IGA Projects

Currently running projects are

VIGNE/VIGNA. Grape genome sequencing initiative

Start/end 2006/2009

Founded by the Ministry of Agriculture and Federazione delle Banche di Credito Cooperativo, Bank Foundations of Udine, Trieste, and Gorizia, Rauscedo Cooperative Nursery (PN), the Eurotech Ltd of Amaro (UD), several local grapevine Industries and Wineries, and the Collio DOC Consortium.

Partners Genoscope Paris (France), VIGNA Consortium (Italy), CRA (Italy)

Project overview VIGNE/VIGNA is French/Italian project aiming to sequence the whole grape genome (approx. 480 million of base pairs) and to exploit the information derived from the DNA decoding in the fields of grape physiology, biochemistry, genetics, and breeding. Plant material was the highly homozygous Pinot Noir inbred line PN40024, developed by the INRA-France. The first draft of the sequence correspondent to the 8,4x assembly has been published on Nature in August 2007; the final 12x assembly has been produced in February 2008.

IGA role IGA is one of the three partners committed to genome sequencing jointly to the CRIBI-University of Padua and Genoscope-Paris. IGA is also actively involved in computational genome assembly and repetitive sequence annotation (e.g. transposable elements). Finally IGA is committed to sequence ‘Tocai friulano’ variety for 1X coverage to detect nucleotide and structural variations in grape.

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Grape breeding for disease resistance

Start/end 2006/2012

Founded by Friuli Venezia Giulia Regional Administration, Federazione delle Banche di Credito Cooperativo, Bank Foundations of Udine, Trieste, and Gorizia, Rauscedo Cooperative Nursery (PN), several local grapevine Industries and Wineries, and the Collio DOC Consortium.

Partners University of Udine, VIGNA Consortium (Italy), INRA (Evry, France), INRA (Colmar, France)

Project overview IGA has joined the University of Udine in a long-term breeding program aiming to study the genetic determinants of disease resistance in grape and to produce novel wine grape cultivars resistant to downy mildew (Plasmopara viticola), powdery mildew (Erysiphe necator) and other diseases. The breeding strategy makes use of either American and Asian sources of resistance already introgressed in Vitis vinifera in ongoing European breeding programs. IGA and University of Udine cooperates with research teams in France, Hungary, Germany, Serbia, and USA for the identification and exchanges of resistant breeding lines.

IGA role IGA is mainly committed to dissecting QTLs and positional cloning of genes involved in the control of resistance to downy mildew in different genetic backgrounds.

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Analysis of clonal variation in grapevine cultivars

Start/end 2007/2009

Founded by Friuli Venezia Giulia Regional Administration and Rauscedo Cooperative Nursery (VCR-Italy)

Partners Vivai Cooperativi Rauscedo (VCR-Italy), Centro per la ricerca e l’innovazione tecnologica in agricoltura (CRITA-Italy)

Project overview Scope of the project is to set up a diagnostic tool for identifying clonal variants within grapevine cultivars with the value of forensic proof. Grapevine is a vegetatively propagated fruit crop. Many grape varieties propagated by grafting since centuries undergo natural mutations (base mutations, indels, transposable element insertions or excisions, and epigenetic modifications) that can lead to the appearance of desirable phenotypic variations. These genetic variants are selected and commercialized as a new clone of a certain cultivar by nurseries, but up to now there is no reliable tool to discriminate clones from one another and clones can not be patented and protected from illegal multiplication.

IGA role IGA has initiated a large scale scanning of grape genome, mainly through 2nd generation sequencing approach (re-sequencing) with the aim of identifying the most suitable kind of mutations. These mutation markers will be transferred to a high throughput, highly automated protocol for the routine analysis of clonal variants.

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Metabolic profiling of grape juice and wine

Start/end 2008/2010

Founded by Friuli Venezia Giulia Regional Administration

Partners University of Udine (Italy), Unione Italiana Vini (UIV-Verona, Italy), Collio DOC Consortium (Italy), IllyCaffé Aromalab (Area Science Park-Trieste, Italy)

Project overview The scope of the project is to develop the analysis of metabolic profiles of grapevine musts as a tool aiming (a) to forecast the quality of wines, (b) the rapid selection of seedlings in grape breeding programs, (c) the analysis of genetic determinants of individual components (metabolites) of the must profiles. The analysis protocols are being developed on the base on SPE/HS-SPME (Solid Phase Extraction, Head Space-Solid Phase Micro Extraction) pre-enrichment strategies and chromatographic/mass spectrometric techniques such GC/MS and HPLC/MS and their recent development.

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TriticeaeGenome. Genomics for Triticeae improvement

Start/end 2008/2012

Founded by EU within the 7th Framework Program

Partners Partners Institut National de la Recherche Agronomique (INRA-France), Leibniz Institute of Plant Genetics and Crop Plant Research (IPK - Germany), Institute of Experimental Botany (IEB - Czech Republic), GSF- National Research Center for Environment and Health (GSF-Germany), Università degli Studi di Milano (UMIL-Italy), University of Haifa (HU-Israel) Maa- ja elintarviketalouden tutkimuskeskus (MTT-Finland), Scottish Crop Research Institute (SCRI-UK), Sabanci University (SABA-Turkey), National Institute of Agricultural Botany (NIAB-UK), John Innes Centre (JIC-UK), Universität Zürich (UZH-Switzerland), INRA Transfert (IT France), Biogemma (BGA-France), Lochow-Petkus GmbH (LP-Germany), University of Bologna (UNIBO-Italy)

Project overview Wheat and barley are among the main cereal crops grown in Europe. Despite their agricultural relevance and the pressing demand of molecular tools supporting genetic improvement of these species, the complexity of their genomes in terms of size (17 Gb for the bread wheat genome), repeat content (>80%) and ploidy level (wheat is hexaploid) has often been considered too challenging for genome-wide investigations. Recently however, several interesting tools have been set up, such as chromosome flow-sorting, BAC libraries, extensive EST collections, transformation systems, wild and induced mutant collections, DNA oligo microarrays. These novel resources and expertise allowed new large scale genomic programs. TriticeaeGenome project aims to produce genetically anchored physical maps of group 1 and 3 chromosomes in wheat and barley, two sister species of the Triticeae tribe, diverged about 10-14 Myrs ago, sharing high colinearity in spite of their different ploidy level (hexaploid and diploid respectively). The TriticeaeGenome project represents a further contribution to the international efforts aiming to improve cereal breeding through map-based gene and QTL isolation. It also contribute to pave the way for a future genome sequencing project.

IGA role IGA is committed to build physical maps of chromosomes 1A, 1B, 3D of Triticum aestivum using a modified version of the High Informative Content Fingerprinting protocol developed by Luo et al. (Genomics 2003). BAC libraries of six chromosome-arm are fingerprinted (400000 clones in total; 15x coverage per chromosome). Moreover IGA will sequence BAC ends of Minimum Tiling Path clones (90000 BES in total; about 50 Mb). These sequences will be used by partners for genome comparison and the development of new markers for reverse anchoring.

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EnergyPoplar. Enhancing Poplar Traits for Energy Applications

Start/end 2008/2012

Founded by EU within the 7th Framework Program

Partners Institut National de la Recherche Agronomique (INRA-France), Sveriges Lantbruksuniversitet (SLU-Sweden), Albert-Ludwigs-Universität Freiburg (ALU-Germany) Flanders Institute for Biotechnology (VIB-Belgium), University of Southampton (SOTON-UK), Georg-August Universität Göttingen (UGOE-Germany), SweTree Biotechnologies (STT-Sweden), Imperial College of Science, Technology and Medicine (Imperial College-UK), INRA Transfert (IT-France).

Project overview ENERGYPOPLAR aims to develop breeding lines with both desirable cell-wall traits and high biomass yield under sustainable low-input conditions to be used as a source of ligno-cellulosic feedstock for bio-ethanol. ENERGYPOPLAR integrates an multidisciplinary approach at molecular, cellular, organism, and community level to optimize the amount, composition, and structure of walls by reducing lignin content and changing wall organisation and composition in order to render poplar biomass more suitable for biofuel production.

IGA role IGA is committed to develop SNP markers to be used in marker assisted selection for the identification of genotypes carrying beneficial alleles for wood quality and yield. These advanced genotypes will serve as parental lines to produce F1 hybrids for energy production.

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Coffee: development of genomic tools in Coffea arabica for bean quality

Start/end 2007/2009

Founded by Illy Caffè Co. Trieste, Italy

Partners IllyCaffé Aromalab (Science Park-Trieste, Italy), University of Trieste

IGA role IGA is committed to sequence ESTs and BAC-ends from Coffea arabica libraries.

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Wheat. High resolution mapping of QTL for seed traits and MAS development

Start/end 2007/2009

Founded by Società Produttori Sementi/Barilla (Bologna, Italy)

Partners Società Produttori Sementi/Barilla (Bologna, Italy)

IGA role IGA is committed to carry out trait/QTL-associated marker analysis on durum wheat lines developed by the Società Produttori Sementi.

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DRUPOMICS. Deciphering peach genome and MAS improving in stone fruit crops

Start/end 2008/2012

Founded by Italian Ministry of Agriculture

Partners CRA (Rome, Italy, project leader), Parco Tecnologico Padano (PTP-Lodi, Italy), National Research Council (CNR, Italy), Metapontum Agrobios (Italy), University of Milan (Italy), Scuola Superiore Sant’Anna (SSSA-Pisa, Italy), University of Bologna (Italy), University of Padua (Italy), University of Udine (Italy), University of Verona (Italy).

Project overview The project is split in 3 phases. The first phase deals with genome sequencing of a peach double haploid genotype. It is carried out in cooperation with USA partners (Clemson University and the Joint Genome Institute) and is based on an integrated approach (6X Sanger and 15X 454/Solexa sequencing) that will produce sequences for a 21X genome coverage. The second phase is committed to the development of molecular tools (EST collections, genetic maps) for mapping and cloning genes/QTLs of interest for peach and apricot breeding. The major traits object of study are fruit quality and ripening and resistance to several diseases. The last phase deals with the management of information: creation of dbases, development of interactive web sites.

IGA role IGA is committed to 3-4X whole genome shotgun sequencing of the peach double haploid and to contribute to sequence assembly.

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CITROMICS. Sequencing and annotation of Citrus genome

[development and implementation in progress]

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