Genome-wide analysis of the AP2/ERF transcription factor superfamily in perennial ryegrass

Abstract

Background: Perennial ryegrass (Lolium perenne L.) is a widely cultivated turfgrass and forage species. AP2/ERF transcription factors play indispensable roles in plant growth and development, particularly in responses to biotic and abiotic stresses. However, comprehensive knowledge of this family in perennial ryegrass remains underexplored. Results: In this study, a total of 172 LpAP2/ERF genes were identified in the perennial ryegrass genome and renamed according to their chromosomal distribution. Phylogenetic and synteny analyses were performed using rice to investigate the evolution of the AP2/ERF genes in perennial ryegrass. These 172 LpAP2/ERF genes were categorized into four distinct subfamilies: the AP2 subfamily (25), the ERF subfamily (84), the DREB subfamily (59), and the RAV subfamily (4). Within each subfamily, gene structure and motif compositions were conserved. The analysis of cis-acting elements in LpAP2/ERF gene promoters suggests that these genes may play crucial roles in plant growth, development, and stress responses. Analysis of the expression patterns of AP2/ERF family genes in endophyte-infected perennial ryegrass under low nitrogen induction showed that a total of 44 LpAP2/ERF genes had significantly different expression levels. 39 genes responded strongly to nitrogen starvation in both endophyte-infected and endophyte-free perennial ryegrass, while 21 genes were expressed in response to infection by endophytic fungi under normal and low nitrogen conditions. Importantly, through GO, KEGG enrichment pathway analysis and protein interaction network prediction, two key core genes (LpAP2/ERF64 and LpAP2/ERF164) were finally identified, which play an important role in enhancing perennial ryegrass’s response to nitrogen starvation by endophytic fungi. Conclusions: This study is the first to identify the characteristics of the AP2/ERF family in perennial ryegrass, providing invaluable information for further evolutionary and functional studies of AP2/ERF. It also contributes to a better understanding of the molecular basis of development and stress tolerance in this species and others.