Diversity of the Soybean SCN Resistance Locus Rhg1

Copy number variation (CNV) and tandem duplication at the soybean cyst nematode (SCN) resistance locus Rhg1 in soybean [Glycine max (L.) Merr.] were previously discovered. In this study, 110 soybean plant introductions (PIs) with SCN resistance reactions were selected and analyzed for their haplotype at the Rhg1 locus. Sixty two PIs carrying the same duplicated sequence at Rhg1 were used for estimation and validation of copy number at the locus. Genomic qPCR and TaqMan assay were used to estimate polymorphism in the duplicated block. One of the Rhg1 genes in the duplicated region was chosen for estimating copy number using qPCR. SNPs located in intergenic sequence in the duplicated region were used for TaqMan assays. These assays indicate a wide distribution (up to 10) of copy number of the tandemly duplicated block. To validate/confirm copy number of the block, whole genome shotgun sequencing (WGS) of selected soybeans was conducted. Using WGS, diverse CNV in soybean and wild Glycine soja was validated. Haplotype phasing methods using SNPs generated from WGS are currently being used to further define this duplicated region at Rhg1.