Common Bean Coordinated Agricultural Project
Soybean Genomics and Improvement
2013 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 design of a custom Illumina iSelect Beadchip referred to as BARCBean6K_3 that contained 5,398 single nucleotide polymorphism (SNP) common bean (SNP) DNA markers. To permit the analysis of genetic mapping populations from the numerous collaborators on the project, a sufficient number of BARCBean6K_3 beadchips were purchased to analyze 6,400 common bean DNA samples. DNA of common bean lines from genetic mapping populations was received from collaborators at the ARS, Prosser, WA; ARS, Beltsville, MD; the Univ. of California, Davis; Michigan St. Univ.; N. Dakota St. Univ.; the Univ. of Wisconsin; the Univ. of Idaho and the Univ. of Puerto Rico and was analyzed with the BARCBean6K_3 beadchip. A total of more than 2,600 common bean DNA samples were analyzed and the SNP DNA marker data were forwarded to the collaborating researchers.