Characterization of Genetic Diversity and Climatic Selection in Wild Common Bean (Phaseolus vulgaris) Using Genotyping By Sequencing (GBS) Technology

During domestication, and subsequent selection, plants were subjected to a severe bottleneck that drastically reduced genetic diversity in cultivated crops. This reduced diversity restricts the ability of breeding improvement in crop plants. Crop wild relatives constitute a valuable genetic resource for broadening the domesticated gene pools, even though they have been poorly characterized and exploited in breeding programs. Common bean (Phaseolus vulgaris) originated in the Americas and diverged into two separated gene pools (e.g., Mesoamerican and Andean), that underwent domestication independently. Wild common beans have a wide geographical distribution from north Mexico to north Argentina, that reflects an adaption to different environments. In this project we aim to genotype, using GBS technology, 284 wild common beans distributed from central to south America. The goal of the project is to generate a high density SNPs resource for wild common beans. These data will be useful for a comprehensive analysis of genetic diversity and signature of climatic selection in this species. After an in silico digestion of common bean reference genome we selected CviAII as the most suitable enzyme for our goals. We tested the approach with a sample of 17 wild and domesticated common bean, and a domesticated P. dumosus. We identified >47k high-quality variants located in ~11k annotated genes. SNPs distribution was positively correlated with chromosome size (r=0.79), with a median of 79 variants/Mb. These results suggest a dense variant distribution suitable for a comprehensive analysis of genetic diversity and signature of climatic selection in common bean.