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Nicola PECCHIONI

Professore Associato
Dipartimento di Scienze della Vita sede ex-Agraria

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Pubblicazioni

- Varietà di Orzo Primaverile 'Doria' [Brevetto]
Pecchioni, Nicola
abstract

Varietà ottenuta dall’incrocio FO 3881 tra la linea FO 3665 (Nure x Zita ) e la linea FO 3667 (Nure x PO 202.169), coniniziale selezione assistita (MAS) seguita da selezione con metodo pedigree. Il mantenimento in purezza della varietà sarà eseguito mediante il metodo di selezione conservatrice dal CRA-GPG già Ist. Sper. per la Cereal. Sezione di Fiorenzuola (PC).

2022 - Anti-Inflammatory Effect of the Natural H2S-Donor Erucin in Vascular Endothelium [Articolo su rivista]
Ciccone, Valerio; Piragine, Eugenia; Gorica, Era; Citi, Valentina; Testai, Lara; Pagnotta, Eleonora; Matteo, Roberto; Pecchioni, Nicola; Montanaro, Rosangela; Di Cesare Mannelli, Lorenzo; Ghelardini, Carla; Brancaleone, Vincenzo; Morbidelli, Lucia; Calderone, Vincenzo; Martelli, Alma
abstract

Vascular inflammation (VI) represents a pathological condition that progressively affects the integrity and functionality of the vascular wall, thus leading to endothelial dysfunction and the onset of several cardiovascular diseases. Therefore, the research of novel compounds able to prevent VI represents a compelling need. In this study, we tested erucin, the natural isothiocyanate H2S-donor derived from Eruca sativa Mill. (Brassicaceae), in an in vivo mouse model of lipopolysaccharide (LPS)-induced peritonitis, where it significantly reduced the amount of emigrated CD11b positive neutrophils. We then evaluated the anti-inflammatory effects of erucin in LPS-challenged human umbilical vein endothelial cells (HUVECs). The pre-incubation of erucin, before LPS treatment (1, 6, 24 h), significantly preserved cell viability and prevented the increase of reactive oxygen species (ROS) and tumor necrosis factor alpha (TNF-alpha) levels. Moreover, erucin downregulated endothelial hyperpermeability and reduced the loss of vascular endothelial (VE)-Cadherin levels. In addition, erucin decreased vascular cell adhesion molecule 1 (VCAM-1), cyclooxygenase-2 (COX-2) and microsomal prostaglandin E-synthase 1 (mPGES-1) expression. Of note, erucin induced eNOS phosphorylation and counteracted LPS-mediated NF-kappa B nuclear translocation, an effect that was partially abolished in the presence of the eNOS inhibitor L-NAME. Therefore, erucin can control endothelial function through biochemical and genomic positive effects against VI.

2022 - Beneficial Effects of Eruca sativa Defatted Seed Meal on Visceral Pain and Intestinal Damage Resulting from Colitis in Rats [Articolo su rivista]
Lucarini, E.; Micheli, L.; Pagnotta, E.; Matteo, R.; Parisio, C.; Toti, A.; Ferrara, V.; Ciampi, C.; Martelli, A.; Testai, L.; Calderone, V.; Savino, M.; Russo, M.; Pecchioni, N.; Ghelardini, C.; Mannelli, L. D. C.
abstract

Most therapies used in patients affected by inflammatory bowel diseases are ineffective in preventing the development of chronic visceral hypersensitivity, mainly due to inflammationinduced enteric neuroplasticity. Glucosinolates, secondary metabolites mainly of Brassicaceae with anti-inflammatory and neuroprotective properties, are effective in treating both neuropathic and arthritis pain through H2S release and Kv7 potassium channel activation. The aim of this work was to investigate the protective and anti-hyperalgesic efficacy of a defatted seed meal from Eruca sativa Mill. (Brassicaceae), rich in glucosinolates, in a rat model of colitis induced by 2,4-dinitrobenzene sulfonic acid (DNBS). The mechanisms of action were also investigated. Visceral pain was assessed by measuring the abdominal response to colorectal distension. Fifteen days after colitis induction, the acute administration of E. sativa defatted seed meal (0.1–1 g kg−1 p.o.) dose-dependently relieved pain. This effect was hampered by co-administering an H2S scavenger or a selective Kv7 blocker. Administering E. sativa (1 g kg−1 ) for 14 days, starting after DNBS injection, contributed to counteracting visceral pain persistence in the post-inflammatory phase of colitis by promoting colon healing from the damage and reducing enteric gliosis. E. sativa defatted seed meal might be employed as a nutraceutical tool for supporting abdominal pain relief in patients.

2022 - Candidate Genes Associated with Abiotic Stress Response in Plants as Tools to Engineer Tolerance to Drought, Salinity and Extreme Temperatures in Wheat: An Overview [Articolo su rivista]
Trono, Daniela; Pecchioni, Nicola
abstract

Wheat represents one of the most important staple food crops worldwide and its genetic improvement is fundamental to meeting the global demand of the growing population. However, the environmental stresses, worsened by climate change, and the increasing deterioration of arable land make it very difficult to fulfil this demand. In light of this, the tolerance of wheat to abiotic stresses has become a key objective of genetic improvement, as an effective strategy to ensure high yields without increasing the cultivated land. Genetic erosion related to modern agriculture, whereby elite, high-yielding wheat varieties are the product of high selection pressure, has reduced the overall genetic diversity, including the allelic diversity of genes that could be advantageous for adaptation to adverse environmental conditions. This makes traditional breeding a less effective or slower approach to generating new stress-tolerant wheat varieties. Either mining for the diversity of not-adapted large germplasm pools, or generating new diversity, are the mainstream approaches to be pursued. The advent of genetic engineering has opened the possibility to create new plant variability and its application has provided a strong complement to traditional breeding. Genetic engineering strategies such as transgenesis and genome editing have then provided the opportunity to improve environmental tolerance traits of agronomic importance in cultivated species. As for wheat, several laboratories worldwide have successfully produced transgenic wheat lines with enhanced tolerance to abiotic stresses, and, more recently, significant improvements in the CRISPR/Cas9 tools available for targeted variations within the wheat genome have been achieved. In light of this, the present review aims to provide successful examples of genetic engineering applications for the improvement of wheat adaptation to drought, salinity and extreme temperatures, which represent the most frequent and most severe events causing the greatest losses in wheat production worldwide.

2022 - Cardiovascular benefits of Eruca sativa mill. Defatted seed meal extract: Potential role of hydrogen sulfide [Articolo su rivista]
Testai, L.; Pagnotta, E.; Piragine, E.; Flori, L.; Citi, V.; Martelli, A.; Mannelli, L. D. C.; Ghelardini, C.; Matteo, R.; Suriano, S.; Troccoli, A.; Pecchioni, N.; Calderone, V.
abstract

Eruca sativa Mill. is an edible plant belonging to the Brassicaceae botanical family with a long story as a medicinal material, mainly linked to the presence of glucoerucin. One of the main products of this glucosinolate is erucin, a biologicallly active isothiocyanate recently recognized as a hydrogen sulfide (H2S) donor. In this work, an Eruca sativa extract has been obtained from a defatted seed meal (DSM), achieving a powder rich in thiofunctionalized glucosinolates, glucoerucin, and glucoraphanin, accounting for 95% and 5% of the total glucosinolate content (17% on a dry weight basis), associated with 13 identified phenolic acids and flavonoids accounting for 2.5%. In a cell-free model, Eruca sativa DSM extract slowly released H2S. Moreover, this extract promoted significant hypotensive effects in hypertensive rats, and evoked dose-dependent cardioprotection in in vivo model of acute myocardial infarct, obtained through a reversible coronary occlusion. This latter effect was sensitive to blockers of mitochondrial KATP and Kv7.4 potassium channels, suggesting a potential role of these mitochondrial channels in the protective effects of Eruca sativa DSM extract. Accordingly, Eruca sativa DSM extract reduced calcium uptake and apoptotic cell death in isolated cardiac mitochondria. Taken together, these results demonstrate that Eruca sativa DSM extract is endowed with an interesting nutraceutical profile on the cardiovascular system due to, at least in part, its H2S releasing properties. These results pave the way for future investigations on active metabolites.

2022 - Genome-Wide Association Study of Leaf Rust and Stem Rust Seedling and Adult Resistances in Tetraploid Wheat Accessions Harvested in Kazakhstan [Articolo su rivista]
Genievskaya, Y.; Pecchioni, N.; Laido, G.; Anuarbek, S.; Rsaliyev, A.; Chudinov, V.; Zatybekov, A.; Turuspekov, Y.; Abugalieva, S.
abstract

Leaf rust (LR) and stem rust (SR) are diseases increasingly impacting wheat production worldwide. Fungal pathogens producing rust diseases in wheat may cause yield losses of up to 50–60%. One of the most effective methods for preventing such losses is the development of resistant cultivars with high yield potential. This goal can be achieved through complex breeding studies, including the identification of key genetic factors controlling rust disease resistance. The objective of this study was to identify sources of tetraploid wheat resistance to LR and SR races, both at the seedling growth stage in the greenhouse and at the adult plant stage in field experiments, under the conditions of the North Kazakhstan region. A panel consisting of 193 tetraploid wheat accessions was used in a genome-wide association study (GWAS) for the identification of quantitative trait loci (QTLs) associated with LR and SR resistance, using 16,425 polymorphic single-nucleotide polymorphism (SNP) markers in the seedling and adult stages of plant development. The investigated panel consisted of seven tetraploid subspecies (Triticum turgidum ssp. durum, ssp. turanicum, ssp. turgidum, ssp. polonicum, ssp. carthlicum, ssp. dicoccum, and ssp. dicoccoides). The GWAS, based on the phenotypic evaluation of the tetraploid collection’s reaction to the two rust species at the seedling (in the greenhouse) and adult (in the field) stages, revealed 38 QTLs (p < 0.001), comprising 17 for LR resistance and 21 for SR resistance. Ten QTLs were associated with the reaction to LR at the seedling stage, while six QTLs were at the adult plant stage and one QTL was at both the seedling and adult stages. Eleven QTLs were associated with SR response at the seedling stage, while nine QTLs were at the adult plant stage and one QTL was at both the seedling and adult stages. A comparison of these results with previous LR and SR studies indicated that 11 of the 38 QTLs are presumably novel loci. The QTLs identified in this work can potentially be used for marker-assisted selection of tetraploid and hexaploid wheat for the breeding of new LR- and SR-resistant cultivars.

2022 - Migration without interbreeding: Evolutionary history of a highly selfing Mediterranean grass inferred from whole genomes [Articolo su rivista]
Stritt, C.; Gimmi, E. L.; Wyler, M.; Bakali, A. H.; Skalska, A.; Hasterok, R.; Mur, L. A. J.; Pecchioni, N.; Roulin, A. C.
abstract

Wild plant populations show extensive genetic subdivision and are far from the ideal of panmixia which permeates population genetic theory. Understanding the spatial and temporal scale of population structure is therefore fundamental for empirical population genetics – and of interest in itself, as it yields insights into the history and biology of a species. In this study we extend the genomic resources for the wild Mediterranean grass Brachypodium distachyon to investigate the scale of population structure and its underlying history at whole-genome resolution. A total of 86 accessions were sampled at local and regional scales in Italy and France, which closes a conspicuous gap in the collection for this model organism. The analysis of 196 accessions, spanning the Mediterranean from Spain to Iraq, suggests that the interplay of high selfing and seed dispersal rates has shaped genetic structure in B. distachyon. At the continental scale, the evolution in B. distachyon is characterized by the independent expansion of three lineages during the Upper Pleistocene. Today, these lineages may occur on the same meadow yet do not interbreed. At the regional scale, dispersal and selfing interact and maintain high genotypic diversity, thus challenging the textbook notion that selfing in finite populations implies reduced diversity. Our study extends the population genomic resources for B. distachyon and suggests that an important use of this wild plant model is to investigate how selfing and dispersal, two processes typically studied separately, interact in colonizing plant species.

2022 - Nitrogen Use Efficiency in Durum Wheat (Triticum durum Desf.) Grown under Semiarid Conditions in Algeria [Articolo su rivista]
Benchelali, S.; Benkherbache, N.; Mefti, M.; Ronga, D.; Louahdi, N.; Russo, M.; Pecchioni, N.
abstract

The proper and sustainable management of nitrogen fertilization is one of the most common problems of cereal cultivation in semiarid regions, which are characterized by a wide variability in climatic conditions. The current work was conducted to evaluate the effects of nitrogen fertilization on the agronomic and economic aspects of durum wheat cultivated under rainfed semiarid conditions in Algeria and to determine the most efficient nitrogen use efficiency (NUE) among four genotypes that are widespread in the country (tall and short, old and modern genotypes). The four genotypes, Bousselam, MBB, Megress, and GTAdur, were investigated under four nitrogen rates from 0 to 120 kg N ha−1 during three cropping seasons (2016 to 2018). The results indicate that the total nitrogen uptake at maturity (NM), nitrogen uptake by grain (NG), nitrogen harvest index (NHI), NUE and its components, such as nitrogen uptake efficiency (NUpE) and nitrogen utilization efficiency (NUtE), were significantly affected by year, genotype, and nitrogen level. From this study, it appears that higher nitrogen rates improved NM and NG. However, no effects on either grain yield or marginal net return (MNR) were observed; conversely, increased nitrogen levels produced a 13% reduction in the economic return. In other words, in the North African environment, the response to nitrogen is more evident in quality than in yield, which in turn is dependent on the yearly weather conditions and cultivated genotypes. Moreover, nitrogen negatively affected NUE and its components (NUpE, NUtE). On average, NUE displayed low values (14.77 kg kg−1), mostly irregular and highly dependent on weather conditions; in the best year, it did not exceed 60% (19.87 kg kg−1) of the global average value of 33 kg kg−1. Moreover, the modern genotypes Megress (tall) and GTAdur (short) showed the best capacity to tolerate different nitrogen conditions and water shortages, providing relatively superior yields, as well as more effective N use from fertilizers and the soil than the other two genotypes.

2022 - Phenolic Acid Composition and Antioxidant Activity of Whole and Defatted Seeds of Italian Hemp Cultivars: A Two-Year Case Study [Articolo su rivista]
Menga, V.; Garofalo, C.; Suriano, S.; Beleggia, R.; Colecchia, S. A.; Perrone, D.; Montanari, M.; Pecchioni, N.; Fares, C.
abstract

The study investigated the nutritional profile and nutraceutical composition of the seeds (whole and defatted) of two monoecious hemp cultivars (Carmaleonte, Codimono) and one dioecious cultivar (CS) grown during the 2018 and 2019 crop seasons. The phenolic acid profiles, both free and bound, antioxidant activity (AA), protein content (PC), total phenolic content (TPC), βcarotene, lutein content, and condensed tannins (CT) were studied, and the effects of genotype (G), year (Y), and GxY interaction were also measured. The results indicated the stronger involvement of the year in the nutritional and antioxidant properties of the whole seeds than in those of the defatted seeds, as indicated by the analysis of the variance. The PC, TPC, AA, sum of phenolics free (SPF), and sum of phenolics bound (SPB) were significantly affected by year, while the lutein and some phenolic acids, free and bound (ferulic and p-coumaric acids and N-trans-caffeoyltyramine), showed significant effects of the genotype. In this respect, the Carmaleonte revealed the highest content of ferulic and p-coumaric acids, as well as CS of N-trans-caffeoyltyramine. A prevalence of Y effect over G was measured in the free and bound fraction of the phenolics of the whole seeds, in contrast to the defatted seeds, in which significant effects of GxY were also measured. Moreover, the Pearson’s correlation coefficients indicated a strict involvement of precipitations in the variation of the phenolics accumulation, above all with bound p-hydroxybenzoic acid (r = 0.71 **), bound syringic acid (r = 0.69 *), bound N-trans-caffeoyltyramine (r = 0.64 *), and SPB (r = 0.60 *). As phenolics bound fractions have strong biological activities, (including antioxidant and anti-inflammatory activities) the high concentrations of N-trans-Caffeoyltyramine B in the CS defatted seeds suggest that it is valuable ingredient for functional foods.

2022 - The Efficacy of Camelina sativa Defatted Seed Meal against Colitis-Induced Persistent Visceral Hypersensitivity: The Relevance of PPAR α Receptor Activation in Pain Relief [Articolo su rivista]
Lucarini, E.; Micheli, L.; Pagnotta, E.; Toti, A.; Ferrara, V.; Ciampi, C.; Margiotta, F.; Martelli, A.; Testai, L.; Calderone, V.; Matteo, R.; Suriano, S.; Troccoli, A.; Pecchioni, N.; Manera, C.; Mannelli, L. D. C.; Ghelardini, C.
abstract

Brassicaceae are natural sources of bioactive compounds able to promote gut health. Belonging to this plant family, Camelina sativa is an ancient oil crop rich in glucosinolates, polyunsaturated fatty acids, and antioxidants that is attracting renewed attention for its nutraceutical potential. This work aimed at investigating the therapeutic effects of a defatted seed meal (DSM) of Camelina sativa on the colon damage and the persistent visceral hypersensitivity associated with colitis in rats. Inflammation was induced by the intrarectal injection of 2,4-dinitrobenzenesulfonic acid (DNBS). The acute administration of Camelina sativa DSM (0.1–1 g kg−1) showed a dose-dependent pain-relieving effect in DNBS-treated rats. The efficacy of the meal was slightly enhanced after bioactivation with myrosinase, which increased isothiocyanate availability, and drastically decreased by pre-treating the animals with the selective peroxisome proliferator-activated receptor alpha (PPAR α) receptor antagonist GW6471. Repeated treatments with Camelina sativa DSM (1 g kg−1) meal counteracted the development, as well as the persistence, of visceral hyperalgesia in DNBS-treated animals by reducing the intestinal inflammatory damage and preventing enteric neuron damage. In conclusion, Camelina sativa meal might be employed as a nutraceutical tool to manage persistent abdominal pain in patients and to promote gut healing.

2021 - Analysis of sequence variability and transcriptional profile of cannabinoid synthase genes in cannabis sativa l. Chemotypes with a focus on cannabichromenic acid synthase [Articolo su rivista]
Fulvio, F.; Paris, R.; Montanari, M.; Citti, C.; Cilento, V.; Bassolino, L.; Moschella, A.; Alberti, I.; Pecchioni, N.; Cannazza, G.; Mandolino, G.
abstract

Cannabis sativa L. has been long cultivated for its narcotic potential due to the accumulation of tetrahydrocannabinolic acid (THCA) in female inflorescences, but nowadays its production for fiber, seeds, edible oil and bioactive compounds has spread throughout the world. However, some hemp varieties still accumulate traces of residual THCA close to the 0.20% limit set by European Union, despite the functional gene encoding for THCA synthase (THCAS) is lacking. Even if some hypotheses have been produced, studies are often in disagreement especially on the role of the cannabichromenic acid synthase (CBCAS). In this work a set of European Cannabis genotypes, representative of all chemotypes, were investigated from a chemical and molecular point of view. Highly specific primer pairs were developed to allow an accurate distinction of different cannabinoid synthases genes. In addition to their use as markers to detect the presence of CBCAS at genomic level, they allowed the analysis of transcriptional profiles in hemp or marijuana plants. While the high level of transcription of THCAS and cannabidiolic acid synthase (CBDAS) clearly reflects the chemical phenotype of the plants, the low but stable transcriptional level of CBCAS in all genotypes suggests that these genes are active and might contribute to the final amount of cannabinoids.

2021 - Comparative analysis based on transcriptomics and metabolomics data reveal differences between emmer and durum wheat in response to nitrogen starvation [Articolo su rivista]
Beleggia, R.; Omranian, N.; Holtz, Y.; Gioia, T.; Fiorani, F.; Nigro, F. M.; Pecchioni, N.; De Vita, P.; Schurr, U.; David, J. L.; Nikoloski, Z.; Papa, R.
abstract

Mounting evidence indicates the key role of nitrogen (N) on diverse processes in plant, including development and defense. Using a combined transcriptomics and metabolomics approach, we studied the response of seedlings to N starvation of two different tetraploid wheat genotypes from the two main domesticated subspecies: emmer and durum wheat. We found that durum wheat exhibits broader and stronger response in comparison to emmer as seen from the expression pattern of both genes and metabolites and gene enrichment analysis. They showed major differences in the responses to N starvation for transcription factor families, emmer showed differential reduction in the levels of primary metabolites while durum wheat exhibited increased levels of most of them to N starvation. The correlation-based networks, including the differentially expressed genes and metabolites, revealed tighter regulation of metabolism in durum wheat in comparison to emmer. We also found that glutamate and γ-aminobutyric acid (GABA) had highest values of centrality in the metabolic correlation network, suggesting their critical role in the genotype-specific response to N starvation of emmer and durum wheat, respectively. Moreover, this finding indicates that there might be contrasting strategies associated to GABA and glutamate signaling modulating shoot vs. root growth in the two different wheat subspecies.

2021 - Genetic and Management Effects on Barley Yield and Phenology in the Mediterranean Basin [Articolo su rivista]
Cammarano, D.; Ronga, D.; Francia, E.; Akar, T.; Al-Yassin, A.; Benbelkacem, A.; Grando, S.; Romagosa, I.; Stanca, A. M.; Pecchioni, N.
abstract

Heading time in barley is considered a key developmental stage controlling adaptation to the environment and it affects grain yield; with the combination of agronomy (planting dates) and genetics being some of the determinants of adaptation to environmental conditions in order to escape late frost, heat, and terminal drought stresses. The objectives of this study are (i) to apply a gene-based characterization of 118 barley doubled haploid recombinants for vernalization, photoperiod, and earliness per se; (ii) use such information to quantify the optimal combination of genotype/sowing date that escapes extreme weather events; and (iii) how water and nitrogen management impact on grain yield. The doubled haploid barley genotypes with different allelic combinations for vernalization, photoperiod, and earliness per se were grown in eight locations across the Mediterranean basin. This information was linked with the crop growth model parameters. The photoperiod and earliness per se alleles modify the length of the phenological cycle, and this is more evident in combination with the recessive allele of the vernalization gene VRN-H2. In hot environments such as Algeria, Syria, and Jordan, early sowing dates (October 30 and December15) would be chosen to minimize the risk of exposing barley to heat stress. To maintain higher yields in the Mediterranean basin, barley breeding activities should focus on allelic combinations that have recessive VRN-H2 and EPS2 genes, since the risk of cold stress is much lower than the one represented by heat stress.

2021 - Genomic approaches to identify molecular bases of crop resistance to diseases and to develop future breeding strategies [Articolo su rivista]
Mores, A.; Borrelli, G. M.; Laido, G.; Petruzzino, G.; Pecchioni, N.; Amoroso, L. G. M.; Desiderio, F.; Mazzucotelli, E.; Mastrangelo, A. M.; Marone, D.
abstract

Plant diseases are responsible for substantial crop losses each year and affect food security and agricultural sustainability. The improvement of crop resistance to pathogens through breeding represents an environmentally sound method for managing disease and minimizing these losses. The challenge is to breed varieties with a stable and broad-spectrum resistance. Different approaches, from markers to recent genomic and ‘post-genomic era’ technologies, will be reviewed in order to contribute to a better understanding of the complexity of host–pathogen interactions and genes, including those with small phenotypic effects and mechanisms that underlie resistance. An efficient combination of these approaches is herein proposed as the basis to develop a successful breeding strategy to obtain resistant crop varieties that yield higher in increasing disease scenarios.

2021 - QTL analysis of five morpho-physiological traits in bread wheat using two mapping populations derived from common parents [Articolo su rivista]
Vitale, P.; Fania, F.; Esposito, S.; Pecorella, I.; Pecchioni, N.; Palombieri, S.; Sestili, F.; Lafiandra, D.; Taranto, F.; De Vita, P.
abstract

Traits such as plant height (PH), juvenile growth habit (GH), heading date (HD), and tiller number are important for both increasing yield potential and improving crop adaptation to climate change. In the present study, these traits were investigated by using the same bi-parental population at early (F2 and F2-derived F3 families) and late (F6 and F7, recombinant inbred lines, RILs) generations to detect quantitative trait loci (QTLs) and search for candidate genes. A total of 176 and 178 lines were genotyped by the wheat Illumina 25K Infinium SNP array. The two genetic maps spanned 2486.97 cM and 3732.84 cM in length, for the F2 and RILs, respectively. QTLs explaining the highest phenotypic variation were found on chromosomes 2B, 2D, 5A, and 7D for HD and GH, whereas those for PH were found on chromosomes 4B and 4D. Several QTL detected in the early generations (i.e., PH and tiller number) were not detected in the late generations as they were due to dominance effects. Some of the identified QTLs co-mapped to well-known adaptive genes (i.e., Ppd-1, Vrn-1, and Rht-1). Other putative candidate genes were identified for each trait, of which PINE1 and PIF4 may be considered new for GH and TTN in wheat. The use of a large F2 mapping population combined with NGS-based genotyping techniques could improve map resolution and allow closer QTL tagging.

2021 - The h2 s-donor erucin exhibits protective effects against vascular inflammation in human endothelial and smooth muscle cells [Articolo su rivista]
Martelli, A.; Piragine, E.; Gorica, E.; Citi, V.; Testai, L.; Pagnotta, E.; Lazzeri, L.; Pecchioni, N.; Ciccone, V.; Montanaro, R.; Mannelli, L. D. C.; Ghelardini, C.; Brancaleone, V.; Morbidelli, L.; Calderone, V.
abstract

Preservation of vascular wall integrity against degenerative processes associated with ageing, fat-rich diet and metabolic diseases is a timely therapeutical challenge. The loss of endothelial function and integrity leads to cardiovascular diseases and multiorgan inflammation. The protective effects of the H2 S-donor erucin, an isothiocyanate purified by Eruca sativa Mill. seeds, were evaluated on human endothelial and vascular smooth muscle cells. In particular, erucin actions were evaluated on cell viability, ROS, caspase 3/7, inflammatory markers levels and the endothelial hyperperme-ability in an inflammatory model associated with high glucose concentrations (25 mM, HG). Erucin significantly prevented the HG-induced decrease in cell viability as well as the increase in ROS, caspase 3/7 activation, and TNF-α and IL-6 levels. Similarly, erucin suppressed COX-2 and NF-κB upregulation associated with HG exposure. Erucin also caused a significant inhibition of p22phox subunit expression in endothelial cells. In addition, erucin significantly prevented the HG-induced increase in endothelial permeability as also confirmed by the quantification of the specific markers VE-Cadherin and ZO-1. In conclusion, our results assess anti-inflammatory and antioxidant effects by erucin in vascular cells undergoing HG-induced inflammation and this protection parallels the preservation of endothelial barrier properties.

2021 - The novel heptyl phorolic acid cannabinoids content in different Cannabis sativa L. accessions [Articolo su rivista]
Linciano, Pasquale; Russo, Fabiana; Citti, Cinzia; Tolomeo, Francesco; Paris, Roberta; Fulvio, Flavia; Pecchioni, Nicola; Vandelli, Maria Angela; Laganà, Aldo; Capriotti, Anna Laura; Biagini, Giuseppe; Carbone, Luigi; Gigli, Giuseppe; Cannazza, Giuseppe
abstract

The recent discovery of the novel heptyl phytocannabinoids cannabidiphorol (CBDP) and Δ9-tetrahydrocannabiphorol (Δ9-THCP) raised a series of questions relating to the presence and abundance of these new unorthodox compounds in cannabis inflorescence or derived products. As fresh inflorescence contains mainly their acid precursors, which are not commercially available, an ad hoc stereoselective synthesis was performed in order to obtain cannabidiphorolic acid (CBDPA) and Δ9-tetrahydrocannabiphorolic acid (THCPA) to be used as analytical standards for quantitative purposes. The present work reports an unprecedented targeted analysis of both pentyl (C5) and heptyl (C7) CBD- and THC-type compounds in forty-nine cannabis samples representing four different chemotypes. Moreover, the ultrahigh performance liquid chromatography coupled to highresolution mass spectrometry-based method was applied for the putative identification of other heptyl homologs of the most common phytocannabinoid acids, including cannabigerophorolic acid (CBGPA), cannabichromephorolic acid (CBCPA), cannabinophorolic acid (CBNPA), cannabielsophorolic acid (CBEPA), cannabicyclophorolic acid (CBLPA), cannabitriophorolic acid (CBTPA), and cannabiripsophorolic acid (CBRPA).

2020 - Characterization of Celiac Disease-Related Epitopes and Gluten Fractions, and Identification of Associated Loci in Durum Wheat [Articolo su rivista]
Taranto, F.; D'Agostino, N.; Catellani, M.; Laviano, L.; Ronga, D.; Milc, J.; Prandi, B.; Boukid, F.; Sforza, S.; Graziano, S.; Gulli, M.; Visioli, G.; Marmiroli, N.; Badeck, F. W.; Minervini, A. P.; Pecorella, I.; Pecchioni, N.; de Vita, P.; Francia, E.
abstract

While durum wheat is a major food source in Mediterranean countries, storage (i.e., gluten) proteins are however responsible for celiac disease (CD), a serious autoimmune disease that occurs in genetically predisposed subjects. Different gluten epitopes—defined as “immunogenic” (IP) and “toxic” (TP) peptides—are involved in the pathology and their content in wheat grain depends on environmental and genetic factors. Detection of IP and TP is not trivial, and no work has been conducted so far to identify the genomic regions associated with their accumulation in wheat. In the present study, a genome-wide association study was performed on a durum wheat collection to identify marker–trait associations (MTAs) between 5730 high quality SNPs and the accumulation of CD-related peptides and gluten protein composition measured in two consecutive cropping seasons (2015/2016 and 2016/2017). High-molecular-weight glutenin subunits (HMW-GS) were more stable between the two years, and differences in total gluten proteins were mainly due to low-molecular-weight glutenin subunits (LMW-GS) and accumulation of gliadins. In the first instance, association tests were conducted on yellow pigment content (YP), a highly inheritable trait with a well-known genetic basis, and several significant MTAs were found corresponding to loci already known for being related to YP. These findings showed that MTAs found for the rest of the measured traits were reliable. In total, 28 significant MTAs were found for gluten composition, while 14 were found to be associated with IP and TP. Noteworthy, neither significant (−log10p > 4.7) nor suggestive (−log10p > 3.3) MTAs for the accumulation of CD-triggering epitopes were found on Gli-A1/Glu-A3 and Gli-B1/Glu-B3 loci, thus suggesting regulatory rather than structural gene effect. A PBF transcription factor on chromosome 5B, known to be involved in the regulation of the expression of CD-related peptides, was identified among the positional candidate genes in the LD-decay range around significant SNPs. Results obtained in the present study provide useful insights and resources for the long-term objective of selecting low-toxic durum wheat varieties while maintaining satisfactory gluten quality.

2020 - Genome-wide association mapping of prostrate/erect growth habit in winter durum wheat [Articolo su rivista]
Marone, D.; Rodriguez, M.; Saia, S.; Papa, R.; Rau, D.; Pecorella, I.; Laido, G.; Pecchioni, N.; Lafferty, J.; Rapp, M.; Longin, F. H.; De Vita, P.
abstract

By selecting for prostrate growth habit of the juvenile phase of the cycle, durum wheat cultivars could be developed with improved competitive ability against weeds, and better soil coverage to reduce the soil water lost by evaporation. A panel of 184 durum wheat (Triticum turgidum subsp. durum) genotypes, previously genotyped with DArT-seq markers, was used to perform association mapping analysis of prostrate/erect growth habit trait and to identify candidate genes. Phenotypic data of plant growth habit were recorded during three consecutive growing seasons (2014–2016), two different growth conditions (field trial and greenhouse) and two sowing periods (autumn and spring). Genome-wide association study revealed significant marker-trait associations, twelve of which were specific for a single environment/year, 4 consistent in two environments, and two MTAs for the LSmeans were identified across all environments, on chromosomes 2B and 5A. The co-localization of some MTAs identified in this study with known vernalization and photoperiod genes demonstrated that the sensitivity to vernalization and photoperiod response are actually not only key components of spring/winter growth habit, but they play also an important role in defining the magnitude of the tiller angle during the tillering stage. Many zinc-finger transcription factors, such as C2H2 or CCCH-domain zinc finger proteins, known to be involved in plant growth habit and in leaf angle regulation were found as among the most likely candidate genes. The highest numbers of candidate genes putatively related to the trait were found on chromosomes 3A, 4B, 5A and 6A. Moreover, a bioinformatic approach has been considered to search for functional ortholog genes in wheat by using the sequence of rice and barley tiller angle-related genes. The information generated could be used to improve the understanding of the mechanisms that regulate the prostrate/erect growth habit in wheat and the adaptive potential of durum wheat under resource-limited environmental conditions.

2020 - Influence of CNV on transcript levels of HvCBF genes at Fr-H2 locus revealed by resequencing in resistant barley cv. ‘Nure’ and expression analysis [Articolo su rivista]
Mareri, L.; Milc, J.; Laviano, L.; Buti, M.; Vautrin, S.; Cauet, S.; Mascagni, F.; Natali, L.; Cavallini, A.; Berges, H.; Pecchioni, N.; Francia, E.
abstract

Resequencing in resistant cultivar ‘Nure’ and structural comparison with the same region of susceptible ‘Morex’ was performed in order to gain a better insight into barley Frost-resistance-H2 locus. Accurate annotation showed copy number variation (CNV) in the proximal part of the locus. In ‘Nure’, two exact copies of the HvCBF4-HvCBF2A region and one of the HvCBF4-HvCBF2B segment were observed, while in ‘Morex’ the corresponding region harboured a single HvCBF4-HvCBF2A (22 kb) segment. Abundance and diversity of repetitive element classes, gene function gain/losses, regulatory motifs and SNPs in gene sequences were identified. An expression study of key HvCBFs with/without CNV on selected genotypes contrasting for frost resistance and estimated HvCBF4-HvCBF2B copy number (2–10 copies) was also performed. Under light stimulus at warm temperature (23 °C), CNV of HvCBF2A and HvCBF4 correlated with their expression levels and reported frost resistance of genotypes; moreover, expression levels of HvCBF2A and HvCBF14 were strongly correlated (r = 0.908, p < 0.01). On the other hand, frost resistance correlated to HvCBF14 expression (r = 0.871, p < 0.01) only after cold induction (6°C) in the dark. A complex interplay of HvCBFs expression levels under different light/temperature stimuli is discussed in light of CNV and presence/number of regulatory elements that integrate different signal transduction pathways.

2020 - Influence of environmental and genetic factors on content of toxic and immunogenic wheat gluten peptides [Articolo su rivista]
Ronga, D.; Laviano, L.; Catellani, M.; Milc, J.; Prandi, B.; Boukid, F.; Sforza, S.; Dossena, A.; Graziano, S.; Gulli, M.; Visioli, G.; Marmiroli, N.; De Vita, P.; Pecchioni, N.; Francia, E.
abstract

The impact of environment, genetic selection and their interactions on grain yield of durum wheat genotypes has been extensively studied; however, limited information is available for their influence on gluten quality associated with effects on the amount and composition of glutenins, gliadins and celiac disease (CD)-triggering peptides. In this study, a set of six commonly cultivated durum wheat genotypes were assessed in a multi-environment trial of eight site-year combinations in different Italian regions during two consecutive harvest years (2016 and 2017). While high-molecular-weight glutenin subunits (HMW-GS) were more stable between years, differences in total gluten proteins were mainly due to low-molecular-weight glutenin subunits (LMW-GS) and gliadins accumulation. After mass separation and quantification, two gliadin proteins – γ-Gli-5 and α-GliA2-6 (41.1 and 33.8 kDa, respectively) – were further studied together with toxic (TP) and immunogenic (IP) celiac disease-triggering peptides obtained via simulated gastrointestinal digestion. While TP accumulation was strongly influenced by the genotypes, IP showed marked variation in the different sites with significant genotype-by-year and genotype-by-site interaction. Specific agrometeorological variables (i.e. growing degree days and aridity index) in different growing phases showed a strong negative correlation with α-GliA2-6 and CD-associated peptides. Statistical analysis revealed that the level of gliadins and TP/IP peptides were uncorrelated with grain protein content and yield. The selection of plant materials with good technological properties but with a low content of CD-triggering peptides should combine with ad hoc environment (e.g. site) selection and management practices reducing crop evapotranspiration in the vegetative phase.

2020 - Quantitative trait loci for agronomic traits in tetraploid wheat for enhancing grain yield in Kazakhstan environments [Articolo su rivista]
Anuarbek, S.; Abugalieva, S.; Pecchioni, N.; Laido, G.; Maccaferri, M.; Tuberosa, R.; Turuspekov, Y.
abstract

Durum wheat (Triticum turgidum L. ssp. durum) is one of the top crops in Kazakhstan, where it is cultivated in different ecological niches, mainly at higher latitudes in the steppe zone of the northern region. Therefore, local breeding programs for durum wheat are primarily focused on selection for high productivity in Northern Kazakhstan based on the introduction of promising foreign germplasm and the adoption of marker-assisted selection. In this study, a world tetraploid wheat collection consisted of 184 primitive and domesticated accessions, which were previously genotyped using 16,425 polymorphic SNP markers, was field-tested in Northern and South-eastern Kazakhstan. The field tests have allowed the identification of 80 durum wheat promising lines in Northern Kazakhstan in comparison with a local standard cultivar. Also, GGE (Genotype and Genotype by Environment) biplot analyses for yield performance revealed that accessions of T. dicoccum, T. carthlicum, and T. turanicum also have potential to improve durum wheat yield in the region. The genome-wide association study (GWAS) has allowed the identification of 83 MTAs (marker-trait associations) for heading date, seed maturation time, plant height, spike length, number of fertile spikes, number of kernels per spike, and thousand kernel weight. The comparison of the 83 identified MTAs with those previously reported in GWAS for durum wheat suggests that 38 MTAs are presumably novel, while the co-localization of a large number of MTAs with those previously published confirms the validity of the results of this study. The MTAs reported herewith will provide the opportunity to implement marker-assisted selection in ongoing durum wheat breeding projects targeting higher productivity in the region.

2020 - Whole Genome Scan Reveals Molecular Signatures of Divergence and Selection Related to Important Traits in Durum Wheat Germplasm [Articolo su rivista]
Taranto, F.; D'Agostino, N.; Rodriguez, M.; Pavan, S.; Minervini, A. P.; Pecchioni, N.; Papa, R.; De Vita, P.
abstract

The first breeding program in the world for durum wheat was conceived in Italy in the early 1900s. Over the decades, pressure exerted by natural and artificial selection could have progressively reduced the genetic diversity of the durum wheat germplasm. In the present study, a large panel of Italian durum wheat accessions that includes landraces, old and modern cultivars was subjected to genotyping using the Illumina iSelect 15K wheat SNP array. The aim was to assess the impact that selection has in shaping Italian durum wheat genetic diversity and to exploit the patterns of genetic diversity between populations to identify molecular signatures of divergence and selection. Relatively small differences in genetic diversity have been observed among accessions, which have been selected and cultivated in Italy over the past 150 years. Indeed, directional selection combined with that operated by farmers/breeders resulted in the increase of linkage disequilibrium (LD) and in changes of the allelic frequencies in DNA regions that control important agronomic traits. Results from this study also show that major well-known genes and/or QTLs affecting plant height (RHT), earliness (VRN, PPD) and grain quality (GLU, PSY, PSD, LYC, PPO, LOX3) co-localized with outlier SNP loci. Interestingly, many of these SNPs fall in genomic regions where genes involved in nitrogen metabolism are. This finding highlights the key role these genes have played in the transition from landraces to modern cultivars. Finally, our study remarks on the need to fully exploit the genetic diversity of Italian landraces by intense pre-breeding activities aimed at introducing a new source of adaptability and resistance in the genetic background of modern cultivars, to contrast the effect of climate change. The list of divergent loci and loci under selection associated with useful agronomic traits represents an invaluable resource to detect new allelic variants for target genes and for guiding new genomic selection programs in durum wheat.

2019 - Anthocyanin profile and antioxidant capacity in coloured barley [Articolo su rivista]
Suriano, S.; Savino, M.; Codianni, P.; Iannucci, A.; Caternolo, G.; Russo, M.; Pecchioni, N.; Troccoli, A.
abstract

The grain of 17 coloured barley F8 recombinant inbred lines from three backcross programs using three barley parental lines were studied. The main objectives were to characterise the anthocyanin profiles and antioxidant activities of these different lines of coloured barley grain when grown in southern Italy. HPLC and spectrophotometric analyses were performed. The overall profile of anthocyanins across the grain of these genotypes comprised 51.8% malvidin 3-glucoside, 12.7% delphinidin 3-glucoside, 5.0% cyanidin, ~2.5% both petunidin and peonidin 3-glucoside, and ~1.4% both delphinidin 3-rutinoside anthocyanidin 3-glucoside, with the remaining 23% as unidentified anthocyanins. Principal component analysis showed that the antioxidant activities of the barley grain were significantly correlated with the levels of phenolic compounds. Furthermore, the grain of some of these coloured barley RILs had the highest radical scavenging activities, which indicated their potential use in preparation of both food and nutraceuticals, for protective effects on human health, and in breeding programs.

2019 - Carbon footprint and energetic analysis of tomato production in the organic vs the conventional cropping systems in Southern Italy [Articolo su rivista]
Ronga, D.; Gallingani, Tommaso; Zaccardelli, M.; Perrone, D.; Francia, E.; Milc, J.; Pecchioni, N.
abstract

Sustainable agriculture aims to reduce its environmental impact. In this research, the carbon footprint and energetic analysis have been performed for three consecutive years to investigate the actual environmental impact of processing tomato production, in the organic (OS) vs the conventional cropping systems (CS), in a specialized Mediterranean area in Southern Italy. The global warming potential (GWP, in term of kg CO 2 -eq) and primary energy demand (PED, in term of MJ) of processing tomato produced in the two systems (average of three years) were compared in this study. Our results indicate that GWP was on average + 22% in the OS than in CS using 1 ton of marketable fresh fruits as FU. On the other hand, GWP recorded in the OS was, on average, −40% compared to the CS, if 1 ha was considered. A similar impact was registered for PED. The OS showed +28% vs −38% of PED than the CS, using 1 t of marketable fresh fruit vs 1 ha. Pesticide and fungicide applications and soil tillage had the highest impacts among management inputs on GWP and PED, for both farming systems. Hence, the environmental efficiency of these practices could be largely improved in the production of processing tomato aiming at sustainable farming. In conclusion, the differences of sustainability observed between the two farming systems were mainly due to the far lower marketable yield recorded in the OS vs the CS. Therefore, the priority future challenge of organic processing tomato farming should be the reduction of the yield gap between the OS and the CS, through the development of both new genotypes and innovative management methods, designed to reduce the gap, but not increasing the environmental impact on the agroecosystem.

2019 - Changes in yield components, morphological, physiological and fruit quality traits in processing tomato cultivated in Italy since the 1930’s [Articolo su rivista]
Ronga, Domenico; Francia, Enrico; Rizza, Fulvia; Badeck, Franz-W.; Caradonia, Federica; Montevecchi, Giuseppe; Pecchioni, Nicola
abstract

Yield of processing tomato (Solanum lycopersicum L.) increased (∼50%) in Italy since the 1930’s. The aim of this work was to assess the changes in yield components associated with morphological, physiological and fruit quality traits in processing tomato cultivars cropped in Italy from the mid-1930s until nowadays, introduced by breeding in six representative cultivars. Marketable yield showed an increase of 0.6% per year of release since the 1930’s. The highest marketable yield was obtained in modern cultivars due to a higher harvest index, fruit number and the ratio between ripe fruit and total fruit in comparison with the old ones. However, no single trait drove the highest marketable yield in modern cultivars. In fact, both morphological (smaller plant height and leaf area index) and physiological (accelerated plant senescence, higher leaf nitrogen status, and lower potential plant water and chlorophyll contents) traits contributed to increase marketable yield in modern cultivars. Moreover, total plant dry weight (shoot+fruit) of a single plant decreased, whereas its total fruit fresh weight and fruit dry matter content were stable and not correlated with the year of release, thus suggesting that a higher sink strength and homogeneity of fruit ripening were also involved in the highest marketable yield showed by modern cultivars. A great effort of breeders was done in the improvement of important fruit quality traits required by Italian canning industries. Fruit colour and Brix yield were positively correlated with the year of release, while viscosity and total carotenoids were negatively correlated with the year of release. However, no improvement was achieved for important traits such as soluble solids content, fruit dry weight and total fruit yield, which instead should be considered in the future breeding programmes, to improve both yield and quality of processing tomato.

2019 - Combined effect of cadmium and lead on durum wheat [Articolo su rivista]
Aprile, A.; Sabella, E.; Francia, E.; Milc, J.; Ronga, D.; Pecchioni, N.; Ferrari, E.; Luvisi, A.; Vergine, M.; De Bellis, L.
abstract

Cadmium (Cd) and lead (Pb) are two toxic heavy metals (HMs) whose presence in soil is generally low. However, industrial and agricultural activities in recent years have significantly raised their levels, causing progressive accumulations in plant edible tissues, and stimulating research in this field. Studies on toxic metals are commonly focused on a single metal, but toxic metals occur simultaneously. The understanding of the mechanisms of interaction between HMs during uptake is important to design agronomic or genetic strategies to limit contamination of crops. To study the single and combined effect of Cd and Pb on durum wheat, a hydroponic experiment was established to examine the accumulation of the two HMs. Moreover, the molecular mechanisms activated in the roots were investigated paying attention to transcription factors (bHLH family), heavy metal transporters and genes involved in the biosynthesis of metal chelators (nicotianamine and mugineic acid). Cd and Pb are accumulated following different molecular strategies by durum wheat plants, even if the two metals interact with each other influencing their respective uptake and translocation. Finally, we demonstrated that some genes (bHLH 29, YSL2, ZIF1, ZIFL1, ZIFL2, NAS2 and NAAT) were induced in the durum wheat roots only in response to Cd.

2019 - Comparative assessment of the yield components of the tetraploid wheat world collection [Articolo su rivista]
Sh. N., Anuarbek; Abugalieva, S. I.; Chudinov, V. A.; Tuberosa, R.; Pecchioni, N.; Turuspekov, Ye. K.
abstract

Nowadays, a large number of cultivars of various origins are attracted to the wheat breeding improvement, and as a result, an assessment of the accessions’ yield in various agroclimatic conditions is required. Genotype-environment interaction is the main reason for the fact that in different years and (or) in other conditions of cultivation, cultivars and lines differ in rank according to the level of the yield. The study aims to investigate the suitability and adaptability of accessions of world tetraploid wheat collection, including durum wheat cultivars, to the Kazakhstan conditions. Three hundred twenty-eight (328) tetraploid wheat accessions of different genetic and geographical origin were grown in 2 randomized replicates in two contrasting regions of Kazakhstan – Kostanay region on the North and Almaty region on the South-east of the country. Phenological observations and structural analysis were conducted following Dospekhov and the Zadoks scale. Correlations coefficients among all characters (days to tillering, days to booting, days to heading, days to anthesis, days to maturity, plant height, peduncle length, number of fertile spikes per plant, spike length, number of kernels per spike, weight of kernels per spike, number of kernels per plant, 1000 kernels weight) were computed using GraphPad software. To assess the contribution of genotypic and environmental variability to the total phenotypic variation of yield and the main economically valuable traits, we evaluated the genotype-environment interaction. Productive and adapted accessions for the both Almaty and Kostanay regions were selected. The data of phenological observations and structural analysis will be used in a genome-wide association study for the traits, related to productivity and quality.

2019 - Comparative transcriptome profiling of the response to Pyrenochaeta lycopersici in resistant tomato cultivar Mogeor and its background genotype—susceptible Moneymaker [Articolo su rivista]
Milc, J.; Bagnaresi, P.; Aragona, M.; Valente, M. T.; Biselli, C.; Infantino, A.; Francia, E.; Pecchioni, N.
abstract

Breeding for resistance is the most effective tool for controlling the corky root disease of tomato caused by Pyrenochaeta lycopersici. A comparative RNA-Seq-based transcriptomic analysis was conducted at 96 hpi (hours post infection) on two tomato cultivars: resistant Mogeor and its genetic background, and susceptible Moneymaker to investigate the differences in their transcriptomic response and identify the molecular bases of this plant-pathogen interaction. The number of differentially expressed genes (DEGs) identified was much higher in the susceptible than in the resistant genotype; however, the proportion of upregulated genes was higher in Mogeor (70.81%) than in Moneymaker (52.95%). Gene Ontology (GO) analysis enabled identification of 24 terms shared by the two cultivars that were consistent with responses to external stimulus, such as fungal infection. On the other hand, as many as 54 GO were enriched solely in Moneymaker, including terms related to defense response and cell wall metabolism. Our results could support the previous observations in other pathosystems, that susceptibility and resistance have overlapping signaling pathways and responses, suggesting that the P. lycopersici resistance gene pyl might be a recessive allele at a susceptibility locus, for which different candidate genes were identified based on the differences in induction or expression levels, observed between the resistant and susceptible genotype. MapMan analysis highlighted a complex hormone and transcription factors interplay where SA- and JA-induced pathways are modulated in a similar way in both genotypes and thus take part in a common response while the ethylene signaling pathways, induced mainly in susceptible Moneymaker, seem putatively contribute to its susceptibility.

2019 - Comparison of gluten peptides and potential prebiotic carbohydrates in old and modern Triticum turgidum ssp. genotypes [Articolo su rivista]
Ficco, Donatella Bianca Maria; Prandi, Barbara; Amaretti, Alberto; Anfelli, Igor; Leonardi, Alan; Raimondi, Stefano; Pecchioni, Nicola; De Vita, Pasquale; Faccini, Andrea; Sforza, Stefano; Rossi, Maddalena
abstract

Old wheat genotypes are perceived by consumers as healthier than modern ones. The release of gluten peptides with in vitro digestion and the content of potentially prebiotic carbohydrates (i.e. resistant fraction of starch and cell-wall associated dietary fiber) were evaluated in tetraploid wheats, namely 9 old and 3 modern Triticum turgidum ssp. genotypes. Simulated digestion of wholemeal flours yielded 152 major peptides, 59 of which were attributed a sequence. Principal component analysis revealed that peptide profiles were variable in old genotypes, unlike in modern ones. Digestion of old genotypes generally yielded peptides in greater concentration. In particular, 5 peptides of γ-gliadin, known to trigger the adaptive immune reaction, and two peptides of α-gliadin, known to be toxic to celiac patients, were particularly abundant in some old varieties. Resistant starch (RS) was negligible in modern genotypes (<0.6%), but it was remarkably abundant in some old varieties, reaching the highest value in Dauno III (8.5%, P < 0.05). Dauno III also presented the highest amount of soluble fiber (4.2%, P < 0.05). Pasta was made with an old and a modern genotype (Dauno III and PR22D89, respectively) with opposite RS content. Pasta making and cooking affected starch digestibility, overtaking differences between genotypes and yielding the same amount of RS for both the varieties (approx. 1.7%). The data herein presented suggest that the wholemeal flours of old tetraploid wheat genotypes could not boast particular claims associated to a lower exposure to gluten peptides and, if cooked, to a prebiotic potential.

2019 - Durum wheat genome highlights past domestication signatures and future improvement targets [Articolo su rivista]
Maccaferri, M.; Harris, N. S.; Twardziok, S. O.; Pasam, R. K.; Gundlach, H.; Spannagl, M.; Ormanbekova, D.; Lux, T.; Prade, V. M.; Milner, S. G.; Himmelbach, A.; Mascher, M.; Bagnaresi, P.; Faccioli, P.; Cozzi, P.; Lauria, M.; Lazzari, B.; Stella, A.; Manconi, A.; Gnocchi, M.; Moscatelli, M.; Avni, R.; Deek, J.; Biyiklioglu, S.; Frascaroli, E.; Corneti, S.; Salvi, S.; Sonnante, G.; Desiderio, F.; Mare, C.; Crosatti, C.; Mica, E.; Ozkan, H.; Kilian, B.; De Vita, P.; Marone, D.; Joukhadar, R.; Mazzucotelli, E.; Nigro, D.; Gadaleta, A.; Chao, S.; Faris, J. D.; Melo, A. T. O.; Pumphrey, M.; Pecchioni, N.; Milanesi, L.; Wiebe, K.; Ens, J.; Maclachlan, R. P.; Clarke, J. M.; Sharpe, A. G.; Koh, C. S.; Liang, K. Y. H.; Taylor, G. J.; Knox, R.; Budak, H.; Mastrangelo, A. M.; Xu, S. S.; Stein, N.; Hale, I.; Distelfeld, A.; Hayden, M. J.; Tuberosa, R.; Walkowiak, S.; Mayer, K. F. X.; Ceriotti, A.; Pozniak, C. J.; Cattivelli, L.
abstract

The domestication of wild emmer wheat led to the selection of modern durum wheat, grown mainly for pasta production. We describe the 10.45 gigabase (Gb) assembly of the genome of durum wheat cultivar Svevo. The assembly enabled genome-wide genetic diversity analyses revealing the changes imposed by thousands of years of empirical selection and breeding. Regions exhibiting strong signatures of genetic divergence associated with domestication and breeding were widespread in the genome with several major diversity losses in the pericentromeric regions. A locus on chromosome 5B carries a gene encoding a metal transporter (TdHMA3-B1) with a non-functional variant causing high accumulation of cadmium in grain. The high-cadmium allele, widespread among durum cultivars but undetected in wild emmer accessions, increased in frequency from domesticated emmer to modern durum wheat. The rapid cloning of TdHMA3-B1 rescues a wild beneficial allele and demonstrates the practical use of the Svevo genome for wheat improvement.

2019 - Effects of solid and liquid digestate for hydroponic baby leaf lettuce (Lactuca sativa L.) cultivation [Articolo su rivista]
Ronga, Domenico; Setti, Leonardo; Salvarani, Chiara; De Leo, Riccardo; Bedin, Elisa; Pulvirenti, Andrea; Milc, Justyna; Pecchioni, Nicola; Francia, Enrico
abstract

Digestate was evaluated as an alternative and sustainable growing medium and nutrient solution in the hydroponic cultivation of baby leaf lettuce (Lactuca sativa L.). Nine hydroponic combinations of substrate and fertilization (agriperlite + standard solution, agriperlite + liquid digestate, solid digestate + standard solution, solid digestate + liquid digestate, soil + standard solution, peat moss + standard solution; peat moss + liquid digestate, pelleted digestate + standard solution and pelleted digestate + liquid digestate) were tested and compared for the cultivation of baby leaf lettuce, in three different experiments. During the crop cycles, yield as other agronomical and microbiological parameters were investigated. The combination of agriperlite + liquid digestate, solid digestate + standard solution and pelleted digestate + standard solution enhanced plant growth by affecting the root, the shoot, the total dry weight and SPAD parameters, in the all investigated experiments (+32%, +40%, +29%, +17% respectively). Based on the obtained results, digestate represents a sustainable and alternative growing media or nutrient solution for the production of baby leaf lettuce cultivated in hydroponic system.

2019 - Measurement of leaf lamina moisture with a low-cost electrical humidity sensor: Case study on a wheat water-mutant [Articolo su rivista]
Rascio, A.; Rinaldi, M.; De Santis, G.; Pecchioni, N.; Palazzo, G.; Palazzo, N.
abstract

Background: The presence and persistence of water on the leaf can affect crop performance and thus might be a relevant trait to select for or against in breeding programmes. Low-cost, rapid and relatively simple methods are of significant importance for screening of large populations of plants for moisture analysis of detached leaves. Leaf moisture can be detected using an electric circuit, where the resistance changes are proportional to the moisture of the measured surface. In this study, we present a protocol to analyse genotypic differences through the electrical properties of living or stored tissues, performed using a commercial device. Expanded and non-expanded leaves were compared to determine the effects of leaf maturity on these data. Two wheat genotypes that differ in tissue affinity for bound water were used to define the influence of water status. Results: The device indirectly estimates leaf moisture content using two electrodes applied to the leaf lamina of fresh and stored samples. Single moisture readings using this moisture meter had mean execution time of ~ 1.0 min. Exponential associations provided good fits for relationships between the moisture meter reading (MMR) and the electrical resistance applied to the electrodes. MMR normalised for the water/ dry matter ratio (MMRnorm) was lower for mature leaves of the water-mutant than those of wild-type, for the fully hydrated fresh leaves. MMR of fully mature leaves when partially dehydrated and measured after 10 min at 27 °C and 40% relative humidity was greater for the water-mutant than the wild-type. Conclusions: This case study provides a low-cost tool to compare electrical-resistance estimates of leaf moisture content, together with a promising and rapid phenotyping protocol for genotypic screening of wheat under standard environmental conditions. Measurement of changes in MMR with time, of fresh and partially dehydrated leaves, or of MMR normalised to tissue water content allowed for differentiation between the genotypes. Furthermore, the differences observed between genotypes that here relate particular to tissue affinity for bound water suggest that not only the free-water fraction, but also other water fractions, can affect these electrically estimated leaf moisture measures.

2019 - Technological Quality and Nutritional Value of Two Durum Wheat Varieties Depend on Both Genetic and Environmental Factors [Articolo su rivista]
Graziano, Sara; Marando, Silvia; Prandi, Barbara; Boukid, Fatma; Marmiroli, Nelson; Francia, Enrico; Pecchioni, Nicola; Sforza, Stefano; Visioli, Giovanna; Gullì, Mariolina
abstract

Durum wheat (Triticum turgidum L. subsp. durum (Desf.) Husn) is a major food source in Mediterranean countries since it is utilized for the production of pasta, leavened and unleavened breads, couscous, and other traditional foods. The technological and nutritional properties of durum wheat semolina depend mainly on the type of gluten proteins and on their amount, which is a genotype- and environment-dependent trait. Gluten proteins are also responsible for celiac disease (CD), an autoimmune enteropathy with a prevalence of about 0.7-2% in the human population. At this purpose, two Italian durum wheat cultivars, Saragolla and Cappelli, currently used for monovarietal pasta, were chosen to compare (i) the reserve and embryo proteome, (ii) the free and bound phenolics, antioxidant activity, and amino acid composition, and (iii) the content of immunogenic peptides produced after a simulated gastrointestinal digestion. The results obtained from 2 years of field cultivation on average showed a higher amount of gluten proteins, amino acids, and immunogenic peptides in Cappelli. Saragolla showed a higher abundance in bound phenolics, antioxidant enzymes, and stress response proteins in line with its higher antioxidant activity. However, the impact of the year of cultivation, largely depending on varying rainfall regimes through the wheat growth cycle, was significant for most of the parameters investigated. Differences in technological and nutritional characteristics observed between the two cultivars are discussed in relation to the influence of genetic and environmental factors.

2019 - The impact of climate change on barley yield in the Mediterranean basin [Articolo su rivista]
Cammarano, D.; Ceccarelli, S.; Grando, S.; Romagosa, I.; Benbelkacem, A.; Akar, T.; Al-Yassin, A.; Pecchioni, N.; Francia, E.; Ronga, D.
abstract

Barley is an important cereal crop for the arid and semi-arid Mediterranean environments. Future climate projections show that Mediterranean countries will get drier and hotter. The objectives of the study are to: i) simulate the impacts of different climate projections and different sowing dates on yield; ii) quantify the importance of heat and drought on barley yield at different growth stages and sowing dates; iii) quantify the contributions of sources of uncertainty among inter-annual variability, adaptation options and climate projections. Nine locations across the Mediterranean basin were used to calibrate and evaluate the Decision Support System for Agrotechnology Transfer (DSSAT) model. At each location the 40 Global Circulation Model (GCM) outputs (RCP4.5, Mid of the Century) showed an increase in mean growing season temperature between 0.9 and 2.16 °C, while changes of growing season rainfall were between -24 and +24%. Therefore, at each location a drier (Dry), mid (Mid), and wetter (Wet) projection was selected. Overall, there was a 9% reduction in grain yield under climate change; but the mean yield change was -27%, +4%, +8%, for the Dry, Mid, and Wet scenarios, respectively. The results of the simulations under the Wet scenario showed a higher variability of yield response. There was an interaction between the soil type, the amount of rainfall, the extractable soil water content and the maximum air temperature. Because of these relationship water-stress during the vegetative stage was experienced, affecting expansive growth. At the same time, the high number of days with Tmax>34 °C caused higher soil water depletion by the plant and therefore lower yields under the Wet scenario. The inter-annual weather variability impacts barley yield irrespective of the sowing dates and the future projected climate. In conclusion, the impact of future climate on barley yield in the Mediterranean is negative but some locations will be less affected than others.

2018 - Evaluation of two groups of quinoa (Chenopodium quinoa Willd.) accessions with different seed colours for adaptation to the Mediterranean environment [Articolo su rivista]
De Santis, Giuditta; Ronga, Domenico; Caradonia, Federica; Ambrosio, Tiziana D.; Troisi, Jacopo; Rascio, Agata; Fragasso, Mariagiovanna; Pecchioni, Nicola; Rinaldi, Michele
abstract

Agronomic and seed-quality traits in 17 quinoa (Chenopodium quinoa Willd.) accessions grouped according to seed colour (i.e. ochre and yellow) were investigated and compared with the white commercial cultivar Regalona-Baer. These accessions were previously selected from a range of accessions of diverse origin and seed colour for their potential value in a breeding program for cultivars adapted to the southern Italian environment. Field trials were conducted over 2 years in Foggia, southern Italy. The aim was to identify elite genotypes suited to the Mediterranean Basin in terms of high yields and seed quality, by using principal component analysis (PCA) and hierarchical cluster analysis. The genotype and year effects were statistically significant for most parameters investigated, whereas the genotype × year interaction was significant only for seed quality. There were significant differences between the two seed-colour groups for most of the investigated traits, but not for total dry weight, days to flowering, and soluble and insoluble fibre. The major difference between the accessions and cv. Regalona-Baer was lower seed yield for the ochre seed group (30% lower, on average); this was associated with increased plant height (13% higher, on average), greater number of days to maturity (+6 days, on average) and shorter panicle length (21% shorter, on average). These results were observed for both growing seasons. The seed yield of the yellow seed group was similar to Regalona-Baer. Focusing on individual accessions, PCA indicated that accessions Q12, Q18 and Q26 were similar to Regalona-Baer for seed yield, 1000-seed weight, seed area and seed perimeter, and accession Q4 had the highest protein and kaempferol contents for both years. Seed area and perimeter, harvest index, and 1000-seed weight showed positive associations with seed yield, whereas days to flowering, days to maturity and quality traits were negatively correlated with seed yield for both years. Cluster analysis carried out on all of the agronomic and seed-quality traits did not show clear clustering of the accessions based on seed colour alone. The results of this study confirm that both the ochre and yellow quinoa seed groups included elite accessions that can be used directly in future selection programs for the development of high-yielding varieties well adapted to the Mediterranean environment.

2018 - Fertilizzante a base di digestato arricchito con microrganismi biostimolanti e metodo per produrlo [Brevetto]
Ronga, Domenico; Pecchioni, Nicola; Francia, Enrico; Bignami, Cristina; Zaghi, Massimo; Bezzi, Guido; Terzi, Valeria
abstract

La presente invenzione si riferisce ad un fertilizzante a base di digestato, sotto forma di pellet o granuli, ed al metodo per produrlo, detto digestato essendo arricchito con microrganismi biostimolanti. Il fertilizzante è caratterizzato dal fatto che detti pellet e/o granuli sono rivestiti con un film biodegradabile atto a sincronizzare i processi della mineralizzazione del fertilizzante con i processi di assorbimento della pianta, detto film essendo arricchito con microrganismi biostimolanti. Il metodo per la produzione di detto fertilizzante è caratterizzato dal fatto di comprendere le seguenti fasi: - separazione del digestato tal quale in digestato solido e digestato liquido; - essiccazione parziale di detti digestato solido e digestato liquido, fino al raggiungimento di un’umidità del 14÷16%; - granulazione e/o pellettizzazione del digestato essiccato; - rivestimento dei granuli e/o dei pellets con un film biodegradabile contenente microrganismi biostimolanti.

2018 - Genetic dissection of the relationships between grain yield components by genome-wide association mapping in a collection of tetraploid wheats [Articolo su rivista]
Mangini, Giacomo; Gadaleta, Agata; Colasuonno, Pasqualina; Marcotuli, Ilaria; Signorile, Antonio M.; Simeone, Rosanna; De Vita, Pasquale; Mastrangelo, Anna M.; Laidò, Giovanni; Pecchioni, Nicola; Blanco, Antonio
abstract

Increasing grain yield potential in wheat has been a major target of most breeding programs. Genetic advance has been frequently hindered by negative correlations among yield components that have been often observed in segregant populations and germplasm collections. A tetraploid wheat collection was evaluated in seven environments and genotyped with a 90K SNP assay to identify major and stable quantitative trait loci (QTL) for grain yield per spike (GYS), kernel number per spike (KNS) and thousand-kernel weight (TKW), and to analyse the genetic relationships between the yield components at QTL level. The genome-wide association analysis detected eight, eleven and ten QTL for KNS, TKW and GYS, respectively, significant in at least three environments or two environments and the mean across environments. Most of the QTL for TKW and KNS were found located in different marker intervals, indicating that they are genetically controlled independently by each other. Out of eight KNS QTL, three were associated to significant increases of GYS, while the increased grain number of five additional QTL was completely or partially compensated by decreases in grain weight, thus producing no or reduced effects on GYS. Similarly, four consistent and five suggestive TKW QTL resulted in visible increase of GYS, while seven additional QTL were associated to reduced effects in grain number and no effects on GYS. Our results showed that QTL analysis for detecting TKW or KNS alleles useful for improving grain yield potential should consider the pleiotropic effects of the QTL or the association to other QTLs.

2018 - Genetic mapping of loci for resistance to stem rust in a tetraploid wheat collection [Articolo su rivista]
Saccomanno, A.; Matny, O.; Marone, D.; Laido, G.; Petruzzino, G.; Mazzucotelli, E.; Desiderio, F.; Blanco, A.; Gadaleta, A.; Pecchioni, N.; De Vita, P.; Steffenson, B.; Mastrangelo, A. M.
abstract

Stem rust, caused by Puccinia graminis f. sp. tritici (Pgt), is a major biotic constraint to wheat production worldwide. Disease resistant cultivars are a sustainable means for the efficient control of this disease. To identify quantitative trait loci (QTLs) conferring resistance to stem rust at the seedling stage, an association mapping panel consisting of 230 tetraploid wheat accessions were evaluated for reaction to five Pgt races under greenhouse conditions. A high level of phenotypic variation was observed in the panel in response to all of the races, allowing for genome-wide association mapping of resistance QTLs in wild, landrace, and cultivated tetraploid wheats. Twenty-two resistance QTLs were identified, which were characterized by at least two marker-trait associations. Most of the identified resistance loci were coincident with previously identified rust resistance genes/QTLs; however, six regions detected on chromosomes 1B, 5A, 5B, 6B, and 7B may be novel. Availability of the reference genome sequence of wild emmer wheat accession Zavitan facilitated the search for candidate resistance genes in the regions where QTLs were identified, and many of them were annotated as NOD (nucleotide binding oligomerization domain)-like receptor (NLR) genes or genes related to broad spectrum resistance.

2018 - Mineral composition of durum wheat grain and pasta under increasing atmospheric CO2concentrations [Articolo su rivista]
Beleggia, Romina; Fragasso, Mariagiovanna; Miglietta, Franco; Cattivelli, Luigi; Menga, Valeria; Nigro, Franca; Pecchioni, Nicola; Fares, Clara
abstract

The concentrations of 10 minerals were investigated in the grain of 12 durum wheat genotypes grown under free air CO2enrichment conditions, and in four of their derived pasta samples, using inductively coupled plasma mass spectrometry. Compared to ambient CO2(400 ppm; AMB), under elevated CO2(570 ppm; ELE), the micro-element and macro-element contents showed strong and significant decreases in the grain: Mn, −28.3%; Fe, −26.7%; Zn, −21.9%; Mg, −22.7%; Mo, −40.4%; K, −22.4%; and Ca, −19.5%. These variations defined the 12 genotypes as sensitive or non-sensitive to ELE. The pasta samples under AMB and ELE showed decreased mineral contents compared to the grain. Nevertheless, the contributions of the pasta to the recommended daily allowances remained relevant, also for the micro-elements under ELE conditions (range, from 18% of the recommended daily allowance for Zn, to 70% for Mn and Mo).

2018 - Phenolic acids profile, nutritional and phytochemical compounds, antioxidant properties in colored barley grown in southern Italy [Articolo su rivista]
Suriano, Serafino; Iannucci, Anna; Codianni, Pasquale; Fares, Clara; Russo, Mario; Pecchioni, Nicola; Marciello, Ugo; Savino, Michele
abstract

Free, soluble conjugated, and insoluble bound phenolic acids and some of the main antioxidant phytochemicals (i.e., total polyphenols, proanthocyanidins, carotenoids) were investigated in 20 genotypes of colored barley. These included 16F8 recombinant inbred lines (RILs) obtained from crosses of four parental lines: ‘2005 FG’ ‘K4-31, ‘L94’ and ‘Priora’. The aim of this work was these to promote the introduction of new barley genotypes with high contents of such natural antioxidants, and of dietary fiber. These new genotypes will enlarge the market of novel functional foods. Large variations were seen in the contents of phytochemicals and β-glucans across these barley genotypes. The highest protein (14.4%) and β-glucan (4.6%) contents were in the blue naked parental genotype ‘2005 FG’. Overall, insoluble bound phenolic acids represented 88.3% of the total phenolic acids, and ferulic acid was the main conjugated phenolic acid. Salicylic and gallic acids were the most represented among the free phenolic acids, with no p-coumaric and cinnamic acids detected. Total polyphenols and proanthocyanidins were highest in the RILs ‘3009′ (2917 μg g−1) and ‘1997′ (1630 μg g−1). The barley line with high total polyphenols (RIL ‘3009′) also showed the highest antioxidant capacities (by both DPPH and ABTS methods: 13.4 μmol g−1 and 15.6 μmol g−1, respectively). Among the RILs examined, ‘3004′ ‘3008′ and ‘3009′ showed 30% higher antioxidant capacities than their parentals, thus providing potential health-promoting benefits.

2018 - Physiological responses to chilling in cultivars of processing tomato released and cultivated over the past decades in Southern Europe [Articolo su rivista]
Ronga, Domenico; Rizza, Fulvia; Badeck, Franz-W; Milc, Justyna; Laviano, Luca; Montevecchi, Giuseppe; Pecchioni, Nicola; Francia, Enrico
abstract

Six processing tomato seedlings, representative of cultivars widely cultivated over the last 80 years in Southern Europe, were compared to assess the physiological responses to chilling. Low temperature stress was applied for 24 h (1 °C, day and night). PEARSON, the oldest cultivar, reported the highest values of chlorophyll content both using DUALEX (ChlDX= 23.11) and SPAD (ChlSPAD= 35.27) and nitrogen balance index (NBIDX= 29.62) measured with DUALEX, before chilling stress. The cultivar E6203 was the least sensitive to chilling with the highest value of maximal photosystem II (PSII) efficiency (Fv/Fm2 = 0.64) at recovery and visual regrowth score (VS3 = 4.0) at regrowth period. As regards chilling tolerance in terms of maximal PSII efficiency, few differences were observed among the cultivars, apart from C33, that was the most sensitive. On the other hand, a better regrowth was recorded in the modern ones. Strong correlations were found between the different parameters investigated both before (SPAD and DUALEX) and after the chilling stress (maximal PSII efficiency, SPAD and electrolyte leakage). SPAD values at regrowth were shown to be a good indicator of tomato chilling status at regrowth period. Analysis of genetic similarity based on microsatellite markers clearly discriminated modern and old varieties according to the year of release. This information could be useful in breeding programs for new cultivars suitable for early transplant, when chilling injury can happen.

2018 - Testing the influence of digestate from biogas on growth and volatile compounds of basil (Ocimum basilicum L.) and peppermint (Mentha x piperita L.) in hydroponics [Articolo su rivista]
Ronga, Domenico; Pellati, Federica; Brighenti, Virginia; Laudicella, Katia; Laviano, Luca; Fedailaine, Maamar; Benvenuti, Stefania; Pecchioni, Nicola; Francia, Enrico
abstract

In this study, a digestate was evaluated for the first time as a sustainable alternative to the conventional growing medium and the nutrient solution in the hydroponic production of aromatic species. Basil (Ocimum basilicum L.) and peppermint (Mentha x piperita L.) were assessed at crop vegetative stage with five fully expanded leaves. Four combinations, i.e. agriperlite (AG) + standard solution (SS), AG + liquid digestate (LD), solid digestate (SD) + SS and SD + LD, were compared. The SD used as the growing medium increased all the investigated agronomical traits, apart the harvest index and shoot dry weight height ratio, that showed the same values compared to agriperlite, on basil and peppermint, respectively. The LD used as the nutrient solution performed as well as the SS on basil and peppermint production, except for the percentage of emergence and total dry weight of basil, showing lower and higher values compared to SS, respectively. Shoot dry weight was the most important agronomical parameter and both basil and peppermint displayed high values using the SD as the growing medium. However, basil recorded the highest dry matter value using SD + LD, while peppermint showed similar values using SD + SS and SD + LD. As regards the volatile compounds of both species, the percentage relative amount of sesquiterpenes was found to be higher under SD + LD and SD + SS conditions in comparison to AG + SS and AG + LD, where the content of monoterpenes and allyl phenol derivatives was higher. SD and LD appear to be sustainable and suitable growing medium and nutrient solution for basil and peppermint grown in hydroponics. Further studies are needed to investigate the influence of the treatments also in advanced developmental stages of the crops, appropriate for the production of plants with high yield and quality.

2018 - Transcriptome profiling of short-term response to chilling stress in tolerant and sensitive Oryza sativa ssp. Japonica seedlings [Articolo su rivista]
Buti, Matteo; Pasquariello, Marianna; Ronga, Domenico; Milc, Justyna Anna; Pecchioni, Nicola; Ho, Viet The; Pucciariello, Chiara; Perata, Pierdomenico; Francia, Enrico
abstract

Low temperature is a major factor limiting rice growth and yield, and seedling is one of the developmental stages at which sensitivity to chilling stress is higher. Tolerance to chilling is a complex quantitative trait, so one of the most effective approaches to identify genes and pathways involved is to compare the stress-induced expression changes between tolerant and sensitive genotypes. Phenotypic responses to chilling of 13 Japonica cultivars were evaluated, and Thaibonnet and Volano were selected as sensitive and tolerant genotypes, respectively. To thoroughly profile the short-term response of the two cultivars to chilling, RNA-Seq was performed on Thaibonnet and Volano seedlings after 0 (not stressed), 2, and 10 h at 10 °C. Differential expression analysis revealed that the ICE-DREB1/CBF pathway plays a primary role in chilling tolerance, mainly due to some important transcription factors involved (some of which had never been reported before). Moreover, the expression trends of some genes that were radically different between Thaibonnet and Volano (i.e., calcium-dependent protein kinases OsCDPK21 and OsCDPK23, cytochrome P450 monooxygenase CYP76M8, etc.) suggest their involvement in low temperature tolerance too. Density of differentially expressed genes along rice genome was determined and linked to the position of known QTLs: remarkable co-locations were reported, delivering an overview of genomic regions determinant for low temperature response at seedling stage. Our study contributes to a better understanding of the molecular mechanisms underlying rice response to chilling and provides a solid background for development of low temperature-tolerant germplasm.

2017 - Advanced imaging tools for plant phenotyping [Abstract in Atti di Convegno]
Costa, C.; Pecchioni, N.; Devita, P.; Menesatti, P.
abstract

High throughput plant phenotyping, also called plant phenomics, is an emerging and fast growing research field that aims to bridge the existing gap between genomics and plant breeding, by solving the so-called phenotyping bottleneck. Moreover, it can supply highly detailed information and tools for the advancement of both plant physiology and agronomy. Plant phenomics takes advantage from the recent developments in the fields of imaging, computer vision and sensor technologies, allowing the nondestructive detection of phenotypic characters. Plant phenomics ranges from basic science to applications in breeding and precision agriculture, combining studies performed under both controlled environments and in the open fields. Last year, Consiglio per la ricerca in agricoltura e l’analisi dell’economia agraria (CREA) joined the Italian Plant Phenotyping Network (ITA-PPN) which gathers the national research centers and universities active in this field. CREA has developed in the last ten years advanced skills for the development of analytical methods for phenotyping, mainly imaging-based. The high-throughput character of our proposed phenotyping methods should help to improve the detection of important plant traits in large field trials as well as help us to reach a better understanding of underlying yield physiological processes and facilitate the genotypephenotype associations. In particular, we developed the following analytic tools for: shape analysis 2d or 3d using landmarks (geometric morphometrics) or outline methods; quantitative color analysis from RGB images (we developed specific algorithms to standardize colors using colorchecker; 3D Thin-Plate Spline); punctual spectrophotometry and hyperspectral imaging; dynamic thermography imaging based; stereovision (multi camera systems for 3d reconstruction). Moreover, we developed an open source conveyor belt prototype multi-sensorized for rapid characterization of experimental wheat field plots. CREA developed advanced analytical approaches based on multivariate methods of prediction and classification (linear approaches and approaches based on artificial neural networks) applied in multi-parametric and multi-sensor metrology for an innovative support in phenomics. All these tools has been developed in Matlab environment, but could be easily exported in open source environments in order to realize highly customizable systems within the phenomics framework.

2017 - Biomass production and dry matter partitioning of processing tomato under organic vs conventional cropping systems in a Mediterranean environment [Articolo su rivista]
Ronga, Domenico; Zaccardelli, Massimo; Lovelli, Stella; Perrone, Domenico; Francia, Enrico; Milc, Justyna Anna; Ulrici, Alessandro; Pecchioni, Nicola
abstract

Modern agriculture should increase crop sustainability while feeding the growing population. The organic cropping system has emerged as an interesting alternative and more sustainable crop management than conventional one. Unfortunately, the current yield gap between organic and conventional systems is significant for most crops, and this limits the organic system's value. Hence, the objective of this study was to investigate biomass production and partitioning of processing tomato genotypes cultivated in organic vs conventional cropping systems in a processing tomato growing area in the Mediterranean. From 2010–2012, field trials were carried out in two farms in Southern Italy. At the end of the crop cycle and in average among years, processing tomato cultivated in organic cropping system showed reductions of: total biomass dry weight (−25%), leaf area (−36%) and radiation use efficiency (−24%). The biomass distribution to fruits and leaves was highly similar under both managements, while a higher fraction of total biomass was allocated to stems (+34%) and to roots (+41%) in the organic cropping system. In the studied environment, a major cause of different fruit dry weight and, consequently, of yield gap between organic and conventional cropping systems was the reduction of the source, i.e. the lower leaf area, that led to a reduction of total biomass dry weight.

2017 - Interventi sui corpi riproduttori: riproduzione e propagazione. [Capitolo/Saggio]
Pecchioni, N.; Noli, E.
abstract

Il testo si articola in quattro parti che analizzano e approfondicono l'agrosistema e i suoi componenti, i sistemi colturali, i sistemi aziendali e i sistemi agricoli. La quinta parte è dedicata alle appendici.

2017 - Pyramiding Ty-1/Ty-3 and Ty-2 in tomato hybrids dramatically inhibits symptom expression and accumulation of tomato yellow leaf curl disease inducing viruses [Articolo su rivista]
Tabein, Saeid; Behjatnia, S. Ali Akbar; Laviano, Luca; Pecchioni, Nicola; Accotto, GIAN PAOLO; Noris, Emanuela; Miozzi, Laura
abstract

Tomato yellow leaf curl disease is a major constraint for tomato production worldwide and availability of new resistant materials is of great importance for breeding programmes. A phenotypic survey was undertaken to evaluate the level of resistance to the main tomato yellow leaf curl disease-inducing viruses Tomato yellow leaf curl virus and Tomato yellow leaf curl Sardinia virus, in several commercial tomato cultivars, never characterised before. Seven weeks post inoculation, two cultivars resulted in high resistant phenotypes to both begomoviruses, and four were tolerant to at least one of them. In the two highly resistant hybrids (SJ12, RFT112), symptoms were completely absent and viral DNA was from 102to 105fold lower than in susceptible plants. Molecular marker analysis revealed that these genotypes harbour the resistant genes Ty-1/Ty-3 and Ty-2. Given their high resistance, they can be considered good candidates for cultivation and breeding in areas where incidence of TYLCD is very elevated.

2017 - Risultati positivi su qualità e rese con l’uso di digestato in vigna [Articolo su rivista]
Ronga, Domenico; Bignami, Cristina; Setti, Leonardo; Laviano, Luca; Hagassou, Djangsou; Caradonia, Federica; Zaghi Massimo, Bezzi; Francia, Enrico; Pecchioni, Nicola
abstract

L’individuazione di fertilizzanti organici innovativi, derivati dal recupero di sottoprodotti delle filiere agricole e agroalimentari, rappresenta un fattore fondamentale per la strutturazione di economie circolari reali. In questa ottica, due fertilizzanti innovativi a base di digestato da impianti di biogas ottenuti anche con l’utilizzo di sottoprodotti della vinificazione sono stati applicati in vigneti dell’Emilia-Romagna sul vitigno Lambrusco salamino per verificarne gli effetti sulla resa produttiva, sulla fermentazione del mosto e sulla qualità del vino, a confronto con fertilizzanti minerale e organo minerale commerciali. Le prove hanno evidenziato che l'impiego dei nuovi formulati costituisce una valida alternativa ai fertilizzanti commerciali classici, in quanto rese produttive, dinamica di fermentazione del mosto e qualità dei vini ottenuti non sono stati alterati dal loro utilizzo. L’impiego di fertilizzanti ottenuti da sottoprodotti della vinificazione permette, inoltre, di creare una vera e propria filiera agroalimentare circolare.

2017 - Speciale grano tenero. Puglia, Campania, Basilicata e Sicilia: dettaglio regionale dei risultati [Articolo su rivista]
Virzi', Nino; Codianni, Pasquale; Licciardello, Stefania; Sciacca, Fabiola; Palumbo, Massimo; Fares, Clara; Pecorella, Ivano; Pecchioni, Nicola
abstract

L'articolo fornisce il dettaglio regionale dei risultati di 6 prove di confronto varietale di Frumento Tenero condotte nell’areale Sud, con il coordinamento del CREA.

2017 - The carotenoid biosynthetic and catabolic genes in wheat and their association with yellow pigments [Articolo su rivista]
Colasuonno, Pasqualina; Lozito, Maria Luisa; Marcotuli, Ilaria; Nigro, Domenica; Giancaspro, Angelica; Mangini, Giacomo; De Vita, Pasquale; Mastrangelo, Anna Maria; Pecchioni, Nicola; Houston, Kelly; Simeone, Rosanna; Gadaleta, Agata; Blanco, Antonio
abstract

Background: In plants carotenoids play an important role in the photosynthetic process and photo-oxidative protection, and are the substrate for the synthesis of abscisic acid and strigolactones. In addition to their protective role as antioxidants and precursors of vitamin A, in wheat carotenoids are important as they influence the colour (whiteness vs. yellowness) of the grain. Understanding the genetic basis of grain yellow pigments, and identifying associated markers provide the basis for improving wheat quality by molecular breeding. Results: Twenty-four candidate genes involved in the biosynthesis and catabolism of carotenoid compounds have been identified in wheat by comparative genomics. Single nucleotide polymorphisms (SNPs) found in the coding sequences of 19 candidate genes allowed their chromosomal location and accurate map position on two reference consensus maps to be determined. The genome-wide association study based on genotyping a tetraploid wheat collection with 81,587 gene-associated SNPs validated quantitative trait loci (QTLs) previously detected in biparental populations and discovered new QTLs for grain colour-related traits. Ten carotenoid genes mapped in chromosome regions underlying pigment content QTLs indicating possible functional relationships between candidate genes and the trait. Conclusions: The availability of linked, candidate gene-based markers can facilitate breeding wheat cultivars with desirable levels of carotenoids. Identifying QTLs linked to carotenoid pigmentation can contribute to understanding genes underlying carotenoid accumulation in the wheat kernels. Together these outputs can be combined to exploit the genetic variability of colour-related traits for the nutritional and commercial improvement of wheat products.

2016 - Agronomic and molecular evaluation of cocksfoot and tall fescue cultivars for adaptation to an Algerian drought-prone environment [Articolo su rivista]
Mefti, M; Bouzerzour, H; Francia, Enrico; Ulrici, Alessandro; Abdelguerfi, A; Barre, P; Pecchioni, Nicola
abstract

A prime objective for improving perennial grasses for Mediterranean environments is the identification and selection of genotypes well adapted to semi-arid conditions. This study was conducted at an experimental site in Algeria over three consecutive seasons, with the aim of evaluating the agronomic performance and genetic diversity of 13 cultivars of two species of perennial grasses: six cocksfoot (Dactylis glomerata L.) and seven tall fescue (Festuca arundinacea Schreb. = syn.Lolium arundinaceum (Schreb.) Darbysh.) cultivars. Variation was found in both species for dry-matter yield, sward recovery, heading date, water-use efficiency (WUE), and summer senescence. Tall fescue cultivars gave greater yield in spring, with earlier heading date and higher WUE than cocksfoot, with no differences for the other traits. Among the genotypes, `Flecha' was the most promising, together with `E-542', `Fraydo' and `Centurion', all of which are tall fescue cultivars. Principal component analysis indicated that persistence of grass cover is relatively independent from dry-matter yield and water-use efficiency. The level of genetic diversity within each species was assessed using AFLP markers, and the molecular variation was analysed together with agronomic trait variation, with identification of molecular markers potentially associated with the relevant traits.

2016 - Copy number variation at the HvCBF4–HvCBF2 genomic segment is a major component of frost resistance in barley [Articolo su rivista]
Francia, Enrico; Morcia, Caterina; Pasquariello, Marianna; Mazzamurro, Valentina; Milc, Justyna Anna; Rizza, Fulvia; Terzi, Valeria; Pecchioni, Nicola
abstract

A family of CBF transcription factors plays a major role in reconfiguring the plant transcriptome in response to low-freezing temperature in temperate cereals. In barley, more than 13 HvCBF genes map coincident with the major QTL FR-H2 suggesting them as candidates to explain the function of the locus. Variation in copy number (CNV) of specific HvCBFs was assayed in a panel of 41 barley genotypes using RT-qPCR. Taking advantage of an accurate phenotyping that combined Fv/Fm and field survival, resistance-associated variants within FR-H2 were identified. Genotypes with an increased copy number of HvCBF4 and HvCBF2 (at least ten and eight copies, respectively) showed greater frost resistance. A CAPS marker able to distinguish the CBF2A, CBF2B and CBF2A/B forms was developed and showed that all the higher-ranking genotypes in term of resistance harbour only CBF2A, while other resistant winter genotypes harbour also CBF2B, although at a lower CNV. In addition to the major involvement of the HvCBF4-HvCBF2 genomic segment in the proximal cluster of CBF elements, a negative role of HvCBF3 in the distal cluster was identified. Multiple linear regression models taking into account allelic variation at FR-H1/VRN-H1 explained 0.434 and 0.550 (both at p < 0.001) of the phenotypic variation for Fv/Fm and field survival respectively, while no interaction effect between CNV at the HvCBFs and FR-H1/VRN-H1 was found. Altogether our data suggest a major involvement of the CBF genes located in the proximal cluster, with no apparent involvement of the central cluster contrary to what was reported for wheat.

2016 - Evaluation of Cucurbita pepo germplasm for staminate flower production and adaptation to the frozen food industry [Articolo su rivista]
Milc, Justyna Anna; Caffagni, Alessandra; Ronga, Domenico; Francia, Enrico; Pasquariello, Marianna; Laviano, Luca; Mazzamurro, Valentina; Pecchioni, Nicola
abstract

Cucurbita pepo is the most economically important species of the genus Cucurbita (Cucurbitaceae). Its edible-fruited cultivated germplasm has been grouped into eight morphotypes (cultivar-groups) divided between two subspecies: pepo and ovifera. In this work, 93 accessions representative of all morphotypes were grown to investigate their genetic variability and to evaluate their potential for production and suitability of male flowers to be used as an Italian frozen food specialty. Results provid the first indications of a plant ideotype for such use. Principal coordinates analysis (PCoA) with nine SSR markers clearly separated the two subspecies, and yielded information on genetically similar vs distant genotypes to be used for parent choice in breeding programs. Analysis of morphological data allowed identification of seven accessions that met all the criteria for the specialty use of male flowers for the frozen food industry: production of many flowers, corolla length of 6–8 cm; and reduced spininess of the foliage. When accessions representing different morphotypes were compared for average male corolla length and average number of male flowers per plant, some accessions of the Pumpkin cultivar-group were observed to be the most suitable for the purpose. Overall, the information collected in the present work is a starting point for exploitation of C. pepo biodiversity in future breeding programs aimed at the production of male flowers for use by the frozen-food industry.

2016 - Marker characterization of vernalization and low-temperature tolerance loci in barley genotypes adapted to semi-arid environments [Articolo su rivista]
Benkherbache, Nadjat; Tondelli, Alessandro; Djekoune, Abdelhamid; Francia, Enrico; Pecchioni, Nicola; Hassous, Liamine; Stanca, Antonio Michele
abstract

For the purpose of marker assisted selection (MAS), six Algerian cultivars and landraces developed locally or introduced from external breeding programs for semi-arid environments were marker characterized at VRN-H1, VRN-H2 and FR-H2 loci. As controls the lines Nure and Tremois were used. Markers available in the literature, known to discriminate efficiently the trait-associated alleles between the two cultivars Nure and Tremois, were used. This study revealed that the used Algerian cultivars carry a dominant (spring) allele for VRN-H1, while the HvZCCT marker generated a polymorphic profile for the second vernalization locus VRN-H2. No cultivars possessed the Nure allele conferring tolerance to low-temperatures at the HvCBF4. Three cultivars possessed the Tremois allele at FR-H2, while the remaining three presented different haplotypes.

2016 - Nuovi fertilizzanti. La risorsa digestato [Articolo su rivista]
Ronga, Domenico; Bignami, Cristina; Tagliavini, Stefano; Zaghi, Massimo; Bezzi, Guido; Francia, Enrico; Pecchioni, Nicola
abstract

Fertilizzanti innovativi organici e organo-minerali ottenuti da digestato sono stati apportati a vigneti del territorio modenese e reggiano per verificarne gli effetti sulla produttività e sulla qualità del prodotto e la capacità di garantire il ritorno continuo della sostanza organica al terreno, contribuendo a migliorare la fertilità del terreno e il bilancio del carbonio del comprensorio. L’uso di digestato e di formulazioni organo-minerali sperimentali a base digestato non ha determinato effetti negativi sulla chioma in termini di area fogliare, percentuale di foglie esterne e di grappoli esposti. I risultati preliminari indicano che questi formulati sembrano comportarsi come i fertilizzanti tradizionali, sia per quanto riguarda gli aspetti vegeto-produttivi delle viti sia per la qualità di base del mosto

2016 - Use of Solid Digestate as Growing Media for the Production of Horticultural Crops. [Abstract in Atti di Convegno]
Ronga, Domenico; Pecchioni, Nicola; Milc, Justyna Anna; Tagliavini, Stefano; Zaghi, Massimo; Francia, Enrico
abstract

Peat is the principal component used for growing media of horticultural crops due to its agronomic characteristics. On the other hand, is a nonrenewable material (Herrera et al., 2008). Previous researches indicated the compatibility of some renewable composted organic wastes in mixture with peat-based media (Herrera et al., 2008; Ronga et al., 2016). However, the composting process might increase the GHGs emissions (Lim et al., 2016). Thus, the aim of this work was to evaluate the use of anuntreated solid digestate as a component in the formulation of growing media for the seedling production of two crop reference species: tomato and basil.

2016 - Use of Spent Coffee Ground Compost in Peat-Based Growing Media for the Production of Basil and Tomato Potting Plants [Articolo su rivista]
Ronga, Domenico; Pane, Catello; Zaccardelli, Massimo; Pecchioni, Nicola
abstract

A spent coffee ground compost (SCGC) was evaluated as an alternative component of growing media to partially replace commercial peat (CP) and fertilizers in the production of potted plants. Seven mixtures (CP 100% + solid mineral fertilizers, CP 100% + liquid mineral fertilizers, CP 90% + SCGC 10%, CP 80% + SCGC 20%, CP 70% + SCGC 30%, CP 60% + SCGC 40%, and CP 100% without fertilizers) were compared for the production of basil and tomato potted plants. SCGC used in a proportion up to 40% enhanced the general plant stand by affecting the dry weight and the measured foliar parameters. Tomato and basil recorded good growth rates on SCGC-amended media, showing quality indices similar to those obtained under fertilization, evidencing compost plant nutrition provision. SCGC appears to be suitable for application as a partial peat substitute in the production of potted plants.

2016 - Valutazione dell’effetto di fertilizzanti innovativi organici e organominerali sulla produzione del vigneto e sulla qualità del prodotto [Relazione in Atti di Convegno]
Ronga, Domenico; Bignami, Cristina; Tagliavini, Stefano; Zaghi, Massimo; Bezzi, Guido; Francia, Enrico; Pecchioni, Nicola
abstract

Evaluation of the effect of innovative organic and organo-mineral fertilizers on vineyard productivity and grape quality - The identification of organic fertilizers is a fundamental objective in sustainable viticulture. The research aimed at formulating and evaluating new fertilizers from digestate containing by-products of the wine industry in two vineyards located in Modena area. Two new experimental fertilizers, an organic (pellets from digestate) and an organo-mineral (organic fraction from digestate) fertilizer, were compared with commercial fertilizers to cv Lambrusco salamino. The results do not indicate negative effects on vegetative-productive indexes. The highest SPAD index values were recorded in plants that received the commercial mineral fertilizer, and similar values were observed using innovative organo-mineral fertilizer was applied. Total number and average weight of bunches, production per plant and must acidity did not differ among thesis. The highest soluble solids content (°Brix) of the must was observed in plants not fertilized.

2015 - CNV and structural variation in plants: prospects of NGS approaches [Capitolo/Saggio]
Francia, Enrico; Pecchioni, Nicola; Policriti, Alberto; Scalabrin, Simone
abstract

Deletion, insertion, and duplications larger than 1 kb are structural variants (SVs) classified as copy number variants (CNVs). Beside single nucleotide variants (SNVs), CNVs are widespread in plants and substantially contribute to intra-species genetic variation. Most CNVs reported so far overlap with protein-coding sequences and result in gains or losses of gene copies that might directly influence transcript dosage. In several cases they proved to play an important role in the adaptive response of plants, by regulating development, and by increasing resistance to biotic and abiotic stresses. The advent of next-generation sequencing (NGS) is giving the possibility to uncover frequency and importance of CNVs. Although complexity of plant genomes and the short read length obtained from NGS platforms posed technical and computational challenges for their discovery, these are currently tackled with five strategies. New developments are expected, by third-generation NGS, the need for comprehensive databases, and the application in plant improvement

2015 - Detection of Single-feature Polymorphisms (SFPs) between two tomato varieties and their application in defining the introgressions of resistance loci [Articolo su rivista]
Milc, Justyna; Infantino, Alessandro; Aragona, Maria; Pecchioni, Nicola
abstract

The objectives of the study were to (i) demonstrate that the hybridization data from microarrays can yield information on sequence variation between two inbred lines, an introgression line 'Mogeor' and its genetic background 'Moneymaker'; (ii) characterize, by means of the identified SFPs, the introgressed genomic segments of 'Mogeor', carrying resistance genes; and (iii) deliver a set of genetically anchored SFPs potentially useful for breeding. In this work, the GeSNP software was used to identify SFPs in tomato using Affymetrix data from a previous experiment. Sequencing of 12 putative polymorphism-containing amplicons yielded a SFP probe set validation rate of 90%. In total, 92 Gene Models putatively harbouring SFPs were identified, distributed as following: 61 Gene Models on chromosome 9, and one to eight on the remaining tomato chromosomes apart from chromosomes 7, 8 and 12. Newly discovered SFPs from microarray data can thus provide not only useful information for definition of introgressed genomic regions, but also identification of candidate genes and new markers for MAS.

2015 - Isolation of a Sequence Homolog to More Axillary Branches MAX2 Gene in Hibiscus rosa-sinensis and its use as Genetic Marker [Articolo su rivista]
Braglia, Luca; Nicoletti, Federica; De Benedetti, Laura; Pecchioni, Nicola; Mercuri, Antonio
abstract

Lateral branching plays an important role in the elaboration of adult plants architecture. Herein, we adopted a modified AFLP approach combined with a degenerate primer amplification to identify and isolate in the underinvestigated ornamental species H. rosasinensis an orthologous element of the MAX2 gene (More Axillary Branches), which acts downstream of the branching inhibition signaling pathway. A specific gene fragment was cloned and sequenced from nineteen H. rosa-sinensis cultivars and twelve Hibiscus botanical species and different significant nucleotide polymorphisms among genotypes that were observed. The comparative analysis revealed a high conservation of DNA sequences among cultivars and wild species sexually compatible with H. rosa-sinensis. The deduced amino acid sequences of the Hibiscus isolated fragments reveal four characteristic repeat regions showing high identity with other F-box/Leucine Reach Repeat MAX2 homologous sequences. The cloned fragment is a likely candidate gene to be validated for association with phenotype to release a gene-derived "perfect marker" for the compact habit trait.

2015 - Pelleting is a successful method to eliminate the presence of Clostridium spp. from the digestate of biogas plants [Articolo su rivista]
Pulvirenti, Andrea; Ronga, Domenico; Mannella, Lorenzo; Pecchioni, Nicola; Zaghi, Massimo; Tomasselli, Anna Rita; Mannella, Lorenzo; Pecchioni, Nicola
abstract

Biogas production is increasing as a sustainable energy supply, with digestate resulting as a by-product of biogas plants. As a result, the high concentration of Clostridium spp. in digestate became a concern in dairy farming areas. Clostridium spores can contaminate soils and crops when digestate is used as fertilizer, causing a con fl ictual cohabitation of biogas with traditional cheese productions. In order to solve the problem, this study aimed to search for a technical solution enabling either a drastic reduction or the elimination of the content of Clostridium spp. within digestate. Results showed a complete elimination of Clostridium spp. in pelleted stored solid digestate; in addition, pelleting caused a reduction of pH and water mass fraction in terms of fresh weight, and a concentration of mineral nutrients compared to stored solid digestate. Pellet can represent a possible sustainable solution both in reducing potential risks linked to the presence of Clostridium spp. in digestate and in improving the transportation and distri- bution of high-value fertilizer. Hence, pelleting of solid digestate could offer a simple and ef ficient method to allow cohesistence of biogas plants and dairy farming

2015 - Physiological responses of processing tomato in organic and conventional Mediterranean cropping systems [Articolo su rivista]
Ronga, Domenico; Lovelli, Stella; Zaccardelli, Massimo; Perrone, Domenico; Ulrici, Alessandro; Francia, Enrico; Milc, Justyna Anna; Pecchioni, Nicola
abstract

Processing tomato is a globally important horticultural crop. It is generally grown in high-input conventional systems, and there is little knowledge regarding its physiological responses in organic cultivation. Therefore, the aim of this work was to determine the influence of organic management on the physiological behavior of cultivars of processing tomato usually cultivated in conventional management in a Mediterranean area. The study was performed by means of: (1) field testing of a set of commercial cultivars for 2 years, in two systems, in one location in Southern Italy, and (2) crop physiological investigations during the growth cycle of processing tomato. Results of the two-year trials indicate that, under the organic cropping system, processing tomato showed, as 2 years average, higher intercellular CO2 concentration (Ci) (+10.3%), transpiration (E) (+15.5%) and stomatal conductance (gs) (+16.5%). Average net assimilation (A) was similar in the two systems and differences were only observed depending on years. In contrast, average leaf area index (LAI) and water use efficiency (WUE) were lower in the organic cropping system (−42% and −17.8%), as were average fruit (FDW) and total (TDW) dry weight (−37.5% and −29%). In our conditions, LAI at the end of the cultivation was highly correlated with total and fruit dry weight. As differences in fruit and total dry weight of processing tomato cannot be explained by differences in net assimilation per leaf area unit, other reasons may be linked to the effects of the organic management on the crop as weeds and pathogens.

2014 - Candidate gene expression profiling in two contrasting tomato cultivars under chilling stress [Articolo su rivista]
Caffagni, Alessandra; Pecchioni, Nicola; Francia, Enrico; D., Pagani; Milc, Justyna Anna
abstract

Tomato (Solanum lycopersicum Mill.) is sensitive to chilling stress during all stages of plant development. Genetic variation for chilling tolerance exists between cultivated tomato and its related wild species, but intra-specific variation has not been thoroughly investigated so far. Seedlings of 63 tomato accessions were evaluated under low temperature and two contrasting cultivars were identified for the trait: Albenga and San Marzano, the former being more chillingtolerant. To clarify the molecular mechanisms of chilling tolerance in tomato, changes in candidate gene expressions in the two tomato genotypes were analysed, using quantitative RT-PCR. Candidate genes were chosen among those known to be induced by chilling and/or with putative roles in CBF/DREB and ROS-mediated pathways. Results show that besides a CBF regulon, whose function is conserved, ROS and C2H2-type zinc finger protein-mediated cold signalling pathways were also involved in chilling tolerance. Under the chilling stress, the up-regulation of respective transcripts was consistently higher in the chilling-tolerant genotype than in the chilling-sensitive ones.

2014 - Caratterizzazione della biodiversità di Cucurbita pepo L. per la produzione di specialità alimentari mediterranee [Abstract in Atti di Convegno]
Ronga, Domenico; Caffagni, Alessandra; Francia, Enrico; Milc, Justyna Anna; Mazzamurro, Valentina; Pecchioni, Nicola
abstract

Tra le Cucurbitaceae lo zucchino rappresenta la specie orticola più coltivata. Generalmente se ne utilizza il frutto, tuttavia in alcune regioni Italiane anche il fiore maschile trova impiego ed interesse. Recentemente il fiore di zucchina pastellato e fritto trova grande impiego in cucina, nella ristorazione e nei catering soprattutto come finger food. Tuttavia, i materiali attualmente coltivati presentano una bassa produzione di fiori maschili. Pertanto obiettivo della ricerca è stato quello di valutare e caratterizzare una collezione di Cucurbita pepo L. col fine di individuare materiali maggiormente adatti alla produzione di fiori maschili.

2014 - Genomics of Low-Temperature Tolerance for an Increased Sustainability of Wheat and Barley Production [Capitolo/Saggio]
Pecchioni, Nicola; Klara, Kosová; P., Vítámvás; Ilia Tom, Prášil; Milc, Justyna Anna; Francia, Enrico; Z., Gulyás; Gabor, Kocsy; Gabor, Galiba
abstract

Stability of high yields in a changing environment becomes the main aim of the future wheat and barley breeding, oriented towards development of frost-tolerant winter and facultative cultivars together with careful selection of growth cycle adaptation and drought tolerance. Since low temperature signal influences both the cold acclimation and vernalization processes the interaction between VRN gene expression and frost tolerance (FT) is discussed. Recent advances in global expression changes driven by cold are reviewed in view of the immense progress in high throughput technological platforms. Different signal transduction pathways in which several transcription factors play an important role regulating the expression of whole sets of genes are presented, including CBF-regulated and CBF-independent hubs. The knowledge acquired from genomics and transcriptome analysis has been then complemented by the description of metabolomics and proteomic approaches to help unraveling the molecular changes that occur under cold stress in the cereal plants. Finally, it is surveyed the great importance of stable and well-characterized genetic resources for future breeding for FT, that could switch from marker-assisted to genomics-assisted selection.

2014 - QTLs for barley yield adaptation to Mediterranean environments in the ‘Nure’ × ‘Tremois’ biparental population [Articolo su rivista]
Tondelli, A.; Francia, Enrico; A., Visioni; J., Comadran; A. M., Mastrangelo; T., Akar; A., Al Yassin; S., Ceccarelli; S., Grando; A., Benbelkacem; F. A., van Eeuwijk; W. T. B., Thomas; A. M., Stanca; I., Romagosa; Pecchioni, Nicola
abstract

Multi-environment trials represent a highly valuable tool for the identification of the genetic bases of crop yield potential and stress adaptation. A Diversity Array Technology®-based barley map has been developed in the ‘Nure’ × ‘Tremois’ biparental Doubled Haploid population, harbouring the genomic position of a gene set with a putative role in the regulation of flowering time and abiotic stress response in barley. The population has been evaluated in eighteen location-by-year combinations across the Mediterranean basin. QTL mapping identified several genomic regions responsible for barley adaptation to Mediterranean conditions in terms of phenology, grain yield and yield component traits. The most frequently detected yield QTL had the early flowering HvCEN_EPS2 locus (chromosome 2H) as peak marker, showing a positive effect from the early winter parent ‘Nure’ in eight field trials, and explaining up to 45.8 % of the observed variance for grain yield. The HvBM5A_VRN-H1 locus on chromosome 5H and the genomic region possibly corresponding to PPD-H2 on chromosome 1H were significantly associated to grain yield in five and three locations, respectively. Environment-specific QTLs for grain yield, and clusters of yield component QTLs not related to phenology and or developmental genes (e.g. on chromosome 4H, BIN_09) were observed as well. The results of this work provide a valuable source of knowledge and tools for both explaining the genetic bases of barley yield adaptation across the Mediterranean basin, and using QTL-associated markers for MAS pre-breeding and breeding programmes.

2014 - Studio di parametri fisiologici nel pomodoro da industria in coltivazione biologica [Abstract in Atti di Convegno]
Ronga, Domenico; Lovelli, Stella; Zaccardelli, Massimo; Francia, Enrico; Milc, Justyna Anna; Pecchioni, Nicola
abstract

Il pomodoro da industria è un importante coltura a livello mondiale. La coltivazione viene generalmente effettuata in sistemi di coltivazione convenzionale, per questo motivo scarse sono le conoscenze fisiologiche della coltura in coltivazione biologica. Quindi l’obiettivo del lavoro è stato valutare l’effetto della coltivazione biologica sulla fisiologia del pomodoro da industria investigando la produzione di sostanza secca di tre cultivar a bacca tonda e tre a bacca allungata, coltivate in un’areale del Sud Italia a confronto con un sistema convenzionale.

2014 - The barley Frost resistance-H2 locus [Articolo su rivista]
Pasquariello, Marianna; Delfina, Barabaschi; Axel, Himmelbach; Burkhard, Steuernagel; Ruvini, Ariyadasa; Nils, Stein; Gandolfi, Francesco; Tenedini, Elena; Bernardis, Isabella; Tagliafico, Enrico; Pecchioni, Nicola; Francia, Enrico
abstract

Frost resistance-H2 (Fr-H2) is a major QTL affecting freezing tolerance in barley, yet its molecular basis is still not clearly understood. To gain a better insight into the structural characterization of the locus, a high-resolution linkage map developed from the Nure x Tremois cross was initially implemented to map 13 loci which divided the 0.602 cM total genetic distance into ten recombination segments. A PCR-based screening was then applied to identify positive bacterial artificial chromosome (BAC) clones from two genomic libraries of the reference genotype Morex. Twenty-six overlapping BACs from the integrated physical-genetic map were 454 sequenced. Reads assembled in contigs were subsequently ordered, aligned and manually curated in 42 scaffolds. In a total of 1.47 Mbp, 58 protein-coding sequences were identified, 33 of which classified according to similarity with sequences in public databases. As three complete barley C-repeat Binding Factors (HvCBF) genes were newly identified, the locus contained13 full-length HvCBFs, four Related to AP2 Triticeae (RAPT) genes, and at least five CBF pseudogenes. The final overall assembly of Fr-H2 includes more than 90 % of target region: all genes were identified along the locus, and a general survey of Repetitive Elements obtained. We believe that this gold-standard sequence for the Morex Fr-H2 will be a useful genomic tool for structural and evolutionary comparisons with Fr-H2 in winter-hardy cultivars along with Fr-2 of other Triticeae crops.

2014 - Update on the genomics and basic biology of Brachypodium. International Brachypodium Initiative (IBI) [Articolo su rivista]
Catalan, Pilar; Chalhoub, Boulos; Chochois, Vincent; Garvin, David F.; Hasterok, Robert; Manzaneda, Antonio J.; Mur, Luis A. J.; Pecchioni, Nicola; Rasmussen, Søren K.; Vogel, John P.; Voxeur, Aline
abstract

The scientific presentations at the First International Bra-chypodium Conference (abstracts available at http://www.brachy2013.unimore.it) are evidence of the wide-spread adoption of Brachypodium distachyon as a model system. Furthermore, the wide range of topics presented (genome evolution, roots, abiotic and biotic stress, com-parative genomics, natural diversity, and cell walls) demonstrates that the Brachypodium research commu-nity has achieved a critical mass of tools and has transi-tioned from resource development to addressing biological questions, particularly those unique to grasses. © 2014 Elsevier Ltd.

2014 - Zucchino da fiore, possibile opportunità di reddito [Articolo su rivista]
Ronga, Domenico; Caffagni, Alessandra; S., Pizzagalli; D., Inglese; L., Ziosi; Pecchioni, Nicola
abstract

Il fi ore maschile di zucchino, trasformato dall’industria in pastellato e prefritto, può raddoppiare i ricavi aziendali rispetto allo zucchino convenzionale, a patto di rispettare gli elevati standard qualitativi richiesti dalla fi liera

2013 - Characterization of an Italian rice germplasm collection with genetic markers useful for breeding to improve eating and cooking quality [Articolo su rivista]
Caffagni, Alessandra; Albertazzi, Giorgia; G., Gavina; S., Ravaglia; A., Gianinetti; Pecchioni, Nicola; Milc, Justyna Anna
abstract

Gelatinization temperature and apparent amylose content are key parameters used to describe the eating and cooking qualities of rice. Sequence variants of SSIIa and Waxy genes are important determinants of gelatinization temperature and apparent amylose content, respectively. A collection of Italian non-glutinous japonica rice accessions was characterized for sequence polymorphisms in SSIIa and Waxy genes, in comparison with non-Italian japonica and indica genotypes. For SSIIa two markers, SNP3 and SNP4, were used. A PCR amplification of multiple specific alleles protocol was developed for the identification of G/T polymorphism in 5′ splice site of first intron and A/C polymorphism in exon 6 of the Waxy gene. Based on simple allele-specific PCR, it can be proposed as a user-friendly, cost-effective tool for marker-assisted selection of amylose content. The collection was characterized also for the (CT)n repeats in exon 1 of the Waxy gene. The results showed that while SSIIa haplotypes were rather similar between Italian and non-Italian japonica rice, the Waxy gene haplotype T/A/(CT)18 was largely predominant in Italian accessions, other haplotypes, well represented in non-Italian japonica [T/A/(CT)19] and indica [e.g. G/C/(CT)20] genotypes, were present at lower frequency. Grain starch quality traits as apparent amylose content and RVA profile were also analysed. The In1/Ex6 SNP haplotypes of Wx gene were found to explain 79 % of variation in apparent amylose content, and 36, 22 and 25 %, of variation in the RVA parameters peak viscosity, breakdown and setback, respectively. The additional use of (CT)n repeats marker further improved the association of haplotypes with RVA parameters.

2013 - Concimazione: meglio se minerale con la giusta dose [Articolo su rivista]
Ronga, Domenico; Pecchioni, Nicola; D., Perrone; M., Zaccardelli
abstract

Se la concimazione organica migliora la consistenza e l’omogeneità della pezzatura rispetto alla concimazione minerale, tuttavia troppo elevato è il divario tra i due sistemi di fertilizzazione per quanto riguarda le rese produttive fornite e le caratteristiche qualitative delle bacche di pomodoro in fase di trasformazione Parcelle

2013 - Determinants of barley grain yield in drought-prone Mediterranean environments [Articolo su rivista]
Francia, Enrico; Alessandro, Tondelli; Fulvia, Rizza; Franz W., Badeck; William T. B., Thomas; Fred Van, Eeuwijk; Ignacio, Romagosa; A., Michele Stanca; Pecchioni, Nicola
abstract

The determinants of barley grain yield in drought-prone Mediterranean environments have been studied in the Nure x Tremois (NT) population. A large set of yield and other morpho-physiological data were recorded in 118 doubled haploid (DH) lines of the population, in multi-environment field trials (18 site-year combination). Agrometeorological variables have been recorded and calculated at each site too. Four main periods of barley development were considered, vegetative, reproductive early and late grain filling phases, to dissect the effect on yield traits of the growth phases. Relationships between agrometeorological variables, grain yield (GY) and its main components (GN and GW) were also investigated by correlation. Results firstly gave a clear indication of the involvement of water consumption in determining GY and GW (r2=0.616, P=0.007 and r2=0.703, P=0.005, respectively) calculated from sowing to the early grain filling period, while GN showed its highest correlation with the total photothermal quotient (PQ) calculated for the same period (r2=0.646, P=0.013). With the only exception of total PQ calculated during the vegetative period, all significant correlations with GY were associated to water-dependent agrometeorological parameters. As a second result, the NT segregating population allowed us to weight the amount of interaction due to genotypes over environments or to environments in relation to genotypes by a GGE analysis; 47.67% of G+GE sum of squares was explained by the first two principal components. Then, the introduction of genomic information at major barley genes regulating the length of growth cycle allowed us to explain patterns of adaptation of different groups of NT lines according to the variants (alleles) harbored at venalization (Vrn-H1) in combination with earliness (Eam6) genes. The superiority of the lines carrying the Nure allele at Eam6 was confirmed by factorial ANOVA testing the four possible haplotypes obtained combining alternative alleles at Eam6 and Vrn-H1. Maximum yield potential and differentials among the NT genotypes was finally explored through Finlay-Wilkinson model to interpret grain yield of NT genotypes together with yield adaptability (Ya), as the regression coefficient bi; Ya ranged from 0.71 for NT77 to 1.20 for NT19. Lines simply harboring the Nure variants at the two genes behaved as highest yielding (3.04 t ha–1), and showed the highest yield adaptability (bi=1.05). The present study constitutes a starting point towards the introduction of genomic variables in agronomic models for barley grain yield in Mediterranean environments.

2013 - Freezing Tolerance in the Triticeae [Capitolo/Saggio]
Galiba, Gabor; Eric J., Stockinger; Francia, Enrico; Milc, Justyna Anna; Gabor, Kocsy; Pecchioni, Nicola
abstract

Species of the Triticeae tribe of the Poaceae, such as wheat and barley, able to acclimate to and to tolerate frost, are one of the best models for studying freezing tolerance in herbaceous, nonwoody plants. This chapter reviews in detail the genetic and genomic knowledge accumulated over the last twenty years in these model species, in terms of genetic loci and sequence variation able to confer higher tolerance to frost. Genomic selection (GS) could be particularly useful for accumulating durable (quantitative) disease resistance quantitative trait loci (QTLs) in wheat, as proposed by Rutkoski and colleagues for stem rust, where the multigenic nature of adult plant resistance hampers the efficiency of MAS-based pyramiding. Lastly, the use of genetic resources, as well as new genomic tools for producing freezing tolerant varieties, is discussed.

2013 - Genome-wide association mapping of frost tolerance in barley (Hordeum vulgare L.) [Articolo su rivista]
Visioni, A; Tondelli, A; Francia, Enrico; Pswarayi, A; Malosetti, M; Russell, J; Thomas, W; Waugh, R; Pecchioni, Nicola; Romagosa, I; Comadran, J.
abstract

Background: Frost tolerance is a key trait with economic and agronomic importance in barley because it is a major component of winter hardiness, and therefore limits the geographical distribution of the crop and the effective transfer of quality traits between spring and winter crop types. Three main frost tolerance QTL (Fr-H1, Fr-H2 and Fr-H3) have been identified from bi-parental genetic mapping but it can be argued that those mapping populations only capture a portion of the genetic diversity of the species. A genetically broad dataset consisting of 184 genotypes, representative of the barley gene pool cultivated in the Mediterranean basin over an extended time period, was genotyped with 1536 SNP markers. Frost tolerance phenotype scores were collected from two trial sites, Foradada (Spain) and Fiorenzuola (Italy) and combined with the genotypic data in genome wide association analyses (GWAS) using Eigenstrat and kinship approaches to account for population structure. Results: GWAS analyses identified twelve and seven positive SNP associations at Foradada and Fiorenzuola, respectively, using Eigenstrat and six and four, respectively, using kinship. Linkage disequilibrium analyses of the significant SNP associations showed they are genetically independent. In the kinship analysis, two of the significant SNP associations were tightly linked to the Fr-H2 and HvBmy loci on chromosomes 5H and 4HL, respectively. The other significant kinship associations were located in genomic regions that have not previously been associated with cold stress. Conclusions: Haplotype analysis revealed that most of the significant SNP loci are fixed in the winter or facultative types, while they are freely segregating within the un-adapted spring barley genepool. Although there is a major interest in detecting new variation to improve frost tolerance of available winter and facultative types, from a GWAS perspective, working within the un-adapted spring germplasm pool is an attractive alternative strategy which would minimize statistical issues, simplify the interpretation of the data and identify phenology independent genetic determinants of frost tolerance.

2013 - Molecular breeding [Capitolo/Saggio]
Sabatini, E.; M., Beretta; T., Sala; N., Acciarri; Milc, Justyna Anna; Pecchioni, Nicola
abstract

Breeding efforts are and will be in the future critical to improve worldwide crop production for food, feed, non-food industrial and environmental aims. The recent development of "omics" sciences, in particular genomics, and bioinformatics give the great opportunity to be either integrated into traditional breeding schemes, or used to generate new breeding schemes and paradigms. There are important expectations from such technologies and from new genome-wide informations to enhance the effectiveness of plant breeding programs, starting from main crops such as tomato. When genotyping tools will not be anymore a limit, one issue crucial for future breeding will be the availability of well characterized germplasm collections. A detailed genetic analysis of the breeder's germplasm aided by DNA technologies will make more and more useful good programs of pre-breeding, to help in planning crosses and guiding the choice of inbred lines for hybrid combinations. As a side-aspect of this, DNA tools can be applied for DUS and hybrid purity testing. Molecular markers enable marker-assisted selection (MAS) for gene and QTL introgression, gene pyramiding and genetic ideotype breeding. MAS application presents several advantages such as increased reliability and efficiency provided by the fact that they can be scored at the seedling stage enabling indirect selection especially for quantitative traits with low heritabilities. MAS becomes particularly useful, or necessary when a phenotypic assay may be influenced by the environment, is particularly costly or technically difficult, MAS integration into classical breeding schemes, as well as the new possibilities are reviewed. Nowadays the cost of genotyping a plant rather than the cost of a datapoint, limited molecular marker polymorphism within cultivated tomato, and thus unavailability of closely-linked markers for all agronomically relevant traits, are the main limitations of MAS. However a trend towards an increased cost accessibility of genomics-based technologies is underway. On the other hand, in developing countries the unfamiliarity of many traditional plant breeders with the use of molecular markers and technologies still represents a major limitation. Eventually, for most crops MAS will be scaled up to the genomic level, consequently the breeder could practice whole genome selection. The expectations from genomics-assisted selection (GAS) are high for many species including tomato. The shifts to second and, soon, to third generation sequencing technologies will provide unique ways in which to conceive plant breeding programs. In addition, the development of phenomics and metabolomics should be taken into great consideration. Transgenic breeding, offers several advantages such as ability to overcome incompatibility barriers and the possibility to incorporate only the specific cloned gene into the recipient, thus avoiding the transfer of undesirable genes in introgressed chromosome regions from wild donors . Very strict release procedures unfortunately severely limit this opportunity, until the development of cisgenics or of other technical alternatives. Pyramiding of transgenes with either similar or complementary and/or additive effects is possible. It is here reviewed how tomato has been modified for improvement of different traits such as fruit quality, parthenocarpy, constitutive overproduction of antifungal compounds, bacterial and viral disease resistance and post-harvest and processing technology.

2013 - TRANSCRIPTOME ANALYSIS IN THE INTERACTION BRACHYPODIUM – PUCCINIA BRACHYPODII [Abstract in Atti di Convegno]
Mazzamurro, Valentina; Laviano, Luca; Thierri, Marcel; Milc, Justyna Anna; Francia, Enrico; Rients, Niks; T., Vozabova; David, Garvin; Enrica, Roncaglia; MALAGOLI TAGLIAZUCCHI, Guidantonio; Bicciato, Silvio; Tagliafico, Enrico; Pecchioni, Nicola
abstract

The model grass Brachypodium distachyon L (Brachypodium) has recently revealed its potential for studying grass-pathogen interactions. In particular, the identification of genomic regions associated with resistance to the false brome rust fungus Puccinia brachypodii offered perspectives to elucidate the genetic and molecular basis of this trait. In this study, we aimed to: 1) provide an initial whole-genome expression dataset for Brachypodium-P. brachypodii interaction in the two inbred lines Bd3-1 (resistant) and Bd1-1 (susceptible), and 2) fine mapping and cloning Rpbq2 and Rpbq3: to increase the resolution of QTL mapping and to reduce the number of candidate genes underlying QTL LOD curves. For the first, aim the two inbred lines have been characterized macroscopically and by confocal microscopy to follow the development of the fungus and the formation of rust infection structures. The expression of six brachypodium genes, homologous to known wheat and barley defence-related genes, was monitored by qRT-PCR analysis in Bd3-1 and Bd1-1 at three time points (18, 24 and 72 hours post infection, hpi). The 18 hpi time point was selected for transcriptome profiling on the basis of the expression profiles of the defence genes. The Affymetrix Brachypodium Tiling Array (BradiAR1b520742) revealed that expression levels of a set of genes (more than 100 in total) were altered in infected plants, mainly in the resistant line Bd3-1. At 18 hpi a significant re-programming of host metabolism occurred in infected leaves, with a modulation of genes involved in different metabolic networks such as defence, glycolysis, aminoacid and nitrogen metabolism. This study represents the first characterization of the functional genomic basis of resistance to a rust species in the model plant Brachypodium, and could be useful for translational genomics to ‘complex’ cereals. For the second aim, fine mapping Rpbq2 and Rpbq3, a new large segregating RIL population has been developed for each QTL separately. Selection of Bd3-1 x Bd1-1 RILs heterozygous for the QTLs has been completed based on flanking marker haplotypes, with the target QTL in a heterozygous state, while the other two QTLs were selected to be homozygous for the susceptible allele. These marker-selected heterozygous RILs have been selfed to obtain large segregating populations for each QTL. These results represent the first steps of a genetic approach towards the cloning of Rpbq2 and Rpbq3 determinants, and for their possible exploitation in cereals.

2013 - Varietà di tondo-squadrato e lungo per l’industria al Sud [Articolo su rivista]
Ronga, Domenico; Pecchioni, Nicola; D., Perrone; M., Zaccardelli
abstract

Le prove hanno riguardato le caratteristiche produttive e qualitative di sei varietà appartenenti alle tipologie tondo- squadrato e lungo; i materiali testati hanno espresso buone produzioni commerciali confermandosi su valori tipici dell’areale di produzione e hanno fornito buoni valori di pH e indice Brix

2012 - A major QTL for resistance to soil-borne cerealmosaic virus derived from an old Italian durum wheat cultivar [Articolo su rivista]
Russo, Ma; Dbm, Ficco; D., Marone; P., De Vita; V., Vallega; C., Rubies Autonell; C., Ratti; P., Ferragonio; V., Giovanniello; Pecchioni, Nicola; L., Cattivelli; Am, Mastrangelo
abstract

The genetic basis of resistance to soil-borne cereal mosaic virus (SBCMV) in the Triticum turgidum L. var. durum cv. Neodur was analyzed in this study, using a linkage mapping approach. We performed phenotypic and molecular analyses of 146 recombinant inbred lines derived from the cross Cirillo (highly susceptible)×Neodur (highly resistant). A major quantitative trait locus (QTL) that explained up to 87% of the observed variability for symptom severity was identified on the short arm of chromosome 2B, within the 40-cM interval between the markers Xwmc764 and Xgwm1128, with wPt-2106 as the peak marker. Three minor QTLs were found on chromosomes 3B and 7B. Two markers coding for resistance proteins co-segregate with the major QTL on chromosome 2B and the minor QTL on chromosome 3B, representing potential candidate genes for the two resistance loci. Microsatellite markers flanking the major QTL were evaluated on a set of 25 durum wheat genotypes that were previously characterized for SBCMV resistance. The allelic composition of the genotypes at these loci, together with pedigree data, suggests that the old Italian cultivar Cappelli provided the SBCMV-resistance determinants to durum cultivars that have been independently bred in different countries over the last century.

2012 - Adaptation to environment in diploid barley: from quantitatively inherited traits, to QTLs and genes ? [Relazione in Atti di Convegno]
Pecchioni, Nicola; Francia, Enrico
abstract

In the last few decades Quantitative Trait Loci (QTL) mapping represented a breakthrough for the study of quantitatively inherited traits. Since then, substantial parts of phenotypic variation for crucial traits in crops have been found as explained by a limited to medium number of loci. Among the most important traits studied by QTL mapping, adaptation to the environment was dissected in its main genetic components. One of the species where the highest significant advances in understanding the genetic architecture of environmental adaptation have been made is the diploid barley in the tribe of Triticeae. An overview will be presented about discovery of genetic bases of such quantitative traits in barley, like regulation of flowering time and tolerance to abiotic stresses, till the identification of several candidate genes. Open questions remain about the past, present and expected future success in molecular breeding for QTL marker- and genomic-assisted selection. By reviewing such aspects, examples about QTL sensitivities to environmental variables will be done. Other questions remain about the biological interpretation of quantitative traits in the "omic" era, in particular for the adaptation to the environment. An overview of recent results in this field will be done, with examples about impact of copy number variation (CNV) on phenotype.

2012 - Barley: Omics approaches for abiotic stress tolerance [Capitolo/Saggio]
Pecchioni, Nicola; Milc, Justyna Anna; Pasquariello, Marianna; Francia, Enrico
abstract

Abiotic stresses such as frost, drought, salinity, hypoxia, and mineral deficiency or toxicity frequently limit growth and productivity of temperate cereal crops, for which barley (Hordeum vulgare L. ssp. vulgare) could represent a model. Improving barley resistance to such constraints is thus fundamental in view of the expected climate change for minimizing the gap between potential and actual yield (the so-called yield gap), increasing the yield stability, and guaranteeing the sustainability of the crop. As different omics technologies have been developed during the past few decades, they enabled systematic analysis of changes that occur in plants in response to abiotic stresses. In this chapter, we focus on the omics contribution to the improvement of abiotic stress tolerance in barley. After a brief summary of the most relevant abioticstresses that limit the crop yields worldwide, successful genomics approaches have been described, starting from the exploitation of germplasm resources. Structural and functional approaches that helped in understanding the mechanisms and the genetic bases of abiotic stress tolerance, when applied to barley and model species(mainly Arabidopsis, rice, and Brachypodium), have been reviewed as an important step toward crop tolerance improvement. Quantitative genetics and genetical genomics of abiotic stress tolerance have been discussed, as they represent both a huge source of information and a challenge for future holistic approaches. Then, we present an overview of the contribution of other omics sciences (e.g., proteomics, epigenomics, metabolomics, ionomics, and phenomics). In the last section, integrative (systems) biology, together with a series of strategies for the future, is proposed and discussed.

2012 - Bioetanolo di 2ª generazione da panico verga, novità in Italia [Articolo su rivista]
Ronga, Domenico; Pasquariello, Marianna; R., Provoli; Caffagni, Alessandra; Francia, Enrico; D., Villecco; Pecchioni, Nicola
abstract

Con produzioni potenziali di 25 t/ha di sostanza secca all’anno per più di 15 anni, bassi input agronomici necessari e l’utilizzo del parco macchine delle colture foraggere, il panico verga fornisce i presupposti per una fi liera corta del bioetanolo di 2ª generazione

2012 - CANDIDATE GENE EXPRESSION PROFILING DURING CHILLING IN TWO DIFFERENTIALLY TOLERANT CULTIVARS OF TOMATO [Abstract in Atti di Convegno]
Caffagni, Alessandra; Pecchioni, Nicola; Milc, Justyna Anna; Francia, Enrico
abstract

Low temperature is a major factor limiting the productivity and geographical distribution of many plant species, including important agricultural crops. The capacity to adapt to a cold environment is significantly different among species, and dividing them in acclimating and notacclimating ones. Many plants of tropical or subtropical origin, such as tomato, maize, soybean, and rice, are severely injured or even killed by exposure to low, nonfreezing temperatures. Most tomato cultivars are sensitive to chilling temperatures during all stages of plant development. Genetic variation for chilling tolerance exists between cultivated Solanum lycopersicum and its related wild species, but intra-specific variation has not been thoroughly investigated and fully exploited so far to improve such tolerance. The general objective of the present study was to give an insight into the molecular processes that underlie chilling tolerance in the chilling-sensitive species S . lycopersicum. Consequently, specific aims have been the selection of two tomato cultivars contrasting for their response to chilling exposure by means of a phenotypic characterization of a large germplasm collection. After the phenotypic screen and the choice of the two contrasting lines, a set of functional candidate genes belonging to gene families regulated by cold in plants have been chosen, and evaluated for cold-modulated expression by RT-PCR in the two cultivars. We report here results of genetic variation in the UniMORE germplasm collection for chilling tolerance (stress treatment at 1°C for 24h) together with the selection of Albenga (tolerant) and San Marzano (susceptible) cultivars. Then, twenty candidate genes induced by chilling and/or with putative roles in abiotic stress-response pathways have been then identified, in this first survey comprising both transcription factors and effector genes. Gene expression profiling was conducted by exposing plants to +1°C at a total of six time points. The study shows a first insight into cold modulated expression profiling of tomato cultivars contrasting for chilling tolerance.

2012 - Effect of the nud gene on grain yield in barley [Articolo su rivista]
Barabaschi, Delfina; Francia, Enrico; A., Tondelli; A., Gianinetti; Stanca, ANTONIO MICHELE; Pecchioni, Nicola
abstract

Naked barleys are less yielding than the hulled ones while the reason for this difference has not beendefinitely clarified. To investigate the effect of the nud gene on yield, a barley doubled haploid (DH, Proctor ×Nudinka) population was initially tested in three environments and a QTL study was run on the entire populationas well as on two nud/NUD DH subpopulations. Among the agronomic traits studied, a QTL effect was found atnud locus on chromosome 7H only for yield and thousand grain weight (TGW), while a second QTL was found on6H, although contributed by the naked parent. Other QTLs for TGW were identified on 2H, 3H and 5H. Most QTLsfound in the entire population were confirmed by the study on the two groups. No interaction was observed betweenQTLs. To provide a more accurate evaluation of the effects of the nud gene upon grain yield, its components andother agronomic traits, sixteen naked advanced backcross (AB) BC5F2 lines in the hulled background of cultivarArda were prepared and evaluated in a replicated yield trial for two years. The only differences found betweenAB lines and Arda in grain yield and TGW were due to hull weight (11.97% of kernel weight). No differences wereobserved in other traits such as grains/m2, grains per spike, plant height, heading date and mildew resistance. Inconclusion, we think to have clarified that the effect of the nud gene on yield is due to hulls, and we did not findany pleiotropic effect of nud on other traits. This suggests, together with the finding of a QTL contributed by thenaked parent, that there is a great potential to improve naked barley up to the yield levels of hulled barley.

2012 - Identification of tomato genes differentially expressed during compatible interaction with Pyrenochaeta lycopersici. [Articolo su rivista]
Milc, Justyna Anna; A., Infantino; Pecchioni, Nicola; M., Aragona
abstract

Breeding for resistance is the most effective tool for controlling the corky root disease of tomato caused by the fungus Pyrenochaeta lycopersici. However, little is known about the molecular bases of tomato-P. lycopersici interaction. In order to identify genes involved in the basal defence response activated in a susceptible cultivar and in disease symptom development, a set of cDNA-AFLP fragments derived from a profiling experiment was analysed. A total of 247 differentially expressed TDFs (transcript-derived fragments), identified as putative tomato genes, were characterized by similarity searches, and classified into 11 broad functional classes. Timings ranging between the early [48, 72 and 96 h post-infection (hpi)] and the late infection stages (20 and 27 dpi) were used. The changes of tomato root transcriptional profiles showed large differences in quantity and quality between the early and late stages of infection. Mechanisms of basal defence were most likely activated at early stages, when a gene coding for a receptor-like serine-threonine protein kinase and other genes of the signalling class were upregulated. At 20 dpi some of the mechanisms involved in defence were still activated, while at 27 dpi a general repression of gene expression was observed.

2012 - Integration and Provenance of Cereals Genotypic and Phenotypic Data [Poster]
Beneventano, Domenico; Bergamaschi, Sonia; Abdul Rahman, Dannaoui; Pecchioni, Nicola
abstract

This paper presents the ongoing research on the design and development of a Provenance Management component, PM_MOMIS, for the MOMIS Data Integration System. MOMIS has been developed by the DBGROUP of the University of Modena and Reggio Emilia (www.dbgroup.unimore.it). An open source version of the MOMIS system is delivered and maintained by the academic spin-off DataRiver (www.datariver.it).PM_MOMIS aims to provide the provenance management techniques supported by two of the most relevant data provenance systems, the "Perm" and "Trio" systems, and extends them by including the data fusion and conflict resolution techniques provided by MOMIS. PM_MOMIS functionalities have been studied and partially developed in the domain of genotypic and phenotypic cereal-data management within the CEREALAB project. The CEREALAB Data Integration Application integrates data coming from different databases with MOMIS, with the aim of creating a powerful tool for plant breeders and geneticists. Users of CEREALAB played a major role in the emergence of real needs of provenance management in their domain.We defined the provenance for the "full outerjoin-merge" operator, used in MOMIS to solve conflicts among values; this definition is based on the concept of "PI-CS-provenance" of the "Perm" system; we are using the "Perm" system as the SQL engine of MOMIS, so that to obtain the provenance in our CEREALAB Application. The main drawback of this solution is that often conflicting values represent alternatives; then our proposal is to consider the output of the "full outerjoin-merge" operator as an uncertain relation and manage it with a system that supports uncertain data and data lineage, the "Trio" system.

2012 - Iodine uptake and distribution in horticultural and fruit tree species. [Articolo su rivista]
Caffagni, Alessandra; Pecchioni, Nicola; P., Meriggi; V., Bucci; E., Sabatini; N., Acciarri; T., Ciriaci; L., Pulcini; N., Felicioni; M., Beretta; Milc, Justyna Anna
abstract

Iodine is an essential microelement for humans and iodine deficiency disorder (IDD) is one of the most widespread nutrient-deficiency diseases in the world. Iodine biofortification of plants provides an attractive opportunity to increase iodine intake in humans and to prevent and control IDD. This study was conducted to investigate the iodine uptake and accumulation in edible portion of two fruit trees: plum and nectarine, and two horticultural crops: tomato and potato. Two type of iodine treatments (soil and foliar spray application), and, for fresh market tomato, two production systems (open field and greenhouse hydroponic culture) were tested. The distribution of iodine in potato stem and leaves, and in plum tree fruits, leaves, and branches was investigated. Iodine content of potato tubers after postharvest storage and processing (cooking), and iodine content of nectarine fruits after postharvest storage and processing (peeling) were also determined. Differences in iodine accumulation were observed among the four crops, between applications, and between production systems. In open field, the maximum iodine content ranged from 9.5 and 14.3 μg 100 g−1 for plum and nectarine fruit, to 89.4 and 144.0 μg 100 g−1 for potato tuber and tomato fruit, respectively. These results showed that nectarine and plum tree accumulated significantly lower amounts of iodine in their edible tissues, in comparison with potato and tomato. The experiments also indicated hydroponic culture as the most efficient system for iodine uptake in tomato, since its fresh fruits accumulated up to 2423 μg 100 g−1 of iodine. Iodine was stored mainly in the leaves, in all species investigated. Only a small portion of iodine was moved to plum tree branches and fruits, and to potato stems and tubers. No differences in iodine content after fruit peeling was observed. A significant increase in iodine content of potato was observed after baking, whereas a significant decrease was observed after boiling. We concluded that iodine biofortified fresh market tomato salad, both from field and hydroponics cultivation, and baked potatoes can be considered as potential functional foods for IDD prevention.

2012 - Natural variation in a homolog of Antirrhinum CENTRORADIALIS contributed to spring growth habit and environmental adaptation in cultivated barley [Articolo su rivista]
J., Comadran; B., Kilian; J., Russell; L., Ramsay; N., Stein; M., Ganal; P., Shaw; M., Bayer; W., Thomas; D., Marshall; P., Hedley; A., Tondelli; Pecchioni, Nicola; Francia, Enrico; V., Korzun; A., Walther; R., Waugh
abstract

As early farming spread from the Fertile Crescent in the Near East around 10,000 years before the present, domesticated crops encountered considerable ecological and environmental change. Spring-sown crops that flowered without the need for an extended period of cold to promote flowering and day length–insensitive crops able to exploit the longer, cooler days of higher latitudes emerged and became established. To investigate the genetic consequences of adaptation to these new environments, we identified signatures of divergent selection in the highly differentiated modern-day spring and winter barleys. In one genetically divergent region, we identify a natural variant of the barley homolog of Antirrhinum CENTRORADIALIS (HvCEN) as a contributor to successful environmental adaptation. The distribution of HvCEN alleles in a large collection of wild and landrace accessions indicates that this involved selection and enrichment of preexisting genetic variants rather than the acquisition of mutations after domestication

2012 - PHYSICAL MAP AND DE NOVO SEQUENCING OF BARLEY FR-H2 FROST RESISTANCE LOCUS [Abstract in Atti di Convegno]
Pasquariello, Marianna; Barabaschi, Delfina; Himmelbach, A; Ariyadasa, R; KNOX A., K; STOCKINGER E., J; Steuernagel, B; Stein, N; Pecchioni, Nicola; Francia, Enrico
abstract

Fr-H2 is one of the two major loci affecting freezing tolerance of barley. Genetic mapping evidences suggested a cluster of more than 14 genes encoding CBF transcription factors as lilely candidates to explain the trait; however, the molecular basis of the Fr-H2 QTL is still to be demonstrated. A large segregating population (2,849 F2 plants) was developed from the ‘Nure’ (frost tolerant) x ‘Tremois’ (frost susceptible) cross for fine mapping and locus dissection. Recombinants identified between seven of the 14 CBFs indicated that the locus spans a total genetic distance of 0.81 cM. Sequencing bacteriophage lambda genomic clones in ‘Nure’, ‘Dicktoo’, ‘Morex’ and ‘Tremois’ provided the first structural insights into Fr-H2. Subsequently, two ‘Morex’ genomic BAC libraries were screened using 10 CBF-specific markers, and their first BAC clone addresses obtained. A High-Information-Content Fingerprinting of the selected BACs was performed to create anchor points between the genetic and physical maps of the region. The Minimal Tiling Path was PCR-screened for the presence of all available CBFs and the physical order confirmed via placement of BAC-end specific markers. De novo 454 sequencing of 27 barcoded and pooled BACs was performed using the GS FLX platform and the sequences assembled under iterative change of parameters of MIRA software. Though the resolution of complex repetitive DNA structures iwas difficult to solve, more than 70% of the assembled sequence contigs were anchored to the physical map of Fr-H2. Altogether, these results throw light on the structural characterization of the 5H genomic region of the Fr-H2 locus and the role of different CBFs in barley.

2012 - Pomodoro da industria, confronto tra biologico e convenzionale. [Articolo su rivista]
Ronga, Domenico; Pecchioni, Nicola; D., Perrone; M., Zaccardelli
abstract

I dati relativi a sei varietà, coltivate secondoil sistema biologico e convenzionale, hannofatto riscontrare differenze importantiper quanto riguarda le rese a ettaro,con ovvie ricadute anche sulla redditività.Sarebbero opportuni, pertanto, programmidi miglioramento genetico volti all’aumentodella produttività in biologico

2012 - QTLs for resistance to the false brome rust Puccinia brachypodii in the model grass Brachypodium distachyon L. [Articolo su rivista]
Barbieri, Mirko; T. C., Marcel; R. E., Niks; Francia, Enrico; Pasquariello, Marianna; Mazzamurro, Valentina; D. F., Garvin; Pecchioni, Nicola
abstract

The potential of the model grass Brachypodium distachyon L. (Brachypodium) for studying grass–pathogen interactions is still underexploited. We aimed to identify genomic regions in Brachypodium associated with quantitative resistance to the false brome rust fungus Puccinia brachypodii. The inbred lines Bd3-1 and Bd1-1, differing in their level of resistance to P. brachypodii, were crossed to develop an F2 population. This was evaluated for reaction to a virulent isolate of P. brachypodii at both the seedling and advanced growth stages. To validate the results obtained on the F2, resistance was quantified in F2-derived F3 families in two experiments. Disease evaluations showed quantitative and transgressive segregation for resistance. A new AFLP-based Brachypodium linkage map consisting of 203 loci and spanning 812 cM was developed and anchored to the genome sequence with SSR and SNP markers. Three false brome rust resistance QTLs were identified on chromosomes 2, 3, and 4, and they were detected across experiments. This study is the first quantitative trait analysis in Brachypodium. Resistance to P. brachypodii was governed by a few QTLs: two acting at the seedling stage andone acting at both seedling and advanced growth stages. The results obtained offer perspectives to elucidate the molecular basis of quantitative resistance to rust fungi.

2012 - RECENT ADVANCES IN THE PHYSICAL MAPPING OF WHEAT CHROMOSOME 5A [Abstract in Atti di Convegno]
Volante, A; Barabaschi, Delfina; Michelotti, V; Lacrima, K; Desiderio, F; Fulgoni, G; Prazzoli, L; Gadaleta, A; Blanco, A; Francia, Enrico; Mazzamurro, Valentina; Pecchioni, Nicola; Fricano, A; Piffanelli, P; MASTRANGELO A., M; Valarik, M; Dolezel, J; Cattonaro, F; Scalabrin, S; Stanca, ANTONIO MICHELE; Cattivelli, L; Valé, G.
abstract

High density genetic maps, needed for anchoring BAC contigs during the construction of a physical map and for DNA sequence assembly, have been developed for the short arm of wheat chromosome 5A (5AS). To undertake this challenge we relied on four mapping populations: [1] Chinese Spring (CS, Triticum aestivum) x Renan (T. aestivum); [2] CS x CS disomic substitution line for chr. 5A (T. turgidum ssp dicoccoides); [3] Latino (T. turgidum ssp durum) x MG5323 (T. turgidum ssp dicoccum); [4] DV92 (T. monococcum) x G3116 (T. monococcum). Different approaches for marker development were implemented: a) a set of SSRs (simple sequence repeats) from databases and literature, b) a set of COS (conserved ortholog set) comparative markers, c) ESTs (expressed sequence tag) specific for 5A, d) SSR, and TE (trasponable elements) junction markers were screened from a 2x coverage of 454 sequences run on 5AS flow sorted DNA. The specificity of these markers for chromosome 5AS has been assessed using nulli-tetrasomic lines derived from the cultivar CS, while their physical position has been assigned to deletion bins of 5AS through the utilization of deletion lines. The anchoring between the four genetic linkage maps and the 4201 BAC clones of the MTP (minimal tiling path), produced after HICF (high information content fingerprinting) analysis of about 45.000 BACs and organized in 3D pools, is in progress. Additional specific markers are being developed from the sequencing of 2000 BAC-ends obtained from BACs of the MTP in order to improve the link between the genetic and physical map. High density genetic maps are under development also for 5AL, and the anchoring to 3D pools of the 6560 MTP-BAC clones deriving from the HICF analysis of about 50.000 BACs, has already started with the available markers mapped.

2012 - RELEASE OF THE CEREALAB DATABASE V 2.0 [Abstract in Atti di Convegno]
Dannaoui, Abdul Rahman; Sala, Antonio; Beneventano, Domenico; Milc, Justyna Anna; Caffagni, Alessandra; Pecchioni, Nicola
abstract

The CEREALAB database is a web-based tool realized for wheat, barley and rice, to help the breeders in choosing molecular markers associated to the most important economically phenotypic traits. It contains phenotypic and genotypic data obtained from the integration of available open source databases with the data obtained by the CEREALAB project. In this paper we describe several significant extensions to the CEREALAB database, derived from real needs of the end-user, the modern breeder that is using molecular tools. Firstly, to offer to the breeders new significant data, the CEREALAB database was extended. As a second aim, to improve and simplify the access to the database, a new user-friendly Graphic User Interface (GUI) was developed. Third, to maximize and optimize the accessibility of the available information, new functionalities and additional tools were realized. In particular, to offer to the breeders an effective tool for the analysis of data, the possibility to obtain structured reports was introduced. Finally, to insert new data in the database, a new data entry module was implemented in the interface. Database URL: http://www.cerealab.org

2012 - Structural characterisation of a chromosome 5H genomic region including the Fr-H2 frost resistance locus [Relazione in Atti di Convegno]
Francia, Enrico; Pasquariello, Marianna; Milc, Justyna Anna; Tondelli, A; Barabaschi, D; Schulte, D; Ariyadasa, R; Himmelbach, A; Knox, Ak; Dhillon, T; Stanca, Am; Stockinger, Ej; Stein, N; Pecchioni, Nicola
abstract

Fr-H2 is one of the two major loci affecting freezing tolerance and winter hardiness of barley. A cluster of more than 14 genes encoding CBF transcription factors maps coincident with Fr-H2 suggesting these as candidates; however, the molecular basis of the QTL is still to be demonstrated. The resistant phenotype could either result from a single CBF, or a copy number variation of CBF genes, or an effect of other sequences independent from the candidates. A large segregating population (2,849 F2) was developed from the ‘Nure’ (frost tolerant) x ‘Tremois’ (frost susceptible) cross (NxT) for fine mapping and locus dissection. These experiments indicated that the locus spans 0.81 cM and identified recombinants between seven of the 14 CBFs. Phenotyping F4/F5 NxT lines harbouring alternative allelic states of the CBF genes was performed through five independent experiments, and highlighted significant differences in frost resistance. Reciprocal QTL-NILs (Near-Isogenic Lines) are also in preparation (now BC4F1 and BC5F1). Sequencing bacteriophage lambda genomic clones in ‘Nure’, ‘Dicktoo’, ‘Morex’ and ‘Tremois’ provided the first structural insights into Fr-H2. Subsequently, two ‘Morex’ genomic BAC libraries were screened using 10 CBF-specific markers, and their first BAC clone addresses obtained. A High-Information-Content Fingerprinting of the selected BACs was performed to create anchor points between the genetic and physical maps of the region. The Minimal Tiling Path was PCR screened for the presence of all available CBFs and the physical order confirmed via placement of BAC-end specific markers. De novo 454 sequencing of barcoded BAC pools is being performed for the structural characterization of the genomic region of barley chromosome 5H, including the Fr-H2 locus. Altogether, the results will hopefully increase knowledge about the role of different CBFs in barley, and will be further efforts to sequence barley chromosome 5H.

2012 - The CEREALAB Database: Ongoing Research and Future Challenges [Relazione in Atti di Convegno]
Beneventano, Domenico; Bergamaschi, Sonia; Dannaoui, Abdul Rahman; Milc, Justyna Anna; Pecchioni, Nicola; Sorrentino, Serena
abstract

The objective of the CEREALAB database is to help the breeders in choosing molecular markers associated to the most important traits. Phenotypic and genotypic data obtained from the integration of open source databases with the data obtained by the CEREALAB project are made available to the users. The first version of the CEREALAB database has been extensively used within the frame of the CEREALAB project. This paper presents the main achievements and the ongoing research related to the CEREALAB database. First, as a result of the extensive use of the CEREALAB database, several extensions and improvements to the web application user interface were introduced. Second, always derived from end-user needs, the notion of provenance was introduced and partially implemented in the context of the CEREALAB database. Third, we describe some preliminary ideas to annotate the CEREALAB database and to publish it in the Linking Open Data network.

2011 - A genotypic and phenotypic informationsource for marker-assisted selection of cereals:the CEREALAB database [Articolo su rivista]
Milc, Justyna Anna; Sala, Antonio; Bergamaschi, Sonia; Pecchioni, Nicola
abstract

The CEREALAB database aims to store genotypic and phenotypic data obtained by the CEREALAB project and to integratethem with already existing data sources in order to create a tool for plant breeders and geneticists. The database can helpthem in unravelling the genetics of economically important phenotypic traits; in identifying and choosing molecularmarkers associated to key traits; and in choosing the desired parentals for breeding programs. The database is dividedinto three sub-schemas corresponding to the species of interest: wheat, barley and rice; each sub-schema is then dividedinto two sub-ontologies, regarding genotypic and phenotypic data, respectively.

2011 - Amplified fragment length polymorphism markers for DNAfingerprinting in the genus Salvia [Articolo su rivista]
Braglia, L.; Casabianca, V.; De Benedetti, L.; Pecchioni, Nicola; Mercuri, A.; Cervelli, C.; Ruffoni, B.
abstract

The interspecific relationships among 51 worldwide collected accessions of Salvia have been investigated using the amplifiedfragment length polymorphism (AFLP) technique. The assessed genetic similarities allowed us to group the genotypes intotwo main c1usters according to their geographical origino Our results are encouraging for further characterization of the genuswith the aim to c1arify Salvia taxonomy.

2011 - Determinanti della Produzione dell’Orzo in Ambienti Siccitosi del Bacino del Mediterraneo [Abstract in Atti di Convegno]
Francia, Enrico; A., Tondelli; F., Rizza; Badeck, F. W.; Thomas, W. T. B.; F., van Eeuwijk; I., Romagosa; A. M., Stanca; Pecchioni, Nicola
abstract

L’orzo è il secondo cereale più diffuso dopo il frumento duro in molti ambienti siccitosi del bacino del Mediterraneo, dove le ridotte precipitazioni e l'estrema erraticità del clima ne influenzano fortemente la produzione. La definizione dei caratteri ecofisiologici critici per l’adattamento e la stabilità produttiva dell'orzo in condizioni stressanti è dunque di fondamentale importanza nella prospettiva dei futuri cambiamenti climatici. In questo lavoro è stata valutata la performance agronomica di una popolazione di 120 linee doppio-aploidi (DH) derivate dall'incrocio tra una varietà invernale -'Nure'- e una primaverile -'Tremois', inclusi i parentali, in 18 ambienti del Mediterraneo.

2011 - Determinants of barley grain yield in a wide range of Mediterranean environments [Articolo su rivista]
Francia, Enrico; A., Tondelli; F., Rizza; F. W., Badeck; O., Li Destri Nicosia; T., Akar; S., Grando; A., Al Yassin; A., Benbelkacem; W. T. B., Thomas; F., Van Eeuwijk; I., Romagosa; Stanca, Antonio Michele; Pecchioni, Nicola
abstract

Barley grain yield in rainfed Mediterranean regions can be largely influenced by terminal drought events.In this study the ecophysiological performance of the ‘Nure’ (winter)בTremois’ (spring) barley mapping population (118 Doubled Haploids, DHs) was evaluated in a multi-environment trial of eighteen site–year combinations across the Mediterranean Basin during two consecutive harvest years (2004 and 2005). Mean grain yield of sites ranged from 0.07 to 5.43 t ha−1, clearly dependent upon both the total water input (rainfall plus irrigation) and the water stress index (WSI) accumulated during the growingseason. All DHs were characterized for possessing molecular marker alleles tagging four genes that regulate barley cycle, i.e. Vrn-H1, Vrn-H2, Ppd-H2 and Eam6. Grain yield differences were initially interpreted in terms of mean differences between genotypes (G), environments (E), and for each combination of genotype and environment (GE) through a “full interaction” ANOVA model. Variance components estimates clearly showed the greater importance of GE over G, although both were much lower than E. Alternative linear and bilinear models of increasing complexity were used to describe GE. A linear model fittingallelic variation at the four genes explained genotype main effect and genotype×environment interaction much better than growth habit itself. Adaptation was primarily driven by the allelic constitution at three out of the four segregating major genes, i.e. Vrn-H1, Ppd-H2 and Eam6. In fact, the three genes together explained 47.2% of G and 26.3% of GE sum of squares. Grain yield performance was more determined by the number of grains per unit area than by the grain weight (phenotypic correlation across all genotypic values: r = 0.948 and 0.559, respectively). The inter-relationships among a series of characters defining grain yield and its components were also explored as a function of the length of the different barley developmental phases, i.e. vegetative, reproductive, and grain filling stages. In most environments, the best performing (adapted) genotypes were those with faster development until early occurrence ofanthesis. This confirmed the crucial role of the period defining the number of grains per unit area in grain yield determination under Mediterranean environments.

2011 - Evaluation of the synteny for 5AS chromosome in Triticum species with different ploidy levels [Abstract in Atti di Convegno]
V., Michelotti; K., Lacrima; F., Desiderio; D., Barabaschi; A., Gadaleta; I., Centomani; A., Giancaspro; S., Giove; Francia, Enrico; Mazzamurro, Valentina; Pecchioni, Nicola; A., Fricano; P., Piffanelli; A. M., Mastrangelo; M., Valarik; A., Blanco; Stanca, ANTONIO MICHELE; L., Cattivelli; G., Valé
abstract

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2011 - Inside the CBF locus in Poaceae [Articolo su rivista]
A., Tondelli; Francia, Enrico; D., Barabaschi; Pasquariello, Marianna; Pecchioni, Nicola
abstract

Several molecular evidences have been gathered in Poaceae that point out a central role of the CBF/DREB1 transcription factors in the signal transduction pathways leading to low-temperature tolerance, although to a quite different extent between crops originating from either temperate or tropical climates. A common feature of the CBF/DREB1 genes in Poaceae is their structural organization at the genome level in clusters of tandemly duplicated genes. In temperate cereals such as barley and wheat, expansion of specific multigene phylogenetic clades of CBFs that map at the Frost Resistance-2 locus has been exclusively observed. In addition, copy number variants of CBF genes between frost resistant and frost sensitive genotypes raise the question if multiple copies of the CBF/DREB1s are required to ensure freezing tolerance. On the other hand, in crops of tropical origin such as rice and maize, a smaller or less-responsive CBF regulon may have evolved, and different mechanisms might determine chilling tolerance. In this review, recent advances on the organization and diversity at the CBF cluster locus in the grasses are provided and discussed.

2011 - Iodine Fortification Plant Screening Process and Accumulation inTomato Fruits and Potato Tubers [Articolo su rivista]
Caffagni, Alessandra; Arru, Laura; Meriggi, P; Milc, Justyna Anna; Perata, Pierdomenico; Pecchioni, Nicola
abstract

Iodine is an essential microelement for human health, and Recommended Daily Allowance (RDA) of such element should range from 40 to 200 µg day-1. Because of the low iodine contents in vegetables, cereals, and many other foods, Iodine Deficiency Disorder (IDD) is one of the most widespread nutrient deficiency diseases in the world. Therefore, investigations of iodine uptake in plants with the aim of their fortification can help reaching the important health and social objective of IDD elimination. This study was conducted to determine the effects of the absorption of iodine from two different chemical forms - potassium iodide (I-) vs. potassium iodate (IO-3) - in a wide range of wild and cultivated plant species. Pot plants were irrigated with different concentrations of I- or IO-3, namely 0.05% and 0.1% (w/v) I-, and 0.05%, 0.1%, 0.2% and 0.5% (w/v) IO-3. Inhibiting effects on plant growth were observed after adding these amounts of iodine to the irrigation water. Plants wereable to tolerate better the higher levels of iodine as IO-3 rather than I- in the root environment. Among cultivated species, barley (Hordeum vulgare L.) showed the lowest, and maize (Zea mays L.) together with tobacco (Nicotiana tabacum L.) the highest biomass reductions due to iodine toxicity. After the screening, cultivated tomato and potato resulted good targets for a fortification rate study among the species screened. When fed with 0.05% iodine salts, potato (Solanum tuberosum L.) tubers and tomato (Solanum lycopersicum L.) fruits absorbed iodine up to 272 and 527 µg/100 g FW from IO-3, and 1,875 and 3,900 µg/100 g FW from I-. These uptake levels were well above the RDA of 150µg day-1 for adults. Moreover, the agronomic efficiency of iodine accumulation of potato tubers and tomato fruits was calculated. Both plant organs showed greater accumulation efficiency for given unit of iodine from iodide than from iodate. This accumulation efficiency decreased in both potato tubers and tomato fruits at iodine concentrations higher than 0.05% for iodide, and at respectively 0.2% and 0.1% for iodate. On the basis of the uptake curve it was finally possible to calculate, although to be validated, the doses of supply in the irrigation water of iodine as iodate (0.028% for potato, and0.014% for tomato) as well as of iodide (0.004% for potato, and 0.002% for tomato), to reach the 150 µg day-1 RDA for adults in 100 g of such vegetables, to efficiently control IDD.

2011 - Mixed model association scans of multi-environmental trial data reveal major loci controlling yield and yield related traitsin Hordeum vulgare in Mediterranean environments [Articolo su rivista]
J., Comadran; J. R., Russell; A., Booth; A., Pswarayi; S., Ceccarelli; S., Grando; A. M., Stanca; Pecchioni, Nicola; T., Akar; A., Al Yassin; A., Benbelkacem; H., Ouabbou; J., Bort; F. A., van Eeuwijk; W. T. B., Thomas; I., Romagosa
abstract

An association panel consisting of 185 accessionsrepresentative of the barley germplasm cultivated inthe Mediterranean basin was used to localise quantitativetrait loci (QTL) controlling grain yield and yield relatedtraits. The germplasm set was genotyped with 1,536 SNPmarkers and tested for associations with phenotypic datagathered over 2 years for a total of 24 year 9 locationcombinations under a broad range of environmental conditions.Analysis of multi-environmental trial (MET) databy fitting a mixed model with kinship estimates detectedfrom two to seven QTL for the major components of yieldincluding 1000 kernel weight, grains per spike and spikesper m2, as well as heading date, harvest index and plantheight. Several of the associations involved SNPs tightlylinked to known major genes determining spike morphologyin barley (vrs1 and int-c). Similarly, the largest QTLfor heading date co-locates with SNPs linked with eam6, amajor locus for heading date in barley for autumn sownconditions. Co-localization of several QTL related to yieldcomponents traits suggest that major developmental locimay be linked to most of the associations. This studyhighlights the potential of association genetics to identifygenetic variants controlling complex traits.

2011 - Molecular strategies for the study of tomato-Pyrenochaeta lycopersici interaction [Relazione in Atti di Convegno]
Valente, Mt; Aragona, M; Infantino, A; Milc, Justyna Anna; Pecchioni, Nicola
abstract

Tomato Corky Root (CRR) is a soil-borne disease, caused by the hemibiotrophic fungus Pyrenochaeta lycopersici that has recently become a disease of concern for many tomato-growing areas including major producers such as China, USA, Italy and Japan, both in greenhouses and in field. The molecular bases of interaction between tomato and P. lycopersici are still poorly understood and breeding for resistance remains the most effective tool for controlling the disease. We are currently investigating the mechanisms behind disease susceptibility and resistance against CRR using different molecular methods. A cDNA-AFLP based approach was employed for transcriptomic analysis of the fungus-plant interaction and led to the identification of fungal genes putatively involved in plant pathogenesis and in the disease symptoms development (Aragona and Infantino, 2008). Among several differentially transcribed fragments we focused on a P. lycopersici sequence having a high similarity with a β-glucanase gene. We cloned the full genomic sequence of the endo-1,4 β-glucanase gene isolated and analyzed its expression in susceptible and resistant tomato cultivars, with the final goal of identifying its role in the interaction with tomato. For expression analysis, a real-time PCR-based approach was conducted on tomato roots artificially infected with P. lycopersici at six different post-infection time points, compared to vegetative mycelium. The quantification of P. lycopersici biomass in relation with plant biomass was assessed and a correlation between expression of the glucanase gene and the progress of P. lycopersici during the time course of root infection was elucidated.

2011 - Pomodoro Da Industria Per Una Coltivazione “Low input” [Abstract in Atti di Convegno]
Ronga, Domenico; S., Lovelli; M., Zaccardelli; Francia, Enrico; D., Perrone; Pecchioni, Nicola
abstract

Nel settore agroindustriale sorge, oggi, la necessità di ripristinare i meccanismi ecologici per ridare vita e fertilità a un sistema che attualmente si trova sfruttato e sbilanciato nelle sue parti funzionali. Nasce, quindi, l’esigenza di gestire le colture assecondando i cicli biologici e le interazioni dell'agroecosistema, e non più intervenendo nell’azienda agraria con input e azioni svincolate da ogni ciclicità. E' stato nostro obiettivo valutare in una zona vocata del Sud Italia, l'impatto di una coltivazione a basso input, come il regime biologico, su varietà di pomodoro da industria di tipologie distinte, a confronto con un regime di coltivazione convenzionale

2011 - Pomodoro da industria, convenzionale batte biologico. [Articolo su rivista]
Ronga, Domenico; Pecchioni, Nicola; D., Perrone; M., Zaccardelli
abstract

SPERIMENTAZIONE. Rese quasi doppie, ma la qualità è simile. Le prove CraOrt nella Piana del Sele peril pomodoro da Industria.Pomodoro da industria, convenzionale batte biologico: i risultatidi un’annata con forti attacchi di Septoria e Alternaria.

2011 - QTLs for resistance to the leaf rust Puccinia brachypodii in the model plant Brachypodium distachyon [Abstract in Atti di Convegno]
Mazzamurro, Valentina; M., Barbieri; D. F., Garvin; T. C., Marcel; R. E., Niks; Francia, Enrico; Pasquariello, Marianna; Pecchioni, Nicola
abstract

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2011 - Sistema sementiero e seminativi, un futuro inscindibile. [Relazione in Atti di Convegno]
Terzi, Valeria; Pecchioni, Nicola
abstract

Relazione ad invito sull'importanza del sistema sementiero per lo sviluppo dei seminativi o grandi colture.

2011 - Usi energetici [Capitolo/Saggio]
Maggiore, T.; Pecchioni, Nicola
abstract

Le destinazioni energetiche principalidella patata sono due: la conversionein bioetanolo e la trasformazionein biogas. Le due trasformazioni,entrambe biochimiche e dipendentida microrganismi, avvengono in unamatrice ideale per le fermentazioni.

2010 - Basal Host Resistance of Barley to Powdery Mildew: Connecting Quantitative Trait Loci and Candidate Genes [Articolo su rivista]
R., Aghnoum; T., Marcel; A., Johrde; Pecchioni, Nicola; P., Schweizer; R., Niks
abstract

The basal resistance of barley to powdery mildew(Blumeria graminis f. sp. hordei) is a quantitatively inheritedtrait that is based on nonhypersensitive mechanismsof defense. A functional genomic approach indicates thatmany plant candidate genes are involved in the defenseagainst formation of fungal haustoria. It is not knownwhich of these candidate genes have allelic variation thatcontributes to the natural variation in powdery mildewresistance, because many of them may be highly conservedwithin the barley species and may act downstream of thebasal resistance reaction. Twenty-two expressed sequencetag or cDNA clone sequences that are likely to play a rolein the barley–Blumeria interaction based on transcriptionalprofiling, gene silencing, or overexpression data, aswell as mlo, Ror1, and Ror2, were mapped and consideredcandidate genes for contribution to basal resistance. Wemapped the quantitative trait loci (QTL) for powderymildew resistance in six mapping populations of barley atseedling and adult plant stages and developed an improvedhigh-density integrated genetic map containing6,990 markers for comparing QTL and candidate genepositions over mapping populations. We mapped 12 QTLat seedling stage and 13 QTL at adult plant stage, ofwhich four were in common between the two developmentalstages. Six of the candidate genes showed coincidencein their map positions with the QTL identified for basalresistance to powdery mildew. This co-localization justifiesgiving priority to those six candidate genes to validatethem as being responsible for the phenotypic effects of theQTL for basal resistance.

2010 - CBF gene copy number variation at Frost Resistance-2 is associated with levels of freezing tolerance in temperate-climate cereals [Articolo su rivista]
Knox, A. K.; Dhillon, T.; Cheng, H.; Tondelli, A.; Pecchioni, Nicola; Stockinger, E. J.
abstract

Frost Resistance-1 (FR-1) and FR-2 are two loci affecting freezing tolerance and winterhardiness of the temperate-climate cereals. FR-1 is hypothesized to be due to thepleiotropic effects of VRN-1. FR-2 spans a cluster of C-Repeat Binding Factor (CBF)genes. These loci are genetically and functionally linked. Recent studies indicate CBFtranscripts are down-regulated by the VRN-1 encoded MADS-box protein or a factor inthe VRN-1 pathway. Here we report that barley genotypes ‘Dicktoo’ and ‘Nure’ carryinga vrn-H1 winter allele at VRN-H1 harbor increased copy numbers of CBF codingsequences relative to Vrn-H1 spring allele genotypes ‘Morex’ and ‘Tremois’. Sequencingbacteriophage lambda genomic clones from these four genotypes alongside DNA blothybridizations indicate approximately half of the eleven CBF orthologs at FR-H2 areduplicated in individual genomes. One of these duplications discriminates vrn-H1genotypes from Vrn-H1 genotypes. The vrn-H1 winter allele genotypes harbor tandemsegmental duplications through the CBF2A–CBF4B genomic region and maintain twodistinct CBF2 paralogs, while the Vrn-H1 spring allele genotypes harbor single copies ofCBF2 and CBF4. An additional CBF gene, CBF13, is a pseudogene interrupted bymultiple nonsense codons in ‘Tremois’ whereas CBF13 is a complete uninterruptedcoding sequence in ‘Dicktoo’ and ‘Nure’. DNA blot hybridization with wheat DNAsreveals greater copy numbers of CBF14 also occurs in winter wheats than in springwheats. These data indicate that variation in CBF gene copy numbers is widespread in theTriticeae and suggest selection for winter hardiness co-selects winter alleles at both VRN-1 and FR-2.

2010 - Dissection of quantitative resistance to leaf rust (Puccinia brachypodii) in Brachypodium distachyon, the model plant for Triticeae [Abstract in Atti di Convegno]
Barbieri, Mirko; Francia, Enrico; Milc, Justyna Anna; Mazzamurro, Valentina; Pasquariello, Marianna; D., Garvin; Tc, Marcel; Re, Niks; Pecchioni, Nicola
abstract

The model plant Brachypodium distachyon (L.) Beauv. has been employed to dissect its quantitative resistance to leaf rust. An F2 mapping population generated between the two B. distachyon diploid inbred lines Bd1-1 and Bd3-1 was used to develop a molecular marker linkage map. The map was initially populated with 192 AFLP marker loci. SSRs and conserved orthologous sequence (COS) markers have also been added to the AFLP framework to provide anchor points for comparative genomics studies with other Brachypodium and Triticeae maps. To locate quantitative resistance loci on the map, the F2 plants were evaluated for their reaction to the leaf rust Puccinia brachypodii. To improve and validate the dissection of the trait, F2-derived F3 families were tested for resistance to leaf rust in two additional independent experiments. Disease evaluations showed continuous, quantitative and transgressive segregation. Interval mapping and MQM mapping were performed on the data of the different experiments by using the software MapQTL 5.0 and then QTL positions were compared. Two major genomic regions involved in resistance to leaf rust were detected and are here discussed according to recent increase of genomic knowledge in Brachypodium. Together they accounted for about 40-50% of the observed phenotypic variation. Our results suggest that leaf rust resistance in B. distachyon is a polygenic trait influenced by few major genes with large effect as observed in the Triticeae. A search for candidates has been started through the Brachypodium distachyon 8x released genomic sequence, to obtain and map candidate gene-derived markers in the QTL intervals.

2010 - Introgression of resistance to two mediterranean virus species causing Tomato Yellow Leaf Curl into a valuable traditional tomato variety [Articolo su rivista]
Barbieri, Mirko; N., Acciarri; E., Sabatini; L., Sardo; G. P., Accotto; Pecchioni, Nicola
abstract

Tomato yellow leaf curl disease (TYLCD) causesdevastation worldwide and in Italy is associated withTomato yellow leaf curl virus (TYLCV) and Tomato yellowleaf curl Sardinia virus (TYLCSV). Starting from thevaluable traditional tomato cv. Eraldo, which is susceptibleto TYLCD, crosses were made with accessions carryingTy-1 and Ty-2 resistance loci. The F2 progenieswere selected using both known and newly developedTy-associated markers. F3 families derived from markerselectedF2 plants were challenged with isolates ofTYLCV and TYLCSV present in Italy, under controlledgreenhouse conditions. Genotypes carrying marker allelesassociated with the Ty-1 gene showed mild symptomsin all cases (tolerance), but the number of plants infectedby TYLCV was much higher than those infected byTYLCSV. The majority of plants carrying the marker allelesassociated to Ty-2 did not allow any TYLCV replicationbut, when challenged with TYLCSV, most ofthem were infected and showed severe yellow leaf curlsymptoms. To our knowledge this is the first report ofTy-1 and Ty-2-carrying tomato plants challenged withthe type-strain of TYLCSV.

2010 - Towards physical mapping and sequencing the Fr-H2 (Frost resistance-H2) region of barley chromosome 5H [Abstract in Atti di Convegno]
Francia, Enrico; Pasquariello, Marianna; Caffagni, Alessandra; Milc, Justyna Anna; Sgarbi, Elisabetta; Barabaschi, Delfina; A., Tondelli; D., Schulte; N., Stein; E. J., Stockinger; Stanca, ANTONIO MICHELE; Pecchioni, Nicola
abstract

Frost resistance-H2 is one of two major quantitative trait loci, located on chromosome 5H, that affect freezing tolerance and winter hardiness of barley. Coincident with Fr-H2 is a cluster of more than 14 genes encoding CBF transcription factors, that are at present the best candidates in barley to explain the effects of frost tolerance given by the QTL. It is not known whether the effect of Fr-H2 is either the result of a single CBF gene, or the combined effect of a subset/all the CBF genes, or an effect of other sequences independent from the CBF genes. As a first step towards Fr-H2 physical mapping we have generated a large mapping population derived from the freezing tolerant genotype ‘Nure’, and the freezing susceptible ‘Tremois’, in order to both fine map the Fr-H2 interval, and to generate recombinants between the different CBF genes. Screens for recombinant individuals from F2 populations consisting of 2,849 plants, and their subsequent phenotypic evaluation in F4 lines provided an estimated refined genomic interval of 4.6 cM for Fr-H2. Recombinants between seven out of the 14 CBF genes under Fr-H2 have been identified and showed that the CBF gene cluster spans 0.81 cM on barley chromosome 5H. A positional cloning effort of Fr-H2 has been undertaken. A genomic BAC library of barley (cv. ‘Morex’) was screened with a total of six CBF markers mapping in this locus. Using a PCR-based screening strategy the first BAC clone addresses were obtained for all the CBF markers assayed. To create anchor points between the genetic map and a ‘future’ physical map of barley, in this region, a high information content fingerprinting (HICF) of the selected BACs has been performed and then the selected BAC clones have been assembled into contigs.To close the gaps between the assembled clones, additional BACs belonging to the contigs detected, have been screened with further CBF markers and a total of three BACs were sequenced and assembled using 454 sequencing. The construction of a single physical contig encompassing the Fr-H2 region will be our next purpose. This will provide further information on gene content and structural locus organization and thus provide a fundamental resource for detailed comparative analyses of the genomic organization of the locus in other barley cultivars, like ‘Nure’ and ‘Tremois’.

2009 - Environment specific and common QTLs for adaptation of barley to a wide range of mediterranean droughted environments [Abstract in Atti di Convegno]
Tondelli, A.; Francia, Enrico; Li Destri Nicosia, O.; Al Yassin, A.; Akar, T.; Benbelkacem, A.; Grando, S.; Romagosa, I.; Thomas, W. T. B.; Van Eeuwijk, F. A.; Stanca, A. M.; Pecchioni, Nicola
abstract

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2009 - Fortificazione con Iodio di specie erbacee ed arboree [Abstract in Atti di Convegno]
Caffagni, Alessandra; Albertazzi, Giorgia; Milc, Justyna Anna; Francia, Enrico; Bucci, V; Perata, P; Acciarri, N.; Sabatini, E; Pecchioni, Nicola
abstract

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2009 - Gene expression in grapevine cultivars in response to BOIS NOIR phytoplasma infection [Articolo su rivista]
Albertazzi, Giorgia; Milc, Justyna Anna; Caffagni, Alessandra; Francia, Enrico; Roncaglia, Enrica; F., Ferrari; Tagliafico, Enrico; Stefani, Emilio; Pecchioni, Nicola
abstract

Bois Noir phytoplasma is an emerging disease of Vitis vinifera in several regions of the world. No completely resistant grapevine cultivars are known and the physiology of disease remains still poorly understood so far. Affymetrix GeneChip® oligonucleotide arrays have been used to identify differentially expressed genes between infected and recovered samples from cv. Chardonnay and between infected and healthy samples from cv. Manzoni Bianco. In the field, cv. Manzoni showed reduced symptoms,while cv. Chardonnay was highly susceptible to the disease. Results showed that expression levels of few hundreds genes were altered in infected plants, both common and specific for each cultivar, with effects on various metabolic pathways. In cv. Chardonnay a serious inhibition of whole photosynthetic chain and photosystem I activity, Calvin-cycle enzymes transcription, lipid metabolism and phenylpropanoid biosynthesis was observed. Increasing physical barriers to limit phytoplsma spread in the plant was observed in both Chardonnay and Manzoni infected plants, with the repression of genes responsible for cell wall degradation and the induction of genes involved in cell wall reinforcement. Interestingly, specifically in cv. Manzoni the expression of a Myb transcription factor, belonging to a gene family that has a role in defense response, was induced.This is the first analysis of gene expression profiling in a grapevine-phytoplasma interaction using Affymetrix GeneChip® array. Presented data provide an interesting picture of the transcriptional response of grapevine to Bois Noir and allowed the selection of several candidate genes for future functional analysis.

2009 - Linkage map development and QTL mapping for leaf rust resistance in the model plant Brachypodium distachyon [Abstract in Atti di Convegno]
Barbieri, Mirko; Francia, Enrico; D., Garvin; R., Niks; T., Marcel; Pecchioni, Nicola
abstract

The model plant Brachypodium distachyon (L.) Beauv. has been employed to analyze the genetics of resistance to leaf rust. An F2 mapping population of 110 individuals generated between the two B. distachyon diploid inbred lines Bd1-1 and Bd3-1 was used to develop a molecular marker linkage map. The map was mainly AFLP-based. In addition to the initial AFLP framework, conservedmarkers between B. distachyon, barley and wheat, such as EST-derived markers, are currently being developed to be added to the map, thus providing anchor points for comparative genomics studies. To locate quantitative resistance loci on the map, the 110 F2 plants were evaluated for their reactionto the leaf rust Puccinia brachypodii. To improve QTL identification, F2-derived F3 families were tested for resistance to leaf rust in two independent experiments. Disease evaluations showed continuous, quantitative and transgressive segregation. Interval mapping and MQM mapping were performed on the data of the different experiments by using the software MapQTL 5.0 and then QTL positions were compared. Two major genomic regions involved in resistance to leaf rust were detected. Together they accounted for about 40-50% of the observed phenotypic variation. Our results suggest that leaf rust resistance in B. distachyon is a polygenic trait influenced by few majorgenes with large effect as observed in the Triticeae.

2009 - Marker-assisted characterization of frost tolerance in barley (Hordeum vulgare L.) [Articolo su rivista]
T., Akar; Francia, Enrico; A., Tondelli; F., Rizza; Stanca, ANTONIO MICHELE; Pecchioni, Nicola
abstract

Five molecular markers associated to two frost tolerance QTLs (Fr-H1 and Fr-H2) were tested both on nine Turkish accessions, classified by breeders as highly frosttolerant, and on a previously described sample of 26 barleys, winter, facultative and spring. Accessions were characterized in terms of frost tolerance under both field conditions and artificial freezing test at -12°C. The Turkish lines resulted to be equal or superior to the most tolerant European genotypes tested, showing that they can be used to improve the frost tolerance of the EU barley germplasm. The marker HvBM5A (Vrn-H1 and Fr-H1) resulted to be the best predictor for assisted selection within this germplasm, because of its high correlation between allelic variation and phenotypic traits. Only HvCBF4 of the 3 HvCBF markers tested at Fr-H2 was associated to the trait, but at lower significance than HvBM5A. The PCR-based molecular marker of Vrn-H1 can thus be used in barley breeding not only for selection of facultative and winter types, but also for fast routine selection of frost tolerant genotypes

2009 - Molecular Characterization Of The Barley Fr-H2 QT Locus [Abstract in Atti di Convegno]
Francia, Enrico; Barabaschi, Delfina; A., Tondelli; N., Stein; Stockinger, E. J.; Stanca, ANTONIO MICHELE; Pecchioni, Nicola
abstract

Frost resistance-H2 is major quantitative trait locus that, in combination with VRN-H1/Fr-H1, affects freezing tolerance of barley. Mapping coincident with Fr-H2 are QTLs regulating COR proteins accumulation and a cluster of more than 14 genes encoding CBF transcription factors – at present the best candidates to explain the effects given by the locus. Expression analyses, conducted on a ‘Nure’ x ‘Tremois’ barley mapping population segregating for VRN-H1/Fr-H1 and Fr-H2, revealed that transcript levels of all cold-induced CBF genes at Fr-H2 were significantly higher in recombinants harboring the vrn-H1 winter allele than in recombinants harboring the Vrn-H1 spring allele. Also, steady-state HvCBF2 and HvCBF4 levels were significantly higher in recombinants harboring the Nure allele at Fr-H2. In a positional cloning effort, a large mapping population consisting of more than 3,698 meiotic events was used to fine map Fr-H2. Recombinants between 12 CBF genes under Fr-H2 have been identified in a total genetic distance of 0.81 cM. The few recombinants between the different HvCBF sub-clusters were chosen and taken to homozygosity in order to separate the effects of the single HvCBF genes. At the same time, a PCR-based screening strategy of the genomic BAC library of cv ‘Morex’ was undertaken, and selected clones assembled into contigs through high information content fingerprinting (HICF). BAC-end sequencing is being used to close remaining gaps and to create anchor points between the genetic and physical maps of the region. Alignment of the genetically colinear region of ‘Nure’ against ‘Tremois’, alongside ‘Dicktoo’ and ‘Morex’, revealed several key molecular differences that we hypothesize accounts for the nature of Fr-H2. The likely scenario is that both a ‘structural’ and a ‘regulatory’ component act together to enhance the tolerance. The first component could be likely due to either allelic or number variation of HvCBF genes at Fr-H2 where “more” CBFs could be better, while the second one would be due to the winter allele of VRN-H1/Fr-H1.

2009 - Patterns of genetic diversity and linkage disequilibrium in a highly structured Hordeum vulgare association-mapping population for the Mediterranean basin [Articolo su rivista]
J., Comadran; Thomas, W. T. B.; van Eeuwijk, F. A.; S., Ceccarelli; S., Grando; Stanca, A. M.; Pecchioni, Nicola; T., Akar; A., Al Yassin; A., Benbelkacem; H., Ouabbou; J., Bort; I., Romagosa; Hackett, C. A.; Russell, J. R.
abstract

Population structure and genome-wide linkagedisequilibrium (LD) were investigated in 192 Hordeumvulgare accessions providing a comprehensive coverage ofpast and present barley breeding in the Mediterraneanbasin, using 50 nuclear microsatellite and 1,130 DArTmarkers. Both clustering and principal coordinate analysesclearly sub-divided the sample into five distinct groupscentred on key ancestors and regions of origin of thegermplasm. For given genetic distances, large variation inLD values was observed, ranging from closely linked markers completely at equilibrium to marker pairs at50 cM separation still showing significant LD. Mean LDvalues across the whole population sample decayed belowr2 of 0.15 after 3.2 cM. By assaying 1,130 genome-wideDArT markers, we demonstrated that, after accounting forpopulation substructure, current genome coverage of 1marker per 1.5 cM except for chromosome 4H with 1marker per 3.62 cM is sufficient for whole genome associationscans. We show, by identifying associations withpowdery mildew that map in genomic regions known tohave resistance loci, that associations can be detected instrongly stratified samples provided population structure iseffectively controlled in the analysis. The population wedescribe is, therefore, shown to be a valuable resource,which can be used in basic and applied research in barley.

2009 - QTL alleles from a winter feed type can improve malting quality in barley [Articolo su rivista]
G., Laido'; Barabaschi, Delfina; A., Tondelli; A., Gianinetti; Stanca, ANTONIO MICHELE; O., LI DESTRI NICOSIA; N., DI FONZO; Francia, Enrico; Pecchioni, Nicola
abstract

Mapping QTLs responsible for malting quality traits in barley populations has been the main genetic approach to malting quality breeding. A ‘winter x spring’ doubled haploid barley population ‘Nure’ x ‘Tremois’, where such traits were segregating, has been recently developed. Our objective was to map QTLs for malting quality from two years of trials in two contrasting locations. QTLs were found on six chromosomes, with a main cluster on chromosome 1H. For wort viscosity and malt extract, favourable alleles at two loci on chromosome 5H were carried by the winter feeding parent ‘Nure’. Doubled-haploids with higher quality than the spring malting cultivar ‘Tremois’ showed either a facultative or a winter growth habit and a level of frost tolerance comparable to that of the winter tolerant parent ‘Nure’. Markers and QTLs of quality traits were further validated on a separate set of DH lines, coming from the same cross, by means of marker-assisted selection. This showed that, at least in the present cross combination, positive contributions to malting quality can be found in winter feed barley.

2009 - Rice marker-assisted breeding for cooking quality. [Abstract in Atti di Convegno]
Albertazzi, Giorgia; Ravaglia, S.; Gavina, G.; Gianinetti, A.; Milc, Justyna Anna; Caffagni, Alessandra; Francia, Enrico; Pecchioni, Nicola
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2009 - Sistemi di controllo della qualita’ del materiale micropropagato nella varieta’ commerciale “Elide” di Gerbera jamesonii [Relazione in Atti di Convegno]
L., Pipino; Francia, Enrico; Pecchioni, Nicola; R., Caccia; Albani, M. M.; A., Giovannini
abstract

The methylation status of the genomic DNA was investigated in the experimental test constituted by the two phenotypes of the commercial variety “Elide”®, the “wild type” and “bushy”, in vitro propagated. The onset of the bushy phenotype was reduced when “Elide” was cultured in the media added with the fungicide Imazalil. The genomic DNA digestion with 10 different methylation-sensitive enzymes showed, for both phenotypes, a low GC content and a high level of methylation. The Methylation-Sensitive Amplification Polymorphism (MSAP) technique, making use of fluorescent primers, has been applied for the first time in Gerbera jamesonii. Different polymorphic bands were obtained, showing different methylation sites in all phenotypic conditions observed.

2009 - Studio delle componenti della produzione in linee quasi-isogeniche di orzo nudo [Abstract in Atti di Convegno]
Barabaschi, D.; Tondelli, A.; Stanca, A. M.; Pecchioni, Nicola; Francia, Enrico
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2008 - Barley adaptation and improvement in the Mediterranean basin [Articolo su rivista]
A., Pswarayi; VAN EEUWIJK, F. A.; S., Ceccarelli; S., Grando; J., Comadran; Russell, J. R.; Francia, Enrico; Pecchioni, Nicola; O., LI DESTRI; T., Akar; A., AL YASSIN; A., Benbelkacem; W., Choumane; M., Karrou; H., Ouabbou; J., Bort; Araus, J. L.; MOLINA CANO, J. L.; Thomas, W. T. B.; I., Romagosa
abstract

To study barley adaptation and improvement in the Mediterraneanbasin, a collection of 188 entries comprising landraces and oldgenotypes and current modern varieties from the Mediterranean basin and elsewhere was tested on moisture-contrasted environments in seven Mediterranean countries, during 2004 and 2005 harvest seasons. The experimental design consisted of an unreplicated trial for all entries, augmented by four repeated checks to which a partial replicate containing a quarter of the entries was added. Best Linear Unbiased Predictions (BLUPs) representing adjusted genotypic means were generated for individual trials using a mixed model. BLUPs were used for genotype by environment interaction analysis using main effectplus genotype by environment interaction (GGE) biplots of yieldranked data and for comparisons of landraces, old and moderngenotypes using analysis of variance. Mean yields ranged from near crop failure to 6 t/ha. Local landraces were better adapted toenvironments yielding below 2 t/ha, thus breeding has mostly benefited environments yielding above 2 t/ha where modern genotypes out yielded landraces and old cultivars by 15%. Current barley selection is leading to specifically adapted genotypes.

2008 - Bioinformatic analysis of cDNA-AFLP derived sequences differentially expressed in a compatible interaction tomato - Pyrenochaeta lycopersici [Abstract in Atti di Convegno]
Milc, Justyna Anna; Aragona, M.; Pecchioni, Nicola; Infantino, A.
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2008 - Changes in allele frequencies in landraces, old and modern barley cultivars of marker loci close to QTL for grain yield under high and low input conditions. [Articolo su rivista]
Pswarayi, A; van Eeuwijk, Fa; Ceccarelli, S; Grando, S; Comadran, J; Russell, Jr; Stanca, M; Pecchioni, Nicola; Tondelli, A; Akar, T; Al Yassin, A; Benbelkacem, A; Ouabbou, H; Thomas, Wtb; I., Romagosa
abstract

Changes in alleles frequencies of markerloci linked to yield quantitative trait loci (QTL) werestudied in 188 barley entries (landraces, old andmodern cultivars) grown in six trials representing lowand high yielding conditions in Spain (2004) and Syria(2004, 2005). A genome wise association analysis wasperformed per trial, using 811 DArT markers ofknown map position. At the first stage of analysis,spatially adjusted genotypic means were created pertrial by fitting mixed models. At the second stage,single QTL models were fitted with correction forpopulation substructure, using regression models.Finally, multiple QTL models were constructed bybackward selection from a regression model containingall significantmarkers from the single QTL analyses. Inaddition to the association analyses per trial, genotypeby environment interaction was investigated across thesix trials. Landraces seemed best adapted to lowyielding environments, while old and modern entriesadapted better to high yielding environments. Thenumber of QTL and the magnitude of their effects werecomparable for low and high input conditions. However,none of the QTL were found within a given bin atany chromosome in more than two of the six trials.Changes in allele frequencies of marker loci close toQTL for grain yield in landraces, old and modernbarley cultivars could be attributed to selection exercisedin breeding, suggesting that modern breeding may have increased frequencies of marker alleles closeto QTL that favour production particularly under highyield potential environments. Moreover, these resultsalso indicate that there may be scope for improvingyield under low input systems, as breeding so far hashardly changed allele frequencies at marker loci closeto QTL for low yielding conditions.

2008 - Genetic structure and proposed conservation strategy for natural populations of Calycanthus chinensis Cheng et S.Y. Chang (Calycanthaceae) [Articolo su rivista]
C. C., Fan; Pecchioni, Nicola; L. Q., Chen
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2008 - Genomic Tools for the Study of the Adaptation of Barley Crop to Climatic Constraints [Relazione in Atti di Convegno]
A., Tondelli; Barabaschi, Delfina; Stanca, ANTONIO MICHELE; VAN EEUWIJK, F. A.; S., Grando; Mastrangelo, A. M.; O., LI DESTRI; T., Akar; A., AL YASSIN; A., Benbelkacem; I., Romagosa; Thomas, W. T. B.; Pecchioni, Nicola; Francia, Enrico
abstract

The Nure x Tremois (NT) population of doubled-haploid lines has been exploited in order to map QTLs for adaptation of barley to climatic constraints. The winter parent - Nure - Italian two-rowed feed-barley cultivar, has a wide range of adaptability, including South European environments. The spring parent - Tremois - French two-rowed malting variety is adapted to fertile environments. Multilocational irrigated vs. non-irrigated field trials of the NT population have been carried out during two years (2003/04 and 2004/05) in Mediterranean Europe, North Africa and West Asia to map QTLs (Quantitative Trait Loci) of yield and drought adaptation traits, under the frame of the European MABDE project. The NT mapping population also represents a valuable resource for genomic analysis of winterhardiness-related traits. The two major loci for low temperature tolerance (Fr-H1 and Fr-H2) were found to segregate on the long arm of chromosome 5H. Moreover, QTLs controlling heading date under controlled photoperiod and vernalization conditions were placed on chromosomes 1H, 2H, 4H and 5H. The agronomic behaviour of the groups of DH lines differentiated for alleles carried at the QTL markers was surveyed. Candidate genes (CGs) involved in barley response to abiotic stresses and plant development have been placed on the NT map, as well. The co-location of QTLs along with CGs putatively related to plant adaptation to environmental conditions is presented and discussed.

2008 - Heading date QTL in the barley ‘Nure’ x ‘Tremois’ mapping population [Abstract in Atti di Convegno]
Tondelli, A.; Francia, Enrico; Barabaschi, D.; Karsai, I.; Stanca, A. M.; Pecchioni, Nicola
abstract

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2008 - Iodine Fortification for the Development of Functional Foods [Relazione in Atti di Convegno]
Caffagni, Alessandra; Albertazzi, Giorgia; Milc, Justyna Anna; Francia, Enrico; P., Meriggi; Perata, Pierdomenico; N., Acciarri; Pecchioni, Nicola
abstract

Major staple crops contain insufficient concentrations of many essential elements to meet the Recommended Dietary Allowance (RDA); therefore, nutrient fortification of the food supply could represent a valuable practice to integrate diet. Iodine is an essential microelement for human health, and the Iodine Deficiency Disorders (IDD) are believed to be one of the commonest human health problems, therefore the natural iodine fortification of vegetable, by means of irrigation water, can be a part of a strategy of functional food constitution. This study was conducted in order to determine the accumulation of iodine in tomato and peach fruits, as well as in potato tubers, by means of fertirrigation. The experiments aim to establish a field protocol for incorporating iodine into the above mentioned food crops, avoiding any detrimental effects on yields. Plants, in field conditions, were irrigated with potassium iodide in different concentrations, in 2007, and in 2008 in Italy. Iodine concentrations were analyzed by means of ICP-MS in fruits and tubers, after treatments, after harvest at commercial maturity, and after a storage period.

2008 - Mapping QTLs for Leaf Rust resistance in the model plant Brachypodium distachyon. Proceedings of the 52nd Italian Society of Agricultural Genetics Annual Congress [Abstract in Atti di Convegno]
Barbieri, Mirko; Francia, Enrico; Garvin, D.; Marcel, T. C.; Niks, R. E.; Pecchioni, Nicola
abstract

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2008 - Mapping adaptation of barley to droughted environments [Articolo su rivista]
Comadran, J; J. R., Russell; F., VAN EEUWIJK; S., Ceccarelli; S., Grando; M., Baum; A. M., Stanca; Pecchioni, Nicola; A. M., Mastrangelo; T., Akar; A., AL YASSIN; A., Benbelkacem; W., Choumane; H., Ouabbou; R., Dahan; J., Bort; J. L., Araus; A., Pswarayi; I., Romagosa; C. A., Hackett; W. T. B., Thomas
abstract

Identifying barley genomic regions influencing the response of yield and its components to water deficits will aid in our understanding of the genetics of drought tolerance and the development of more drought tolerant cultivars. We assembled a population of 192 genotypes that represented landraces, old, and contemporary cultivars sampling key regions around the Mediterranean basin and the rest of Europe. The population was genotyped with a stratified set of 50 genomic and EST derived molecular markers, 49 of which were Simple Sequence Repeats (SSRs), which revealed an underlying population sub-structure that corresponded closely to the geographic regions in which the genotypes were grown. A more dense whole genome scan was generated by using Diversity Array Technology (DArT1) to generate 1130 biallelic markers for the population. The population was grown at two contrasting sites in each of seven Mediterranean countries for harvest 2004 and 2005and grain yield data collected. Mean yield levels ranged from 0.3 to 6.2 t/ha, with highly significant genetic variation in low-yielding environments. Associations of yield with barley genomic regions were then detected by combining the DArT marker data with the yield data in mixed model analyses for the individual trials, followed by multiple regression of yield on markers to identify a multi-locus subset of significant markers/QTLs. QTLs exhibiting a predefined consistency across environments weredetected in bins 4, 6, 6 and 7 on barley chromosomes3H, 4H, 5H and 7H respectively.

2008 - Marker-assisted selection of the TYLCD resistance genes Ty-1 and Ty-2 in tomato [Abstract in Atti di Convegno]
Barbieri, Mirko; Acciarri, N.; Sabatini, E.; Accotto, G. P.; Sardo, L.; Pecchioni, Nicola
abstract

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2008 - Physical mapping of the barley Fr-H2 (Frost resistance-H2) locus [Abstract in Atti di Convegno]
Barabaschi, D.; Francia, Enrico; Tondelli, A.; Schulte, D.; Stein, N.; Stanca, A. M.; Pecchioni, Nicola
abstract

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2008 - Transcriptional changes in grapevine in response to Bois Noir infection [Abstract in Atti di Convegno]
Albertazzi, Giorgia; Caffagni, Alessandra; Milc, Justyna Anna; Francia, Enrico; Roncaglia, Enrica; Ferrari, Francesco; Tagliafico, Enrico; Pecchioni, Nicola
abstract

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2008 - Yield performance of naked barley NILs and QTL analysis of yield traits in a naked x hulled DH population [Abstract in Atti di Convegno]
Barabaschi, D.; Francia, Enrico; Tondelli, A.; Stanca, A. M.; Pecchioni, Nicola
abstract

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2007 - Caratteri ecofisiologici dell’orzo per l’adattamento della coltura ad ambienti siccitosi del Mediterraneo [Relazione in Atti di Convegno]
Pecchioni, Nicola; Francia, Enrico; I., Romagosa; Thomas, W. T. B.; F., VAN EEUWIJK; Stanca, ANTONIO MICHELE
abstract

L’orzo assieme al frumento duro è la coltura cerealicola più diffusa negli ambienti del WANA (West Asia e Nord Africa). Gli ambienti del Mediterraneo sono caratterizzati da ridotte precipitazioni e da estrema erraticità del clima che influenzano fortemente la produzione della coltura. Pertanto conoscere i caratteri ecofisiologici critici per l’adattamento e la stabilità produttiva della coltura in tali condizioni, è essenziale per migliorare la produzione cerealicola dell’area del Mediterraneo. L’approccio usato in questo studio è stata la valutazione del comportamento di un ampia collezione di germoplasma di orzo e di popolazioni di mappaggio genetico in multilocational yield trias irrigate e non in sette paesi del bacino del Mediterraneo per tre anni. Le due tipologie di materiale vegetale utilizzate: 1) una collezione di 192 genotipi di orzo collezionati all'interno del progetto MABDE (Mapping Adaptation of Barley to Drought Environments) e comprendenti landraces, varietà antiche o varietà moderne provenienti dal Nord Europa, Nord e Sud Mediterraneo e Turchia; 2) una popolazione di linee doppio-aploidi derivate dall'incrocio tra una varietà italiana da zootecnia invernale -'Nure'- e una da malto primaverile -'Tremois'. I risultati presentati riguardano l’importanza dei diversi caratteri ecofisiologici della specie per la stabilità della produzione di granella in ambienti moderatamente siccitosi e in ambienti marginali con scarsa disponibilità idrica.

2007 - Coltivazioni innovative: pomodoro ad alto contenuto di carotenoidi. [Articolo su rivista]
Milc, Justyna Anna; Caffagni, Alessandra; L., Zanzi; Pecchioni, Nicola; P., Meriggi
abstract

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2007 - Development of an On-Line Database of Molecular and Phenotypic Data for Marker Assisted Selection of Cereals. [Abstract in Atti di Convegno]
Milc, Justyna Anna; Albertazzi, Giorgia; Caffagni, Alessandra; Sala, Antonio; Francia, Enrico; Barbieri, Mirko; Bergamaschi, Sonia; Pecchioni, Nicola
abstract

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2007 - Expression levels of barley CBF genes at Frost-resistance H2 are dependent upon alleles at Fr-H1 and Fr H2 [Articolo su rivista]
Stockinger, E. J.; Skinner, J. S.; Gardner, K. G.; Francia, Enrico; Pecchioni, Nicola
abstract

Genetic analyses have identified two loci in wheat and barley that mediate the capacity to overwinter in temperate climates. One locus co-segregates with VRN-1, which affects the vernalization requirement. This locus is known as Frost resistance-1 (Fr-1). The second locus, Fr-2, is coincident with a cluster of more than 12 Cbf genes. Cbf homologs in Arabidopsis thaliana play a key regulatory role in cold acclimatization and the acquisition of freezing tolerance. Here we report that the Hordeum vulgare (barley) locus VRN-H1/Fr-H1 affects expression of multiple barley Cbf genes at Fr-H2. RNA blot analyses, conducted on a `Nure'×`Tremois' barley mapping population segregating for VRN-H1/Fr-H1 and Fr-H2, revealed that transcript levels of all cold-induced Cbf genes at Fr-H2 were significantly higher in recombinants harboring the vrn-H1 winter allele than in recombinants harboring the Vrn-H1 spring allele. Steady-state Cbf2 and Cbf4 levels were also significantly higher in recombinants harboring the Nure allele at Fr-H2. Additional experiments indicated that, in vrn-H1 genotypes requiring vernalization, Cbf expression levels were dampened after plants were vernalized, and dampened Cbf expression was accompanied by robust expression of Vrn-1. Cbf levels were also significantly higher in plants grown under short days than under long days. Experiments in wheat and rye indicated that similar regulatory mechanisms occurred in these plants. These results suggest that VRN-H1/Fr-H1 acts in part to repress or attenuate expression of the Cbf at Fr-H2; and that the greater level of low temperature tolerance attributable to the Nure Fr-H2 allele may be due to the greater accumulation of Cbf2 and Cbf4 transcripts during normal growth and development.

2007 - Fine Mapping of a HvCBF gene cluster at Fr-H2, a QTL controlling frost resistance in barley. [Abstract in Atti di Convegno]
Francia, Enrico; Barabaschi, Delfina; A., Tondelli; G., Laido'; Stanca, ANTONIO MICHELE; Stockinger, E. J.; Pecchioni, Nicola
abstract

Barley (Hordeum vulgare) is an economically important diploid model for the Triticeae. We developed a new resource for genetic analysis of winterhardiness-related traits, the ‘Nure’ (winter) x ‘Tremois’(spring) barley mapping population. Two low temperature QTLs were found to segregate on the long arm of chromosome 5H. A first distal QTL for low-temperature tolerance was identified at the VrnH1/Fr1 region (Fr-H1). A second proximal QTL for low-temperature tolerance was identified (Fr-H2) and it was coincident with the QTLs regulating the accumulation of two different and well characterized COR proteins (COR14b and TMC-Ap3). Six barley genes with the CBF transcription factor signature have been mapped in a single gene cluster in this region, and they represented the candidate genes underlying this Fr-H2. A population of 1,849 recombinant plants (F2 and BC1F2) was constructed and the resulting F3 families harboring none, both and only one QTL were phenotypically tested for validation of the two QT loci Fr-H1 and Fr-H2. The study was then focused towards the isolation of the determinant of Fr-H2, and a high-resolution genetic map of the HvCBF gene cluster was constructed by using the large segregating population. In this phase a shorter confidence interval (P=0.05) for the frost tolerance QTL effect was estimated. After fine mapping, recombinations between the HvCBF genes were observed. The few recombinants between the different HvCBF sub-clusters were chosen and taken to homozygosity in order to separate the effects of the single HvCBF genes. Reciprocal QTL-NILs at Fr-H2 are also being devloped.

2007 - Fine mapping of a HvCBF gene cluster at the frost resistance locus Fr-H2 in barley. [Articolo su rivista]
Francia, Enrico; D., Barabaschi; A., Tondelli; G., Laido'; F., Rizza; Stanca, A. M.; M., Busconi; C., Fogher; Stockinger, E. J.; Pecchioni, Nicola
abstract

Barley is an economically important model for the Triticeae tribe. We recently developed a new resource: the ‘Nure’ x ‘Tremois’ mapping population. Two low temperature QTLs were found to segregate on the long arm of chromosome 5H (Fr-H1, distal; Fr-H2, proximal). With the final aim of positional cloning of the genetic determinants of Fr-H1 and Fr-H2, a large segregating population of 1,849 F2 plants between parents ‘Nure’ and ‘Tremois’ was prepared. These two QT loci were first validated by using a set of F3 families, marker-selected to harbor pairs of reciprocal haplotypes, with one QTL fixed at homozygosity and the alternate one in heterozygous phase. The study was then focused towards the isolation of the determinant of Fr-H2. Subsequent recombinant screens and phenotypic evaluation of F4 segregants allowed us to estimate (P < 0.01) a refinedgenomic interval of Fr-H2 (4.6 cM). Several barley genes with the CBF transcription factor signature had been already roughly mapped in cluster at Fr-H2, and they representlikely candidate genes underlying this QTL. Using the large segregating population (3,698 gametes) a high-resolution genetic map of the HvCBF gene cluster was then constructed, and after fine mapping, six recombinations between the HvCBFs were observed. It was therefore possible to genetically divide seven HvCBF subclusters in barley, in a region spanning 0.81 cM, with distances among them varying from 0.03 to 0.32 cM. The few recombinants between the different HvCBF subclusters are being marker selected and taken to homozygosity, to phenotypically separate the effects of the single HvCBF genes.

2007 - Genetic Aspects of Floral Fragrance in Plants. [Articolo su rivista]
Xiang, L; Milc, Justyna Anna; Pecchioni, Nicola; AND L. Q., Chen
abstract

It is generally assumed that compounds are emitted from flowers in order to attract and guide pollinators. Due tothe invisibility and the highly variable nature of floral scent, no efficient and reliable methods to screen for genetic variationhave been developed. Moreover, no convenient plant model systems are available for flower scent studies. In the past decade,several floral fragrancerelated genes have been cloned; the biosynthesis and metabolic engineering of floral volatiles havebeen studied with the development of biotechnology. This review summarizes the reported floral fragrancerelated genes andthe biosynthesis of floral scent compounds, introduces the origin of new modification enzymes for flower scent, comparesdifferent methods for floral fragrancerelated gene cloning, and discusses the metabolic engineering of floral scent. Finally,the perspectives and prospects of research on floral fragrance are presented.

2007 - Haplotype structure around the nud locus in barley and its association with resistance to leaf stripe (Pyrenophora graminea) [Articolo su rivista]
Barabaschi, Delfina; L., Campani; Francia, Enrico; H., TOUBIA RAHME; Vale', Giampiero; A., Gianinetti; G., Delogu; Stanca, A. M.; Pecchioni, Nicola
abstract

The naked/hulled kernel trait is controlled in barley by a single gene called nud, on chromosome 7H. The first aim of this work was use bulked segregant analysis to find, new PCR-based markers linked to nud for marker-assisted selection (MAS). A new SCAR marker (sJ14) was developed, which is useful for introgressing the naked trait. This, and three other SCARs, were placed on the ‘Proctor’ x ‘Nudinka’ map to detail a 0.9-cM fragment tagging nud. In order to evaluate the haplotypes around the nud locus, a phenotypically differentiated collection of naked/hulled genotypes was characterized by means of the above markers. Eight different marker haplotypes were found in the breeding germplasm, and a new allele for the marker sKT7 was found. The same barley collection has been surveyed for resistance/susceptibility to leaf stripe (Pyrenophora graminea), in order to investigate any possible association between this and other traits. The naked/hulled seed trait was not associated with resistance/susceptibility to the fungus.

2007 - Molecular Genetic Analyses Of The CBF Genes At The Barley Frost Resistance-H2 Locus. [Relazione in Atti di Convegno]
Francia, Enrico; Tondelli, A.; Knox, A. K.; Dhillon, T.; Stockinger, E. J.; Stanca, A. M.; Pecchioni, Nicola
abstract

Frost resistance-H2 is one of two major quantitative trait loci that affects freezing toleranceand winter hardiness of barley. Mapping coincident with Fr-H2 is a cluster of more than 14 genesencoding CBF transcription factors. To explore the possibility that the Cbfs may be the underlyingmolecular basis of Fr-H2, we have generated a large mapping population derived from the morefreezing tolerant genotype ‘Nure’, and the less freezing tolerant genotype ‘Tremois’, to both finemap the Fr-H2 interval, and to generate recombinants between the different Cbf genes.Concurrently, we have sequenced most of genetically colinear region encompassing the Cbf genesfrom these two barley genotypes with the goal of uncovering the underlying molecular basisexplaining Fr-H2. Screens for recombinant individuals from F2 populations consisting of morethan 3,698 meiotic events, and their subsequent phenotypic evaluation in F4 lines provided anestimated refined genomic interval of 4.6 cM for Fr-H2. Recombinants between seven of theestimated 14 Cbf genes under Fr-H2 have been identified and showed that the Cbf gene clusterspans 0.81 cM. Sequencing of the colinear genomic region revealed several key moleculardifferences that we hypothesize accounts for the phenotypic differences. Determining whether theCbfs underlie Fr-H2, and which gene or genes confers the capacity for greater freezing tolerancewill require the creation of near isogenic lines differing in their Fr-H2 alleles such thatrecombinants between the different Cbf gene orthologs and paralogs may be analyzed for theirphysiological capacity to survive freezing temperatures.

2007 - Obiettivi e traguardi dell’innovazione varietale. [Speciale Grano Tenero] [Articolo su rivista]
Pecchioni, Nicola
abstract

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2007 - The nuclear–cytoplasmic interaction controls carotenoid content in wheat [Articolo su rivista]
ATIENZA S., G; Martin, A; Pecchioni, Nicola; Platani, C; Cattivelli, L.
abstract

In greenhouse studies of three alloplasmicwheat series, plant height, Xowering date and yieldper plant were least aVected when the native cytoplasmwas replaced by donor cytoplasm of the Triticum–Aegilops complex than when replaced byHordeum chilense cytoplasm. On the other hand, signiWcantdiVerences for seed lutein content were foundbetween euplasmic controls and their respective alloplasmiclines in all the alloplasmic lines studied,underscoring the important role of the cytoplasm todetermine the seed carotenoid content. Both T. aestivumsubesp. macha and Ae. squarrosa cytoplasmsincreased the lutein content. They may be the mostuseful sources of cytoplasmic variability for broadeningthe genetic diversity of wheat for seed carotenoidcontent since both cytoplasm types do not produceany detrimental eVect on agronomic traits, as previouslyreported by other researchers. These Wndingsdemonstrate the role of the nuclear x cytoplasm interaction in the accumulation of carotenoids inwheat.

2007 - Workshop CEREALAB [Esposizione]
Pecchioni, Nicola
abstract

Le Biotecnologie non-OGM nel settore Sementiero: i Risultati del Laboratorio CEREALABGiovedì 31 Maggio 2007 - ore 14.30Aula Magna "Pietro Manodori"dell'Università di Modena e Reggio EmiliaViale Allegri, 9 - Reggio EmiliaCEREALAB è un Laboratorio promosso dalla Regione Emilia-Romagna dedicato alla ricerca industriale e al trasferimento tecnologico nel campo della innovazione varietale di specie cerealicole.CEREALAB aggrega partner di ricerca pubblica ed industriali per sviluppare nuove conoscenze in questo settore e promuoverne l'impatto tecnologico sulla realtà produttiva. Attraverso la struttura a rete CEREALAB mette a disposizione competenze qualificate, tecnologie, e attività a favore delle imprese del settore sementiero.14.30 - Registrazione partecipanti14.40 - SalutiGiancarlo Pellacani - Magnifico Rettore Università degli Studi di Modena e Reggio EmiliaPierluigi Saccardi - Assessore alle Attività Produttive della Provincia di Reggio Emilia14.50 - Introduzione al Laboratorio CEREALABNicola Pecchioni - Responsabile Scientifico Laboratorio CEREALAB15.10 - La Rete Alta Tecnologia della Regione Emilia-Romagna nel Settore AgroalimentareEnzo Bertoldi - ASTER Scienza Tecnologia Impresa15.20 - Risultati del Laboratorio CEREALABBreeding Assistito per la Resistenza alle malattie dei cerealiMichele Stanca - CRA di Fiorenzuola d'ArdaSelezione assistita per la sostenibilità produttiva del frumento duroRoberto Tuberosa - Università degli Studi di BolognaDemo del dBase CEREALABSonia Bergamaschi - Università degli Studi di Modena e Reggio EmiliaLe imprese di CEREALAB:Metodi innovativi per la selezione varietale in frumento duroAndrea Demontis - PSB S.p.a. ArgelatoMetodi innovativi per la selezione varietale con particolare riferimento al risoStefano Ravaglia - SIS S.p.a. San Lazzaro di Savena16.10 - Ruolo delle tecnologie avanzate nello sviluppo varietaleMarco Nardi - Segretario Associazione Italiana Sementi16.30 - Conclude Duccio CampagnoliAssessore alle Attività Produttive, Sviluppo Economico e Piano Telematico Regione Emilia-Romagna

2007 - dBase CEREALAB [Software]
Pecchioni, Nicola; Milc, Justyna Anna; Sala, Antonio; Bergamaschi, Sonia
abstract

The CEREALAB database; an information system for breeders is a source of molecular and phenotypic data, realized by integrating two already existing web databases, Gramene and Graingenes together with the source storing the information achieved by research groups of the CEREALAB project. The new data derives from a systematic genotyping work using already known markers and some brandly new protocols developed by the discovery workpackage of the project.This integration is obtained using the MOMIS system (Mediator Environment for Multiple Information Sources). The result obtained is a queriable virtual view that integrates the three sources and allows performing selection of cultivars of barley, wheat and rice based on molecular data and phenotypic traits, regardless of the specific languages of the three source databases. The phenotypic characters to be included in the database have been chosen among those of major interest for the breeders and divided into six categories: Abiotic Stress, Biotic Stress, Growth and Development, Quality and Yield. As far as molecular data is concerned the major categories for the query are: Trait, Qtl, Gene and Marker.

2006 - Dual-purpose barley and oat in a Mediterranean environment [Articolo su rivista]
Francia, Enrico; Pecchioni, Nicola; O., LI DESTRI NICOSIA; G., Paoletta; L., Taibi; V., Franco; M., Odoardi; Stanca, ANTONIO MICHELE; G., Delogu
abstract

In Mediterranean environments, forage production for livestock is both difficult and costly due to erratic rainfall. As an alternative, barley, oat and triticale can be used as dual-purpose autumn-sown cereals, thus serving as winter grazing and grain for feed. The present study was aimed at estimating the influence of different management systems (dual-purpose with one and two grazings, soft-dough harvest for silage, full maturity grain only) on grain yield, forage and whole plant production, and on quality-related traits of barley (Hordeum vulgare L.) and oat (Avena sativa L.). The trials were conducted over 2 years (1998/1999 and 1999/2000) in a Southern Italy Mediterranean environment using a flock of sheep for grazing and mechanically clipping the plots, thus simulating the dual-purpose, to obtain forage samples for analyses. Effect of the years was not significant, whereas both crops underwent significant reductions of grain yield, harvest index, thousand kernel weight and seeds/m(2) in the dual-purpose plots but not in the grain only plots. The most drastic yield reduction was recorded in oat after two grazings by comparison to the ungrazed treatment (2.4 t/ha versus 3.9 t/ha). Grain protein content was not affected by dual-purpose in oat, and it was independent of the number of grazings in barley. Barley had a higher production of total biomass and milk feed units than oat in the dual-purpose management systems, except for the soft-dough and grain only treatments. In addition, barley reacted positively to both the dual-purpose systems (one and two grazings). More specifically, whole plant biomass increased from 9.6 t/ha when grown for grain only to 13.6 t/ha in the single grazing system, and milk feed units similarly increased, from 7680 to 9216 MFU/ha. Green forage quality was comparable between the two cereals, even though barley whole plants showed lower fibre content, especially after two grazings. The soft-dough stage of both crops had better forage quality parameters, nevertheless, the lower biomass yields and total milk feed units (in the case of barley) rendered this system non-profitable for the environment studied. Barley demonstrated a clear superiority for the dual-purpose systems in Mediterranean Italy and should thus be preferred to oat, except when using oat to interrupt barley monocropping. (c) 2006 Elsevier B.V. All rights reserved.

2006 - Genetic variability among different Italian populations of the aphid Myzus persicae [Articolo su rivista]
A., Criniti; E., Mazzoni; Pecchioni, Nicola; D., Rau; Cassanelli, Stefano; D., Bizzaro; Manicardi, Gian Carlo
abstract

Aphids life cycle includes cyclical or obligate parthenogenesis, therefore low genetic variation is expected in these insects. Genetic diversity in crop pest aphids such as Myzus persicae, is also influenced by the extensive use of insecticides which favoured the selection of few resistant strains. In the present work, 18 M. persicae populations collected in different Italian regions, were studied by RAPD-PCR (Random Amplified Polymorphic DNA) to assess genetic variability among populations. Twelve different random primers, selected out of 24 previously investigated, were employed for genomic DNA amplification. A total of 150 fragments from the aphid M. persicae populations, and 31 fragments in two outgroups were identified. An UPGMA cluster analysis based on NEI and LI's genetic distance revealed that the M. persicae populations could be divided into two groups: aphids from Central and Southern Italy were generally located in the same cluster, while aphids from Northern Italy were more often located in the other. The presence of a positive correlation between genetic and geographical distance suggests that at least a portion of the interpopulation polymorphism evidenced could be caused by restricted gene flow.

2006 - Impiego di marcatori molecolari in garofano e loro applicazione per il miglioramento della qualità post-raccolta [Articolo su rivista]
DE BENEDETTI, L; S., Bruna; A., Mercuri; G., Burchi; Pecchioni, Nicola; C. BIANCHINI E. T., Schiva
abstract

Le tecniche di indagine dei polimorfismi del DNAsono sempre più numerose e perfezionate e il loro utilizzoper lo studio delle specie ornamentali si è dimostratovalido oltre che per la caratterizzazione varietaleanche per l’individuazione diretta di geni che controllano controllanocaratteri qualitativi e quantitativi importanti(Arùs, 2000).In garofano, il saggio della longevità è nella praticail primo tesi effettuato dai breeders sui nuovi genotipiselezionati e, partendo dai semi F1, si impieganoalmeno due anni per effettuare tale screening. Ladurata in vaso è un carattere complesso di tipo quantitativo,in cui sono coinvolti più geni i cui effetti sonodi tipo prevalentemente additivo (Burchi et al., 1999).La disponibilità e l’utilizzo di marcatori molecolaricorrelati a questo carattere permetterebbero una precoceidentificazione dei genotipi più longevi migliorandol’efficienza dei programmi di breeding con unametodologia avanzata (selezione assistita).Allo scopo di identificare tali marcatori sono statireperite sia progenie segreganti per longevità, siavarietà commerciali ben differenziate per il carattere,ed analizzate mediante tecniche RAPD (RandomAmplified Polymorphic DNA), AFLP (AmplifiedFra gment Lenght Polymorphism) e SSCP (Single-Strand Confo rmation Polymo rphism).

2006 - Le proprietà salutistiche dei cereali autunno-vernini e del riso. [Articolo su rivista]
Pecchioni, Nicola; G., Dinelli; P., Meriggi
abstract

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2006 - Mapping candidate genes for drought tolerance in barley [Abstract in Atti di Convegno]
Tondelli, A.; Francia, Enrico; G., Laidò; D., Barabaschi; Stanca, A. M.; Pecchioni, Nicola
abstract

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2006 - Mapping regulatory genes as candidates for cold and drought stress tolerance in barley [Articolo su rivista]
A., Tondelli; Francia, Enrico; Barabaschi, Delfina; A., Aprile; Skinner, J. S.; Stockinger, E. J.; Stanca, ANTONIO MICHELE; Pecchioni, Nicola
abstract

Cereal crop yield is greatly affected in many growing areas by abiotic stresses, mainly low temperature and drought. In order to find candidates for the tolerance genes for these stresses, 13 genes encoding for transcription factors and upstream regulators were screened by amplification and SSCP on six parental genotypes of three barley mapping populations ('Nure' x 'Tremois', 'Proctor' x 'Nudinka', and 'Steptoe' x 'Morex'), and mapped as newly developed STS, SNP, and SSCP markers. A new consensus function map was then drawn using the three maps above, including 16 regulatory candidate genes (CGs). The positions of barley cold and drought tolerance quantitative trait loci (QTLs) presently described in the literature were added to the consensus map to find positional candidates from among the mapped genes. A cluster of six HvCBF genes co-mapped with the Fr-H2 cold tolerance QTL, while no QTLs for the same trait were positioned on chromosome 7H, where two putative barley regulators of CBF expression, ICE1 and FRY1, found by homology search, were mapped in this work. These observations suggest that CBF gene(s) themselves, rather than their two regulators, are at present the best candidates for cold tolerance. Four out of 12 drought tolerance QTLs of the consensus map are associated with regulatory CGs, on chromosomes 2H, 5H, and 7H, and two QTLs with effector genes, on chromosomes 5H and 6H. The results obtained could be used to guide MAS applications, allowing introduction into an ideal genotype of favourable alleles of tolerance QTLs.

2006 - Survey of molecular diversity at nud locus in barley. [Relazione in Atti di Convegno]
Barabaschi, Delfina; G., Laido'; Francia, Enrico; A., Tondelli; A., Gianinetti; Stanca, ANTONIO MICHELE; Pecchioni, Nicola
abstract

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2006 - The genetic basis of vernalization response in barley. [Capitolo/Saggio]
COOPER LLD, L. L. D.; J., VON ZITZEWITZ; Skinner, J. S.; P., Szucs; I., Karsai; Francia, Enrico; Stanca, ANTONIO MICHELE; Pecchioni, Nicola; Laurie, D. A.; Chen, T. H. H.; Hayes, P. M.
abstract

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2006 - Towards the fine mapping of Fr-H2 – a major QTL controlling frost resistance in barley. [Abstract in Atti di Convegno]
Francia, Enrico; D., Barabaschi; A., Tondelli; G., Laidò; F., Rizza; Stanca, A. M.; M., Busconi; C., Fogher; Stockinger, E. J.; Pecchioni, Nicola
abstract

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2006 - ‘Diomede’, A winter barley for dual-purpose in comparison to oats grown in a Mediterranean environment. [Abstract in Atti di Convegno]
Odoardi, M.; Francia, Enrico; Pecchioni, Nicola; O., Li Destri Nicosia; G., Paoletta; L., Taibi; V., Franco; Stanca, A. M.; G., Delogu
abstract

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2005 - A new barley consensus function map of abiotic stress-related genes [Abstract in Atti di Convegno]
Tondelli, A.; Francia, Enrico; D., Barabaschi; G., Laidò; A., Aprile; A., Caffagni; A. M., Stanca; Pecchioni, Nicola
abstract

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2005 - Development of three genetic maps for the dissection of the genetic bases of agronomical key traits in durum wheat [Abstract in Atti di Convegno]
Marone, D.; E., Mazzucotelli; L., Matteu; Pecchioni, Nicola; L., Cattivelli; A. M., Mastrangelo
abstract

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2005 - Effetti del pascolamento di orzo e avena in ambiente mediterraneo sulla produzione di granella e sulla qualità della pianta intera. [Abstract in Atti di Convegno]
Pecchioni, Nicola; Delogu, G.; Li Destri Nicosia, O.; Paoletta, G.; Taibi, L.; Franco, V.; Stanca, A. M.
abstract

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2005 - Genetic bases of barley resistance to the leaf stripe agent Pyrenophora graminea. [Relazione in Atti di Convegno]
Valè, G.; Pecchioni, Nicola; D., Bulgarelli; G., Tacconi; E., Dall’Aglio; G., Delogu; A. M., Stanca
abstract

Leaf stripe, caused by Pyrenophora graminea, is a serious disease of barley in many productionareas. Genetic mapping of major genes and quantitative trait loci for this disease has revealedresistance loci on the chromosomes 1(7H), 2 (2H) and 3(3H). QTLs for partial resistance have beenidentified in segregating populations derived from the crosses between Proctor and Nudinka, L94and Vada, L94 and C123, Steptoe and Morex. Major genes conferring useful range of activity havebeen identified in the barley cultivars Vada and Thibaut. The Thibaut resistance gene, named asRdg2a, has been subjected to high resolution mapping and a syntenic relationship of the resistancegene locus with rice chromosome 6 has been established. In the course of the mapping of major andquantitative disease resistance loci, molecular markers for resistance breeding for disease controlusing gene technology have been identified and validated for utilization in marker assisted selectionof disease resistance.

2005 - Genetic bases of resistance to abiotic stresses in durum wheat (Triticum turgidum ssp. durum) [Capitolo/Saggio]
Mastrangelo, A. M.; C., Mare’; E., Mazzucotelli; Francia, Enrico; Arru, Laura; N., DI FONZO; Pecchioni, Nicola; L., Cattivelli
abstract

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2005 - Il Pianeta Acqua nel Continente Agricoltura (Congresso Nazionale dell’Associazione Italiana delle Società Scientifiche Agrarie – AISSA) [Altro]
Stanca, Am; Arru, Laura; Bignami, Cristina; Conte, Angela; Endrighi, Emiro; Franchini, ; Lofiego, D; Manicardi, Gian Carlo; Orlandini, Stefano; Pellegrini, ; Ulrici, Alessandro; Bacarella, Borin; Dazzi, Espen; Gallerani, Giupponi; Magnani, ; Pecchioni, Nicola; Poni, Rossi; Zanni,
abstract

Nell’era della specializzazione nel settore della Ricerca Scientifica, il Convegno ha l’ambizione di mettere insieme i singoli componenti del mondo scientifico agrario, di farli interagire tra di loro e di tentare di affrontare il problema Acqua in modo interdisciplinare. L’avanzamento delle conoscenze sul ruolo dell’acqua nel “Continente Agricoltura” garantirà ricadute di notevole interesse a breve, medio e lungo termine, per migliorare ulteriormente l’interazione “Organismi viventi di interesse agrario e forestale - Terreno – Atmosfera”. L’obiettivo finale è infatti quello di assicurare per il futuro uno sviluppo sostenibile, grazie alla razionale gestione di un fattore ambientale ed economico primario, l’Acqua.

2005 - Influenza dei principali fattori agronomici sulla qualità del pomodoro da industria [Articolo su rivista]
P., Meriggi; G., Villani; Francia, Enrico; Pecchioni, Nicola
abstract

L’influenza da parte dell’ambiente di coltivazione, del clima dell’annata e delle pratiche agronomiche sulle qualità intrinseche del pomodoro da industria è in parte conosciuta. Esistono però ancora interrogativi su come le tecniche di coltivazione influenzino i singoli parametri qualitativi. Recentemente tale problematica ha assunto una rilevante importanza anche in relazione alle Normative che stabiliscono il sistema di valutazione qualitativa del pomodoro conferito e la relativa differenziazione del prezzo.

2005 - Lo Iodio nell’alimentazione umana ed il ruolo delle colture erbacee. [Articolo su rivista]
P., Perata; Pecchioni, Nicola; P., Meriggi; Arru, Laura; D., Barabaschi; Caffagni, Alessandra; S., Poggiolini
abstract

Lo iodio è un micronutriente troppo spesso sottovalutato. In Italia sono 5-6 milioni i soggetti che hanno problemi di gozzo, cioè presentano un ingrossamento della tiroide (nell’Italia meridionale il 25% dei ragazzi delle scuole dell’obbligo). La causa è principalmente il deficit di iodio ambientale. Il presente contributo si pone come obbiettivo di conoscere meglio questo elemento e di introdurre il possibile contributo dell’agricoltura alla attività di prevenzione.

2005 - Localization of QTLs and candidate genes involved in the regulation of frost tolerance in cereals [Relazione in Atti di Convegno]
G., Galiba; Pecchioni, Nicola; A., Vagujfalvi; Francia, Enrico; B., Toth; Barabaschi, Delfina; S., Barilli; C., Crosatti; L., Cattivelli; Stanca, ANTONIO MICHELE
abstract

The recent advances in the molecular investigation of the stress response have led to the identification of a great number of genes whose expression is associated to cold acclimation. In the model species Arabidopsis thaliana, a crucial role in the regulation of the gene set involved in cold tolerance has been clearly demonstrated for a family of transcription factors named C-repeat binding factor (CBF). Genes similar to the Arabidopsis CBF genes were identified in the EST database of many crop species including barley and wheat. In Triticeae, CBF is a multigene family with more than six members per genome and most of the CBF-cereal homologous sequences are clustered together on the long arm of chromosome 5. On the other hand, parallel genetic studies have identified several major genes and QTLs responsible for frost resistance or for components associated to frost restistance on each member of the 5th homoeologous chromosome of Triticeae. Soon after the discovery of the CBF transcription factors it was suggested that the CBF-cereal homologous genes might represent candidate genes for the loci controlling stress tolerance in cereals. Recent findings have demonstrated that the CBF locus cosegregates with one of the major QTLs for frost tolerance in barley and einkorn. This result represent one of the best successful examples of candidate gene approach for unraveling a complex phenotype such as the tolerance to abiotic stress.

2005 - Molecular analysis of Limonium genus through RAPD markers. [Articolo su rivista]
Bruna, S.; G., Burchi; L., DE BENEDETTI; A., Mercuri; Pecchioni, Nicola; C. BIANCHINI T., Schiva
abstract

RAPD analysis was used to determine the genetic similarity in wild species and cultivatedvarieties of Limonium genus and for verification of hybridity in progenies of interspecific crosses.Eleven wild species and ten commercial varieties were tested with ten selected RAPDprimers. A total of 254 bands were scored and used for calculating genetic distances amongentries. Two cultivars were grouped together with L. sinensis. The species L. bellidifolium, L.otolepis and L. caspia were clustered together. The largest cluster grouped five varieties and L.latifolium. The remaining three cultivars, belonging to the ‘Altaica’ group, resulted related toL. gmelinii. The wild species L. tataricum, L. perezii, L. sinuatum and L. longifolium were clearlyseparated from all of the other genotypes.Seven putative interspecific hybrids and their parents were characterised by means of nineselected RAPD primers. The putative parentage was confirmed for only two hybrids; the remainingfive genotypes, on the basis of RAPD patterns, were identified as apomixis and/orself-pollinations.Our results demonstrated that RAPD analysis is a useful tool for the molecular characterizationof Limonium genotypes. This simple technique may enable ornamental plant breedersto improve the efficiency of their breeding programs.

2005 - Molecular and structural characterization of barley vernalization genes [Articolo su rivista]
J., VON ZITZEWITZ; P., Szucs; J., Dubcovsky; Yan, L. L.; Francia, Enrico; Pecchioni, Nicola; A., Casas; Chen, T. H. H.; Hayes, P. M.; Skinner, J. S.
abstract

Vernalization, the requirement of a period of low temperature to induce transition from the vegetative to reproductive state, is an evolutionarily and economically important trait in the Triticeae. The genetic basis of vernalization in cultivated barley (Hordeum vulgare subsp. vulgare) can be defined using the two-locus VRN-H1/VRN-H2 model. We analyzed the allelic characteristics of HvBM5A, the candidate gene for VRN-H1, from ten cultivated barley accessions and one wild progenitor accession (subsp. spontaneum), representing the three barley growth habits - winter, facultative, and spring. We present multiple lines of evidence, including sequence, linkage map location, and expression, that support HvBM5A being VRN-H1. While the predicted polypeptides from different growth habits are identical, spring accessions contain a deletion in the first intron of HvBM5A that may be important for regulation. While spring HvBM5A alleles are typified by the intron-localized deletion, in some cases, the promoter may also determine the allele type. The presence/absence of the tightly linked ZCCT-H gene family members on chromosome 4H perfectly correlates with growth habit and we conclude that one of the three ZCCT-H genes is VRN-H2. The VRN-H2 locus is present in winter genotypes and deleted from the facultative and spring genotypes analyzed in this study, suggesting the facultative growth habit (cold tolerant, vernalization unresponsive) is a result of deletion of the VRN-H2 locus and presence of a winter HvBM5A allele. All reported barley vernalization QTLs can be explained by the two-locus VRN-H1/VRN-H2 model based on the presence/absence of VRN-H2 and a winter vs. spring HvBM5A allele.

2005 - Produzione di granella e qualità maltaria di linee doppio-aploidi di orzo cresciute in ambienti contrastanti del mediterraneo [Abstract in Atti di Convegno]
Francia, Enrico; Laidò, G.; Pecchioni, Nicola; Gianinetti, A.; Mastrangelo, A.; Li Destri Nicosia, O.; Di Fonzo, N.; Rizza, F.; Stanca, A. M.
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2005 - Survey of molecular diversity at nud locus in barley [Abstract in Atti di Convegno]
Barabaschi, D.; L., Campani; Francia, Enrico; A., Tondelli; A., Gianinetti; A. M., Stanca; Pecchioni, Nicola
abstract

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2004 - Development of PCR-based markers on chromosome 5H for assisted selection of frost-tolerant genotypes in barley [Articolo su rivista]
B., Toth; Francia, Enrico; F., Rizza; Stanca, ANTONIO MICHELE; G., Galiba; Pecchioni, Nicola
abstract

Frost tolerance is an important trait for barley breeding. Field selection for this trait is not always efficient since, especially in Southern Europe, severe winter frost occurs erratically. Recent advances of cloned genes and molecular markers in barley provide molecular breeders with the means to develop new, simple PCR-based molecular markers, which can be used to select frost-tolerant genotypes quickly without stress simulation. This paper reports the development of two STS markers derived from the RFLP probes WG644 and PSR637, chosen as they are located on the long arm of homoeologous group 5 chromosomes of Triticeae, known to harbour the most important loci for frost tolerance. The two STS markers were validated together with one selected RAPD marker, OPA17, by separating two sets of winter and spring barley genotypes with different levels of frost tolerance. The ability of the developed markers to select segregant frost-tolerant and frost-susceptible genotypes was then investigated in a population of doubled haploid lines derived from a cross between a highly tolerant ('Nure') and a susceptible ('Tremois') genotype. In this population only two markers, OPA17 and Psr637 demonstrated their efficiency in dividing the phenotypes according to the parental alleles. These two markers mapped on the long arm of chromosome 5H, tightly linked to two frost tolerance QTLs. Two polymorphic bands of the WG644 STS were mapped: the former on the long arm of chromosome 5H (Wg644c) and the latter (Wg644b) on the long arm of chromosome 2H.

2004 - Mapping adaptation of barley to Mediterranean environments [Relazione in Atti di Convegno]
Francia, Enrico; A., Tondelli; Barabaschi, Delfina; F., Rizza; O., Li Destri Nicosia; A., Mastrangelo; N., Di Fonzo; Pecchioni, Nicola
abstract

Barley (Hordeum vulgare) is an important diploid model for the Triticeae. In order to study inan unique genetic system drought and cold stresses, together with malting quality, a newgenetic map based on the Nure x Tremois (NT) doubled-haploid population has beendeveloped. The winter parent - Nure - is a modern, high yielding two-rowed feed-barleycultivar released by the ISC section of Fiorenzuola. It has a wide range of adaptability,including South European environment, and it belongs to the RLT (Recommended-ListTrials) of Italy. The spring parent - Tremois - is a modern, high yielding French two-rowedmalting variety; it is adapted to fertile environments and included in the RLT.To construct a functional map for the study of the drought tolerance trait, twenty barleyabiotic stress-induced and cold-related genes were placed on the NT map. Moreover, sixtycandidate genes were collected by looking for sequences of gene families involved in droughttolerance. Amongst them genes encoding for LEA proteins, kinases and transcription factorslike DREB/CBF, MYB and bZIP are being mapped. A multilocational irrigated vs. nonirrigatedfield trial on the NT population in Mediterranean Europe, North Africa and WestAsia is being carried out in 2004 for mapping QTLs of yield and drought adaptation traits.As a valuable tool to study low temperature tolerance, two QTLs - corresponding to theVrnH1/Fr-H1 and Fr-H2 loci for frost resistance - were mapped on the long arm ofchromosome 5H (Francia et al. 2004). Fine mapping of these QTLs has been started by usinga large F2 population.Understanding the genetic loci responsible of adaptation to drought environments will allowus to select, by means of molecular markers, superior genotypes for drought tolerance.

2004 - Marker-Assisted Selection and resistance gene pyramiding in barley [Abstract in Rivista]
Pecchioni, Nicola; Francia, Enrico; D., Barabaschi; Delogu, Giovanni; J., Ovesna; L., Kucera; J., Vacke; V., Sip
abstract

The soil-borne barley yellow mosaic virus complex (BaMMV-BaYMV), the aphid-borne barley yellow dwarf virus (BYDV) and the seed-borne fungus Pyrenophora graminea (leaf stripe) are the most serious diseases for the barley crop in Southern Europe. Moreover, resistance to BaYMV, still not present in Czech Republic, is a target of quarantine breeding for this as well as for other Eastern European Countries, and resistance to leaf stripe an increasingly important trait for organic barley crop in Europe. Nevertheless, breeding for multiple diseases encounters several economical and technical problems, and cultivars resistant to all the former diseases are not yet available. In this view, two schemes of marker-assisted selection (MAS) have been followed in winter barley to develop high yielding advanced lines: an assisted pedigree by introducing the two virus resistances, and a "gene pyramiding" scheme to introduce four loci of resistance - two to leaf stripe, and one each to BYDV and BaYMV. STS and SSR markers have been selected for the aim and applied to segregating progenies together with phenotypic selection for agronomic traits.Results of the two MAS processes are here presented, including yield performances of the advanced breeding lines.

2004 - QTL mapping of malting quality traits and characterization of doubled haploid lines by means of molecular markers [Abstract in Atti di Convegno]
Laidò, G.; Francia, Enrico; D., Barabaschi; F., Finocchiaro; A., Gianinetti; A. M., Stanca; G., Paoletta; Pecchioni, Nicola
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2004 - QTLs and candidate genes in the ‘Nure’ x ‘Tremois’ mapping population. [Abstract in Rivista]
Francia, Enrico; D., Barabaschi; A., Tondelli; G., Laido'; A., Caffagni; A., Aprile; A., Gianinetti; Stanca, ANTONIO MICHELE; G., Galiba; Hayes, P. M.; Pecchioni, Nicola
abstract

In order to study in an unique genetic system cold and drought stress-related traits, together with malting quality traits, a new barley genetic map based on the 'Nure' (winter and feeding) x 'Tremois' (spring and malting) doubled-haploid population has been developed. Two low temperature tolerance QTLs were mapped on chromosome 5H. A first, distal QTL for low temperature tolerance and vernalization requirement was identified at the VrnH1/FrH1 region. A second proximal QTL of cold tolerance was coincident with two QTLs regulating the accumulation of two different COR (COld Regulated) proteins (COR14b and TMC-Ap3); the peak position of this QTL, named FrH2, is coincident with the genetic locus of the HvCBF4 barley gene, that is in turn the candidate gene underlying this QTL. The ‘Nure’ x ‘Tremois’ population is also being tested for malting quality related traits. For this purpose, two separate replicated yield trials have been set up, the first fall-sown in one location (2001/2002), and the second one for validation in different locations in Italy (2002/2003). Moreover, a multilocational irrigated vs. non-irrigated field trial in Mediterranean Europe, North Africa and West Asia is being carried out in 2004 for mapping QTLs and candidate genes for drought tolerance.

2004 - Towards the identification of the genetic bases for drought tolerance in durum wheat [Abstract in Atti di Convegno]
Mastrangelo, A. M.; D., Marone; E., Mazzucotelli; F., Rizza; F., Badek; O., Li Destri; Pecchioni, Nicola; N., Di Fonzo
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2004 - Two loci on chromosome 5H determine low-temperature tolerance in a Nure (winter) × Tremois (spring) barley map. [Articolo su rivista]
Francia, Enrico; F., Rizza; L., Cattivelli; Stanca, A. M.; G., Galiba; B., Toth; Hayes, P. M.; Skinner, J. S.; Pecchioni, Nicola
abstract

Barley (Hordeum vulgare subsp. vulgare) is an economically important diploid model for the Triticeae; and a better understanding of low-temperature tolerance mechanisms could significantly improve the yield of fallsown cereals. We developed a new resource for genetic analysis of winter hardiness-related traits, the ‘Nure’ x ‘Tremois’ linkage map, based on a doubled-haploid population that is segregating for low-temperature tolerance and vernalization requirement. Three measures oflow-temperature tolerance and one measure of vernalizationrequirement were used and, for all traits, QTLs were mapped on chromosome 5H. The vernalization response QTL coincides with previous reports at the Vrn-1/Fr1 region of the Triticeae. We also found coincident QTLs at this position for all measures of low-temperature tolerance. Using Composite Interval Mapping, a second proximal set, of coincident QTLs for low-temperaturetolerance, and the accumulation of two different COR proteins (COR14b and TMC-Ap3) was identified. The HvCBF4 locus, or another member of the CBF loci clustered in this region, is the candidate gene underlying this QTL. There is a CRT/DRE recognition site in the promoter of cor14b with which a CBF protein could interact. These results support the hypothesis that highly conserved regulatory factors, such as members of theCBF gene family, may regulate the stress responses of a wide range of plant species.

2004 - Use of RAPD Markers for the Genetic Characterization of Limonium Species [Relazione in Atti di Convegno]
S., Bruna; L., De Benedetti; A., Mercuri; T., Schiva; G., Burchi; Pecchioni, Nicola; C., Agrimonti
abstract

The genus Limonium (fam. Plumbaginaceae) consists of about 300 species ofmostly herbaceous perennials, some low shrubs, and annuals. Most botanical speciesare endemics in the Mediterranean region, but many species have their centre oforigin in Caucaso, Turkestan, Caspian Sea, Russia, Iran, China, and South Africa.Limonium is grown in several regions of the world for use as a cut flower for bothfresh and dry-flower arrangements.In this work, RAPD analyses were used for thestudy of genetic relationships in Limonium. Thirteen wild species were tested with 10primers. A total of 244 bands were scored and used for the analysis of geneticdistances. The dendrogram obtained from cluster analysis showed high similarityamong three species that some authors report as synonymous and that appearedvery similar from our previous phenotypic observations (L. caspia, L. bellidifoliumand L. otolepis). In order to clarify the genetic relationships, further analyses werecarried out on several genotypes belonging to these species. The new dendrogram,obtained scoring 151 RAPD bands, showed that the genotypes did not group in clearclusters. Analysis of molecular variance (AMOVA) confirmed this trend: the highestgenetic variation resulted among genotypes and only 6,58 % of the total variationresulted among the species. These results suggest that the species can be consideredsynonymous. The use of RAPD markers in our case was thus useful for clarifying thehighly probable identity of the three Limonium species, in a plant genus that isnotably of difficult interpretation.

2003 - A cluster of CBF genes on chromosome 5H regulates the accumulation of the COR14b and TMC-Ap3 cold-induced proteins and frost tolerance in barley [Abstract in Atti di Convegno]
Francia, Enrico; D., Barabaschi; A., Aprile; A., Tondelli; C., Crosatti; A. M., Stanca; G., Galiba; P. M., Hayes; Pecchioni, Nicola
abstract

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2003 - Advanced high yielding lines of hulless winter barley for the development of functional foods [Relazione in Atti di Convegno]
D., Barabaschi; Pecchioni, Nicola; Francia, Enrico; M., Baronchelli; F., Finocchiaro; B., Ferrari; A., Gianinetti
abstract

Barley is interesting from a nutritional point of view for the typical grain composition that makes it an ideal cereal for the production of "functional foods". Such components are mainly beta-glucans (soluble fiber) and tocols (vitamin E). The beta-glucans are an heterogeneous family of polysaccharides, typical of barley and oats, that constitute the cellular walls of the seed endosperm, and that, introduced into diet, can contribute to the lowering of hematic cholesterol and of hematic glucose content. Therefore, the interest of researchers is for the production of baked foods containing barley flour, then rich in dietary fiber, i.e. beta-glucans. Also by using specific techniques for the enrichment of flour in beta-glucans (e.g. turboseparation), it has been possible to produce high beta-glucan bread and bakery products made of mixed wheat and enriched barley flour with organolectic characteristics not too far from those made of pure wheat flour. Hulless barley, lacking of glumelets, gives a grain of superior quality for food respect to hulled barley, although it yields generally less, for both the absence of the glumelets and the lower efforts on the improvement of the hulless germplasm. In the Istituto Sperimentale per la Cerealicoltura it had been active a breeding program for winter hulless barley, with the main objective of yield stability, and based on pedigree and backcross schemes that lead to the release of cultivar 'Zacinto' (2000). Inside the frame of the programme, a SCAR marker has been developed for the recognition of heterozyigous genotypes in hulled x hulless backcrosses, and this marker has been used for the acceleration of such breeding schemes. In a second phase, the resistance to the soil-borne mosaic virus complex (BaMMV-BaYMV), and to the yellow dwarf virus (BYDV) have been introduced in the programme, by means of molecular Marker-Assisted Selection. A specific replicated yield trial has been recently set up in which the advanced high yielding hulless lines, together with hulled and hulless checks have been evaluated in different locations in Italy for the average production of beta-glucans and tocols, and for the evaluation of the effects of the genotype x environment interaction on the production of such compounds. In the last years, the virus-resistant advanced lines have been also crossed to Canadian and Australian hulless waxy lines with the aim to develop high yielding, virus-resistant and high beta-glucan winter barleys. In fact it is well-known that waxy barley genotypes contain consistently higher-beta-glucans respect to the ones with normal starch. The most recent results of the hulless barley breeding programme for the production of functional foods at the Istituto Sperimentale per la Cerealicoltura are here presented.

2003 - Advances in understanding barley-Pyrenophora graminea interaction [Relazione in Atti di Convegno]
Vale', Giampiero; G., Tacconi; Francia, Enrico; E., Dall’Aglio; C., Govoni; Pecchioni, Nicola; Arru, Laura; Delogu, Giovanni; A., PORTA PUGLIA; Stanca, ANTONIO MICHELE
abstract

Pyrenophora graminea Ito and Kuribayashi (anamorph Drechslera graminea) is a seed-borne pathogen causing barley leaf stripe. The disease is widely distributed in most barley growing areas, where it causes serious damage and yield losses. At present disease control is focused mainly on the application of fungicides, but the risk of naturally occurring resistance within the pathogen populations and the increasing legal limitations to the use of fungicides requires the development of new strategies for disease control. To this aim we are currently applying breeding procedures and studying the molecular bases of P. graminea-barley interaction. The interaction P. graminea-barley provides a good model for understanding the molecular basis of diseases caused by seed-borne pathogens. The expression of defence-related genes occurs in barley tissues inoculated with P. graminea, a response that is regulated by several factors depending on both the fungal isolate and the barley cultivar. The induction of these genes was monitored in barley cultivars inoculated with two highly virulent isolates of the pathogen Dg2 and Dg5 (also called I2 and I5 in previous papers) and in barley tissues infected with a hypovirulent mutant of the isolate Dg2. In the former, it was found that plants challenged by the isolates Dg2 and Dg5 responded with the induction of genes coding for peroxidases, thionins and thaumatin-like proteins. A single genetic factor controlling complete resistance to P. graminea, derived from Hordeum laevigatum via cv "Vada", has been introduced into most resistant North-European two-rowed spring barley cvs. This "Vada resistance" was probably introgressed into the barley genome along with the MlLa (Laevigatum) powdery mildew resistance, because the two factors have been found to be linked; this resistance, named as Rdg 1a, has been mapped on the long arm of barley chromosome 2. It is also known that cvs quantitatively resistant to leaf stripe are widespread in Europe. A major QTL conferring resistance to barley leaf stripe was identified in the cv "Proctor" by means of QTL analysis; this QTL accounted for 58.5% of the variation in the trait and was mapped on the centromeric region of barley chromosome 1. The cv "Thibaut" was identified as highly resistant to the most virulent Italian isolate, isolate Dg2. We have described the characterization of the genetic basis of the cv "Thibaut" resistance, the mapping of the locus harbouring this resistance gene and the development of PCR-based molecular markers associated with the resistance, and useful for marker-assisted selection. Near-isogenic lines (NILs) carrying resistance of the cv "Thibaut" against the highly virulent isolate Dg2 were obtained by introgressing the resistance into the genetic background of the susceptible cv "Mirco". The "Thibaut resistance gene" was mapped and called Rdg2a. A PCR-based marker (MWG2018) associated with the resistance gene has been developed to assess the leaf stripe resistant phenotype in barley breeding programs. Several resistant genotypes were identified and among them four were shown to possess the same allele of the cultivar Thibaut at the marker locus. One of them, the cultivar Rebelle, is being used as a source of leaf stripe resistance in winter barley breeding programs. In several resistant lines obtained from five crosses, in which Rebelle acted directly or indirectly as donor of the resistance, the allelic composition at the MWG2018 locus was verified. The results showed that the resistant phenotype of the lines was always associated with the resistance allele of the molecular marker, thereby demonstrating its reliability for selecting the leaf stripe resistance.

2003 - Isolate-specific QTLs of resistance to leaf stripe (Pyrenophora graminea) in the ‘Steptoe’ x ‘Morex’ spring barley cross [Articolo su rivista]
Arru, Laura; Francia, Enrico; Pecchioni, Nicola
abstract

Leaf stripe caused by the fungus Pyrenophoragraminea represents a serious threat to grain yield in organicallygrown barley and in conventional Nordic andMediterranean districts, for which resistant cultivars arenecessary. A medium-density, molecular marker map derivedfrom a ‘Steptoe’ (partially resistant) × ‘Morex’(susceptible) spring barley cross and its derived doubledhaploidmapping population inoculated with the fungusmade it possible to identify QTLs of resistance to leafstripe. In order to investigate isolate-specificity of partialresistance, the ‘Steptoe’ × ‘Morex’ segregating populationwas inoculated with two highly virulent P. gramineaisolates, Dg2 and Dg5. The present study demonstratesthat partial resistance to leaf stripe of cv ‘Steptoe’ is governedin part by shared loci and in part by isolate-specificones. One QTL is common to the resistance for the twoisolates, on the long arm of chromosome 2 (2H), twoQTLs are linked on chromosome 3 (3H), and the remainingtwo are isolate-specific, respectively for isolate Dg2on chromosome 2 (2H) and for isolate Dg5 on chromosome7 (5H). The QTL in common is that with the majoreffect on the resistance for each isolate, explaining 18.3%and 30.9% R2 respectively for Dg2 and Dg5. The isolatespecificQTLs mapped in the ‘Steptoe’ × ‘Morex’ barleyreference map support the assumption of Parlevliet andZadoks (1977) that partial resistance may be due to minorgene-for-minor-gene interactions. Map comparisons ofthe QTLs with the known qualitative resistance genes toleaf stripe, Rdg1 (2H) and Rdg2 (7H), as well as with otherQTLs of partial resistance in barley, show that the QTLfor resistance to both isolates mapped on the long arm ofchromosome 2 (2H) does not coincide with the qualitativeRdg1 gene but is linked to it at about 30 cM. One isolate-specific QTL of resistance to P. graminea, mappedon the short arm of chromosome 2 (2H), is coincidentwith a QTL for resistance to Pyrenophora teres previouslymapped in the ‘Steptoe’ × ‘Morex’ cross.

2003 - Marker-assisted selection for virus and low temperature tolerance in barley. [Relazione in Atti di Convegno]
Pecchioni, Nicola; Francia, Enrico; D., Barabaschi; G., Laidó; F., Reggiani; B., Toth; V., Sip; F., Rizza; G., Delogu
abstract

The soil-borne barley yellow mosaic virus (BaYMV), the aphid-borne barley yellow dwarf virus (BYDV) and the seed-borne fungus Pyrenophora graminea (leaf stripe) are the most serious diseases for the barley crop in Southern Europe environments, where mildew and other foliar diseases have a relatively small or not significant effect on yields. The development of barley cultivars resistant to the three diseases is thus an urgent objective of barley breeding for the area, in a context of increasing organic farming for cereals. Nevertheless, breeding for multiple diseases encounters several economical and technical problems, and cultivars resistant to the former diseases are not yet available. The bottlenecks of barley breeding for resistance to BYDV are the availability of sources of resistance, mainly based on semi-dominant Yd2 gene, and the labour-intensive inoculation test made with infected aphids. Availability of resistant germplasm and inoculation test are easier for BaYMV and, in relative terms, also for leaf stripe resistance. In this view, two schemes of marker-assisted selection (MAS) have been followed to develop high yielding advanced lines: an assisted pedigree by introducing the two virus resistances, and a "gene pyramiding" scheme to introduce four loci of resistance - two to leaf stripe, and one each to BYDV and BaYMV. STS and SSR markers have been selected for the aim and applied to segregating progenies together with phenotypic selection for agronomic traits.Results of the two MAS processes are here presented, including yield performances of the advanced breeding lines.

2003 - The PCR-based marker MWG2018 linked to the Rdg2a leaf stripe resistance gene is a useful tool for assessing barley resistance in breeding programs [Articolo su rivista]
Arru, Laura; N., Faccini; C., Govoni; L., Cattivelli; Pecchioni, Nicola; G., Delogu; Stanca, ANTONIO MICHELE; G., Vale'
abstract

Leaf stripe, caused by the fungus Pyrenophora graminea Ito et Kuribayashi [anamorph Drechslera graminea (Rabenh. ex. Schlech.) Shoemaker], is an important seed-borne disease of barley (Hordeum vulgare L.). The objective of this study was to verify the reliability of a PCR-based marker (MWG2018) associated with the resistance gene Rdg2a and to assess the leaf stripe resistant phenotype in barley breeding programs. A large number of barley cultivars and accessions were thus evaluated for their reaction to a highly virulent monoconidial isolate (Dg2) of the pathogen and genotyped for the allele of the molecular marker. Several resistant genotypes were identified and four were shown to possess the same allele as the cultivar Thibaut (the resistant parent of the original mapping population in which Rdg2a was identified) at the marker locus. One of them, cv. Rebelle, is being used as a source of leaf stripe resistance in winter barley breeding programs. The allelic composition at the MWG2018 locus was verified in several resistant lines bred from five crosses, in which Rebelle acted directly or indirectly as donor of the resistance. The results showed that the resistant phenotype of the lines was always associated with the resistance allele of the molecular marker, thereby demonstrating its reliability for selecting leaf stripe resistance. The MWG2018 PCR-based marker can therefore be proposed as a tool to assess the resistant phenotype.

2003 - Use of RAPD markers for the genetic characterization of Limonium wild species [Abstract in Atti di Convegno]
Bruna, S.; G., Burchi; L., De Benedetti; A., Mercuri; Pecchioni, Nicola; C., Agrimonti; T., Schiva
abstract

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2002 - Barley. [Capitolo/Saggio]
Pecchioni, Nicola; L., Cattivelli; G., Delogu; P., Faccioli; V., Terzi; G., Vale'; A. M., Stanca
abstract

Book Review by Ian Wardlaw - Ann Bot (2003) 91(4): 500-501.This book covers the evolution and domestication of six important cereal crops (rice, wheat, maize, barley, sorghum and pearl millet), and each chapter has been written by authors associated with major national or international research centres. The strength of the book does lie, as stated by the editors, in bringing together information on the development and improvement of the major crops into a single publication. However, not all chapters are presented in the same detail, or with the same emphasis, and it is difficult to generalize across all the presentations.While the chapter on rice does cover changes that have occurred during and following domestication and the attributes associated with the wide‐ranging cultural practices associated with growth of this crop, it is strongly centred on origins, taxonomy and breeding procedures. The chapter on wheat covers the evolutionary history and genetic changes that have taken place during domestication. There is a relatively short section on adaptation, with the main emphasis being on breeding and breeding techniques, genetics and plant genome analysis. As to be expected, aspects of the CIMMYT wheat breeding programme are included in this chapter. A more recent publication that might interest readers is Evolution of wild emmer and wheat improvement (Nevo et al., 2002). The chapter on maize gives a good insight into the nature of the plant, its taxonomic classification, origin, evolution and geographical and racial diversity. There is more emphasis on the adaptation of the crop to a range of abiotic and biotic stresses, and much less emphasis on detailed genetic analyses. The chapter on barley, with seven authors, is the longest. This covers taxonomy and genetic relationships, evolution and domestication, and breeding achievements. There is considerable emphasis in this chapter on modern molecular techniques, including a short discussion of barley transformation. There is also a relatively detailed assessment of adaptation to abiotic and biotic stress. A final point worth mentioning is the inclusion of website details where the reader can gain further information. The chapter on sorghum is the shortest,........Two earlier books come to mind when reading this volume: the second edition of Crops and man by Harlan (1992) and Crop evolution, adaptation and yield by Evans (1993). The current volume is, in a sense, complementary to these earlier publications in that the overall emphasis is more on the genetics and plant breeding systems associated with the individual crops, while the earlier publications were concerned more with the historical development of cropping and the morphological and physiological changes associated with crop improvement.......It is stated in the preface that the book is written for students, teachers, researchers and others interested in the biology, improvement and use of the crops discussed. While a lot of the material is of general interest, to get the most out of this book it would help for the reader to have a background in genetics, including the more molecular aspects of the topic. This book should certainly be available in all libraries supporting agricultural research and plant breeding.

2002 - Chromosome regions and stress-related sequences involved in resistance to abiotic stress in Triticeae [Articolo su rivista]
Cattivelli, L; Baldi, P; Crosatti, C; DI FONZO, N; Faccioli, P; Grossi, M; MASTRANGELO A., M; Pecchioni, Nicola; Stanca, A. M.
abstract

Drought, low temperature and salinity are the most important abiotic stress factors limiting crop productivity.A genomic map of major loci and QTLs affecting stress tolerance in Triticeae identified the crucial role of thegroup 5 chromosomes, where the highest concentration of QTLs and major loci controlling plant’s adaptation tothe environment (heading date, frost and salt tolerance) has been found. In addition, a conserved region with amajor role in drought tolerance has been localized to the group 7 chromosomes. Extensive molecular biologicalstudies have led to the cloning of many stress-related genes and responsive elements. The expression of somestress-related genes was shown to be linked to stress-tolerant QTLs, suggesting that these genes may represent themolecular basis of stress tolerance. The development of suitable genetic tools will allow the role of stress-relatedsequences and their relationship with stress-tolerant loci to be established in the near future.

2002 - Genomic regions determining resistance to leaf stripe (Pyrenophora graminea) in barley [Articolo su rivista]
Arru, Laura; Re, Niks; P., Lindhout; G., Vale'; Francia, Enrico; Pecchioni, Nicola
abstract

Leaf stripe is a seed-borne disease of barley (Hordeum vulgare) caused by Pyrenophora graminea. Little is known about the genetics of resistance to this pathogen. In the present work, QTL analysis was applied on two recombinant inbred line (RIL) populations derived from two- and six-rowed barley genotypes with different levels of partial resistance to barley leaf stripe. Quantitative trait loci for partial resistance were identified using the composite interval mapping (CIM) method of PLABQTL software, using the putative QTL markers as cofactors. In the L94 x 'Vada' mapping population, one QTL for resistance was detected on chromosome 2H; the same location as the leaf-stripe resistance gene Rdg1 mapped earlier in 'Alf', where it confers complete resistance to the pathogen. An additional minor-effect QTL was identified by further analyses in this segregating population on chromosome 7H. In L94 x C123, two QTLs for resistance were mapped, one each on chromosomes 7H and 2H.

2002 - La concia del seme. [Articolo su rivista]
Gianinetti, A.; G., Vale'; Pecchioni, Nicola; A. M., Stanca
abstract

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2002 - L’ “Elmintosporiosi” del riso: studio sulla resistenza varietale dell’ospite e sulla virulenza del fungo. [Articolo su rivista]
Gianinetti, A.; G., Vale'; Pecchioni, Nicola; A., Infantino; N., Pucci; A. M., Stanca
abstract

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2002 - Validation of a chlorophyll fluorescence-based method for selection for winterhardiness in cereals. [Abstract in Atti di Convegno]
Rizza, F.; Crosatti, C.; Pagani, D.; Francia, Enrico; Pecchioni, Nicola; Galiba, G.; Cattivelli, L.
abstract

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2001 - A four resistance loci pyramiding MAS scheme in barley [Relazione in Atti di Convegno]
Pecchioni, Nicola; G., Valé; G., Delogu
abstract

The most serious diseases for the barley crop in Southern Europe environments, where mildew and other leaf fungi have a relatively small or not significant effect on yields, are the soil-borne barley yellow mosaic virus (BaYMV), the aphid-borne barley yellow dwarf virus (BYDV) and the seed-borne fungus Pyrenophora graminea (leaf stripe). Developing barley cultivars resistant to the three diseases, while being an urgent objective of barley breeding, in a context of increasing organic farming for cereals, encounters several problems and cultivars resistant to all the former diseases are not yet available. The problems of barley breeding for resistance to BYDV are the availability of sources of resistance, mainly based on semi-dominant Yd2 gene, and the labour-intensive inoculation test made with infected aphids. Availability of resistant cultivars and inoculation test is easier for BaYMV and, in relative terms, also for leaf stripe. Indeed, in normal breeding schemes is quite difficult and anyway expensive to perform all resistance tests on the segregating progenies. For these reasons, it has been developed few years ago a "gene pyramiding" MAS (molecular-assisted selection) scheme to introduce four loci of resistance - two to leaf stripe, and one each to BYDV and BaYMV - into the elite winter barley cultivar Nure. Nure is in fact a highly yielding cultivar, adapted to Southern European environments, but lacking of most important resistances. STS and SSR markers have been adapted to the aim and applied to segregating progenies together with phenotypic selection for agronomic traits. The four loci have been introgressed successfully in couples at homozygosity into F3 families, for the final consolidation of the four into the Nure winter type background.In this work it is reported the molecular-assisted breeding history of the resistance gene pyramiding into this cultivar.

2001 - Amido non food: dalla sintesi alla trasformazione industriale. [Articolo su rivista]
Cavallero, A.; A., Gianinetti; Pecchioni, Nicola; G., Vale'; A. M., Stanca
abstract

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2001 - Development of a 'winter' x 'spring' and 'feeding' x 'malting' two-rowed barley map [Relazione in Atti di Convegno]
Pecchioni, Nicola; Francia, Enrico; Arru, Laura; Baldi, P; Cattivelli, L; Gianinetti, A; Stanca, ANTONIO MICHELE
abstract

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2001 - Expressed sequence tags (ESTs) from cold-acclimated barley to identify novel plant genes [Articolo su rivista]
Faccioli, P; Pecchioni, Nicola; Cattivelli, L; STANCA A., M; Terzi, V.
abstract

Expressed sequence tags (ESTs) databases are being created for severalplant species. ESTs have the potential to analyse the expressed part ofthe genome, and to be used in a wide range of applications from thetheoretical aspect of plant biology to the breeding process. The presentstudy is based on a cold-stressed cDNA library as a source of ESTs inbarley: partial cDNA sequencing of randomly isolated clones yielded960 ESTs. The strategy of random sequencing cDNA clones at their5' ends allows one to obtain information on the steady-state level of thetranscripts in a cold-stressed green leaf of barley. Repetitive sequencingof nearly identical ESTs provides, in addition, useful information onthe existence of multigene families. The results of a BLAST searchperformed on this set of ESTs showed that 18.5% of the tags exhibitedno significant homology to known genes, 10% had significant levels ofhomology with known cold or other stress-related genes, about 26%proved homologous to enzymes involved in several metabolic pathways and about 15% encoded for ribosomal proteins, cytoskeletonproteins, histones, ubiquitin, elongation factors and others. Redundancy was found for some classes of tag: RuBisCo, cab proteins,carbonic anhydrase, glutamate decarboxylase and stress relatedproteins.

2001 - Identification and mapping of a new leaf stripe resistance gene in barley (Hordeum vulgare L.) [Articolo su rivista]
Tacconi, G; Cattivelli, L; Faccini, N; Pecchioni, Nicola; STANCA A., M; Valé, G.
abstract

Pyrenophora graminea is the seed-bornepathogen causal agent of barley leaf stripe disease. Nearisogeniclines (NILs) carrying resistance of the cv “Thibaut”against the highly virulent isolate Dg2 were obtainedby introgressing the resistance into the geneticbackground of the susceptible cv “Mirco”. The segregationof the resistance gene was followed in a F2 populationof 128 plants as well as on the F3 lines derived fromthe F2 plants; the segregation fitted the 1:2:1 ratio for asingle gene. By using NILs, a RAPD marker associatedwith the resistance gene was identified; sequence-specific(STS) primers were designed on the basis of the ampliconsequence and a RILs mapping population with anAFLP-based map were used to position this molecularmarker to barley chromosome 1 S (7HS). STS and CAPSmarkers were developed from RFLPs mapped to thetelomeric region of barley chromosome 7HS and threepolymorphic PCR-based markers were developed. Thesegregation of these markers was followed in the F2 populationand their map position with respect to the resistancegene was determined. Our results indicate that theThibaut resistance gene, which we designated as Rdg2a,maps to the telomeric region of barley chromosome 7HSand is flanked by the markers OPQ-9700 and MWG 2018at distances of 3.1 and 2.5 cM respectively. The suitabilityof the PCR-based marker MWG2018 in selectionassistedbarley breeding programs is discussed.

2001 - Identificazione in orzo di Rdg2, un nuovo gene di resistenza alla striatura bruna, e di marcatori molecolari per la selezione assistita [Relazione in Atti di Convegno]
Tacconi, G.; L., Cattivelli; Pecchioni, Nicola; G., Delogu; A., Porta Puglia; A. M., Stanca; G., Valé
abstract

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2001 - Orzo nudo, alternativa percorribile. [Articolo su rivista]
Porfiri, O.; A., Petrini; Pecchioni, Nicola; G., Delogu
abstract

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2001 - Phyletic relationships within the genus Hordeum using PCR-based markers [Articolo su rivista]
Terzi, V.; Pecchioni, Nicola; P., Faccioli; L., Kucera; A. M., Stanca
abstract

Fifteen Hordeum species and subspecies belonging to groups with different genomes were studied usingPCR-based markers to establish phylogenetic relationships within the genus. Two hundred and seventeen RAPDand STS markers were used to calculate genetic distances and construct phylogenetic trees. The phenetic analysisclearly separated the primary gene pool, represented by H. vulgare ssp. vulgare, H. vulgare ssp. vulgare convar.vulgare f. agriochriton and H. vulgare ssp. spontaneum, from the secondary gene pool, represented by H.bulbosum and the tertiary gene pool, represented by American wild barleys and H. bogdanii. Data obtained fromPCO analysis are in complete agreement with taxonomic classifications proposed previously, which werecomparisons of numerous morphological, cytological and reproductive characters.

2001 - QT loci regulating the accumulation of COR14 and TMCAP3 cold-induced proteins in barley [Abstract in Atti di Convegno]
Francia, Enrico; C., Crosatti; Pecchioni, Nicola
abstract

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2001 - RAPD and AFLP genetic markers for the characterisation of Osteospermum germplasm. [Articolo su rivista]
T., Berio; G., Morreale; A., Giovannini; A., Allavena; Arru, Laura; P., Faccioli; V., Terzi; Pecchioni, Nicola
abstract

The level of genetic diversity was assayed within the accessions of three breeding groups in an Osteospermum collection. The NA-profiling via RAPD revealed high levels of polymorphism. enetic variation was highest in the English material, intermediate in the Italian and lowest in the Danish breeding group. The most requent similarity classes were 0.5-0.6 for the English, 0.6-0.7 for he Italian and 0.7-0.8 for the Danish group. Furthermore, an FLP analysis has been carried out on a sample of eight accessions representative of the three groups. Preliminary results indicate that AFLP analysis is suitable to give polymorphism in Osteospermum. RAPD and AFLP analysis can therefore be a useful tool for evaluating genetic diversity for breeding purposes, and for protecting intellectual property rights of new varieties.

2001 - Random amplified polymorphic DNA (RAPD) analysis for the genetic characterization of potential parents in a breeding program on pot Alstroemeria [Articolo su rivista]
Burchi, G.; L., De Benedetti; A., Mercuri; Pecchioni, Nicola; T., Schiva
abstract

Random amplified polymorphic DNA (RAPD) markers were used for the characterization of potential parents in a breeding program on Alstroemeria for pot plant production. A similarity matrix was constructed to estimate the genetic similarity values between genotypes. Cluster analysis was performed to examine the relationships among genotypes. The classification of genotypes through the use of four selected primers is in agreement with the expectations based on geographical origin and pedigree data. On the basis of RAPD data, the most distantly related genotypes were selected to start the breeding program. RAPD analysis thus resulted an effective tool for the genetic characterization of potential parents that may enable ornamental plant breeders to improve the efficiency of the breeding programs

2000 - Genetic diversity in Osteospermum as revealed by random amplified polymorphic DNA analysis [Articolo su rivista]
Faccioli, P.; V., Terzi; Pecchioni, Nicola; T., Berio; A., Giovannini; A., Allavena
abstract

A collection of 28 Osteospermum clones and cultivated varieties ofdi}erent origin were evaluated by random amplifed polymorphic DNA (RAPD) analysis. All the clones were identifed by 12 decamers selectedfrom a set of 29. This is the first characterization by molecular markersof the genetic material of Osteospermum. The level of genetic diversityamong genotypes was assayed and all the accessions tested were thenclassified into six groups by UPGMA cluster analysis. The clustering ofgenotypes using the RAPD data proved to be in accordance with theirbreeding group origin. RAPD analysis can therefore be a useful toolfor evaluating genetic variability in other Osteospermum germplasmcollections for breeding purposes and for protecting intellectual property rights of improved varieties

2000 - QTL mapping of leaf stripe (Pyrenophora graminea) resistance in two- and six-rowed barleys [Relazione in Atti di Convegno]
Arru, Laura; Delogu, G; Busconi, M; Reggiani, F; Pecchioni, Nicola
abstract

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2000 - Random amplified polymorphic DNA (RAPD) analysis for the verification of hybridity in interspecific crosses of Alstroemeria. [Articolo su rivista]
DE BENEDETTI, L.; G., Burchi; A., Mercuri; Pecchioni, Nicola; P., Faccioli; T., Schiva
abstract

Random amplified polymorphic DNA (RAPD) markers were used to verify interspecific hybridization in Alstroemeria. Five putative interspecific hybrids and their parents were analysed by means of four preselected RAPD primers. The putative parentage was confirmed in four hybrids and was excluded in one that showed completely different RAPD patterns from its putative parents and a different phenotype.Our results demonstrated that this molecular technique is a powerful tool for verifying hybridity rapidly if the putative parents are given. This tool will allow screening of small immature seedlings for verification of hybridity and should improve the efficiency of breeding programmes.

2000 - Surveying plant metabolism by sequencing analysis of expressed clones in Triticeae [Articolo su rivista]
Faccioli, P.; Pecchioni, Nicola; R., Pisani; A. M., Stanca; V., Terzi
abstract

The paper describes how it can be possible to survey the plant metabolism by sequencing analysis of expressed clones, particularly referring to Triticeae. In Triticeae the Expressed sequence tags (ESTs) databases are being created for severalplant species. ESTs have in fact the potential to analyse the expressed part ofthe genome, and to be used in a wide range of applications from thetheoretical aspect of plant biology to the breeding process. The presentstudy describes the cold-stressed cDNA library as a source of ESTs inbarley: partial cDNA sequencing of randomly isolated clones yielded960 ESTs. The strategy of random sequencing cDNA clones at their5' ends allows one to obtain information on the steady-state level of thetranscripts in a cold-stressed green leaf of barley. Repetitive sequencingof nearly identical ESTs provides, in addition, useful information onthe existence of multigene families. The results of a BLAST searchperformed on this set of ESTs showed that 18.5% of the tags exhibitedno significant homology to known genes, 10% had significant levels ofhomology with known cold or other stress-related genes, about 26%proved homologous to enzymes involved in several metabolic path-ways and about 15% encoded for ribosomal proteins, cytoskeletonproteins, histones, ubiquitin, elongation factors and others. Redund-ancy was found for some classes of tag: RuBisCo, cab proteins,carbonic anhydrase, glutamate decarboxylase and stress relatedproteins.The result of the survey is a sort of "genomic Northern" analysis of the cold acclimation process.

2000 - The resistance of barley to leaf stripe caused by Pyrenophora graminea [Articolo su rivista]
Pecchioni, Nicola; G., Tacconi; Arru, Laura; L., Bellini L; G., Valè
abstract

Leaf stripe is a seed-borne barley disease, caused by Pyrenophora graminea.Reactions of cultivars to leaf stripe show great variability, and one race-specific resistancesystem (Rdg1a gene) has been described. In this work it was studied the response of seventwo-rowed and two six-rowed cultivars, and of a two-rowed line to the highly virulent isolatesDg2 and Dg5 of Pyrenophora graminea.NILs have been developed from two highly resistant six-rowed winter cultivars, Thibaut andOnice, after six backcrosses to susceptible cultivar Mirco, in order to map these new sourcesof resistance by means of BSA (Bulked Segregant Analysis).Colinear maps of barley chromosome 1(7H) have been drawn, where the major QTL ofresistance of cv. 'Proctor' to leaf stripe, and two other resistance (R) genes to barley pathogenshave been mapped. These R genes, RsmMx to the seed-borne virus BSMV (Barley StripeMosaic Virus), and Rpt4 to Pyrenophora teres, are associated to common markers in thebarley genome and could help to explain the biological role of the leaf stripe QTL.

1999 - Aliseo: nuova varietà di orzo polistico resistente al virus del mosaico giallo (BaYMV). [Articolo su rivista]
Faccini, N.; R., Alberici; M., Baronchelli; D., Pagani; Pecchioni, Nicola; G., Vale; V., Terzi; A. M., Stanca; G., Delogu
abstract

Il lavoro descrive la costituzione e le caratteristiche della varietà di orzo Aliseo, alla cui costituzione N Pecchioni ha contribuito.

1999 - Amplified fragment length polymorphism (AFLP) markers for barley malt fingerprinting. [Articolo su rivista]
Faccioli, P.; Pecchioni, Nicola; A. M., Stanca; V., Terzi
abstract

Barley is the cereal par excellence in the production of malt for beer and other alcoholic beverages. Inthis work, biochemical (hordein A-PAGE) and molecular (RAPDs, AFLPs) markers have beencompared for their efficiency in malt fingerprinting. To overcome the difficulties related to the qualityof the DNA extracted from grain malt, malted coleoptiles are proposed as useful tissue for theextraction. On the basis of our data, we exclude a fingerprinting system based on A-PAGE hordeinanalysis because of the degradation of these proteins during the malting process. Comparing molecularmarkers for their efficiency and repeatability, we indicate AFLP analysis based on template DNAextracted from the tissue of grain malt coleoptile as an excellent tool for malt fingerprinting.

1999 - Barley-Pyrenophora graminea interaction: QTL analysis and gene mapping [Articolo su rivista]
Pecchioni, Nicola; G., Vale'; H., TOUBIA RAHME; P., Faccioli; V., Terzi; G., Delogu
abstract

Pyrenophora graminea is a seed-borne pathogen and is the causal agentof the barley leaf stripe disease. Our aim is to study the genetic basis ofbarley resistance to leaf stripe. A qualitatively acting resistance factorhas been identi_ed in the cultivar Vada and the partial resistance ofthe cultivar Proctor to a P. graminea isolate has been demonstratedto be dominated by a major quantitative trait locus (QTL) mapped onbarley chromosome 1(7H). Map colinearity between the leaf stripe Proctorresistance QTLs, Vada resistance to leaf stripe, and other diseaseresistance loci have been investigated in this work using molecularmarkers. Moreover, since inoculation of barley rootlets by the fungushad been shown to induce the accumulation of several PR (pathogen-related) mRNA families, seven barley PR genes have been mapped asRFLPs, and one assigned to a chromosome arm via ditelosomic analysisto verify possible map associations with resistance QTLs. This workdiscusses the genetic relationships between the known leaf stripe resistance loci, resistance loci towards other seed!borne pathogens anddefence gene loci.

1999 - Detection of genetic diversity in barley using tools from DNA technologies [Relazione in Atti di Convegno]
Terzi, V; Faccioli, P; Pecchioni, Nicola; Pisani, R; Arru, Laura; Stanca, ANTONIO MICHELE
abstract

Characterization of genetic resources has been traditionally based upon morphophysiological traits and, more recently, isozymes and seed storage proteins. The limitations of these descriptors lie in their restricted number, in the small portion of variability studied and in the influence of environmental conditions.In our work, we have developed different kinds of molecular markers that can be proposed as valuable tools for study barley genetic variability.

1999 - Effects of cadmium stress on hairy roots of Daucus carota. [Articolo su rivista]
SANITA DI TOPPI, L.; M., Lambardi; Pecchioni, Nicola; L., Pazzagli; M., Durante; R., Gabbrielli
abstract

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1999 - Genetic analysis of barley resistance to leaf stripe [Relazione in Atti di Convegno]
Pecchioni, Nicola; TOUBIA RAHME, H; Tacconi, G; Arru, Laura; Bellini, L; Val, G.
abstract

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1999 - High expression level of a gene coding for a chloroplastic amino acid selective channel protein is correlated to cold acclimation in cereals [Articolo su rivista]
Baldi, P; Grossi, M; Pecchioni, Nicola; Valé, G; Cattivelli, L.
abstract

A cold-regulated gene (cor tmc-ap3) coding for a putative chloroplastic amino acid selective channel protein wasisolated from cold-treated barley leaves combining the differential display and the 50-RACE techniques. Cor tmcap3is expressed at low level under normal growing temperature, and its expression is strongly enhanced aftercold treatment. A positive correlation between the expression of cor tmc-ap3 and frost tolerance was found bothamong barley cultivars and among cereal species. The COR TMC-AP3 protein was expressed in vitro, purifiedand used to raise a polyclonal antibody.Western analysis showed that the cor tmc-ap3 gene product is localized tothe chloroplastic outer envelope fraction, supporting its putative function. The frost-resistant winter cultivar Oniceaccumulated COR TMC-AP3 more rapidly and at a higher level than the frost-susceptible spring cultivar Gitane.After 28 days of cold acclimation the winter cultivar had about 2-fold more protein than the spring genotype.All these results suggest that an increased amount of a chloroplastic amino acid selective channel protein couldbe required for cold acclimation in cereals. Hypotheses about the role of COR TMC-AP3 during the hardeningprocess are discussed.

1999 - Mapping Lrk10 wheat rust resistance gene in barley [Relazione in Atti di Convegno]
Arru, Laura; Bellini, L; Gandolfi, R; Valé, Gp; Steffenson, Bj; Pecchioni, Nicola
abstract

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1999 - Pyrenophora graminea-barley: a model for biomolecular studies of seed-borne desease [Abstract in Rivista]
Porta Puglia, A; Delogu, G; Vannacci, G; Aragona, M; Arru, Laura; Bellini, L; Cristani, C; Faccini, N; Haegi, A; Montigiani, M; Pecchia, S; Pecchioni, Nicola; Stanca, ANTONIO MICHELE; Valé, G; Vergara, R.
abstract

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1999 - The wheat leaf rust resistance gene Lrk 10 maps to barley chromosome 1 HS [Articolo su rivista]
Pecchioni, Nicola; Arru, Laura; L., BELLINI L; Stanca, ANTONIO MICHELE; G., Vale'
abstract

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1999 - Tocoli e beta-glucani dell'orzo nudo per lo sviluppo di alimenti "funzionali". [Articolo su rivista]
Cavallero, A.; R., Alberici; N., Faccini; L., Cattivelli; Pecchioni, Nicola; G., Vale'; G., Delogu; N., DI FONZO; E., Fiori; A. M., Stanca
abstract

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1998 - Attivazione dei geni di difesa nella interazione orzo-Pyrenophora graminea: clonaggio e regolazione [Relazione in Atti di Convegno]
Valè, G; Aragona, M; Bellini, L; Cristani, C; Arru, Laura; Pecchioni, Nicola
abstract

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1998 - Barley [Capitolo/Saggio]
P., Faccioli P; M., Grossi; Pecchioni, Nicola; G., Vale’; A. M., Stanca
abstract

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1998 - Development and applications of molecular markers for genetic variation studies in the Triticeae [Relazione in Atti di Convegno]
V., Terzi; Pecchioni, Nicola; P., Faccioli
abstract

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1998 - Diffusione delle virosi dell’orzo in Lombardia e Piemonte. [Articolo su rivista]
Faccini, N.; R., Alberici; P., Caciagli; P., Gotta; Pecchioni, Nicola; G., Delogu
abstract

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1998 - Effetti dell'anossia sullo sviluppo dell'orzo: moderne strategie biotecnologiche. [Articolo su rivista]
D., Rau; G., Attene; Arru, Laura; G., Valé; Pecchioni, Nicola
abstract

.

1998 - Uptake and agronomic efficiency of nitrogen in winter barley and winter wheat. [Articolo su rivista]
Delogu, G.; L., Cattivelli; Pecchioni, Nicola; D., DE FALCIS; T., Maggiore; A. M., Stanca
abstract

Nitrogen (N) uptake and utilization efficiency (NUtE) of the high-yielding cultivars ‘Gemini’ of wheat and ‘Jaidor’of barley were tested with N rates of 0, 140 and 210 kg ha−1 and 0, 80 and 140 kg ha−1, respectively. The differentgrain yield response was linked to their difference in nitrogen uptake and utilization efficiency. The highest yield inbarley was recorded with 80 kg N ha−1 and in wheat with 210 kg N ha−1. Nitrogen application affected theaccumulation of biomass up to heading in wheat and barley. While N uptake during grain filling did not show anycorrelation to N applied in barley, it was markedly correlated in wheat. At N0 and N140 N applied, barley exhibiteda 32 and 8% higher NUtE than wheat. N agronomic efficiency, a parameter representing the ability of the plant toincrease yield in response to N applied, was similar in barley and wheat (8.7 and 9.2 kg kg−1 of N applied,respectively), suggesting that both species respond equally to nitrogen fertilization. Nevertheless, due to its lowerNUtE, wheat requires high N fertilization to optimize yields; by contrast, in barley the lower N rate needed to achievehighest yields enables this crop to perform better in low-input conditions. As a results, the reduced N requirementsfor barley highest yield associated with a better RF value (apparent N fertilizer recovery of 63% in barley and 49% inwheat at N140) makes barley crop a better choice to reduce ground-water pollution due to nitrate leaching in winterand early spring.

1997 - Analisi di caratteri morfologici, biochimici e molecolari per l’identificazione varietale nelle piante coltivate. [Articolo su rivista]
Terzi, V.; P., Faccioli; G., Vale; P., Baldi; Pecchioni, Nicola; G., Delogu
abstract

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1997 - Analisi genetico-molecolare per lo studio della biodiversità nel genere Hordeum [Capitolo/Saggio]
V., Terzi; P., Faccioli; Pecchioni, Nicola
abstract

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1997 - Characterization of ornamental Datura plants transformed by Agrobacterium rhizogenes. [Articolo su rivista]
Giovannini, A.; Pecchioni, Nicola; M., Rabaglio; A., Allavena
abstract

Datura arborea and D. sanguinea hairy roots were produced by cocultivation of leaf fragments with Agrobacteriumrhizogenes strain NCPP 1855. Adventitious buds emerged spontaneously-, without exogenous growth regulators, fiom sevenhairy root clones of D. arborea and from one hairy, root clone of D. sanguinea. Regenerated plants were successfullyacclimatized in the greenhouse. The integration of the bacterial TL-DNA into the genome of the putative transformed plantswas confirmed by Southern blot analysis. Transgenie plants displayed increased ability to root in vivo. Morphological traitswith relevant ornamental value like plant height, leaf number, size and shape, internode numbe~, and internode length werealso affected. Transformation by wild-type Ri TL-DNA provided the chance to study plant growth and differentiation andto select improved genotypes.

1997 - Cucurbita pepo L. can be transformed by Agrobacterium rhizogenes. [Articolo su rivista]
SANITA DI TOPPI, L.; Pecchioni, Nicola; M., Durante
abstract

Two-week-old in vitro grown Cucurbita pepo L. intact plants and cotyledons (detached and undetached from themother-plant) were transformed by Agrobacterium rhizogenes strain NCPPB 1855, grown for 48 h at 25 C onYMB medium. All infected material formed vigorous hairy roots in about seven days. The transformed roots weresuccessfully grown in liquid MS medium without plant growth regulators for an indefinite number of transfers.Genetic transformation of root DNA was proven by Southern analysis performed with a rolABC probe and a virprobe. Our results demonstrate that, in contrast with previous literature, A. rhizogenes could represent an efficientand reproducible system to transform C. pepo plants. Furthermore, we verified that plant age and incubationtimes/temperatures of bacterial strain influence transformation efficiency.

1997 - Orzo, l’uso della granella dai mangimi alla tavola. [Articolo su rivista]
Faccioli, P.; F., Rizza; Pecchioni, Nicola; A. M., Stanca
abstract

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1997 - Prove di concimazione azotata su orzo. [Articolo su rivista]
Alberici, R.; M., Baravelli; G., Bianchi; G., Vale; Pecchioni, Nicola; A. M., Stanca; M., Snidaro
abstract

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1996 - Genetic transformation of lisianthus (Eustoma grandiflorum Griesb.) by Agrobacterium rhizogenes [Articolo su rivista]
Giovannini, A.; Pecchioni, Nicola; A., Allavena
abstract

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1996 - Molecular markers for genotype identification in small grain cereals [Articolo su rivista]
Pecchioni, Nicola; P., Faccioli; A., Monetti; A. M., Stanca; V., Terzi
abstract

Review about the molecular and statistical methods necessary to evaluate the genetic distance as well the varietal characterization in plants.

1996 - Produzione di malto in Italia: effetti ambientali sulla qualità [Articolo su rivista]
Faccioli, P.; M., Baronchelli; R., Alberici; Pecchioni, Nicola; P., Baldi; G., Delogu
abstract

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1996 - Quantitative resistance to barley leaf stripe (Pyrenophora graminea) is dominated by one major locus [Articolo su rivista]
Pecchioni, Nicola; Faccioli, P; TOUBIA RAHME, H; Valé, G; Terzi, V.
abstract

A major gene underlying quantitative resistance to barley leaf stripe (Pyrenophora graminea), a seed-borne pathogen causing leaf stripe, was mapped with molecular markers in a barley doubled haploid (DH) population, derived from the cross Proctor x Nudinka (PN). The quantitative locus accounts for r2= 58.5% and was mapped on barley chromosome 1, tightly linked to the "naked" gene. A second resistance QTL, accounting for 29.3% of phenotypic variation, was identified on the P arm of barley chromosome 2. Another two minor QTLs were detected in further analyses. None of the QTLs were found in the chromosome 2 "vada" region studied by Giese et al. (1993).

1995 - B-Hordein STSs markers for barley genotype identification: comparison with RFLPs, hordein A-PAGE and morpho-physiological traits. [Articolo su rivista]
Faccioli, P.; V., Terzi; A., Monetti; J., Nicola; Pecchioni, Nicola
abstract

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1994 - Barley winter hardiness in laboratory and field examinations [Articolo su rivista]
Rizza, F.; A., Portesi; Pecchioni, Nicola; V. Terzi And A. M., Stanca
abstract

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1994 - L'orzo perlato nell'alimentazione umana [Articolo su rivista]
Terzi, V.; N., Faccini; G., Vale'; Pecchioni, Nicola; G., Delogu
abstract

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1993 - Effetto della concimazione azotata sulla produttività dell'orzo (Hordeum vulgare L.) autunnale in successione a diverse colture. [Articolo su rivista]
Cattivelli, L.; G., Vale'; Pecchioni, Nicola; F., Rizza; A., Portesi; G., Delogu
abstract

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1993 - RFLP analysis of highly polymorphic loci in barley [Articolo su rivista]
Pecchioni, Nicola; A. M., Stanca; V., Terzi; L., Cattivelli
abstract

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1993 - Uso di tecniche molecolari (RFLP e PCR) per il riconoscimento varietale di specie di interesse agrario [Articolo su rivista]
Pecchioni, Nicola; C., Peveri; A., Monetti; P., Faccioli; M., Grossi; G., Vale'; A., Portesi; V., Terzi; A. M., Stanca
abstract

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1992 - Analisi della risposta genetico-molecolare allo stress termico e possibili applicazioni al miglioramento genetico di Gerbera jamesonii hybrida (H.B.) [Articolo su rivista]
Pecchioni, Nicola; G., Di Cola; T., Schiva; N., Marmiroli
abstract

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1991 - Acclimatamento e resistenza al freddo nei cereali [Articolo su rivista]
Cattivelli, L.; M., Grossi; Pecchioni, Nicola; V., Terzi
abstract

Il lavoro descrive in termini tecnici il fenomeno dell'accllimatamento nei cereali autunno-vernini e di come questo influenzi le rese di granella. Conclude poi descrivendo i nuovi approcci e le nuove ricerche che possono definire quali siano i motivi biologici del fenomeno, e che quindi possano aiutare a migliorare i risultati produttivi.

1991 - La biologia molecolare al servizio del miglioramento genetico: polimorfismo dei frammenti di restrizione (RFLP) [Articolo su rivista]
Terzi, V.; Pecchioni, Nicola; C., Peveri
abstract

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