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Uncovering signatures of selection in the soybean genome using SSR diversity near QTLs of agronomic importance

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Abstract

The cultivated soybean [Glycine max (L.) Merr.] is widely considered to descend from the wild soybean (G. soja Sieb. & Zucc.). This study was designed to evaluate the genetic variability and differentiation between G. soja and G. max, and to detect signatures of the selection that may have occurred during the domestication process from G. soja to G. max. A total of 192 G. soja accessions and 104 G. max accessions were genotyped using eight selected simple sequence repeat (SSR) markers assigned to three SSR groups. Four SSRs in group A were not located near any known QTL. Three SSRs in group B were associated with seed protein content, and an SSR in group C was associated with resistance to Sclerotinia stem rot. The number of alleles per locus and the level of genetic variability in G. soja were higher than those in G. max. A total of 122 out of 125 alleles were present in G. soja, but only 59 alleles were detected in G. max. The average gene diversity was 0.74 in G. soja and 0.64 in G. max. Four SSRs near QTLs of agronomic importance showed strong genetic differentiation and shift change in high frequency alleles in groups B and C between G. soja and G. max, revealing selection signatures that may reflect the domestication events and recent selective breeding. With reduced diversity in G. max, some undomesticated genes from G. soja should be prime candidates for introgression to increase the pool of diversity in G. max.

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Author notes

  1. Tae-Hwan Jun

    Present address: Dept. of Entomology, Ohio State University, 1680 Madison Ave., Wooster, OH, 44691, USA

Authors and Affiliations

  1. Department of Plant Science and Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Korea

    Tae-Hwan Jun, Kyujung Van, Moon Young Kim & Suk-Ha Lee

  2. National Institute of Biological Resources, Incheon, 404-708, Korea

    Myounghai Kwak

  3. Plant Genomic and Breeding Research Institute, Seoul National University, Seoul, 151-921, Korea

    Suk-Ha Lee

Authors
  1. Tae-Hwan Jun
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  2. Kyujung Van
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  3. Moon Young Kim
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  4. Myounghai Kwak
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  5. Suk-Ha Lee
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Correspondence to Suk-Ha Lee.

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Jun, TH., Van, K., Kim, M.Y. et al. Uncovering signatures of selection in the soybean genome using SSR diversity near QTLs of agronomic importance. Genes Genom 33, 391–397 (2011). https://doi.org/10.1007/s13258-010-0159-6

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  • DOI: https://doi.org/10.1007/s13258-010-0159-6

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