Genome-wide characterization and expression profiling of EIN3/EIL family genes in Oryza sativa var. japonica
摘要
EIN3/EIL proteins are nuclear-localized, DNA-binding transcription factors that regulate plant growth and development under diverse environmental conditions and act as central integrators linking ethylene signaling with other hormonal and stress-responsive pathways. Despite extensive studies in other crops, this gene family has not yet been characterized in Oryza sativa var. japonica. This study investigated the ethylene-insensitive 3-like (EIN3/EIL) gene family in the rice subspecies O. sativa var. japonica. A genome-wide analysis identified seven putative EIL members in the japonica genome. OsEIL proteins exhibited both acidic and basic properties, with most predicted to localize in the nucleus and a smaller proportion in the chloroplast. The 74 amino acid sequences of OsEIL proteins have evolutionary relationships among C3 and C4 plants across both monocot and dicot species. The OsEIL proteins of rice shared conserved DNA-binding characteristics and similar structural features with Arabidopsis EIN3. The OsEIL genes under each phylogenetic group had specific conserved exon–intron structures and motif compositions. Duplicate gene pairs exhibiting identical numbers of exons and introns imply shared functional characteristics and motif patterns. Protein–protein interaction analysis revealed a complex network connecting OsEILs with other ethylene-responsive proteins. The functionalities of the cis-acting regulatory elements—present in the OsEIL gene family—were linked with plant growth and development, phytohormone responsiveness, and abiotic and biotic stress responses. RNA-seq expression profiling demonstrated that OsEIL1 and OsEIL3 exhibit significantly elevated transcript levels across multiple tissues. These results provide valuable insights for the functional characterization and selection of candidate genes involved in key biological processes in O. sativa var. japonica.