Domestication of Common Bean

Common bean (Phaseolus vulgaris) is the most important food legume for human consumption.  The recently completed draft sequence enables investigations into the evolutionary and domestication history of this major societal crop that has consistently been shown to have undergone two domestication events from unique wild gene pools.  A pooled resequencing project collected SNP data from two wild and six landrace populations.  A joint allele frequency spectrum analysis dated the split of the wild Andean population from an ancestral Mesoamerican (MA) population (n=168k) at ~165kya.  The wild Andean population underwent a bottleneck (n=3590) not observed for the wild MA population.  A strong asymmetric gene flow into the wild Andean population was observed.  The diversity of the wild Andean population was 23% that of the wild Mesoamerican population.  During domestication, MA landrace diversity was reduced slightly, while Andean landrace diversity increased slightly.  As defined by a combined statistic utilizing diversity ratios and F_ST, 74Mb underwent a sweep during MA domestication and 60Mb during Andean domestication.  Only 7.2Mb were shared.  Based on the same criteria, 1424 genes were noted as MA domestication candidates, while only 748 Andean candidates were detected.  Notably, only 59 domestication candidate genes were shared between the two gene pools, which points to the unique domestication trajectory within each common bean gene pool.  Among the MA domestication candidates, a number associated with plant growth were noted.  Several seed weight candidates were confirmed using a GWAS analysis.