Genome-wide discovery of short sequence repeat markers useful for genetic diversity studies in Lima bean (Phaseolus lunatus L.)

Lima bean is an underutilized legume that holds potential as a food crop in the context of climate change, nevertheless very few studies have been done on its genetic structure. The aim of this study was to identify genome-wide SSR loci informative for genetic diversity studies in Lima bean. First, a Lima bean reference genome was used to identify a total of 109,698 SSR loci. Then, 27,376 loci were genotyped in silico using WGS data from 60 wild and domesticated Lima bean accessions that belong to the two major gene pools, namely the Mesoamerican and Andean gene pools. Of these loci, 9346 loci were polymorphic for the Andean gene pool and 13,496 loci for the Mesoamerican one. Genetic structure was studied by means of Bayesian analysis (Structure), principal component analysis, genetic distances and neighbor-joining topologies. Genetic diversity indexes showed a strong reduction of genetic diversity due to domestication, more severe in Mesoamerica (50%) than in the Andes (33%). Outlier SSR loci likely to be associated with domestication traits were identified, 211 for the Mesoamerican gene pool and 123 loci for the Andean one. Interestingly, only six outlier loci were shared among gene pools, possibly indicating different genetic avenues to domestication. A comparison with genome-wide SNP data validated the use of SSR loci for genetic diversity studies in Lima bean. Finally, 16 outlier loci located within genes related to agronomic traits were experimentally validated by PCR. The identified SSR loci could be useful to unravel the genetic basis of agronomic traits of interest for genetic improvement.