Mining resistance genes of soybean cyst nematode based on genome-wide association study

Soybean cyst nematode disease is one of the major threats to global soybean production, characterized by its widespread distribution, severe damage, and strong pathogenicity. Identifying and regulating key resistance genes, as well as incorporating them into cultivated varieties through genetic transformation, represents a relatively efficient and cost-effective prevention and control strategy. From 2022 to 2023,at the Chengzi and Xiqiao experimental bases of the Chifeng Academy of Agriculture and Animal Sciences, this study utilized 206 soybean materials for resistance evaluation under two-year, four-site environmental conditions. Based on 101,549 high-quality single nucleotide polymorphism (SNP) loci derived from sequencing data, phylogenetic analysis and principal component analysis were conducted. Genome-wide association study (GWAS) identified 19 SNP loci significantly associated with resistance to soybean cyst nematode, distributed across 11 chromosomes. Among these, four loci (Chr18_56072377, Chr08_159841, Chr15_50312327, and Chr16_32880873) were detected under multiple environmental conditions, with effect values ranging from -35.75 to 24.25.The genes associated with these loci were enriched in multiple pathways, including cell wall construction, root development, and amino acid metabolism. The disease resistance function of the candidate gene Glyma.18G279900 was preliminarily validated. This study addresses the gap in identifying stable resistance loci across diverse environments, advances the understanding of resistance-related metabolic regulatory mechanisms, provides new markers and gene resources for disease-resistant molecular breeding, and offers direct application value for cultivating resistant varieties adapted to local ecological conditions.