A roadmap for functional structural variants in the soybean genome

Justin E. Anderson, Michael B. Kantar, Thomas Y. Kono, Fengli Fu, Adrian O. Stec, Qijian Song, Perry B. Cregan, James E. Specht, Brian W. Diers, Steven B. Cannon, Leah K. McHale, Robert M. Stupar

Research output: Contribution to journalArticle

Abstract

Gene structural variation (SV) has recently emerged as a key genetic mechanism underlying several important phenotypic traits in crop species. We screened a panel of 41 soybean (Glycine max) accessions serving as parents in a soybean nested association mapping population for deletions and duplications in more than 53,000 gene models. Array hybridization and whole genome resequencing methods were used as complementary technologies to identify SV in 1528 genes, or approximately 2.8%, of the soybean gene models. Although SV occurs throughout the genome, SV enrichment was noted in families of biotic defense response genes. Among accessions, SV was nearly eightfold less frequent for gene models that have retained paralogs since the last whole genome duplication event, compared with genes that have not retained paralogs. Increases in gene copy number, similar to that described at the Rhg1 resistance locus, account for approximately one-fourth of the genic SV events. This assessment of soybean SV occurrence presents a target list of genes potentially responsible for rapidly evolving and/or adaptive traits.

Original languageEnglish (US)
Pages (from-to)1307-1318
Number of pages12
JournalG3: Genes, Genomes, Genetics
Volume4
Issue number7
DOIs
StatePublished - 2014

Keywords

  • CNV nested association mapping
  • Glycine max soybean structural variation

ASJC Scopus subject areas

  • Molecular Biology
  • Genetics
  • Genetics(clinical)

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  • Cite this

    Anderson, J. E., Kantar, M. B., Kono, T. Y., Fu, F., Stec, A. O., Song, Q., Cregan, P. B., Specht, J. E., Diers, B. W., Cannon, S. B., McHale, L. K., & Stupar, R. M. (2014). A roadmap for functional structural variants in the soybean genome. G3: Genes, Genomes, Genetics, 4(7), 1307-1318. https://doi.org/10.1534/g3.114.011551