Genome-wide characterization and expression profiling of EIN3/EIL family genes in Zea mays

The ethylene-insensitive3/Ethylene-insensitive3-like (EIN3/EIL) protein family functions as an important factor for plant growth and development under various environmental conditions. EIN3/EIL protein is a DNA-binding nuclear-localized protein that contributes to the broad array of plant metabolic pathways in plants. There is no comprehensive study available on EIN3/EIL protein family in Zea mays. This study detected nine ZmEIL genes through genome-wide characterization and profiled their expression utilizing available RNA sequencing data. Phylogenetic analysis grouped 81 EIL proteins of ten plant species into three clades based on sequence alignment. ZmEIL protein homology modeling depicted that the DNA binding features and protein structure were similar with Arabidopsis EIN3. The ZmEIL genes were conserved in exon-intron and motif distribution according to their pertaining phylogenetic group. The protein-protein interaction predicted the intricate network of other ethylene responsive proteins with ZmEILs. The nine ZmEIL genes were distributed among six of the ten Z. mays chromosomes, with one segmentally duplicated paralogue. Analysis of cis-elements revealed that the ZmEIL genes are widespread in functions including tissue-specific, stress and hormone sensitive expressions. In addition, RNA-sequencing-based expression profiling indicated that the genes ZmEIL1 and ZmEIL9 displayed comparatively higher expression in various tissues. Characterization of the EIL genes will assist in the selection of potential genes responsible for biological functions in Z. mays and related species.