Targeted Genome Enrichment and Next Generation Sequencing Allow the Identification of the Rhg4 Gene, GmSHMT, Conferring Resistance to Soybean Cyst Nematode within Soybean Hg-Type Indictor Lines

The identification of the soybean (Glycine max (L.) Merr.) genes conferring resistance to soybean cyst nematode (SCN), Heterodera glycines Ichinohe is very important but highly challenging step to the management of the SCN disease. We previously identified the soybean Rhg4 gene, serine hydroxymethyltransferase (GmSHMT), conferring resistance to SCN on chromosome 8, by positional cloning, fairly labor intensive and very time consuming method. To explore a simple and reliable alternative method for the identification of soybean quantitative trait loci controlling SCN resistance and to collect more genomic information about the Rhg4 locus among soybean lines, we used targeted genome enrichment and next generation sequencing to identify genes at the Rhg4 locus that underlie resistance to SCN, following the sequencing of a 300Kb chromosomal regions harboring the Rhg4 gene (about 150Kb upstream and downstream GmSHMT). The comparison of SNPs and InDels within the  300Kb Rhg4 genomic DNA sequences of four soybean lines including SCN susceptible line Essex and SCN resistant lines Forrest, Peking and PI88788, identified 1060 SNPs and InDels and showed that the identified GmSHMT in our previous studies is the sole candidate gene conferring resistance to SCN at the Rhg4 locus; Two specific SNPs, the C156824G and A157600T, both lead to the amino acid changes of the predicted GmSHMT protein, selected from the 10 SNPs and 1 insertion strongly associated with the resistance at the Rhg4 locus. The data indicates that targeted chromosomal enrichment and next generation sequencing is a reliable and simple method for the identification of soybean SCN resistance genes.