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Current lines of research


Genetics and genomics
The Centre coordinates the Italian participation at the international initiative for wheat genome sequencing with the responsibility for the analysis of the genomic BAC libraries for creating a physical map of the wheat chromosome 5A.
Mapping, fine mapping and positional cloning of genes controlling disease resistance, tolerance to abiotic stress as well as mutated phenotypes are in progress in several crop species. Several Recombinant Inbred Lines (RILs) segregating for agronomically important traits were developed in barley, bread wheat, durum wheat and rice with the aim of identifying loci involved in relevant phenotypes. In barley several segregating population are being developed with a specific focus on the resistance toward Phyrenophora tesres. Available tetraploid wheat RIL populations include Sachem x Lloyd, Triticum dicoccum MG5323 x Latino, Zardak x 249 landrace. Hexaploid wheat RIL populations include Victo x Spada and Agadir x Artico. For these populations, SSRs and SNPs (Illumina 90K SNP array)-based genetic maps were recently developed for mapping yield-related and resistance (leaf rust, powdery mildew, yellow rust) traits. The fine mapping of QTLs conferring resistance to leaf rust and powdery mildew is ongoing.
The genetic bases of rice resistance to the blast fungus in Italian temperate japonica rice genotypes is carried out with dedicated mapping population (Gigante Vercelli x Vialone Nano; Salvo x Maratelli, Augusto x Vialone Nano) (read more about the RISINNOVA project). High resolution maps based on genotyping by sequencing have been developed for Salvo x Maratelli andAugusto x Vialone Nano. A whole genome re-sequencing work is currently carried out for the characterization of traditional Italian rice cultivars.
In the last years the novel approach of association genetics has been also adopted with the aim to improve our ability to dissect quantitative traits. Through national and international collaborations, germplasm collections of different crop species have been assembled. Among them, the Hordeum vulgare Cultivar Collection, representing a core sample of barley varieties grown in Europe in the last century, has been extensively genotyped with Illumina 9K SNP array, allowing us to finely characterize the genetic diversity and evolution of cultivated barley, and map QTLs for several agronomic traits.
The Centre is partner of the WHEALBI consortium, an FP7 project that combine genomics, genetics and agronomy to improve European wheat and barley production in competitive and sustainable cropping systems. WHEALBI will generate original data from expressed genome sequences of 1000 wheat and barley genetic resources and provide models and tools to integrate these data in breeding programmes (read more about the WHEALBI project).
The Centre participates also to the CLIMBAR project, focused on an integrated approach to evaluate and harvest genetic diversity for breeding climate-resilient barley.

Functional genomics
High-throughput expression analysis (transcriptomics) and identification of microRNA are carried on for the characterization of different experimental systems. Currently, several RNAseq analysis are being conducted aiming at characterization of chloroplast defective barley mutants for the study of nucleo-chloroplast interaction, drought response in durum wheat, response to CO2 enrichment in durum wheat, analysis of plant/rootstock interaction in grape; cold response in olive tree, plant-pathogen interaction in rice-Magnaporthe oryzae (rice blast) and kiwifruit-Pseudomonas syringae pv actinidiae (Psa). The Centre is partner of the FP7 project DROPSA focused at the understanding of the molecular interaction between kiwifruit and Psa.
A specific work is dedicated to the functional characterization of some ubiquitin ligases enzymes that control drought/cold tolerance in barley and wheat. This work aims to the understanding of the mechanism involved in activation, regulation and attenuation of molecular responses to abiotic stresses.
Standard protocols for stable transformation in barley, Arabidopsis and tobacco as well as transient transformation are well established.

Bioinformatics
Most of the activity is devoted to the high-throughput analysis of gene expression data and to the development of in silico approaches for the functional annotation of coding and non coding genes.
Conserved and species-specific microRNAs coding genes and the corresponding target genes are studied in several crop species with or without a fully sequenced genome available.
A specific activity is also dedicated to computational analysis of complex regulatory circuits involving microRNAs and transcription factors in plants. Bioinformatic pipelines for RNAseq analysis and detection of differentially expressed microRNAs with next-generation sequencing technologies have been developed in Perl, Python and R programming languages.

Proteomics
The main lines of research are focused on the study of relevant post-translational protein modifications -phosphorylation, ubiquitination and sumoylation- implicated in the signal transduction and regulation of the response to pathogens and abiotic stresses in barley and wheat. Approaches based on typical proteomic workflows (2DE/MS) are associated to affinity-based enrichment techniques followed by MS, and yeast two hybrid system. The goal is the identification of modified proteins and the study of the modification pathways, with the final objective of understanding the functional roles of these modifications in stress response.

Molecular breeding
Breeding programs are currently active in barley, oat, and triticale. The main breeding targets are: pathogen resistance, yield potential and stability, stress resistance, and genotypes more suited for or the production of functional foods and malt. The traditional breeding work has been implemented with knowledge from molecular genetics (Marker Assisted Selection).
Collaborations have been established with private breeding companies for breeding in barley, oat and triticale and for the characterization of new varieties.

Agri-environmental innovations
The Centre is involved in MIC-CERES project aimed to characterize the response of wheat to colonisation by arbuscular mycorrhizal fungi (AMF) and symbiotic beneficial bacteria (SBB), with a view of employ AMF and SBB as natural biofertilizers and bioprotectors.
Mycotoxin monitoring in Italian small grain cereals and malt-beer production chain is a well established activity, together with genomic characterization of mycotoxigenic Fusaria.
The use of natural molecules and of their synthetic derivatives as fungistatic and fungicide in crop protection is studied at molecular level.

Food quality
Pigmented cereals (rice, wheat, barley) are a good source of antioxidant compounds, especially polyphenols. The HPLC/MS characterization of the main antioxidant compounds of pigmented cereals is carried out in parallel with screening of total antioxidant capacity and total polyphenol content. Rice population have been developed to perform segregation mapping for minor genes effecting polyphenol content in the caryopsis of pigmented rice. A study is dedicated to gene expression for genes involved in the regulation of biosynthesis of polyphenols in the caryopsis of pigmented rice and wheat.A breeding program for barley with high β-glucan and high amylose contents is aimed to produce new varieties whose flour can be introduced in bakery products to reduce human blood glycemic response and cholesterol.

Plant physiology and Phenotyping
Research is currently developing screening methods for the assessment of tolerance/susceptibility to cold and drought stress. A large Free Air CO2 Enrichment (FACE) experiment is in progress to study the effects of the climate changes on the yield and quality of durum wheat (read more about the DUCO project).
Studies on seed dormancy are performed using red rice as a model system to investigate the role of phytohormones and the biochemical modifications taking place during the after-ripening process (breaking of dormancy in the dry seed).

Biodiversity
The Centre is committed to conservation, characterization and exploitation of crop biological diversity. Research activities are currently focused on barley, wheat, rice and oat genetic resources - belonging to the primary, secondary and tertiary gene pools. Characterization of variability for Fusarium resistance, anti-oxidant content and cold response in a wide germplasm collection of oat is underway. New bi- and multi-parental populations useful for mapping studies are continuously developed for research and breeding. Advanced mapping populations (NAM and MAGIC) have been generated in barley for gene mapping as well as for pre-breeding and breeding purposes.
A grapevine DNA bank with about 1000 grape accessions, including both wine and table varieties, has been genotyped with SNP markers (Illumina 20K SNP array) for genetic variability evaluation and association mapping studies. A “bar-coding” system for grapevine based on DArT markers has also been implemented for the identification of the molecular signatures of each genotype.

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The Genomics Research Centre holds a collection of more than one hundred barley mutants.

Our contacts

Genomics Research Centre
Via S. Protaso, 302
29017 Fiorenzuola d'Arda (PC) - ITALY
Phone:
+39 0523 983758
Fax:
+39 0523 983750
E-mail:
gpg@entecra.it
How to find us

We thank Renzo Alberici, Donata Pagani and Gianni Tacconi for setting up the picture collection.