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

Abstract

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.

Genetic Diversity, Population Structure, and Linkage Disequilibrium in a Spanish Common Bean Diversity Panel Revealed through Genotyping-by-Sequencing

“…The region of 45 Mbp, in which the candidate gene, PHAVU_001G189200g , has been located, was not identified in the MLM-GWAS. Determinacy is a complex trait that has been selected during domestication of common bean, and leguminous crops in general [ 68 ]. Multiple origins have been proposed for determinacy in common bean based on the broad mutational spectrum observed in PvTFL1y , including retrotransposon insertion and deletion [ 69 ], so the possibility of other genes apart from PvTFL1y involved in the genetic control of determinacy cannot be discarded.…”

Characterization of the BnA10.tfl1 Gene Controls Determinate Inflorescence Trait in Brassica napus L.

“…The functions of TFL1 homologous were studied in some plants. In Vigna radiata, Li and Ding et al found that the VrDet1 gene was transformed into the A. thaliana tfl1 mutant, the progeny transgenic plants showed indeterminate traits similar to wild-type A. thaliana, and the expression level of VrDet1 at the SAMs of indeterminate plants was higher than that in determinate plants [10]. In Punica granatum L., PgTFL1 was transformed into the tfl1-14 mutant, and the determinate trait restored growth to an indeterminate plant [50].…”

B-box Proteins in Arachis duranensis: Genome-Wide Characterization and Expression Profiles Analysis

“…A chromosomal distribution map was generated using Mapinspect software (Mike Lischke, Berlin, Germany). To investigate the synteny relationships of related genome regions in different species, putative orthologous genes surrounding CO orthologs/homologs from soybean and A. duranensis were identified by a BLASTP search as previously described [46,47], and the blast results were used to generate a synteny map. To analyze the duplicated gene pairs, we clustered AdBBX, AiBBX, and AhBBX genes using OrthoMCL software [48] with amino acid sequences more than 70% similar, and visualized the duplicated gene pairs using Circos software as previously described, respectively [49,50].…”