RNA-Seq analysis reveals early defense activation and responses associated with resistance to Fusarium thapsinum stalk infection in sorghum

Fusarium stalk rot in sorghum is caused by Fusarium thapsinum and affects sorghum production globally. In this study, we investigated genome-wide transcriptional responses associated with resistance to sorghum stalk rot. Transcriptomes of two sorghum genotypes, a resistant (SC599) and a susceptible (BTx3042) genotype, were analyzed at 24 and 48 h post-inoculation (hpi) with F. thapsinum at flowering. A total of 24 RNA-seq libraries were generated. Differentially expressed genes (DEGs) ranged from 360 to 6,178 (FDR < 0.05), with earlier and stronger transcriptional responses observed in the resistant genotype. Key defense-related genes, including nucleotide-binding site leucine-rich repeat (Sobic.005G226400), pathogenesis-related proteins (Sobic.001G401200), disease resistance-response genes (Sobic.009G021300), wall-associated kinase (Sobic.008G170800 and Sobic.002G249600), and flavonoid synthase (Sobic.004G050200) genes, were upregulated in SC599 at 24 hpi, whereas expression of these genes was lower or delayed in BTx3042. Gene ontology and KEGG analyses revealed enrichment of defense responses, flavonoid biosynthesis, and signal transduction at 24 hpi in the resistant genotype, whereas the susceptible genotype showed delayed activation of stress-related pathways. These results highlight the importance of early and coordinated activation of defense responses and provide insight into the temporal regulation of resistance mechanisms in sorghum against F. thapsinum and may provide a framework for future studies to understand the genes and pathways underlying the molecular mechanisms of Fusarium stalk rot resistance in sorghum.