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

Adzuki is a significant legume representing East Asian culinary culture, yet the origin of its domestication remains debated. Using ~700 wild and cultigen accessions across Asia, we showed that the initial domestication happened 3-5 kya in central Japan during the Jomon period, followed by a range expansion into China and secondary hybridization with the Chinese wild population. We mapped, validated, and dated key genes associated with seed coat color evolution (VaPAP1 for loss of black and VaANR1 for gain of red colors). The frequency increase of seed-color-associated mutants substantially predated that of the yield-ensuring pod-non-shattering phenotype and the wild-cultigen divergence. Despite the moderate connections between VaANR1 and seed permeability, our results challenge the progressive view of domestication and support archaeobotanical evidence of early weak selection.

Methods
Adzuki accessions of 327 wild and cultigen accessions across Asia were collected/obtained from the National Agriculture and Food Research Organization (NARO) in Japan and the germplasm center of the Taiwan Agricultural Research Institute (TARI) in Taiwan. These 327 accessions were re-sequenced by illumina whole genome sequencing (WGS) and mapped to the reference genomes, Shumari or Miyagi. GWAS was performed using the dataset with GEMMA. For the selection-sweep scanning, pure populations (JP_W, JP_C, CN_Cn) were obtained from the dataset, and the vcf with the non-variant and bi-allele sites was used in the analyses. Pi  and FST values were calculated by PIXY with windows size = 10,000. For XP-CLR analysis, the dataset was analyzed using an xpclr script. The window size and step size were set to 10 kb and 5 kb, respectively. For XP-EHH analysis, the iHS values were first calculated for each population of interest by the R package, rehh. The window size was set to 10 kb. The ies2xpehh function was then used to calculate the XP-EHH values in each window between the two interested groups.