Time- and Genotype-Dependent Root-Transcriptomic Responses of Soybean to Combined Soybean Aphid and Soybean Cyst Nematode Infestation

The soybean aphid (Aphis glycines) and soybean cyst nematode (Heterodera glycines) are major aboveground and belowground pests of soybean (Glycine max) in the U.S. Midwest, but the molecular basis of their combined effects on soybean defense remains poorly understood. This study examines how soybean genotypes influence demographic and root-transcriptomic responses to single and combined pest infestation. Soybean cyst nematode reproduction increased under combined infestation in the susceptible cultivar but remained unchanged in the resistant cultivar, whereas soybean aphid populations declined when plants were also infested with nematodes. Root RNA-seq revealed strong time-dependent transcriptional responses, with substantially more differentially expressed genes at 30 days post-infestation than at 5 days post-infestation. Co-expression and enrichment analyses showed that early responses were associated with defense signaling, plant–pathogen interaction, and cutin, suberin, and wax biosynthesis, whereas later responses involved redox processes, isoflavonoid biosynthesis, phenylpropanoid metabolism, and one-carbon metabolism. Several differentially expressed soybean genes co-localized with known soybean cyst nematode resistance quantitative trait loci, including genes near the rhg1 region. Together, these results suggest that soybean genotypes strongly influence soybean aphid–soybean cyst nematode interactions and identify candidate genes and pathways that may contribute to durable resistance against interacting aboveground and belowground pests.