Genomic Insight into the Breeding of Edible Podded Beans in a Snap

New genomics technologies are capable of providing unprecedented insight into the genetic diversity of agricultural crops. This can provide a window into the past through the characterization of genetic diversity and genetic relationships between cultivars, and by uncovering the selection preferences in modern germplasm. It can also enable insight for future selection by providing the molecular tools to elucidate genotype-phenotype relationships and to enhance the accuracy and efficiency of breeding programs to deliver superior cultivars for sustainable agriculture. We employed ApeKI based genotyping-by-sequencing (GBS) in concert with the recently released reference genome for common bean to discover and genotype 40,023 SNPs in a panel of 378 snap bean cultivars of diverse origins and market classes, many of them previously under plant variety protection (PVP). We employed this SNP dataset to characterize the genetic diversity, population structure, and linkage disequilibrium that exists within this germplasm. Valuable phenotypic information was extracted from the PVP certificates and a wealth of additional phenotypic data was acquired to combine with our genotypic data in order to explore the potential for genome-wide association studies. We provide proof of the utility of these combined datasets to identify associations between highly significant SNPs and economically important traits under both simple and complex inheritance. The Snap bean Association Panel (SnAP) provides a public platform for allele discovery in snap beans, and its exploration may also provide unique insight and/or alleles for genomics-assisted improvement of common bean worldwide.