Evolution and Selection of Soybean Nematode Resistance Locus

We have shown that theRhg1 locus is a multi-gene repeat of non-canonical resistance genes in strict tandem formation. Using whole-genome sequencing and PCR assays, we show that different soybean germplasm accessions contain one to 10 copies of a tandemly duplicated unit of 31.2 kb. The individual repeated units were classified into four types by using haplotype phasing techniques, with some Rhg1 loci carrying up to three different types of repeat unit. The Rhg1 locus shows strong signatures of selection and significant linkage disequilibrium in the genome around the boundaries of the repeat within a large population of over 15,000 accessions. The regions surrounding the repeat show indications of non-neutral evolution and high genetic variability in populations from different geographic locations. The linkage disequilibrium around the Rhg1 repeat in accessions carrying different repeat types allows the Rhg1 genotype of germplasm accessions to be inferred using large public SNP array datasets, revealing over 800 new potential sources of resistance.