Developing an Improved Bean Genotyping Chip

To provide a tool for breeders and geneticists to identify genes or QTL associated with their traits of interest, 6000 SNPs were selected from the successful markers on the BARCBean6K_1 and BARCBean6K_2 BeadChips for inclusion in the BARCBean6K_3 BeadChip. Only SNPs that had a minor allele frequency (MAF) >0.05 and with missing or ambiguous allele calls <10% among 365 dry bean and 134 snap bean accessions (Table S1) from the Association Mapping Population of the BeanCAP (http://www.beancap.org/) were selected for inclusion in the BARCBean6K_3 BeadChip. In addition, SNPs that were polymorphic in more than one common bean market class, that were located on different scaffolds, or that were located in different bins of the linkage maps of the Stampede × Red Hawk population were preferentially selected when possible, so that the number of SNPs, especially in the heterochromatic regions which had very low recombination rates, was greatly reduced. This procedure of SNP selection, which was based on the genetic distance/physical distance ratio in the heterochromatic and euchromatic regions, was previously reported in soybean (Song et al. 2013 (link)).