DOI: 10.5061/dryad.8w9ghx3xv
title: Data from: A single domestication origin of adzuki bean in Japan and the evolution of domestication genes

description: 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.
description: 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.
 <em>Pi</em>  and <em>F<sub>ST
 </sub></em>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.
description: # Data from: A single domestication origin of adzuki bean in Japan and the
 evolution of domestication genes
 [https://doi.org/10.5061/dryad.8w9ghx3xv](https://doi.org/10.5061/dryad.8w9ghx3xv) ## Description of the data and file structure These data provide GWAS results (association data) for the red seed coat color, the mottled black seed coat color, and the seed water permeability traits of the adzuki bean. The genotypic data was used from the sequencing data mapped to the cultivar, Shumari, and the wild accession, Miyagi, respectively. The selection sweep scanning was performed by the analyses of genome-scale 𝜋 ratio, *FST*, XP-EHH, and XP-CLR values. ### Files and variables #### File: adzuki\_GWAS\_data.zip **Description:**  1. mapped_to_Miyagi_mottled_black_seedcoat.maf_0.05.assoc.txt: GWAS results for the mottled black seed coat color. Genotypic data are from the mapping results of the wild adzuki, Miyagi. 2. mapped_to_Miyagi_red_seedcoat.maf_0.05.assoc.txt: GWAS results for the red seed coat color. Genotypic data are from the mapping results of the wild adzuki, Miyagi. 3. mapped_to_Miyagi_water_permeability.maf_0.05.assoc.txt: GWAS results for the water permeability of seeds. Genotypic data are from the mapping results of the wild adzuki, Miyagi. 4. mapped_to_Shumari_mottled_black_seedcoat.maf_0.05.assoc.txt: GWAS results for the mottled black seed coat color. Genotypic data are from the mapping results of the cultivated adzuki, Shumari. 5. mapped_to_Shumari_red_seedcoat.maf_0.05.assoc.txt: GWAS results for the red seed coat color. Genotypic data are from the mapping results of the cultivated adzuki, Shumari. 6. mapped_to_Shumari_water_permeability.maf_0.05.assoc.txt: GWAS results for the water permeability of seeds. Genotypic data are from the mapping results of the cultivated adzuki, Shumari. These GWAS files contain the following columns: 1. chr -- Chromosome number where the SNP is located 2. rs --  SNP identifier (if available, otherwise it may be missing or a dot ".") 3. pos -- Physical position of the SNP on the chromosome (in base pairs) 4. n-miss -- Number of missing genotype calls for this SNP 5. allele1 -- The minor allele used for association testing 6. allele0 -- The reference or major allele 7. af -- Allele frequency of allele1 in the sample population 8. beta -- Effect size of allele1 representing the estimated change in phenotype per allele 9. se -- Standard error of the beta estimate 10. logl_h1 -- Log-likelihood of the alternative hypothesis (H1), which assumes a genetic effect 11. l_remle -- Log-likelihood from the restricted maximum likelihood (REML) estimation 12. l_mle -- Log-likelihood from the maximum likelihood estimation (MLE) 13. p_wald -- P-value from the Wald test, used to assess the significance of the SNP-phenotype association 14. pval -- P-value from the likelihood ratio test (LRT) for SNP significance 15. p_score -- P-value from the score test for SNP significance #### File: selection\_sweep\_scanning.xlsx **Description:** 1. pi_ratio: 𝜋 ratio of the genome between JP_W and North_C (JP_C, CN_Cn) 2. Fst: *FST* values of the genome between JP_W and North_C (JP_C, CN_Cn) 3. XP-EHH: XP-EHH values of the genome between JP_W and North_C (JP_C, CN_Cn) 4. XP-CLR: XP-CLR values of the genome between JP_W and North_C (JP_C, CN_Cn) These datasets contain the following columns: 1. Population 1 -- the first testing population name 2. Population 2 -- the second testing population name 3. Chromosome -- chromosome ID 4. Position_start -- starting nucleotide position of the chromosome 5. Position_end -- the end postion of the nucleotides in the chromosome 6. 𝜋 ratio -- 𝜋 values from Population 1 divided by 𝜋 values from Population 2 7. *FST --* *FST* values of the region 8. XP-EHH -- XP-EHH values of the region 9. XP-CLR -- XP-CLR values of the region