| Domesticated soybean, Glycine max, is an important world commodity accounting for 68% of world protein meal and 56% of world oilseed production. Soybean cyst nematode (SCN, Heterodera glycines) causes billions of dollars of economic losses annually and is considered the most economically damaging soybean disease. A previously identified locus, termed Rhg1, has a significant impact on SCN resistance, and is currently deployed in most commercially utilized SCN resistant soybean cultivars. The mechanism underlying Rhg1-mediated SCN resistance has remained elusive. This dissertation focuses on functional and computational approaches to define and characterize the genes underlying Rhg1-mediated SCN resistance.;We identified three tightly clustered genes at the Rhg1 locus that each contributes to SCN resistance. We further discovered that the DNA encoding these genes is present in multiple copies in SCN-resistant parents, and this causes elevated expression of the genes. Two of the identified genes, Glyma18g02580 and Glyma18g02610, did not carry amino acid polymorphisms between resistant and susceptible Rhg1 haplotypes. The third gene, Glyma18g02590, encoding a predicted α-SNAP protein did contain amino acid polymorphisms relative to the reference soybean genome Williams 82, which is SCN-susceptible. Transgenic expression of any one of these three genes in soybean roots did not discernibly improve resistance, but simultaneous expression of all three genes did enhance SCN resistance. To further explore the evolution and diversity of Rhg1, we used whole genome sequencing, fiber-FISH and related techniques to examine the structural and nucleic acid variation in the genomes of four-dozen soybean accessions. We discovered that the Rhg1 locus is commonly arranged in a single copy in all tested SCN susceptible germplasm, but is present as either a low-copy or high-copy type in SCN-resistant germplasm. These repeat copy classes are also distinguishable by expression level differences, and the presence of related but distinct alleles of the previously identified α-SNAP protein. We also identified differential DNA-methylation at the locus between SCN-resistance and susceptible lines. The identification of the genes that control Rhg1-mediated resistance, and an understanding of their evolution and diversity, should foster efforts to improve the disease resistance that is available to reduce the deleterious impacts of SCN. |
