Parallel domestication with a broad mutational spectrum of determinate stem growth habit in leguminous crops

Stem growth habit is a key plant architecture trait determining yield potential in grain legumes, and the phenotypic change from the indeterminate stem growth habit of wild mungbeans (Vigna radiata) to the determinate stem growth habit of cultivated mungbeans is a critical domestication transition. Here we show that indeterminate stem growth in wild mungbean is modulated by a single gene, VrDet1, which encodes a signaling protein of shoot apical meristems. The transition from an indeterminate to a determinate stem growth habit was achieved by selection of two linked point mutations in two putative cis-regulatory elements, resulting in a significant reduction in gene expression. Both the wild-type nucleotides corresponding to the two point mutations were essential for VrDet1 function. In addition, two highly diverse haplotypes of Vrdet1 were found in cultivated mungbeans, suggesting dual domestication of Vrdet1. VrDet1 was orthologous to Dt1 in wild soybean and PvTFL1y in wild common bean, where multiple loss-of-function mutations altering the coding sequences of individual genes were selected to produce determinate stems in cultivated accessions. Interspecific comparison of these orthologs in the wild and cultivated accessions reveals the most conservative interspecific and intraspecific parallel domestication events with the broadest mutational spectrum of a domestication trait in leguminous crops. We also found that interspecifically and functionally conserved promoters possess cis-regulatory elements that are highly conserved in kind but greatly variable in number and order, demonstrating the evolutionary dynamics of regulatory sequences. This work provides insights into the origins of cultivated mungbean and exemplifies the conservativeness and plasticity of the domestication processes of related crops.