A Novel Mechanism Underlying Resistance to Soybean Cyst Nematode in the Resistant Soybean HN531

The soybean cyst nematode (Heterodera glycines, SCN) is the leading pathogen causing economic losses in soybean production worldwide. Using resistant cultivars is the most sustainable control method, yet the molecular basis of this resistance remains unclear. Heinong 531 (HN531), a high-yield soybean variety rich in seed oil, shows broad resistance to multiple SCN races. In this research, we studied HN531’s resistance to SCN races 3 and 5 through phenotypic assessment and comparative transcriptomics. Although initial infection rates were similar between resistant HN531 and the susceptible Dongsheng 1 (DS1), HN531 limited later nematode development inside roots, with fewer progressing to the J2 stage and maturing females. RNA-seq at 5 days post-infection revealed 1459 differentially expressed genes (DEGs) in HN531, mainly involved in secondary metabolite pathways, especially phenylpropanoid biosynthesis. We pinpointed a β-glucosidase gene (Glyma.12G053800, BGLU) upregulated after SCN infection and naturally more expressed in HN531 roots than DS1. Functional tests using Agrobacterium rhizogenes-mediated hairy root transformation showed that overexpressing Glyma.12G053800 in the susceptible DS1 significantly decreased SCN development and adult female counts by around 65%, without affecting initial infection. These findings suggest Glyma.12G053800 contributes to SCN resistance via phenylpropanoid-driven secondary metabolism, offering new insights into nematode resistance pathways and a valuable genetic resource for breeding broad-spectrum resistant soybean varieties.