Genome-wide identification and expression analysis of EIN3/EIL gene family in rice (Oryza sativa)

The nuclear-localized ethylene-insensitive3/ethylene-insensitive3-like (EIN3/EIL) proteins regulate the ethylene signaling pathway for growth and stress responses. This study presents a genome-wide analysis of nine Oryza sativa EIN3/EIL genes, exhibiting three clads in an ML phylogenetic tree. These proteins are conserved in both exon-intron organization and motif architecture aligned with their phylogenetic clustering. The EIN3/EIL proteins harbor the EIN3, EIN3 superfamily, and RDV-p3 conserved domains. OsEIN3/EIL expression profiling revealed consistently high transcript levels of LOC_Os03g20790 and LOC_Os02g36510 in leaf blades across vegetative and reproductive stages and in the endosperm, indicating a potential role in growth and yield enhancement. Additionally, LOC_Os03g20790, LOC_Os02g36510, LOC_Os07g48630, and LOC_Os09g31400 are highly expressed at later stages of root development, showing potential in nutrient signaling for seed-filling. Moreover, elevated expression of LOC_Os04g38400, LOC_Os09g31400, LOC_Os03g20790, LOC_Os08g39830, and LOC_Os07g48630 were detected under mannitol treatment, while LOC_Os04g38400 and LOC_Os08g39830 were highly upregulated in root and leaf tissues under drought stress exposure. Additionally, EIN3/EIL genes intricately interacted with MPK1, MPK5, and MYC genes, underscoring their potential involvement in growth and stress tolerance. Our findings lay a foundation for improved rice growth and yield enhancement.