De novo assembly of soybean wild relatives for pan-genome analysis of diversity and agronomic traits

Ying Hui Li, Guangyu Zhou, Jianxin Ma, Wenkai Jiang, Long Guo Jin, Zhouhao Zhang, Yong Guo, Jinbo Zhang, Yi Sui, Liangtao Zheng, Shan Shan Zhang, Qiyang Zuo, Xue Hui Shi, Yan Fei Li, Wan Ke Zhang, Yiyao Hu, Guanyi Kong, Hui Long Hong, Bing Tan, Jian SongZhang Xiong Liu, Yaoshen Wang, Hang Ruan, Carol K.L. Yeung, Jian Liu, Hailong Wang, Li Juan Zhang, Rong Xia Guan, Ke Jing Wang, Wen Bin Li, Shou Yi Chen, Ru Zhen Chang, Zhi Jiang, Scott A. Jackson, Ruiqiang Li, Li Juan Qiu

Research output: Contribution to journalArticlepeer-review


Wild relatives of crops are an important source of genetic diversity for agriculture, but their gene repertoire remains largely unexplored. We report the establishment and analysis of a pan-genome of Glycine soja, the wild relative of cultivated soybean Glycine max, by sequencing and de novo assembly of seven phylogenetically and geographically representative accessions. Intergenomic comparisons identified lineage-specific genes and genes with copy number variation or large-effect mutations, some of which show evidence of positive selection and may contribute to variation of agronomic traits such as biotic resistance, seed composition, flowering and maturity time, organ size and final biomass. Approximately 80% of the pan-genome was present in all seven accessions (core), whereas the rest was dispensable and exhibited greater variation than the core genome, perhaps reflecting a role in adaptation to diverse environments. This work will facilitate the harnessing of untapped genetic diversity from wild soybean for enhancement of elite cultivars.

Original languageEnglish
Pages (from-to)1045-1052
Number of pages8
JournalNature Biotechnology
Issue number10
StatePublished - 1 Oct 2014
Externally publishedYes

ASJC Scopus subject areas

  • Biotechnology
  • Bioengineering
  • Applied Microbiology and Biotechnology
  • Molecular Medicine
  • Biomedical Engineering


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