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The adzuki bean (Vigna angularis), an essential crop supporting traditional Japanese cuisine such as wagashi (traditional Japanese sweets) and sekihan (steamed rice with adzuki beans), has long been believed to have been introduced to Japan from the Asian continent, similar to rice and wheat. However, recent archaeological excavations have revealed that between approximately 6,000 and 4,000 years ago (during the Late Jomon period in Japan) adzuki bean seeds were undergoing size enlargement in Japan earlier than in China. These findings have led to the proposal of a Japan-origin hypothesis for adzuki bean domestication. Nevertheless, scientific evidence confirming that domestication occurred in Japan has remained insufficient until now.

To investigate the origin of adzuki bean domestication, a research team from NARO and National Taiwan University conducted whole-genome sequencing of 693 accessions. These included cultivated adzuki beans and their wild progenitor, V. angularis var. nipponensis, collected from various regions across Asia. In plant domestication studies, regions with higher genetic diversity are generally considered potential centers of origin. The analysis of the nuclear genome showed that Chinese cultivated adzuki beans have greater genetic diversity than those from Japan, which appeared to support the hypothesis of a continental origin. On the other hand, the analysis of the chloroplast genome, which is maternally inherited, revealed that Chinese cultivated adzuki beans share the same chloroplast haplotype as Japanese wild adzuki beans, and are clearly distinct from Chinese wild populations. This finding supports the hypothesis that adzuki bean was first domesticated in Japan and later spread to China.

To resolve the contradiction between the two hypotheses, the research team conducted a more detailed analysis of nuclear genome sequences. The results suggested that the high genetic diversity observed in Chinese cultivated adzuki beans was caused by introgression from Chinese wild V. angularis. In other words, adzuki bean was first domesticated from wild V. angularis var. nipponensis in Japan, then spread to China, where it subsequently hybridized with local wild populations, resulting in genetically diverse cultivated varieties. These findings are consistent with recent archaeological evidence. This study serves as a valuable example of how detailed genomic analysis can unravel complex crop evolutionary histories and provide useful information about domestication origins, which can be leveraged in breeding programs and the use of genetic resources.

This study was published in Science on May 29, 2025.