Genome-wide identification of the EIN3/EIL transcription factor family and their responses under abiotic stresses in Alfalfa (Medicago sativa)

Background Alfalfa ( Medicago sativa ) is known as the "king of forage" due to its high protein, mineral, carbohydrate, and digestive nutrient content. However, various abiotic stresses inhibit the growth and development of alfalfa, ultimately leading to a decrease in yield and quality. The ethylene-insensitive 3 (EIN3)/ethylene-insensitive 3-like (EIL) transcription factors are core regulators in plant ethylene signaling, playing important roles in plant development and response to abiotic stresses. However, a comprehensive genome-wide analysis of EIN3/EIL genes in alfalfa has not yet been conducted. Results In this study, we identified ten MsEIN3/EIL genes from the alfalfa (cv.Zhongmu No.1) genome, which were classified into four clades based on phylogenetic analysis. The motif 1, motif 2, motif 3, motif 4, and motif 9 of the MsEIN3/EIL genes constitute the conserved structural domains. Gene duplication analyses suggest that segmental duplication (SD) is a major driver of the expansion of the MsEIN3/EIL gene family during evolution. The analysis of the cis -acting elements in the promoter of MsEIN3/EIL genes showed their ability to respond to various hormones and stresses. The analysis of tissue expression revealed that group A and group C members were highly expressed in flowers and seeds, while group D members were highly expressed in roots and stems. Furthermore, RNA-Seq analysis demonstrated that the expression of MsEIN3/EIL genes were responsive to ABA treatment and different abiotic stresses (e.g., salt, cold, and drought stress). Conclusion This study investigated MsEIN3/EIL genes in alfalfa and identified three candidate MsEIN3/EIL transcription factors involved in the regulation of abiotic stresses. These findings will provide valuable insights into uncovering the molecular mechanisms underlying various stress responses in alfalfa.