Transcriptomic Responses of Perennial Ryegrass to Resident Epichloë Endophytes During Early Stages of Seed Germination

Asexual fungal endophytes of the genus Epichloë form mutualistic associations with Pooideae grasses and are transmitted vertically through seeds. Although these associations can improve pasture performance and persistence, global host transcriptional responses to resident endophytes during early seed germination remain poorly understood. This study investigated changes in the perennial ryegrass (Lolium perenne) transcriptome associated with three taxonomically distinct Epichloë strains during seed imbibition and early seedling development. The Alto-SE, Alto-NEA12 and Alto-NEA11 associations were compared with endophyte-free Alto-WE seeds. During seed imbibition, 2627, 2695 and 3022 host genes were differentially expressed in Alto-SE, Alto-NEA12 and Alto-NEA11, respectively, followed by a sharp decrease in differentially expressed genes on day 2. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses showed that the differentially expressed genes (DEGs) were primarily associated with transcription and RNA processing, genome maintenance, molecular transport, and defence- and stress-related responses. Differential expression of multiple transcription factor families and genes associated with histone modification, DNA methylation and chromatin remodelling indicated extensive regulatory reprogramming, with both shared and strain-specific host responses. Germination performance assessments and functional validation were not conducted, and the surface disinfection design limits the separation of endophyte-associated transcriptional responses from potential treatment-related effects in the present study. Nevertheless, the findings provide a foundation for further investigation of the molecular processes associated with seed-mediated endophyte transmission and the establishment of a successful host–endophyte symbiosis. Future physiological, histological and functional studies will be required to determine their relationship with seed performance and endophyte transmission success.