Microsatellite diversity and genetic structure among common bean (Phaseolus vulgaris L.) landraces in Brazil, a secondary center of diversity

Abstract

Brazil is the largest producer and consumer of common bean (Phaseolus vulgaris L.), which is the most important source of human dietary protein in that country. This study assessed the genetic diversity and the structure of a sample of 279 geo-referenced common bean landraces from Brazil, using molecular markers. Sixty-seven microsatellite markers spread over the 11 linkage groups of the common bean genome, as well as Phaseolin, PvTFL1y, APA and four SCAR markers were used. As expected, the sample showed lower genetic diversity compared to the diversity in the primary center of diversification. Andean and Mesoamerican gene pools were both present but the latter gene pool was four times more frequent than the former. The two gene pools could be clearly distinguished; limited admixture was observed between these groups. The Mesoamerican group consisted of two sub-populations, with a high level of admixture between them leading to a large proportion of stabilized hybrids not observed in the centers of domestication. Thus, Brazil can be considered a secondary center of diversification of common bean. A high degree of genome-wide multilocus associations even among unlinked loci was observed, confirming the high level of structure in the sample and suggesting that association mapping should be conducted in separate Andean and Mesoamerican Brazilian samples.

Fig. 1

Collecting sites of common bean landraces in Brazil

Fig. 2

Structure bar plot of membership coefficients for all the accessions of common bean in the study sample sorted in the same order and classified according to successive selected preset K values ranging from 2 to 10. For K = 2 and K = 5, the groups are identified. G2 and G4: groups 2 and 4, respectively. Hybrid represents a large group of accessions resulting from hybridization mostly among Mesoamerican groups

Fig. 3

Neighbor-joining tree reconstructed for the Brazilian germplasm collection of landraces based on the C.S. Chord distances and all 73 polymorphic molecular markers. Branches are colored according to the Structure simulation for K = 3. 271: hybrid accession identified at K = 2 (posterior probability < 0.80); gray branches hybrid accessions identified at K = 3 (see Fig. 2 and text)

Fig. 4

Magnitude of multilocus associations as measured by r ² (a) and D′ (b) among Brazilian landraces. The abscissa represents the genetic distance expressed in cM for locus pairs within linkage groups (LG). Along the same axis, “Across LG” represents the r ² and D′ values for locus pairs distributed among linkage groups