SNP Assay Development for Linkage Map Construction, Anchoring Whole Genome Sequence and Other Genetic and Genomic Applications in Common Bean

A total of 992,682 SNPs was identified as ideal for Illumina Infinium II BeadChip design after sequencing a diverse set of 17 common bean (Phaseolus vulgaris L) varieties with the aid of next-generation sequencing technology. From these, two BeadChips each with >5,000 SNPs were designed. The BARCBean6K_1 BeadChip was selected for the purpose of optimizing polymorphism among market classes and, when possible, SNPs were targeted to sequence scaffolds in the Phaseolus vulgaris 14x genome assembly with sequence lengths >10kb. The BARCBean6K_2 BeadChip was designed with the objective of anchoring additional scaffolds and to facilitate orientation of large scaffolds. Analysis of 267 F2 plants from a cross of varieties Stampede x Red Hawk with the two BeadChips resulted in linkage maps with a total of 7,040 markers including 7,015 SNPs. With the linkage map, a total of 432.3Mb of sequence from 2,766 scaffolds was anchored to create the Phaseolus vulgaris v1.0 assembly which accounted for approximately 89% of the 487 Mb of available sequence scaffolds of the Phaseolus vulgaris v0.9 assembly. A core set of 6,000 SNPs (BARCBean6K_3 BeadChip) with high genotyping quality and polymorphism was selected based on the genotyping of 365 dry bean and 134 snap bean accessions with the BARCBean6K_1 and BARCBean6K_2 BeadChips. The BARCBean6K_3 BeadChip is a useful tool for genetics and genomics research and it is widely used by breeders and geneticists in the U.S. and abroad.

View Publication