Genetic mapping of soybean cyst nematode resistance and evaluation of resistant germplasm in soybean and pennycress
Authors:   , Basnet Pawan 
Published: February 2023

A single mode of genetic resistance derived from PI 88788 (rhg1-b) has dominated the $57.5 B US soybean market for almost three decades. The breakdown of resistance and selection of virulent nematode populations poses a significant threat to soybean production, estimated at a $1.5 billion loss annually. Breeding for soybean cyst nematode (SCN) resistant soybean to effectively combat the widespread increase in virulent SCN populations presents a significant challenge. Moreover, insufficient or an ambiguous understanding of SCN resistance loci effectiveness against different SCN populations is a major obstacle to developing SCN-resistant soybeans. Here, we aimed to understand the genetic resistance in a highly resistant but underutilized soybean accession, PI 90763. With recent reports demonstrating the significance of PI 90763 in managing SCN through resistance rotation with PI 88788 (rhg1-b), unraveling the genetics governing SCN resistance in PI 90763 is essential. To decode the genetic architecture of SCN resistance in PI 90763, we mapped SCN resistance quantitative trait loci (QTL) through linkage and biparental mapping analyses. QTL on chromosomes 11 and 18, corresponding to the rhg1-a and rhg2 loci, respectively, were determined to govern SCN resistance through an epistatic interaction. We fine-mapped the rhg2 gene to a 169 Kbp region and pinpointed GMSNAP11 as the strongest candidate gene. Screening different combinations of resistance genes/QTL, we further presented the evidence of strong SCN resistance imparted by rhg1-a and rhg2 genes and pinpointed their indispensable roles in resistance gene/QTL pyramiding for SCN management. In addition to the mapping study, we utilized resistant cultivars with unique resistance genes/QTL in continuous and rotated schemes to understand their effects on SCN population density and SCN virulence through a 3-year microplot field study. This study showed two rotated treatments: (1) rhg1-b+cqSCN-006/007+qSCN10 rotated with rhg1-a+rhg2+Rhg4 (PI 90763), and (2) rhg1-a+Rhg4 (PI 437654) rotated with rhg1-b+cqSCN-006/007+qSCN10 reduced SCN density without selecting nematode populations with a broader virulence. These findings show the importance of rotating rhg1-b+cqSCN-006/007+qSCN10 with the unique resistance genes rhg1-a+rhg2+Rhg4 from PI 90763 to combat the number one yield limiting pathogen of soybean. With SCN already being a single major pathogen in soybean, newer prospects of incorporating pennycress, an alternative SCN host, as an oilseed cover crop in the Midwest's corn-soybean production system could be counterproductive. Hence, we optimized several factors to standardize the SCN screening strategy in pennycress and utilized the optimized protocol to identify resistant and susceptible pennycress germplasm. We identified one common susceptible germplasm, eight resistant germplasm against HG type 1.2.5.7, and four resistant germplasm against HG type 7. The resistant pennycress germplasm identified here opens a new research avenue for unraveling SCN-pennycress interaction through molecular and genomic studies, which is crucial for developing SCN-resistant pennycress cultivars. Results from these studies lay the foundation for the next generation of SCN resistance breeding in soybean and pennycress to combat the number one pathogen of soybean.