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Overview:

The International Barley Sequencing Consortium (IBSC), including the US, Germany, UK, Finland, Australia, and Japan (http://barleygenome.org/) was formalized at the 18th annual International Triticeae Mapping Initiative (ITMI) workshop (Victor Harbor, Australia; August 27 – 31, 2006).  The priority near-term need of community is the identification of the remainder of ~50,000 genes, including the 5’ and 3’ regulatory regions (by end of 2008), and the longer-term goal an ordered physical map anchored to the genetic map (by end of 2010) to accelerate crop improvement.

Germany will provide a whole-genome physical map integrated with the current NSF-funded map (PI Close, Award #0321756).  Australia will provide new BAC libraries for physical mapping in addition to targeted sequencing efforts on 7H (to be linked with wheat group 7).  An SCRI-led effort will provide BAC-end sequences anchored to the genetic map.  Japan will provide additional gene discovery and targeted BAC sequencing from Haruna Nijo, a second haplotype.  Currently, there is > 60 Gb of contributed Barley1 GeneChip expression data in PLEXdb.  Large groups of tightly co-regulated genes are at our fingertips, thus, the near-term need is not only to identify the rest of the genes, but also their regulatory regions to access gene networks for a number of key traits.

Activities:

Among recent complementary initiatives of the consortium are:

  • Advancing the Barley Genome: Tim Close, Stefano Lonardi, University of California, Riverside; Gary Muehlbaeur, University of Minnesota; Jeff Bennetzen, University of Georgia

    Funding: $1 million for two years September 1, 2009 - August 31, 2011 from U.S. Department of Agriculture - Cooperative State Research, Education, and Extension Service (USDA/CSREES).

    Objective Set 1: Determine the sequences of nearly all Morex barley genes, including 5’ and 3’ flanking regions. This will assist with annotation of BACs and the genome in general. Sequence to be generated using Roche 454 Titanium.

    • 1A. High Cot fractions (2 runs, 1 Gb total); Bennetzen
    • 1B. Hypomethylated partially restricted DNA (4 runs, 2 Gb total); Bennetzen
    • 1C. Diverse cDNA library (1 run, 0.5 Gb total); Close and Lonardi.

    Objective Set 2: Sequence ~2000 previously mapped gene-bearing BACs from an existing minimal tiling path, mainly from chromosomes 4H, 5H and 6H. Structured on a combinatorial design for 2197 BACs for gene-BAC deconvolution. Close and Lonardi.

    Objective Set 3: Assemble, annotate, release data for public access. All investigators.

  • ERA-PG Project: Genomics-assisted dissection of barley morphology and development: a collaboration between Robbie Waugh (SCRI, PI), Nils Stein (IPK-Gatersleben, Co-I) and Michele Morgante (Uni. of Udine) funded through the European Reaseach Area - Plant Genomics program.  

    Funding: 1.7 million Euros

    Goals: To integrate state of the art genomics technologies with advanced biological resources systematically generated over the last 30 years. This project represents a collision between historical mutation-genetics research and advanced genomics technology. Within three clearly defined objectives we aim to:

    • Genetically map 480 morphological mutant loci onto the barley genome (at low to medium resolution) combining use of a high throughput gene-based SNP genotyping platform with an unique series of available nearly isogenic mutant lines (the Bowman Series).
    • Develop approximately 400Mbp of barley BAC-end sequence data linked directly to a High Information Content Fingerprint (HICF) BAC contig-based physical map.
    • Identify, isolate and validate at least three morphologically and / or developmentally important barley genes that are perturbed in specific mutant lines.
  • The project will build upon ongoing research programs in the partner organizations, benefiting from existing in-house and international informatics resources for storage, analysis and graphical display of genotypic and sequence data.

  • BARLEX: Exploring the Barley Genome: anchoring the barley physical map by explorative genomic sequencing consortium by 4 partners: IPK (Nils Stein, PI of the consortium; Uwe Scholz, co-PI), FLI Jena (Mathias Platzer, co-PI), MIPS GSF Munich (Klaus Mayer, co-PI), BAZ Quedlinburg (Frank Ordon, co-PI).

    Funding: 6.2 million EURO for 3.5 years, 01.07.07 - 31.12.10, provided by German Ministry of Education and Research (BMBF).

    Goals:

    • Add 200,000 clones to the HICF project to achieve 12-15x genome coverage, including construction of a third (MboI or PstI) Morex BAC library to complement the current HindIII and EcoRI libraries.
    • Sample sequencing of 3000 BACs (BAC pools using barcoded adaptors and 454 technology) to harness gene content information for surveying the barley genome and anchoring of the physical to the genetic map.
    • Anchoring 1000 gene or BACend derived markers to the physical map.
    • Anchoring DArT markers to the physical map.
    • Map based cloning of two virus resistance genes by taking advantage of the barley physical map resources.
    • Build bioinformatics environment for integrating barley genomic
  • 4,500 single nucleotide polymorphisms (SNPs) on three Illumina 1,526 SNP Oligo pool assays (OPAs) for high throughput mapping and genotyping; the first from the Close, Waugh, and Graner NSF, SCRI, & IPK projects respectively, and two additional OPAs from the USDA-CSREES Barley CAP project (PI Muehlbauer, Award #2005-05128) and UK DEFRA LINK project (PI Waugh, Award# SA LINK BB/D522003/1).  These will quickly leverage the genomic efforts into plant breeding.
  • 5,000 full length (FL) barley cDNAs from cv. Haruna Nijo (K. Sato, Okayama University, Japan, nearly complete).  Another 30,000 FL cDNAs from the same cDNA pool will be produced at Tsukuba in the next three years. In addition, 500 BAC clones on barley chromosome 3 (syntenic with rice chromosome 1) that target important agronomic traits has been initiated for cv. Haruna Nijo by K. Sato. This also will link with French, UK, US, and Australian efforts to physically map and sequence chromosomes 3A, 3B, and 3D from wheat.
  • Large-scale sequencing of 7H (to be linked with wheat group 7) by the ACPFG in Australia.