Transcriptomic Analysis of Soybean Defense Mechanism Against Aphid and Nematode Co-Infestation

Soybean aphid (SBA), Aphis glycines Matsumura (Hemiptera: Aphididae), and soybean cyst nematode (SCN), Heterodera glycines Ichinoe (Tylenchida: Heteroderidae), are major pests of soybean, Glycine max L. Merr., in the U.S. Midwest. This study examined three-way interactions among soybean, SBA, and SCN using demographic and transcriptomic analyses. SCN-resistant and SCN-susceptible cultivars were evaluated under three treatments (SBA, SCN, SCN+SBA) in a randomized complete block design with six replicates, repeated eight times in greenhouse cone-tainers. Plants were infested with 2,000 SCN eggs at planting or 15 SBA at the V2 stage. Aphid populations were counted at 5-, 15-, and 30-days post-infestation (dpi), and SCN eggs sampled at 30 dpi. SCN egg density increased significantly in the susceptible cultivar but remained unchanged in the resistant cultivar in the presence of SBA, while SBA populations declined under SCN infestation. RNA-seq identified 4,637 differentially expressed genes (DEGs) at 5 dpi and 19,032 DEGs at 30 dpi. Analyses focused on DEGs shared across treatments but discordantly expressed in resistant cultivars during SBA–SCN interactions. Weighted Gene Co-expression Network Analysis revealed seven and nine modules at 5 and 30 dpi, respectively. Enrichment analyses identified ‘Plant–Pathogen Interaction’ and ‘Cutin, Suberin, and Wax Biosynthesis’ at 5 dpi, and ‘Isoflavonoid Biosynthesis’ and ‘One-Carbon Pool by Folate’ at 30 dpi. Several DEGs overlapped with SCN resistance QTLs, identifying candidate genes for cross-resistance breeding.