Triticeae Genome

Results

The results of the fourth (and last) project year are now available!

After four years of activity, the TriticeaeGenome project has reached all milestones and deliverables on time. Results and resources produced by the project are already available to the wheat and barley communities. The main achievements for each WP are as follows:

•    WP1: Publicly available BAC libraries have been constructed for the wheat chromosomes 3B, 3DS, 3DL, 1AS, 1AL, 1BS, and 1BL and are available to the community (see INRA-CNRGV website). Using FPC and the newly developed LTC algorithms, BAC contigs were build using HIC Fingerprints and MTP were designed for each chromosome. BAC end sequences were produced for each MTP. These resources were used for (i) constructing anchored physical maps of the wheat chromosomes 1A, 1B, 3B and 3D in WP2 , (ii) providing a substrate for map-based cloning in WP3 and (iii) for future sequencing of these chromosomes. A guidelines for physical map assembly has been produced and adopted by the IWGSC.

•    WP2: Integrated physical maps of wheat chromosomes 1AS, 1AL, 1BS, 1BL, 3B, 3DS, and 3DL and barley chromosomes 1H and 3H were produced by screening 5,400 BAC contigs with approximately 140,000 molecular markers (SSR, STS, COS, genes, ISBPs). Anchoring was performed by combinations of various approaches ranging from individual PCR to high throughput hybridizations of 3-D MTP pools and sequence- based anchoring using tags generated by BAC pool sequencing. In total, 4301 wheat contigs covering more than 75% of the target chromosomes have been anchored. For barley, 560 contigs and 668 contigs were anchored and ordered along chromosomes 1H and 3H, respectively. High resolution mapping populations of 2600 and 4455 RILs were obtained for fine mapping and anchoring in wheat and barley, respectively. Genes anchored to the physical maps and shotgun sequences produced from the TG chromosomes were used to refine the syntenic relationships between the homoeologous group 1 and group 3 chromosomes. Wheat and barley high resolution mapping populations are available to the community (contact Pierre Sourdille from INRA for wheat and Viktor Korzun from KWL for barley).

•    WP3: Fine mapping and isolation of candidate genes for two Mendelian loci (YrH52, cul4) and three QTLs underlying fungal disease resistance, yield and quality traits (PV-QTL, QYld-idw, QSng.sfr) located on wheat and barley chromosomes 1BS, 1BL, 3BS and 3H was performed. High resolution has been achieved for all traits through the development/characterization of segregating populations and diversity panels, and through marker enrichment of target intervals using synteny and information from the physical maps built in WP1/2. For all traits but one, the genetic interval is now smaller than 1 cM and physical contigs have been identified at or near the target loci. Final resolution of the target locus to a single BAC and candidate gene has been successful in the cul4 project on chromosome 3H, two candidate genes that need further validation were identified for the PV-QTL in 1BL, reduced physical intervals of 200kb to 3Mb were identified for the QYld-idw and YrH52 on chromosomes 3BS and 1BS. Functional validation and allele mining have been initiated for the various CGs.

•    WP4: Association studies to identify traits of agronomic interest and develop molecular markers linked to these traits for supporting the creation of new varieties by marker-assisted selection was performed using a panel composed of 376 winter wheat varieties from France, the UK, Germany maximizing the phenotypic and genetic diversity of the European material. The panel was evaluated for yield and development related traits at 3 locations over 2 years and was genotyped with DArT markers, markers for major adaptation genes and SNP markers derived from COS developed in WP2. Genome-Wide Association Analyses were conducted for heading date, grain yield and plant height. Known and new chromosomal locations were identified. The TG panel has been multiplied for distribution to partners and is available to the community (contact Nick Gosman from NIAB).

•    WP5: bioinformatics tools and resources have been developed to support the construction of the wheat and barley physical maps, assist in contig assembly and anchoring, analyze and annotate Triticeae genomic sequences and, integrate data and analysis tools in a platform for Triticeae genomics. Two databases have been established at the INRA-URGI and HGMU-MIPS databases. WP5 also developed LTC, a new algorithm for physical map assembly and a comparative viewer called CrowsNest to enable the visualisation of both physical and genetic maps of single plant species and their comparisons with other genomes. Finally, the semi-automated online annotation pipeline TriAnnot is available for BAC and chromosome sequence annotation.

•    WP6: Nine training courses in emerging technological approaches have been organized for project members and external scientists and students. Results from the TG project were disseminated at more than 249 events with a global audience size estimated at 85 000. Since May 2010, the public website has received 11 000 visits from all over the world. A brochure and 3 posters showing the project results have been presenting, 20 articles referring to the TG project have been published and a TG newsletter have been published.

•    WP7: The efficient management of the project permitted to submit deliverables and periodic reports on time as well as organize the project meetings as scheduled. In addition, to the daily management of the project, WP7 ensures coordination of the TG activities with other initiatives worldwide. This is performed through a TriticeaeGenome Network that comprises now 24 laboratories.