Title

Resequencing 302 wild and cultivated accessions identifies genes related to domestication and improvement in soybean

Authors

Zhengkui Zhou, Institute of Genetics and Developmental Biology Chinese Academy of Sciences
Yu Jiang, Kunming Institute of Zoology Chinese Academy of Sciences
Zheng Wang, Institute of Genetics and Developmental Biology Chinese Academy of Sciences
Zhiheng Gou, Kunming Institute of Zoology Chinese Academy of Sciences
Jun Lyu, Kunming Institute of Zoology Chinese Academy of Sciences
Weiyu Li, Institute of Genetics and Developmental Biology Chinese Academy of Sciences
Yanjun Yu, Institute of Microbiology Chinese Academy of Sciences
Liping Shu, Kunming Institute of Zoology Chinese Academy of Sciences
Yingjun Zhao, Kunming Institute of Zoology Chinese Academy of Sciences
Yanming Ma, Institute of Genetics and Developmental Biology Chinese Academy of Sciences
Chao Fang, Institute of Genetics and Developmental Biology Chinese Academy of Sciences
Yanting Shen, Institute of Genetics and Developmental Biology Chinese Academy of Sciences
Tengfei Liu, Institute of Genetics and Developmental Biology Chinese Academy of Sciences
Congcong Li, Institute of Genetics and Developmental Biology Chinese Academy of Sciences
Qing Li, Institute of Genetics and Developmental Biology Chinese Academy of Sciences
Mian Wu, Institute of Genetics and Developmental Biology Chinese Academy of Sciences
Min Wang, Institute of Genetics and Developmental Biology Chinese Academy of Sciences
Yunshuai Wu, Institute of Genetics and Developmental Biology Chinese Academy of Sciences
Yang Dong, Kunming Institute of Zoology Chinese Academy of Sciences
Wenting Wan, Kunming Institute of Zoology Chinese Academy of Sciences
Xiao Wang, Kunming Institute of Zoology Chinese Academy of Sciences
Zhaoli Ding, Kunming Institute of Zoology Chinese Academy of Sciences
Yuedong Gao, Kunming Institute of Zoology Chinese Academy of Sciences
Hui Xiang, Kunming Institute of Zoology Chinese Academy of Sciences
Baoge Zhu, Institute of Genetics and Developmental Biology Chinese Academy of Sciences
Suk Ha Lee, Seoul National University
Wen Wang, Kunming Institute of Zoology Chinese Academy of Sciences
Zhixi Tian, Institute of Genetics and Developmental Biology Chinese Academy of Sciences

Abstract

Understanding soybean (Glycine max) domestication and improvement at a genetic level is important to inform future efforts to further improve a crop that provides the world's main source of oilseed. We detect 230 selective sweeps and 162 selected copy number variants by analysis of 302 resequenced wild, landrace and improved soybean accessions at >11× depth. A genome-wide association study using these new sequences reveals associations between 10 selected regions and 9 domestication or improvement traits, and identifies 13 previously uncharacterized loci for agronomic traits including oil content, plant height and pubescence form. Combined with previous quantitative trait loci (QTL) information, we find that, of the 230 selected regions, 96 correlate with reported oil QTLs and 21 contain fatty acid biosynthesis genes. Moreover, we observe that some traits and loci are associated with geographical regions, which shows that soybean populations are structured geographically. This study provides resources for genomics-enabled improvements in soybean breeding.

Publication Title

Nature Biotechnology

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