Genetic data of 326 diverse common beans and genetic and phenotypic data of two RIL populations segregating for pod shattering

Here, we investigate the loss of seed dispersal via pod shattering during
common bean (Phaseolus vulgaris L.) domestication. We identified PvMYB26
mutations in all three main gene pools of common bean, including an 8 kb
deletion in Middle American lines eliminating the gene’s transcription
start site and promoter; a frameshift/truncation deletion in the
independently domesticated Andean population; and another
frameshift/truncation insertion in the genetic background of the
"undomesticated" debouckii population. Mutants with the 8 kb
deletion express PvMYB26 at <1% of the level of wild types and
produce 44% less pod lignin. RNA in situ hybridization and fluorescence
microscopy show that PvMYB26 is expressed in the lignified fiber layer of
pods, while mutants show no visible expression and have a greatly reduced
fiber layer. Sequencing of 327 accessions revealed that the mutation is
nearly diagnostic for domestication status among Middle American common
bean and identified a 125 kb hard selective sweep, indicating the gene’s
importance in domestication. The main Andean frameshift mutation is found
in 84.5% of Andean domesticates but 0% of wild lines, while the debouckii
truncation was identified in six domesticated lines of Race Peru,
suggesting a third proto-domestication of common bean may have occurred in
Ecuador and/or northern Peru. Wild haplotypes most like Middle American
domesticates are found in eastern Jalisco, Mexico, strongly suggesting
West-Central Mexico as the site of common bean domestication and the rise
of agriculture in Middle America.