Host-Associated Temporal Transcriptomics of Fusarium poae During Barley and Wheat Spike Infection

Fusarium head blight (FHB) is a destructive disease of wheat and barley caused by a complex of Fusarium species, including Fusarium poae. However, the transcriptional responses of F. poae during spike colonization remain insufficiently characterized. This study aimed to characterize and compare the temporal transcriptomic responses of F. poae during barley and wheat spike infection. We profiled the in planta transcriptome of F. poae isolate GA18W 5.2.4 in barley cv. Stander and wheat cv. SS8641 at 0, 24, 48, 72, and 96 h after inoculation (HAI). RNA sequencing, differential expression analysis, functional enrichment, and evidence-supported protein annotation characterized temporal and host-associated transcriptional patterns. Likelihood ratio tests identified 7,852 time-responsive genes in barley and 5,464 in wheat. Relative to 0 HAI, 2,858 to 3,868 genes were upregulated in barley and 1,631 to 3,921 in wheat, whereas downregulated genes were uncommon. Shared upregulated genes increased from 1,410 at 24 HAI to 3,192 at 96 HAI. Upregulated genes in both hosts were enriched for protein synthesis, energy metabolism, intracellular transport, and protein homeostasis. Curated DEG categories comprised candidates representing cell wall-degrading enzymes, effectors, biosynthetic gene cluster core genes, transcription factors, transporters, signaling proteins, and stress/detoxification proteins. Many categories were represented earlier or more broadly in barley but increased later in wheat, with several approaching or exceeding barley by 96 HAI. These findings reveal a shared core transcriptional program with host-associated temporal differences and provide a basis for further prioritization and functional validation of candidate genes involved in F. poae colonization and FHB development.