Developmental Pleiotropy Shaped the Roots of the Domesticated Common Bean Phaseolus vulgaris L.

Roots have been omitted from previous domestication analyses owing mostly to their subterranean nature. We hypothesized that domestication-associated changes in common bean (Phaseolus vulgaris) roots were due to direct selection for some aboveground traits that also affect roots, and to indirect selection of root traits that improved aboveground plant performance. To test this hypothesis, we compared the root traits of wild and domesticated accessions and performed a multistep quantitative trait locus (QTL) analysis of an intra-Andean recombinant inbred family derived from a landrace and a wild accession. Multivariate analysis of root traits distinguished wild from domesticated accessions and showed that seed weight affects many root traits of young seedlings. Sequential and methodical scanning of the genome confirmed the significant effect of seed weight on root traits and identified QTLs that control seed weight, root architecture, shoot and root traits, and shoot traits alone. The root domestication syndrome in the common bean was associated with genes that were directly selected to increase seed weight but had a significant effect on early root growth through a developmental pleiotropic effect. The syndrome was also associated with genes that control root system architecture and that were apparently the product of indirect selection.