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Resequencing of 31 wild and cultivated soybean genomes identifies patterns of genetic diversity and selection

Nature Genetics volume 42, pages 1053–1059 (2010)Cite this article

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An Addendum to this article was published on 29 March 2011

Abstract

We report a large-scale analysis of the patterns of genome-wide genetic variation in soybeans. We re-sequenced a total of 17 wild and 14 cultivated soybean genomes to an average of approximately ×5 depth and >90% coverage using the Illumina Genome Analyzer II platform. We compared the patterns of genetic variation between wild and cultivated soybeans and identified higher allelic diversity in wild soybeans. We identified a high level of linkage disequilibrium in the soybean genome, suggesting that marker-assisted breeding of soybean will be less challenging than map-based cloning. We report linkage disequilibrium block location and distribution, and we identified a set of 205,614 tag SNPs that may be useful for QTL mapping and association studies. The data here provide a valuable resource for the analysis of wild soybeans and to facilitate future breeding and quantitative trait analysis.

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Figure 1: Analysis of the phylogenetic relationship, population structure and LD decay of wild and cultivated soybeans.
Figure 2: Summary of resequencing data of 17 wild and 14 cultivated soybean accessions.
Figure 3: Patterns of LD blocks in two genomic regions.

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Acknowledgements

T. Han, X. Yan, H. Liao, B. Zhuang and Y.-K. Lau provided valuable advice, information and other aid. This work was partially supported by the Hong Kong RGC General Research Fund 468610 (to H.-M.L.), the Hong Kong UGC AoE Center for Plant and Agricultural Biotechnology Project AoE-B-07/09 and a special fund from the Resource Allocation Committee, The Chinese University of Hong Kong (to H.-M.L. and S.S.-M.S.). We also acknowledge the funding support from the National Natural Science Foundation of China (30725008), the Chinese 973 program (2007CB815703; 2007CB815705), Chinese Ministry of Agriculture (948 program), the Shenzhen Municipal Government of China and grants from Shenzhen Bureau of Science Technology & Information, China (ZYC200903240077A; CXB200903110066A). We thank L. Goodman for assistance in editing the manuscript.

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Author notes

  1. Hon-Ming Lam, Xun Xu, Xin Liu, Wenbin Chen and Guohua Yang: These authors contributed equally to this work.

Authors and Affiliations

  1. State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong

    Hon-Ming Lam, Xin Liu, Fuk-Ling Wong, Man-Wah Li, Guihua Shao & Samuel Sai-Ming Sun

  2. BGI-Shenzhen, Shenzhen, China

    Xun Xu, Xin Liu, Wenbin Chen, Guohua Yang, Weiming He, Nan Qin, Bo Wang, Jun Li, Min Jian, Jian Wang, Jun Wang & Gengyun Zhang

  3. Key Laboratory of Genomics, Ministry of Agriculture, BGI-Shenzhen, China

    Xun Xu & Gengyun Zhang

  4. Institute of Crop Sciences, The Chinese Academy of Agricultural Sciences, Beijing, China

    Guihua Shao

  5. Department of Biology, University of Copenhagen, Copenhagen, Denmark

    Jun Wang

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  1. Hon-Ming Lam
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Contributions

H.-M.L., G.Z., S.S.-M.S. and Jun Wang managed the project. H.-M.L., X.X., X.L, N.Q. and G.Y. designed the experiments and led the data analysis. W.H., B.W., J.L., W.C., M.J. and Jian Wang contributed to DNA sequencing and bioinformatics. F.-L.W., M.-W.L. and G.S. prepared samples and contributed to data analysis. H.-M.L., X.X. and X.L. wrote the manuscript.

Corresponding authors

Correspondence to Hon-Ming Lam, Jun Wang, Samuel Sai-Ming Sun or Gengyun Zhang.

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The authors declare no competing financial interests.

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Lam, HM., Xu, X., Liu, X. et al. Resequencing of 31 wild and cultivated soybean genomes identifies patterns of genetic diversity and selection. Nat Genet 42, 1053–1059 (2010). https://doi.org/10.1038/ng.715

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