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United States Department of Agriculture

Agricultural Research Service

Research Project: Common Bean Coordinated Agricultural Project

Location: Soybean Genomics and Improvement

2012 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.


3.Progress Report:

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 genetic analysis of 517 common bean cultivars representing a range of market classes (pinto, black, navy, great northern, small red, dark red kidney, light red kidney, white kidney, and snap bean). The cultivars were analyzed with two Illumina iSelect “Beadchips”. Each contained more than 5,000 Single Nucleotide Polymorphism (SNP) DNA markers. These molecular genetic data permit the analysis of the genetic relationships among the 517 common bean cultivars. In addition, a set of wild common bean accessions, the presumed ancestors of today’s common bean cultivars, were analyzed with the same set of more than 10,000 SNP DNA markers. Combining the resulting molecular genetic data from the cultivars and the wild common bean accessions will facilitate an analysis of the relationship between the two groups of common bean lines.


Last Modified: 4/21/2014
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