High-Resolution Genomic Resources for Trait Mapping and Precision Breeding for Adzuki Bean (Vigna angularis)

Adzuki bean (Vigna angularis), a globally important legume crop, faces breeding bottlenecks due to limited genomic resources and an insufficient understanding of its genetic basis for key traits, which constrains the efficient utilization of its genetic diversity in breeding programs. To address this, a high-quality genome assembly is developed for the elite cultivar ZH20 and a comprehensive genetic variation map is constructed by resequencing of 546 diverse adzuki bean accessions. Genomic and phenotypic analyses of this diversity panel reveal distinct population structures and identify genomic variations underlying key agronomic traits, including seed coat color, size, shape, and flowering time, linked to adaptation and selection. This analysis pinpointed 251 loci significantly associated with eight key agronomic traits, highlighting promising candidate genes, such as ANKRD50 and NAC73 for seed morphology, ANR1 for flavonoid content, and NPF5.4 for flowering time. Furthermore, comparative genomics provides insights into domestication processes. These datasets are integrated to develop AdzukiBeanAtlas (https://www.cgris.net/AdzukiBeanAtlas), a versatile toolkit to facilitate breeding strategies. These resources provide a valuable foundation for understanding adzuki bean diversity, while AdzukiBeanAtlas serves as a user-friendly, cross-platform tool for molecular marker development, helping to accelerate future breeding programs.