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Title: A roadmap for functional structural variants in the soybean genome

item ANDERSON, JUSTIN - University Of Minnesota
item KANTAR, MICHAEL - University Of Minnesota
item KONO, THOMAS - University Of Minnesota
item FU, FENGLI - University Of Minnesota
item STEC, ADRIAN - University Of Minnesota
item Song, Qijian
item Cregan, Perry
item SPECHT, JAMES - University Of Minnesota
item DIERS, BRIAN - University Of Illinois
item Cannon, Steven
item MCHALE, LEAH - The Ohio State University
item STUPAR, ROBERT - University Of Minnesota

Submitted to: Genes, Genomes, Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 5/20/2014
Publication Date: 5/22/2014
Citation: 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. Genes, Genomes, Genetics. DOI:10.1534/g3.114.011551.

Interpretive Summary: Variation in the DNA content of genes among different plant accessions of the same species has recently been shown to influence the expression of traits in crop plants. In this study the whole genome DNA sequences of 41 diverse soybean accessions were compared and DNA sequence variation was observed in 1,528 of the over 53,000 soybean genes. In many cases genes that were associated with resistance to disease showed increased copy numbers. Approximately, one quarter of the genes with increased copy numbers were genes controlling resistance to disease. This information will be useful to plant geneticists who want to use DNA sequence data to find accessions with increased copy number of genes that control a disease for which they are looking for greater resistance.

Technical 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 accessions serving as parents in a soybean nested association mapping population for deletions and duplications in over 53,000 gene models. Array hybridization and whole genome resequencing methods were used as complementary technologies to identify SV in 1,528 genes, or approximately 2.8% of the soybean gene models. Though SV occurs throughout the genome, SV enrichment was noted in families of biotic defense response genes. Among accessions, SV was nearly eight-fold less frequent for gene models that have retained paralogs since the last whole genome duplication event, compared to 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 initial assessment of soybean SV occurrence presents a target list of genes potentially responsible for rapidly evolving and/or adaptive traits.