Identification of Novel Genetic Resources for Broad-Based Soybean Cyst Nematode Resistance Independent of Conventional Loci

Soybean cyst nematode (SCN, Heterodera glycines Ichinohe) is the most economically damaging soil-borne pathogen affecting soybean, causing significant yield losses in the United States and worldwide. Current commercial cultivars rely heavily on a limited genetic resistance base, primarily from PI 88788 and Peking, which has led to the emergence of virulent SCN populations that threaten the durability of this resistance. To address this challenge, we performed a comprehensive allelic analysis of key resistance loci (rhg1, Rhg4, qSCN10 (O), and qSCN18 (G)) using whole-genome resequencing data from 1,110 diverse soybean accessions. Our study identified novel non-synonymous SNPs in 27 accessions, including PI 602492 (Glycine max) and two Glycine soja accessions (PI 522226, PI 522228), which display strong to moderate resistance across multiple SCN HG types (Heterodera glycines) or SCN races. Additionally, we identified two G. soja accessions, PI 507380B and PI 507752 that exhibited strong resistance to HG type 2.5.7 (Race 5). Notably, accessions with genotypes similar to these five showed variable resistance phenotypes, suggesting the presence of additional, yet unidentified, genes contributing to broad-based SCN resistance. Among these, PI 602492 stands out as a valuable new resistance source with strong activity against multiple HG types (races), making it an excellent candidate for gene discovery and breeding efforts to enhance resistance independently of conventional germplasm. These findings provide important, underutilized genetic resources that can expand the resistance base and drive the development of more durable SCN-resistant soybean cultivars.