Analysis of Genetic Diversity, Evolution and Signature of Environmental Selection in Wild Phaseolus vulgaris using Genotyping-By-Sequencing (GBS) and Landscape Genomics

Wild common bean (P. vulgaris) constitutes a very useful resource for broadening the genetic diversity and breeding improvement of its two domesticated gene pools. However, this resource is still under-exploited due to the scarcity of information regarding genetic diversity and markers, which are essential for an efficient breeding program. For this reason, we applied Genotyping-By-Sequencing (GBS) to a panel of 271 wild common bean representative of the genetic diversity and geographical distribution of this species. With this approach, we identified 19,126 variants in the common bean genome across 246 wild individuals. We used this dataset to analyze genetic diversity, population structure, and phylogenetic relationship among the different wild gene pools of this species, but also for evolutionary studies using coalescent simulation and Approximate Bayesian Computation (ABC). In addition, we applied a landscape genomic approach by coupling genotypic information with GIS data and bio-climatic databases, and identified several markers correlated with environmental variables, potentially involved in local adaptation. This is the first study reporting a genome-wide genetic characterization of wild Phaseolus vulgaris using state-of-the-art genotyping technologies. The results delivered will allow a more efficient germplasm management for this species, and will facilitate breeding improvement of domesticated common bean by introgessing abiotic resistance traits from the wild gene pool.