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Justyna Anna MILC

Personale tecnico amministrativo
Dipartimento di Scienze della Vita sede ex-Agraria

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Pubblicazioni

2023 - Evaluating the impact of drought stress in Nure and Tremois barleys (Hordeum vulgare) treated with plant growth promoting rhizobacteria (PGPR) at seedling phase [Poster]
Caccialupi, Giovanni; Cattabiani, Nicolò; Nur Avci, Fatma; Milc, Justyna; Francia, Enrico; Caradonia, Federica
abstract

Barley is the fifth cultivated herbaceous crop in the world, and its important is due to its economic and nutritional value. Climate change is posing a new challenge to barley production. While drought stress was traditionally associated with the flowering and caryopsis filling stages in barley plants, a new form of drought is now emerging in seedling stage. To mitigate the impact of environmental stresses, plant growth promoting rhizobacteria (PGPR) have been proposed to promote nutrient absorption and plant growth with the production of a range of beneficial substances, such as phytohormones, organic acids, and enzymes. The aim of this study was to evaluate the genotype response and the impact of PGPR treatment on two cultivars of barley, Nure (Italian feeding barley, winter habitus) and Tremois (French malting barley, spring habitus) in seedling phase under drought stress. At sowing, the soil was treated with PGPR and after two weeks of control condition two different water regimes were applied on seedlings (control at 25% and stressed at 12% of soil moisture). The results showed that both genotypes exhibited analogous stress response, however the PGPR treatment showed different effects on the two cultivars. Specifically, PGPR treatment increased root dry weight in stress conditions in Nure seedlings (by 36.6%) and increased dry weight in control conditions in Tremois seedlings (by 31.1%). Furthermore, the treatment increased the photosynthesis efficiency (PhiPS2) in Tremois seedlings (by 6.2%) and generally in both cultivars (by 7.6%) under drought stress. These findings suggest that the use of PGPR could be a useful tool for protecting barley seedlings against drought stress in early stages of development. However, further research is needed to fully understand the mechanisms of action to determine the optimal conditions for using this approach in the field.

2023 - The Triticeae CBF Gene Cluster—To Frost Resistance and Beyond [Articolo su rivista]
Caccialupi, Giovanni; Milc, Justyna; Caradonia, Federica; Nasar, Muhammad Fazail; Francia, Enrico
abstract

2022 - Characterization of Leaf Transcriptome of Grafted Tomato Seedlings after Rhizospheric Inoculation with Azospirillum baldaniorum or Paraburkholderia graminis [Articolo su rivista]
Caradonia, Federica; Buti, Matteo; Flore, Alessia; Gatti, Roberto; Morcia, Caterina; Terzi, Valeria; Ronga, Domenico; Moulin, Lionel; Francia, Enrico; Milc, Justyna Anna
abstract

2022 - Effect of foliar fertlizers from fish by-product on growth and development of Lettuce (L. sativa)in green-house conditions [Poster]
Ben Hassine, M.; Caradonia, F.; Milc, J. A.; Caccialupi, G.; Masino, F.; Pulvirenti, A.; Francia, E.; Antonelli, A.
abstract

In Liguria Region, as in all coastal areas, fish represents a relevant part of human diet due to its high-quality protein content, low fat content, and importance as a source of vitamins and minerals (Prato and Biandolino, 2015). Therefore, in the contest of circular economy, the huge quantity of fish by-product produced could be a resource instead of an environmental issue, thus producing materials with high added value. Such an example are fertilizers or biostimulants obtained from fish by-product that can be used to increase the sustainability of crops cultivation. Under the frame of project “FISH – Fertilizzante Innovativo Suolo e Habitat” (PSR Regione Liguria 2014 – 2020 Misura 16), the effect of foliar fertilizers obtained from fish by-product were evaluated on the growth and development of lettuce (Lactuca sativa L. ‘Summerbel’) in green-house conditions.

2022 - Effects of Fish protein hydrolysate on lettuce growth/development under controlled conditions. [Abstract in Atti di Convegno]
Mortadha, B. H.; Caradonia, F.; Milc, J. A.; Pulvirenti, A.; Cocchiara, S.; Masino, F.; Antonelli, A.; Francia, Enrico; E., (2022).
abstract

2022 - Extensive allele mining discovers novel genetic diversity in the loci controlling frost tolerance in barley [Articolo su rivista]
Guerra, D.; Morcia, C.; Badeck, F.; Rizza, F.; Delbono, S.; Francia, E.; Milc, J. A.; Monostori, I.; Galiba, G.; Cattivelli, L.; Tondelli, A.
abstract

Key message: Exome sequencing-based allele mining for frost tolerance suggests HvCBF14 rather than CNV at Fr-H2 locus is the main responsible of frost tolerance in barley. Abstract: Wild relatives, landraces and old cultivars of barley represent a reservoir of untapped and potentially important genes for crop improvement, and the recent sequencing technologies provide the opportunity to mine the existing genetic diversity and to identify new genes/alleles for the traits of interest. In the present study, we use frost tolerance and vernalization requirement as case studies to demonstrate the power of allele mining carried out on exome sequencing data generated from > 400 barley accessions. New deletions in the first intron of VRN-H1 were identified and linked to a reduced vernalization requirement, while the allelic diversity of HvCBF2a, HvCBF4b and HvCBF14 was investigated by combining the analysis of SNPs and read counts. This approach has proven very effective to identify gene paralogs and copy number variants of HvCBF2 and the HvCBF4b-HvCBF2a segment. A multiple linear regression model which considers allelic variation at these genes suggests a major involvement of HvCBF14, rather than copy number variation of HvCBF4b-HvCBF2a, in controlling frost tolerance in barley. Overall, the present study provides powerful resource and tools to discover novel alleles at relevant genes in barley.

2022 - Mendelizing Barley VRN-H1/FR-H1 and FR-H2 Quantitative Trait Loci in alternative backgrounds [Poster]
Caccialupi, Giovanni; Rizza, Fulvia; Badeck, Franz; Terzi, Valeria; Milc, Justyna Anna; Francia, Enrico
abstract

Freezing temperatures is one of the major limitations among the abiotic stress in cereals. In Triticeae tribe, several genetic studies have revealed the phenotypic variation for frost tolerance (FT) is attributed to two QTLs located in the long arm of homoeologous group 5 chromosome: Frost Resistance 1 (FR-1) and Frost Resistance 2 (FR-2). Besides these QTLs, the genotype background might also play a role in the phenotype. Considering barley as a model specie for the Triticeae tribe, in order to study the impact of the FR-H1 (VRN-H1), FR-H2 (cluster of 13 CBFs) locus and the genotype background, a series of experiments in controlled environment (Votsch chamber) has been carried out to test the freezing resistance of the QTL-NILs (Nure or Tremois x DH/RIL), Nure (winter genotype, resistance FT) and Tremois (spring genotype, susceptible FT). Temperature stress ranges from -10°C to -12°C. Plants at seedling stage (1-2 leaves) were firstly acclimated at 3/1°C (200 uE, 8/16H light/dark regime) for 4 weeks. Frost resistance score was measured using chlorophyll fluorescence analysis (Fv/Fm parameter). A marker-assisted backcross scheme was used to develop four QTL-Near Isogenic Lines aiming at separating FR-H1 and FR-H2 genomic regions in different alternative backgrounds. PCR-based molecular markers for HvCBF3 (Fr-H2) and HvBM5 (Vrn-H1/Fr-H1) were used to select plant with the desired allelic state, and after at least BC4 generation, heterozygous plants multiple selfing generations were obtained. At early selfing generations, the genotypic status of the lines was tested using 19 polymorphic SSR markers scattered throughout the barley genome. Moreover, a Cod42 Nu-Fr-H2 in Tremois background and Cod44 Tr-Fr-H2 in Nure were genotyped with barley 50K chip (Trait genetics). The result of the freezing tests showed that putatively the Fr-H2 (CBF cluster) appears to have a greater effect compared to FR-H1 (VRN-H1). Moreover, the data showed a difference between Nure and the QTL-NILs with Nure background with at least one allele from the spring Tremois. It can be hypothesized that the spring allelic state at the locus negatively affected the phenotype even in a winter background. All the treatments showed that the role of the background is secondary compared to the two FR locus. To confirm these hypothesises, gene expression analysis will be carried out to evaluate VRN-H1, the impact of the whole cluster and each CBF gene on the FT phenotype. Additionally, further investigation will be assessed on open field trials to evaluate recombinants genotype coming from the cross between Nure (winter genotype, resistance FT) and Pamina (facultative genotype, highly resistance FT).

2022 - Un nuovo biostimolante dai sottoprodotti della filiera ittica [Articolo su rivista]
Caser, M; Masino, F; Gervasio, S; Fassio, F; Ben Hassine, M; Benedetti, P; Caradonia, F; Cocchiara, S; Milc, J. A.; Caccialupi, G; Pulvirenti, A; Antonelli, A; Torri, L; Cevasco, R; Rovera, F; Scariot, V; Francia, E; Bertora, C; Ertani, A; Bertelli, C.
abstract

I sottoprodotti della pesca contengono proteine, grassi e amminoacidi, rendendoli così ottimi candidati per la produzione di biostimolanti. Il progetto FiSH (Fertilizzante idrolizzato Suolo e Habitat), al quale collaborano sei aziende agricole liguri, ha come obiettivo lo studio di un idrolizzato proteico fermentato derivato da scarti del pescato sulla crescita, resa e qualità di diverse colture floricole e orticole (Ranunculus asiaticus, Anemone x hybrida ‘Mistral Blu’, Solanum tuberosum ‘Quarantina’, Ocimum basilicum, Cucurbita pepo ‘Trombetta d’Albenga’, Allium sativum e Allium cepa). Durante il primo anno di progetto (2020-2021) sono stati testati in campo quattro concentrazioni (0,3 ml/L, 0,5 ml/L, 1 ml/L e 2 ml/L) del prototipo Fish n.7 in applicazione fogliare. Su patata è stata prevista anche un’applicazione su tubero preimpianto e valutato l’attacco di peronospora (Phytophthora infestans). I risultati ottenuti hanno evidenziato un’ampia variabilità di risposta. Tra le sei varietà di ranuncolo, ‘Elengance bianco’ ha mostrato una tendenza a produrre piante più rigogliose e fiori più grandi in risposta alla dose più elevata di Fish n.7, mentre la dose 0,5 ml/L ha indotto un maggiore sviluppo vegetativo e maggior produzione di rizomi nella varietà ‘Venere’. Su patata i risultati suggeriscono di evitare l’immersione del tubero, di mantenere i trattamenti rameici e di utilizzare concentrazioni < 1 ml/L. Su basilico e zucchina è stata osservata una maggiore produzione di biomassa nelle piante trattate alla concentrazione 2 ml/L. Nessun effetto è emerso in anemone, cipolla e aglio anche se, i dati delle ultime due specie sembrano indicare un beneficio fornito dalla dose 1 ml/L. Sulla base dei risultati, sono in corso valutazioni con otto nuovi prodotti.

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 - In silico identification of myb and bhlh families reveals candidate transcription factors for secondary metabolic pathways in cannabis sativa L [Articolo su rivista]
Bassolino, L.; Buti, M.; Fulvio, F.; Pennesi, A.; Mandolino, G.; Milc, J.; Francia, E.; Paris, R.
abstract

Plant secondary metabolic pathways are finely regulated by the activity of transcription factors, among which members of the bHLH and MYB subfamilies play a main role. Cannabis sativa L. is a unique officinal plant species with over 600 synthesized phytochemicals having diverse scale-up industrial and pharmaceutical usage. Despite comprehensive knowledge of cannabinoids’ metabolic pathways, very little is known about their regulation, while the literature on flavonoids’ metabolic pathways is still scarce. In this study, we provide the first genome-wide analysis of bHLH and MYB families in C. sativa reference cultivar CBDRx and identification of candidate coding sequences for these transcription factors. Cannabis sativa bHLHs and MYBs were then classified into functional subfamilies through comparative phylogenetic analysis with A. thaliana transcription factors. Analyses of gene structure and motif distribution confirmed that CsbHLHs and CsMYBs belonging to the same evolutionary clade share common features at both gene and amino acidic level. Candidate regulatory genes for key metabolic pathways leading to flavonoid and cannabinoid synthesis in Cannabis were also retrieved. Furthermore, a candidate gene approach was used to identify structural enzyme-coding genes for flavonoid and cannabinoid synthesis. Taken as a whole, this work represents a valuable resource of candidate genes for further investigation of the C. sativa cannabinoid and flavonoid metabolic pathways for genomic studies and breeding programs.

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.

2019 - A meta-analysis of comparative transcriptomic data reveals a set of key genes involved in the tolerance to abiotic stresses in rice [Articolo su rivista]
Buti, M.; Baldoni, E.; Formentin, E.; Milc, J.; Frugis, G.; Schiavo, F. L.; Genga, A.; Francia, E.
abstract

Several environmental factors, such as drought, salinity, and extreme temperatures, negatively affect plant growth and development, which leads to yield losses. The tolerance or sensitivity to abiotic stressors are the expression of a complex machinery involving molecular, biochemical, and physiological mechanisms. Here, a meta-analysis on previously published RNA-Seq data was performed to identify the genes conferring tolerance to chilling, osmotic, and salt stresses, by comparing the transcriptomic changes between tolerant and susceptible rice genotypes. Several genes encoding transcription factors (TFs) were identified, suggesting that abiotic stress tolerance involves upstream regulatory pathways. A gene co-expression network defined the metabolic and signalling pathways with a prominent role in the differentiation between tolerance and susceptibility: (i) the regulation of endogenous abscisic acid (ABA) levels, through the modulation of genes that are related to its biosynthesis/catabolism, (ii) the signalling pathways mediated by ABA and jasmonic acid, (iii) the activity of the “Drought and Salt Tolerance” TF, involved in the negative regulation of stomatal closure, and (iv) the regulation of flavonoid biosynthesis by specific MYB TFs. The identified genes represent putative key players for conferring tolerance to a broad range of abiotic stresses in rice; a fine-tuning of their expression seems to be crucial for rice plants to cope with environmental cues.

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 - 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 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 - Effects of innovative biofertilizers on yield of processing tomato cultivated in organic cropping systems in northern Italy [Relazione in Atti di Convegno]
Ronga, D.; Caradonia, F.; Setti, L.; Hagassou, D.; Giaretta Azevedo, C. V.; Milc, J.; Pedrazzi, S.; Allesina, G.; Arru, L.; Francia, E.
abstract

Nowadays agriculture needs to increase crop sustainability and the organic cropping system has emerged as an interesting alternative approach with respect to the conventional one. On the other hand, the current unfavorable yield gap between organic and conventional systems reduces the organic system’s value. Processing tomato is a globally important horticultural crop and used as crop model. The objective of this study was to investigate different biofertilizers that could improve the yield and quality of processing tomato in organic cropping system. An experiment was conducted in Po Valley, northern Italy, during spring-summer 2017. The cultivar used was ‘Barone Rosso’ blocky fruit genotype, using 2.8 plants m-2, in randomized complete block design with seven biofertilizer treatments (pelleted digestate, granular biofertilizer, biochar, compost tea as foliar spray biostimulant, SiO2 as foliar spray biostimulant, compost tea + SiO2 as foliar spray biostimulant, zero biofertilizer as a control) and three replications. Agronomical and physiological parameters were recorded during the crop cycle. Results showed that tomato grown with biochar recorded the maximum commercial yield (136 t ha-1), followed by pelleted digestate (117 t ha-1) and compost tea + SiO2 as foliar spray biostimulant (113 t ha-1) while the minimum production (71 t ha-1) was recorded in untreated plots. On average, the results revealed that biochar, pelleted digestate and compost tea + SiO2 as foliar spray biostimulant, increased the vegetative vigor of plant (+10%), the number of flowers (+13%) and fruits (+41%), the average weight of fruits (+20%), the total biomass production (+48%), the harvest index (+15%) and the Brix t ha-1 (+49%), with respect to the control. Considering the overall performance, innovative biofertilizers could be promising to improve yield and quality of processing tomato cultivated in organic cropping systems, reducing the yield gap with conventional one.

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.

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 - 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 - 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 - SUSTAINABILITY OF AGRICULTURAL ENVIRONMENT: CONTRIBUTIONS OF PLANT GENETICS AND PHYSIOLOGY [Abstract in Atti di Convegno]
Buti, Matteo; Leonarduzzi, Cristina; Ronga, Domenico; Milc, Justyna Anna; Beretta, Massimiliano; Malatrasi, M; Setti, Leonardo; Hagassou, Djangsou; Arru, Laura; Francia, Enrico
abstract

Tomato (Solanum lycopersicum L.) is one of the most widely cultivated vegetable crops, and its production for both processing and fresh market is widespread in the Mediterranean area, especially in Italy. With 26,500 ha cultivated with processing tomato, Emilia-Romagna region is the Italian leader in production. Low temperature stress and blossom-end rot (BER) physiopathy are two of the major limiting factors for the local processing tomato production, while length of growth cycle strongly influences the fructification timeframe, an essential trait for transformation industry. Understanding the molecular basis of chilling tolerance, BER resistance and crop earliness would be crucial to identify the correlated molecular markers and to characterize their allelic variants: this would allow developing new processing tomato cultivars carrying these desirable traits. A thorough literature survey allowed us to identify candidate genes and QTLs linked to the three mentioned traits. The position of candidate genes was directly inferred from the annotated genome (version SL2.50), while QT loci were physically positioned using the sequences of associated flanking and peak markers. This allowed the detection of genomic regions putatively associated with the 3 selected traits, and SolCAP database was searched to identify a set of SNPs located within or nearby the genomic regions of interest. In total 1,564 and 312 SNPs putatively correlated to chilling and BER tolerance, respectively, while identification of SNPs linked to crop cycle length is still in progress. A processing tomato collection of 124 accessions (both lines and hybrids) with a wide phenotypic range for the three traits was assembled and grown in filed and in controlled conditions during 2017. Phenotyping and genotyping using SNPs putatively associated with the studied traits of these accessions are currently in progress, aiming at the identification of a set of locus specific SNPs (and respective allelic variants) that could be used for assisted selection in breeding programs. European ERDF fund supported this research as a part of Emilia Romagna regional project GENBACCA.

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 - 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.

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 - 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 - 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.

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 - 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 - 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.

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 - 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 - 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 - 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 - 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 - 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 - 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.

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 - 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 - 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 - 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
abstract

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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.
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 - 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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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 - 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 - 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.

2002 - Isolation of porcine expressed sequence tags for the construction of a first genomic transcript map of the skeletal muscle in pig [Articolo su rivista]
Davoli, R.; Fontanesi, F.; Zambonelli, P.; Bigi, D.; Gellin, J.; Yerle, M.; Milc, Justyna Anna; Braglia, S.; Cenci, V.; Cagnazzo, M.; Russo, V.
abstract

To identify genes with effects on meat quality and production traits we developed an adult porcine skeletal muscle cDNA library. After pre-screening this library with seven genes highly expressed in skeletal muscle, 385 non-hybridizing clones were sequenced from both ends to yield 5 10 expressed sequence tags (ESTs). Together with those ESTs previously generated from this library, we have produced 701 porcine skeletal muscle ESTs. These ESTs were grouped into 306 different cDNA species and compared with the human skeletal muscle transcriptional profiles obtained from different databases. Furthermore we mapped 107 of these cDNAs using a somatic cell hybrid panel with genes mapping over all the autosomes (except on chromosome 11) and on chromosome X. The mapping of these cDNAs contributed to the construction of a first genomic transcript map of the skeletal muscle tissue in pig

2001 - The porcine ATPase, Ca++ transporting, plasma membrane 1 (ATP2B1) gene maps to chromosome band 5q23. [Articolo su rivista]
Zambonelli, P; Milc, Justyna Anna; Davoli, R; Russo, V; Kubícková, S; Rubes, J; Cepica, S.
abstract

An approximately 1.6 kb recombinant ATP2B1 (ATPase, Ca++ transporting, plasma membrane 1) clone was isolated from porcine skeletal muscle cDNA library. Precise localization of the gene was determined on the basis of FLpter values using computer assisted linkage analysis

2001 - The porcine sarcolipin (SLN) gene: identification of an SNP and linkage mapping to chromosome 9. [Articolo su rivista]
Fontanesi, L; Davoli, R; Milc, Justyna Anna; Russo, V.
abstract

Sarcolipin (SLN) is a 31-amino acid proteolipid that regulates the activity of SERCA1 (ATP2A1), a fasttwitch skeletal muscle sarcoplasmic reticulum Ca2+-ATPase. Two alleles were identified by SSCP analysis in the 218 bp fragment of the porcine SLN gene. Mendelian segregation was confirmed in three-generation families of the PiGMaP Consortium. The DNA samples belonging to six threegeneration families of the PiGMaP Consortium were genotyped at the SLN locus obtaining 98 informative meiosis. Multipoint sex-averaged map of porcine chromosome 9, placed SLN between markers PPP2ARB and CRYAB (PPP2ARB± 24.7 cM ± SLN ± 3.1 cM ± CRYAB ±). This assignment confirms the physical mapping of the porcine SLN gene to chromosome9p24-(1/3p21) previously obtained

2000 - Linkage mapping of the alpha-B-crystallin (CRYAB) gene to porcine chromosome 9. [Articolo su rivista]
Fontanesi, L; Davoli, R; Milc, Justyna Anna; Russo, V.
abstract

An expressed sequence tag (EST) that showed homology with human (M28638) a-B-crystallin (CRYAB) gene sequence was isolated from a porcine skeletal muscle cDNA library (Z98816). Two alleles were identified in the 115-bp fragment of the porcine CRYAB 3'-untranslated region. A multipoint sex-averaged map of porcine chromosome 9, placed CRYAB between markers PPP2ARB and APOA1

2000 - Ricerca di marcatori in geni candidati per il miglioramento della produzione e della qualità della carne. [Relazione in Atti di Convegno]
Russo, V.; Davoli, R.; Fontanesi, L.; Zambonelli, P.; Nanni Costa, L.; LO FIEGO, Domenico Pietro; Cagnazzo, M.; Milc, Justyna Anna
abstract

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1996 - Biocompatibility of glass-crystalline materials obtained by the sol-gel method: effect on macrophage function. [Articolo su rivista]
Turyna, B; Milc, Justyna Anna; Laczka, A; Cholewa, K; Laczka, M.
abstract

The aim of this work was to confirm in vitro biocompatibility of a new gel-derived glass-crystalline material containing hydroxyapatite and wollastonite phases. For the purpose of comparison, studies were also carried out for a material of the same chemical composition obtained by the traditional melting method. We examined the behaviour and response of cells cultured in the presence of the studied materials. The level of activation of macrophages in culture was determined using three different methods: measurement of respiratory burst by chemiluminescence, nitrite assay and by bioassay of secreted cytokines after immunoelectrophoresis of acute phase proteins from hepatoma cells. All our results show a relatively low, close to control level, activation of macrophages exposed to the studied materials. This indicates a good biocompatibility of both the gel-derived material and the material obtained by the traditional melting method