Conservation Genetics

, Volume 12, Issue 5, pp 1145–1157 | Cite as

Genetic diversity and association mapping in a collection of selected Chinese soybean accessions based on SSR marker analysis

  • Ying-Hui Li
  • Marinus J. M. Smulders
  • Ru-Zhen Chang
  • Li-Juan QiuEmail author
Research Article


For broadening the narrow genetic base of modern soybean cultivars, 159 accessions were selected from the Chinese soybean collection which contained at least one of seven important agronomic traits: resistance to soybean cyst nematode (SCN) or soybean mosaic virus (SMV), tolerance to salt, cold, or drought, high seed oil content or high protein content. Genetic diversity evaluation using 55 microsatellite loci distributed across the genome indicated that a large amount of genetic diversity (0.806) and allelic variation (781) were conserved in this selected set, which captured 65.6% of the alleles present in Chinese soybean collection (1,863 accessions). On average, 9.4 rare alleles (frequency <5%) per locus were present, which were highly informative. Using model-based Bayesian clustering in STRUCTURE we distinguished four main clusters and a set of accessions with admixed ancestry. The four clusters reflected different geographic regions of origin of the accessions. Since the clusters were also clearly different with respect to the seven agronomic traits, the inferred population structure was introduced when association analysis was conducted. A total of 21 SSR markers on 16 chromosomes were identified as significantly (P < 0.01) associated with high oil content (6), high protein content (1), drought tolerance (5), SCN resistance (6) and SMV resistance (3). Twelve of these markers were located in or near previously identified quantitative trait loci (QTL). The results for both genetic relationship and trait-related markers will be useful for effective conservation and utilization of soybean germplasm.


Population structure Genetic diversity Association mapping Selected accessions Soybean 



This research was supported by National Key Technologies R&D Program in the 11th Five-Year Plan (No. 2006BAD13B05), the State Key Basic Research and Development Plan of China (973) (2010CB125900 and 2004CB117203), State High-tech (863) (No. 2006AA10A110, 2006AA10Z164), Crop Germplasm Conservation (NB08-2130315-(25-31)-06, NB08-2130315-(25-30)-06 and NB2010-2130135-25-05) the Academy and Institute Foundation for Basic Scientific Research in Institute of Crop Science, Chinese Academy of Agricultural Sciences.


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Copyright information

© Springer Science+Business Media B.V. 2011

Authors and Affiliations

  • Ying-Hui Li
    • 1
  • Marinus J. M. Smulders
    • 2
  • Ru-Zhen Chang
    • 1
  • Li-Juan Qiu
    • 1
    Email author
  1. 1.The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI)/Key Lab of Germplasm Utilization (MOA), Institute of Crop ScienceChinese Academy of Agricultural SciencesBeijingPeople’s Republic of China
  2. 2.Plant Research InternationalWageningen UR Plant BreedingWageningenThe Netherlands

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