SNP Identification By Next Generation Sequencing of the Soybean Targeted Genome Segment for High-Throughput Selection of Soybean Cyst Nematode Resistance

Soybean cyst nematode (SCN) is the most economically devastating pathogen of soybean. Two resistant loci, Rhg1 on chromosome 18 and Rhg4 on chromosome 8 contribute to the main SCN race 3 resistance. Peking-type soybean requires both Rhg1 and Rhg4 alleles, whereas PI 88788-type soybean only requires Rhg1 allele, for their SCN resistance. For high-throughput selection of soybean cyst nematode resistance, we developed a targeted genome enrichment-next generation sequencing approach to identify the SNPs and InDels at rhg1 locus (about 300-kb) of the Peking-type soybeans (Peking and Forrest), PI 88788-type soybean (PI 88788), and SCN-susceptible soybean (Essex), compared to the Williams 82 reference genome sequence. The sequence comparison indicated 10 specific SNPs and InDels in the gene Glyma18g02590 (SNAP) at rhg1 locus between SCN-resistant and SCN–susceptible soybeans, which cause 9 amino acids changes of the predicted SNAP protein. Furthermore, of those 10 specific SNPs and InDels, 7 SNPs can be used to differentiate PI88788-type soybeans from Peking-type soybeans. Those results suggest that those specific SNPs and InDels identified at rhg1 locus may be used for high-throughput selection of soybean cyst nematode resistance, which is being conducted.