The Search for Functional Structural Variants and Adaptive Traits in Soybean

Genic structural variation (SV), such as gene deletion or duplication, underlies several key phenotypic traits in crop species. We screened a panel of diverse soybean (Glycine max) accessions for deletions and duplications in more than 53,000 genes. Array hybridization and whole genome resequencing methods were used to identify SV in 1,528 genes, approximately 2.8% of the soybean gene models. These SV are distributed throughout the genome but were enriched for families of biotic defense response genes.  A number of agronomically important loci (e.g. Rhg1, Rsv1) related to soybean disease resistance show interesting patterns of SV.  Similar patterns can also be found in some genes related to abiotic stress. Approximately 60% of the soybean genes have retained a syntenic paralog since the most recent whole genome duplication event. We found nearly eightfold fewer SV associated with genes retaining a paralog compared with genes that have not retained a paralog. This assessment of soybean SV occurrence identifies genes potentially responsible for rapidly evolving and/or adaptive traits.