Identification of loci controlling adaptation in Chinese soya bean landraces via a combination of conventional and bioclimatic GWAS

Ying hui Li, Delin Li, Yong qing Jiao, James C. Schnable, Yan fei Li, Hui hui Li, Huai zhu Chen, Hui long Hong, Ting Zhang, Bin Liu, Zhang xiong Liu, Qing bo You, Yu Tian, Yong Guo, Rong xia Guan, Li juan Zhang, Ru zhen Chang, Zhiwu Zhang, Jochen Reif, Xin an ZhouPatrick S. Schnable, Li juan Qiu

Research output: Contribution to journalArticlepeer-review


Landraces often contain genetic diversity that has been lost in modern cultivars, including alleles that confer enhanced local adaptation. To comprehensively identify loci associated with adaptive traits in soya bean landraces, for example flowering time, a population of 1938 diverse landraces and 97 accessions of the wild progenitor of cultivated soya bean, Glycine soja was genotyped using tGBS®. Based on 99 085 high-quality SNPs, landraces were classified into three sub-populations which exhibit geographical genetic differentiation. Clustering was inferred from STRUCTURE, principal component analyses and neighbour-joining tree analyses. Using phenotypic data collected at two locations separated by 10 degrees of latitude, 17 trait-associated SNPs (TASs) for flowering time were identified, including a stable locus Chr12:5914898 and previously undetected candidate QTL/genes for flowering time in the vicinity of the previously cloned flowering genes, E1 and E2. Using passport data associated with the collection sites of the landraces, 27 SNPs associated with adaptation to three bioclimatic variables (temperature, daylength, and precipitation) were identified. A series of candidate flowering genes were detected within linkage disequilibrium (LD) blocks surrounding 12 bioclimatic TASs. Nine of these TASs exhibit significant differences in flowering time between alleles within one or more of the three individual sub-populations. Signals of selection during domestication and/or subsequent landrace diversification and adaptation were detected at 38 of the 44 flowering and bioclimatic TASs. Hence, this study lays the groundwork to begin breeding for novel environments predicted to arise following global climate change.

Original languageEnglish
Pages (from-to)389-401
Number of pages13
JournalPlant Biotechnology Journal
Issue number2
StatePublished - 1 Feb 2020
Externally publishedYes

Bibliographical note

Publisher Copyright:
© 2019 The Authors. Plant Biotechnology Journal published by Society for Experimental Biology and The Association of Applied Biologists and John Wiley & Sons Ltd.


  • adaptation
  • associated SNP
  • bioclimatic variable
  • flowering time
  • soya bean landrace

ASJC Scopus subject areas

  • Biotechnology
  • Agronomy and Crop Science
  • Plant Science


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