Investigation of the domestication of common bean (Phaseolus vulgaris) using multilocus sequence data

Abstract

Multilocus sequence data collected from domesticated and related wild relatives provides a rich source of information on the effect of human selection on the diversity and adaptability of a species to complex environments. To evaluate the domestication history of common bean (Phaseolus vulgaris L.), multilocus sequence data from landraces representing the various races within the Middle American (MA) and Andean gene pools was evaluated. Across 13 loci, nucleotide diversity was similar between landraces and wild germplasm in both gene pools. The diversity data were evaluated using the approximate Bayesian computation approach to test multiple domestication models and estimate population demographic parameters. A model with a single domestication event coupled with bidirectional migration between wild and domesticated genotypes fitted the data better than models consisting of two or three domestication events in each genepool. The effective bottleneck population size was ~50% of the base population in each genepool. The bottleneck began ~8200 and ~8500 years before present and ended at ~6300 and ~7000 years before present in MA and Andean gene pools respectively. Linkage disequilibrium decayed to a greater extent in the MA genepool. Given the (1) geographical adaptation bottleneck in each wild gene pool, (2) a subsequent domestication bottleneck within each gene pool, (3) differentiation into gene-pool specific races and (4) variable extents of linkage disequilibrium, association mapping experiments for common bean would more appropriately be performed within each genepool.