Molecular markers for assessing the inter- and intra-racial genetic diversity and structure of common bean

The Mesoamerican and Andean gene pools of the common bean are distinguished into specific races. Knowledge of their structure and genetic diversity is an important prerequisite for plant conservation and breeding. The aim of this study was to estimate the inter- and intra-racial genetic diversity of genotypes representative of the six common bean races using simple sequence repeats (SSRs) and single nucleotide polymorphism (SNPs). Ninety-four accessions were genetically analyzed, using 24 SSR and 4.820 SNPs markers with minor allele frequencies (MAF) >= 5%. Based on SSR, 163 alleles were identified (13.8 alleles/marker). For the whole samples, the average values for expected (H-e) and observed heterozygosity (H-o) were 0.780 and 0.045, respectively, and 5.5 x 10(-31) for probability of identity (PI). While for the gene pools analyzed separately, similar H-e estimates were obtained for the Andean (H-e = 0.731) and Mesoamerican gene pools (H-e = 0.733). Population structure and clustering analyses revealed subdivision predominantly by gene pool (K = 2). The overall linkage disequilibrium extension (r(sv)(2)) was 58 kb. Estimated H-e was 0.327 and H-o 0.025, with slightly higher values for the Mesoamerican (H-e= 0.303) when compared to its Andean counterpart (H-e = 0.269). Population structure was observed in the Andean (K = 2 and K = 3) and Mesoamerican (K = 2) gene pools. The molecular analyses did not reveal clear differentiation between the bean races. Although sampling may be having an effect on the analysis, our results reinforce that distinction among races appeared to have resulted from selection caused by domestication.

Automated summary

This study estimated the inter- and intra-racial genetic diversity of common bean races using SSR and SNP markers. The results showed that there was not a clear differentiation between the bean races, and the population structure primarily divided by gene pool.