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Genetic structure and diversity of cultivated soybean (Glycine max (L.) Merr.) landraces in China

Theoretical and Applied Genetics volume 117, pages 857–871 (2008)Cite this article

Abstract

The Chinese genebank contains 23,587 soybean landraces collected from 29 provinces. In this study, a representative collection of 1,863 landraces were assessed for genetic diversity and genetic differentiation in order to provide useful information for effective management and utilization. A total of 1,160 SSR alleles at 59 SSR loci were detected including 97 unique and 485 low-frequency alleles, which indicated great richness and uniqueness of genetic variation in this core collection. Seven clusters were inferred by STRUCTURE analysis, which is in good agreement with a neighbor-joining tree. The cluster subdivision was also supported by highly significant pairwise F st values and was generally in accordance with differences in planting area and sowing season. The cluster HSuM, which contains accessions collected from the region between 32.0 and 40.5°N, 105.4 and 122.2°E along the central and downstream parts of the Yellow River, was the most genetically diverse of the seven clusters. This provides the first molecular evidence for the hypotheses that the origin of cultivated soybean is the Yellow River region. A high proportion (95.1%) of pairs of alleles from different loci was in LD in the complete dataset. This was mostly due to overall population structure, since the number of locus pairs in LD was reduced sharply within each of the clusters compared to the complete dataset. This shows that population structure needs to be accounted for in association studies conducted within this collection. The low value of LD within the clusters can be seen as evidence that much of the recombination events in the past have been maintained in soybean, fixed in homozygous self-fertilizing landraces.

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Acknowledgments

This research was supported by the State Key Basic Research and Development Plan of China (973) (No.2004CB117203), National Key Technologies R&D Program in the 11th Five-Year Plan (No.2006BAD13B05), the National Natural Science Foundation of China (No.30490251 and 30471096) and the Academy and Institute Foundation for Basic Scientific Research in Institute of Crop Science, Chinese Academy of Agricultural Sciences. Dr. Wim J.M. Koopman (Plant Research International, Wageningen UR, The Netherlands) is thanked for a batch program for NTSYS, and Dr. Alain Charcosset and two anonymous reviewers for useful suggestions.

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  1. The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI)/Key Lab of Germplasm and Biotechnology (MOA), Institute of Crop Science, Chinese Academy of Agricultural Sciences, 100081, Beijing, People’s Republic of China

    Yinghui Li, Rongxia Guan, Zhangxiong Liu, Yansong Ma, Lixia Wang, Linhai Li, Fanyun Lin, Weijiang Luan, Zhe Yan, Yuan Guan, Li Zhu, Xuecheng Ning, Wei Li, Rihua Piao, Yanhua Cui, Zhongmei Yu, Min Guan, Ruzhen Chang & Lijuan Qiu

  2. Department of Crop, Soil, and Environmental Sciences, University of Arkansas, Fayetteville, AR, 72701, USA

    Pengyin Chen, Anfu Hou, Ainong Shi, Bo Zhang & Shenlong Zhu

  3. Plant Research International, Wageningen UR, P.O. Box 16, 6700 AA, Wageningen, The Netherlands

    Marinus. J. M. Smulders

  4. Soybean Research Institute of Heilongjiang Academy of Agricultural Sciences, 150086, Harbin, People’s Republic of China

    Yansong Ma

  5. Northwest A & F University, 712100, YangLing, People’s Republic of China

    Linhai Li, Fanyun Lin & Weijiang Luan

  6. Xinjiang Agricultural University, 830046, Urumqi, People’s Republic of China

    Zhe Yan, Yuan Guan, Li Zhu & Xuecheng Ning

  7. Soybean Research Institute, Key Laboratory of Soybean Biology, Ministry of Education, Northeast Agricultural University, 150030, Harbin, People’s Republic of China

    Wei Li, Rihua Piao, Yanhua Cui, Zhongmei Yu & Min Guan

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Correspondence to Lijuan Qiu.

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Communicated by A. Charcosset.

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122_2008_825_MOESM1_ESM.doc

Table S1. Description of the 59 SSR loci, population-genetic statistics for the complete dataset, and most frequent alleles in each of the seven model-based clusters (DOC 253 kb)

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Li, Y., Guan, R., Liu, Z. et al. Genetic structure and diversity of cultivated soybean (Glycine max (L.) Merr.) landraces in China. Theor Appl Genet 117, 857–871 (2008). https://doi.org/10.1007/s00122-008-0825-0

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Keywords

  • Linkage Disequilibrium
  • Simple Sequence Repeat Marker
  • Allelic Richness
  • Rare Allele
  • Core Collection