Quantitative trait loci and gene-specific markers associated with resistance to soybean cyst nematode HG type 2.5.7

Soybean cyst nematode (SCN) is one of the most damaging soybean (Glycine max) pests worldwide. More than 95% of SCN-resistant commercial cultivars in North America are derived from a single source of resistance named PI 88788, and the widespread use of this source in the past three decades has led to the selection of virulent biotypes of SCN, such as HG (Heterodera glycines) type 2.5.7 that can overcome the PI 88788-type resistance. The objectives of this study were to identify quantitative trait loci (QTL) and candidate genes underlying the resistance to HG type 2.5.7 isolate and to measure the impact of the resistance factors on seed yield. To achieve the goals, a recombinant inbreed line (RIL) population was established from a cross between an SCN-susceptible high-yielding elite soybean cultivar, OAC Calypso, and the cultivar LD07-3419, resistant to SCN HG type 2.5.7. The RILs resistant to HG type 2.5.7 were identified using greenhouse bioassay tested for differentiation of resistant sources using Kompetitive Allele-Specific PCR (KASP) assay at rhg1 and Rhg4 loci and also for rhg1 copy number variation using TaqMan assay. The RILs were also genotyped using genotype-by-sequencing and three SCN-related QTL were identified on chromosomes 9, 12, and 18 using composite interval mapping. In addition, 31 genes involved in protein kinase activity were identified within QTL regions as potential causal candidate genes underlying the resistance. No significant correlation was found between seed yield and the resistance to SCN in the RIL population evaluated under non-SCN-infested environments.

Automated summary

This study identified QTL and candidate genes for resistance to HG type 2.5.7 isolate in soybeans, as well as evaluated their impact on seed yield. Three SCN-related QTL were located on chromosomes 9, 12, and 18, with 31 genes involved in protein kinase activity identified as potential causal candidate genes. Interestingly, no significant correlation was found between seed yield and SCN resistance in non-infested environments among the RIL population.