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., 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 ies2xpeh..., , # 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 ...,

赤小豆（Adzuki bean）是代表东亚饮食文化的重要豆科作物，但其驯化起源始终存在争议。本研究利用亚洲范围内约700份野生与栽培种质材料，证实最初的驯化事件发生于距今3000至5000年前的绳文时代日本中部地区，随后其分布范围扩张至中国，并与中国野生种群发生二次杂交。我们对与种皮颜色演化相关的关键基因进行了定位、验证并确定其演化时间，其中VaPAP1与黑色种皮的丢失相关，VaANR1与红色种皮的获得相关。与种皮颜色相关的突变体的频率上升，显著早于保证产量的豆荚不落粒表型的出现以及野生与栽培种群的分化。尽管VaANR1与种子透性存在中等程度的关联，本研究结果挑战了驯化的渐进式演化观点，并支持早期弱选择的考古植物学证据。

本研究共收集了分布于亚洲的327份野生与栽培赤小豆种质材料，这些材料取自日本国立农业与食品研究开发机构（National Agriculture and Food Research Organization, NARO）以及中国台湾地区台湾农业研究所种质资源中心。对这327份材料进行了Illumina全基因组测序（whole genome sequencing, WGS），并将测序数据比对至参考基因组Shumari或Miyagi。使用GEMMA软件对该数据集进行全基因组关联分析（genome-wide association study, GWAS）。在选择扫荡扫描分析中，我们从数据集中筛选得到纯合种群JP_W、JP_C及CN_Cn，并使用包含非变异位点与双等位基因位点的VCF文件开展分析。使用PIXY软件以10kb为窗口大小计算核苷酸多样性（π）与群体分化指数（FST）值。在XP-CLR分析中，使用xpclr脚本对数据集进行处理，窗口大小与步长分别设置为10kb与5kb。在XP-EHH分析中，首先使用R包rehh为各目标种群计算整合单倍型得分（integrated haplotype score, iHS），窗口大小设置为10kb。[原文截断] 数据来源：《赤小豆单次驯化起源于日本及驯化基因演化》

https://doi.org/10.5061/dryad.8w9ghx3xv

## 数据与文件结构说明
本数据集包含赤小豆红色种皮、斑驳黑色种皮以及种子透水性性状的全基因组关联分析（GWAS）结果（关联分析数据）。基因型数据分别取自比对至栽培品种参考基因组Shumari与野生种质参考基因组Miyagi的测序数据。选择扫荡扫描通过基因组水平的π比值、FST、XP-EHH及XP-CLR值分析完成。

### 文件与变量
#### 文件：adzuki_GWAS_data.zip
**描述：**
1. mapped_to_Miyagi_mottled_black_seedcoat.maf_0.05.assoc.txt：斑驳黑色种皮性状的GWAS分析结果，基因型数据取自野生赤小豆Miyagi的基因组比对结果。
2. mapped_to_Miyagi_red_seedcoat.maf_0.05.assoc.txt：[原文截断]