2007 Y2 Barley CAP Continuation of Grant Proposal - PDF - 5.52mb
2006 Barley CAP Research Proposal - PDF - 154kb
Obj. 1. High-Throughput Marker Development – Develop an integrated 3,000 single nucleotide polymorphism (SNP) -based genetic/physical/expression map of the barley genome. Our aim is to develop a saturated genetic map with SNP markers for marker-assisted selection, haplotype-block analysis, and QTL identification through association genetics. The SNP mapping is a collaboration with Robbie Waugh at the Scottish Crop Research Institute. In addition, we will integrate the SNP map with the BAC-based physical map.
Specific Outcomes from Objective 1:
- Map positions of 3,000 informative SNP markers for U.S. barley germplasm
- SNP map integrated with BAC-based physical map
Obj. 2. Worldwide Web Access – Develop an integrated web portal and database for efficient access to map, gene expression, and trait data. Our objective is to develop The Hordeum Toolbox (THT), as an integrated public resource for discovery and dissemination of large-scale SNP data sets as they apply to genetic, phenotypic, and trait data. The development of THT will proceed via a collaboration with the Scottish Crop Research Institute.
Specific Outcomes from Objective 2:
- Web-accessible pedigree, trait, SNP database integrated with gene expression datasets
- Software for SNP analysis, haplotype, and germplasm analysis and sorting
- THT development as a prototype database for other organisms
Obj. 3. Genes and Traits – Provide access to economically important genes using association genetics and diverse breeding germplasm. We will obtain genotype and phenotype data from 3,840 breeding lines that are important to 10 U.S. barley breeding programs. We will also develop QTL miner software to facilitate mixed-model analysis of breeding program data. These data, the QTL miner software and THT database will be used to map QTL for important traits using association genetics. These data and tools will also be used to understand the haplotype block structure of barley breeding materials in the US.
Specific Outcomes from Objective 3:
- Web-based database of the location of QTL for important traits
- Haplotype block structure of U.S. barley
- Comprehensive SNP genotypes of breeding lines to facilitate MAS and germplasm exchange
- Candidate genes for QTL
- “QTL Miner” software to facilitate mixed-model analysis of breeding program data
Obj. 4. Superior Germplasm – Develop elite barley germplasm using high-throughput marker-assisted selection (MAS). As SNP markers or haplotypes are identified that are associated with desirable QTL alleles, they will be employed in MAS by the participating breeding programs.
Specific Outcomes from Objective 4:
- Implementation of MAS approaches to develop improved barley germplasm
- Improved barley germplasm
- Breeder-friendly markers posted on the web
Obj. 5. Education and Outreach - Educate students, scientists, farmers, processors, and consumers in use of genomics technology for gene discovery and crop improvement.
Specific Outcomes from Objective 5:
- Graduates and post-graduates educated in translating genomics to crop improvement
- User-friendly “QTL Miner” software, user guide and tutorials released for general use
- Workshops at national meetings that describe the outcomes of the barley CAP
- Enhanced linkages with barley end users on the applied outcomes of the project
- Short courses on applied association-based MAS breeding