A single domestication origin of adzuki bean in Japan and the evolution of domestication genes

Adzuki is a central legume in East Asian culinary culture, yet its domestication origin remains debated. Using ~700 accessions across Asia, we show that the initial domestication happened three to five thousand years ago in central Japan during the Jomon period, followed by a range expansion into China and secondary hybridization with Chinese wild populations. We mapped, validated, and dated key genes associated with seed coat color evolution (VaPAP1 for loss of mottled black and VaANR1 for gain of red colors). The frequency increases of variants affecting key domestication syndrome substantially predated the wild-cultigen divergence. Together, our results resolve the conflict between genetic and archaeological evidence about adzuki origins and reconstruct the evolutionary trajectory of archaeobotanically unobservable traits, consistent with a role of early weak selection during domestication.