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

Abstract

A total of 992,682 single-nucleotide polymorphisms (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 >5000 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 14× genome assembly with sequence lengths >10 kb. 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 × Red Hawk with the two BeadChips resulted in linkage maps with a total of 7040 markers including 7015 SNPs. With the linkage map, a total of 432.3 Mb of sequence from 2766 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 6000 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 United States and abroad.

Identification of QTL Associated with Drought Tolerance in Andean Common Bean

“…Pod weight per plant was moderately correlated with HI (r = 0.29, p < 0.01) and PPI (r = 0.24, p < 0.05). Generally, the order of linkage groups and orientation agreed with those in the Stampede ´ Red Hawk linkage map (Song et al, 2015). As expected, positive correlations were observed among yield component traits and partitioning traits, consistent with previous studies (Ramirez-Vallejo and Mukeshimana et al, 2014), suggesting that mechanisms associated with drought responses could be associated with pleiotropic effects on traits contributing to performance under drought in this population.…”

“…The DNA from the samples used in this study were genotyped using an Illumina BARC_ Bean6K_3BeadChip with 5398 single nucleotide polymorphisms (SNPs; Song et al, 2015) in the Soybean Genomics and Improvement USDA Laboratory (USDA-ARS, Beltsville Agricultural Research Center) in Maryland. Genome Studio software from Illumina was used to call SNPs (Song et al, 2015).…”

Climatic adaptation and ecological descriptors of wild beans from Mexico

“…The use of environmental information in breeding programs has been promoted by the use of methodologies that can predict the presence of specific traits in germplasm growing at specific locations with consequent savings of time and cost (Cortés et al., 2013; Parra‐Quijano et al., 2012; Rodriguez et al., 2015; Song et al., 2015; Thormann et al., 2015; von Wettberg, Marques, & Murren, 2016). However, conservation programs are not considered important by the government and have therefore not received economic support, resulting in the low representation of wild crop relatives in germplasm banks (Castañeda‐Álvarez et al., 2016; Maxted et al., 2016).…”

A Phaseolus vulgaris Diversity Panel for Andean Bean Improvement

“…The trial was planted in December 2013 with two replications in a RCBD. The ADP was genotyped with the Illumina (Illumina Inc., San Diego, CA) BARCBean6K_3 SNP array (Song et al, 2015), which permits the analysis of 5398 SNP markers distributed across the 11 pairs of common bean chromosomes. Common bacterial blight (CBB) disease, caused by Xanthomonas axonopodis pv.…”