An Operational SNP Panel Integrated to SSR Marker for the Assessment of Genetic Diversity and Population Structure of the Common Bean

Abstract

The common bean, an important source of protein and minerals for humans, complements cereals both nutritionally and as a rotation crop, supplying nitrogen and reducing soil pathogens. The aim of this study was to develop an operational SNP-based panel for common bean in order to facilitate SSR employment in genetic diversity and population structure analyses, and its use in breeding programs. A set of 88 diverse and important common bean cultivars/lines (53), landraces (33) and wild accessions (2) were genotyped. Overall, the 58 SSRs performed better at evaluating genetic diversity (Ā = 7.38; He = 58.7 %; PI = 1.20E−45) than the 345 SNPs, of which the SSRs dinucleotides (SSR-di) were more informative (Ā = 9.92; He = 72.5 %; PI = 3.40E−26) and a selected set of 13 SSRs (Ā = 15.31/locus; He = 84.5 %; PI = 1.03E−19) allowed for the discrimination of all individuals. For the 345 high-quality scored SNPs a low combined PI (4.70E−119) and high PE (100 %) was obtained for the assessment of parentage and identity. The SNPs were very useful for linkage mapping in inter- (78.2 %) and intra-gene pool (17.7 %) crosses. Both markers afforded high resolution detection of inter-gene pool structure, with greater differentiation based on SNPs (K = 2, F ST = 0.759). The SSRs-di differentiated cultivars/lines and landraces (K = 3) of Mesoamerican origin. A set of 16 SSRs was selected to establish a routine and operational analysis of Genbank accessions allowing an efficient origin-based discrimination of common bean accessions. Operational genotyping panels based on SSRs and SNPs were derived, contributing to the growing integration of genomics with molecular breeding programs of the common bean.