Genetic diversity of common bean (Phaseolus vulgaris L.) germplasm from Serbia, as revealed by single sequence repeats (SSR)

Abstract

Genetic diversity and structure of common bean (Phaseolus vulgaris L.) germplasm from Serbia, comprising 118 landraces and 18 cultivars, was assessed with the application of 27 Single Sequence Repeats (SSR) markers. Thirteen accessions from Agricultural Institute of Slovenia were used as references for gene pool determination. Main parameters of genetic diversity were calculated for each SSR loci, i.e. number of different and rare alleles, number of effective alleles, Shannon’s information index, observed and expected heterozygosity and polymorphic information content. A total of 445 allelic variants, with 16.5 alleles per locus on average, were detected. Mean gene diversity (He = 0.79) indicated sufficient reservoir of genetic variation preserved in studied bean germplasm. Landraces displayed higher variability compared to cultivars (405 in relation to 233 allelic variants). Genetic structure and relatedness of accessions was assessed by model-based method and hierarchical clustering method in combination with genetic distance calculation. The Bayesian clustering model implemented in STRUCTURE software, on the primary level (K = 2), revealed clear separation of accessions into two groups, corresponding to gene pool affiliation. Mesoamerican gene pool (M) was represented with 23.5% of accessions, while Andean (A) was larger, composed of 68.4% of studied germplasm. Small group (8.1%) showed admixed genetic structure between two gene pools. Additional variation in respect to two recognized gene pools was revealed (K = 3), whose basis was acknowledged to be within Andean gene pool. Further subdivision of accessions (K = 8), mainly according to the seed forms, was observed. Genetic distance analysis associated with Neighbour-joining clustering method revealed grouping pattern of landraces and cultivars corresponding to the gene pool and their seed phenotypes. Classification and structuring of the bean accessions according to and beyond the gene pool of origin should facilitate conservation strategies and breeding of this material. Combining the information of phenotypic variation obtained in previous research and molecular data reveled in this study will assist in selection of parental components for breeding, or in the choice of smaller sample in order to further acknowledge their breeding value. In addition, obtained results of this work should serve as an additional information on common bean germplasm variation in Western Balkans and beyond, in Europe.