A Roadmap for Gain of Function Copy Number Variants in the Soybean Genome

Gene copy number variation (CNV) has recently emerged as a key genetic mechanism underlying several important QTL in crop species.  We screened over 52,000 gene models in soybean for deletions and duplications among the 41 parental accessions that are being used to develop the soybean Nested Association Mapping population.  Array hybridization and whole genome resequencing methods were used as complementary technologies to identify CNV in upwards of 1,500 genes.  These variants occurred throughout the genome, but were enriched for families of biotic defense response genes.  Increases in gene copy number, as previously described at the Rhg1 locus, account for approximately one fourth of the events and appear to be under purifying selection.  This first generation roadmap of soybean CNV presents a target list of genes potentially responsible for disease resistance and other traits associated with environmental factors.