A reference genome for common bean and genome-wide analysis of dual domestications

TLDR

Common bean (Phaseolus vulgaris) is the most important grain legume for human consumption and supports sustainable agriculture through nitrogen fixation. The authors assembled a 473‑Mb genome, anchored 98 % onto 11 chromosome‑scale pseudomolecules, compared it to soybean to identify polyploidy‑induced changes, and resequenced 60 wild and 100 landrace individuals from Mesoamerican and Andean gene pools to confirm two independent domestications. The study found two independent domestications of common bean, with less than 10 % of domestication‑related sequences shared, identified genes linked to increased leaf and seed size, and suggested these genes could aid genomics‑enabled crop improvement.

Abstract

Scott Jackson, Jeremy Schmutz, Phillip McClean and colleagues report the genome sequence of the common bean (Phaseolus vulgaris) and resequenced wild individuals and landraces from Mesoamerican and Andean gene pools, showing that common bean underwent two independent domestications. Common bean (Phaseolus vulgaris L.) is the most important grain legume for human consumption and has a role in sustainable agriculture owing to its ability to fix atmospheric nitrogen. We assembled 473 Mb of the 587-Mb genome and genetically anchored 98% of this sequence in 11 chromosome-scale pseudomolecules. We compared the genome for the common bean against the soybean genome to find changes in soybean resulting from polyploidy. Using resequencing of 60 wild individuals and 100 landraces from the genetically differentiated Mesoamerican and Andean gene pools, we confirmed 2 independent domestications from genetic pools that diverged before human colonization. Less than 10% of the 74 Mb of sequence putatively involved in domestication was shared by the two domestication events. We identified a set of genes linked with increased leaf and seed size and combined these results with quantitative trait locus data from Mesoamerican cultivars. Genes affected by domestication may be useful for genomics-enabled crop improvement.