Common Bean Coordinated Agricultural Project
Soybean Genomics and Improvement
2011 Annual Report
1a.Objectives (from AD-416)
Objectives are for the identification of genetic variability for nutritional traits in common bean, the discovery of the genes or quantitative trait loci (QTL) controlling that variability and the development of DNA markers that can be used by plant breeders to incorporate QTL into new and more nutritional common bean cultivars.
1b.Approach (from AD-416)
Single Nucleotide Polymorphism (SNP) DNA markers will be discovered via the use of high throughput DNA sequence analysis using the Illumina/Solexa Genome Analyzer as well as via the analysis of common bean DNA gene fragments amplified using polymerase chain reaction (PCR) primers designed to orthologous soybean genes. Because common bean market classes fall into three distinct groups based on their geographic origins in Central or S. America, three sets of 768 SNP panels specific to the three groups will be developed. These three sets of SNPs will be used to characterize common bean populations segregating for nutritional traits for purposes of QTL discovery. The SNP analysis will be conducted using the Illumina GoldenGate assay which is analyzed on the Illumina BeadStation.
Funds from North Dakota State University, Fargo, ND are provided by the Agriculture and Food Research Initiative (AFRI) of the USDA, National Institute of Food and Agriculture (NIFA). The overall objectives of the collaborative project are the identification of genetic variability for nutritional traits in common bean, the discovery of the genes or quantitative trait loci (QTL) controlling that variability and the development of DNA markers that can be used by plant breeders to incorporate QTL into new and more nutritional common bean cultivars. Progress was made in the development of a Single Nucleotide Polymorphism (SNP) DNA marker Illumina iSelect “Beadchip” that permits the analysis more than 5,000 SNP DNA markers in common bean on many hundreds of DNA samples in a period of a few days. This Beadchip was used to create a SNP DNA marker based genetic map of a common bean mapping population developed at North Dakota State University from a cross of the pinto bean variety Stampede with the dark red kidney bean variety Red Hawk. In addition, the same set of SNP markers was used to analyze a group of 192 diverse common bean varieties which included beans from the various market classes (pinto, black, navy, great northern, small red, dark red kidney, light red kidney, white kidney, and snap bean) with the objective of defining genetic variability within and among the market classes.