The prevalence of deleterious mutations during the domestication and improvement of soybean

Shichao Sun, Yumin Wang, He Wei, David E. Hufnagel, Ya Wang, Shiyu Guo, Yinghui Li, Li Wang, Li juan Qiu

Research output: Contribution to journalArticlepeer-review


Soybean (Glycine max L.) is a protein and oil crop grown worldwide. Its fitness may be reduced by deleterious mutations, whose identification and purging is desirable for crop breeding. In the published whole-genome re-sequenced data of 2214 soybean accessions, including 221 wild soybean, 1132 landrace cultivars and 861 improved soybean lines, we identified 115,275 deleterious single-nucleotide polymorphisms (SNPs). Numbers of deleterious alleles increased from wild soybeans to landraces and decreased from landraces to modern improved lines. Genes in selective-sweep regions showed fewer deleterious mutations than the remaining genes. Deleterious mutations explained 4.3%–48% more phenotypic variation than randomly selected SNPs for resistance to soybean cyst nematode race 2 (SCN2), soybean cyst nematode race 3 (SCN3) and soybean mosaic virus race 3 (SMV3). These findings illustrate how mutation load has shifted during soybean domestication, expansion and improvement and provide candidate sites for breeding out deleterious mutations in soybean by genome editing and/or conventional breeding focused on the selection of progeny with fewer deleterious alleles.

Original languageEnglish
Pages (from-to)523-530
Number of pages8
JournalCrop Journal
Issue number2
StatePublished - Apr 2023
Externally publishedYes

Bibliographical note

Publisher Copyright:
© 2022 Crop Science Society of China and Institute of Crop Science, CAAS


  • BAD_Mutations
  • Deleterious mutations
  • Domestication cost
  • Expansion load
  • Soybean cyst nematode

ASJC Scopus subject areas

  • Agronomy and Crop Science
  • Plant Science


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