Comparative transcriptomic analysis revealed specific modules and hub heat-responsive genes in perennial ryegrass

Perennial ryegrass (<italic>Lolium perenne</italic>) is one of the most important cool-season grasses used for forage and turf purposes. Heat stress is the primary abiotic factor threatening its pasture/turf persistence. In this study, heat-responsive genes common between or specific to two ryegrass varieties with contrasting heat tolerance traits were analyzed at the transcriptomic level. The result identified 5,399 common heat-responsive differentially expressed genes (DEGs) between the two ryegrass varieties enriched in KEGG pathways such as ribosomes, spliceosomes, ribosome biogenesis, photosynthetic antenna proteins, etc. Weighted gene co-expression network analysis (WGCNA) revealed specific DEGs in the heat-tolerant ryegrass variety that were mainly enriched in glyoxylate and dicarboxylate metabolism, glycolysis, protein processing in the endoplasmic reticulum, spliceosome, and ascorbate-glutathione cycle, etc. Furthermore, heat-tolerant variety-specific hub DEGs and transcription factors were also identified using Core Gene Co-expression Network analysis. Knowledge gained from this study provides a basis for the genetic improvement of heat-tolerant ryegrass and other cool-season perennial grass species.