SNP Identification through Genotyping By Sequencing and Genome-Wide Association Study (GWAS) of Pod Traits in Common Bean

The common bean or Phaseolus vulgaris L. (2n = 2x = 22), is one of the most important crops all around the world due to constitutes the main source of vegetable protein, minerals and vitamins, provides interesting features to study the process of plant domestication. The restriction-based approaches, genotyping-by-sequencing (GBS), is an easy and affordable method that restriction-based approaches requires no prior sequencing of plant genome and is capable of producing high-density, low-cost genotype information to generate genome-wide single nucleotide Polymorphism (SNP) markers. The objective of this study was to determine association between Single Nucleotide Polymorphism (SNP) and pod trait in common bean. In this study, a total of 43,018 SNPs markers were developed from 173 common bean accessions through Genotyping by Sequencing assays. After filtering and removed monomorphic,16,366 SNPs were used to perform an association analysis by using a general linear model (GLM) as implemented in the TASSEL software.  We identified 45 SNPs that were significantly associated with all eight traits for pod (Pod lenght, lenght of beak, pod median width, pod transverse thickness, ratio pod transverse thickness, pod lightness value, pod Hue value and pod chroma value). This study demonstrate that the power and feasibility of SNPs for GWAS to explore complex traits in common bean.