Genome-wide association study and molecular marker development for resistance to soybean cyst nematode in soybean

Soybean (Glycine max) is a major crop for grain and oil production worldwide. However, soybean cyst nematode (SCN) disease is a serious threat to soybean cultivation, causing major challenges for agriculture in China and globally. In this study, 306 soybean germplasms were evaluated for resistance to SCN HG type 0 using the female index (FI), a metric quantifying nematode reproduction on soybean roots. Furthermore, we performed a genome-wide association analysis study using 1,332,548 high-density single nucleotide polymorphism (SNP) markers. Through this analysis, the study identified quantitative trait nucleotides (QTN) and pinpointed candidate genes that are linked to resistance against SCN HG type 0. A total of 77 SNPs and 117 candidate genes associated with soybean resistance to SCN HG type 0 were identified. Subsequently, two kompetitive allele-specific PCR (KASP) markers, S19_rs8522772 and S19_rs8384176, along with four cleaved amplified polymorphic sequence (CAPS) markers (S19_rs838271, S19_rs8522589, S19_rs8466511 and S19_rs8481473) were developed. These markers were found to be closely linked to soybean resistance to SCN based on the results of beneficial allele analysis of candidate genes. These markers not only expanded the soybean germplasm resource, but also provided a solid foundation for molecular breeding of soybean varieties resistant to SCN.