Comparative transcriptomic dynamics reveal molecular responses of susceptible and resistant Triticum aestivum genotypes to wheat stripe mosaic virus

Soil-borne wheat mosaic disease (SBWMD), caused by wheat stripe mosaic virus (WhSMV), poses an emerging threat to wheat production in South America. In this study, we analyzed the transcriptomic responses of two Triticum aestivum genotypes exhibiting contrasting resistance levels to WhSMV. The resistant cultivar, Embrapa 16, displayed low viral accumulation and either mild or no symptoms, whereas the susceptible cultivar, BRS Guamirim, exhibited pronounced chlorosis, stunting, and elevated virus titers. RNA-Seq analysis identified 13,225 differentially expressed genes (DEGs) across four genotype-infection contrasts. In Embrapa 16, WhSMV infection resulted in the enrichment of Gene Ontology (GO) terms associated with defense responses, kinase activity, and hormone signaling, with marked induction of genes such as RPP13-like, RGA3, and shikimate kinase. In contrast, BRS Guamirim demonstrated extensive downregulation of photosynthesis-related genes and a disrupted hormonal response, indicating compromised metabolic homeostasis under stress. KEGG and Plant Reactome pathway analyses revealed the activation of MAPK signaling and plant–pathogen interaction pathways in the resistant genotype. These results suggest that effective resistance to WhSMV entails coordinated activation of signaling cascades, secondary metabolism, and chloroplast protection mechanisms, providing molecular insights to inform breeding strategies aimed at durable virus resistance in wheat.