Genome-wide identification and expression analysis of the Auxin-Response factor (ARF) gene family in Medicago sativa under abiotic stress

Abstract

Background Alfalfa (Medicago sativa) is the most widely planted legume forage and one of the most economically valuable crops in the world. The periodic changes in its growth and development and abiotic stress determine its yield and economic benefits. Auxin controls many aspects of alfalfa growth by regulating gene expression, including organ differentiation and stress response. Auxin response factors (ARF) are transcription factors that play an essential role in auxin signal transduction and regulate the expression of auxin-responsive genes. However, the function of ARF transcription factors is unclear in autotetraploid-cultivated alfalfa. Result A total of 81 ARF were identified in the alfalfa genome in this study. Gene Ontology (GO) terms and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways were analyzed, identifying that ARF genes are mainly involved in transcriptional regulation and plant hormone signal transduction pathways. Phylogenetic analysis showed that MsARF was divided into four clades: I, II, III, and IV, each containing 52, 13, 7, and 9 genes, respectively. The promoter region of the MsARF gene contained stress-related elements, such as ABRE, TC-rich repeats, MBS, LTR. Proteins encoded by 50 ARF genes were localized in the nucleus without guide peptides, signal peptides, or transmembrane structures, indicating that most MsARF genes are not secreted or transported but only function in the nucleus. Protein structure analysis revealed that the secondary and tertiary structures of the 81 MsARF genes varied. Chromosomal localization analysis showed 81 MsARF genes were unevenly distributed on 25 chromosomes, with the highest distribution on chromosome 5. Furthermore, 14 segmental duplications and two sets of tandem repeats were identified. Expression analysis indicated that the MsARF was differentially expressed in different tissues and under various abiotic stressors. The quantitative reverse transcription polymerase chain reaction (qRT-PCR) analysis showed that the expression profiles of 23 MsARF genes were specific to abiotic stresses such as drought, salt, high temperature, and low temperature, as well as tissue-specific and closely related to the duration of stress. Conclusion This study identified MsARF in the cultivated alfalfa genome based on the autotetraploid level, which GO, KEGG analysis, phylogenetic analysis, sequence characteristics, and expression pattern analysis further confirmed. Together, these findings provide clues for further investigation of MsARF functional verification and molecular breeding of alfalfa. This study provides a novel approach to systematically identify and characterize ARF transcription factors in autotetraploid cultivated alfalfa, revealing 23 MsARF genes significantly involved in response to various stresses.

A Comprehensive Analysis of Auxin Response Factor Gene Family in Melastoma dodecandrum Genome

“…Specifically, we observed an abundance of promoter elements related to the BHLH and bZIP families in multiple members of the MedARF16s subgroup, indicating that they might be regulated by downstream genes targeted by the BHLH and bZIP transcription factors [45], thereby exhibiting similar regulatory functions. They may co-regulate complex controlling the transcription of MedARFs and thereby influencing gene expression during the growth of M. dodecandrum [46].…”

Comprehensive analyses of the ARF gene family in cannabis reveals their potential roles in regulating cannabidiol biosynthesis and male flower development

“…Duplication events, including tandem duplication and segmental/whole duplication, are the major forces for gene family expansion and functional differentiation during evolution. Previous studies have reported that plant ARF genes expand by undergoing tandem duplication and segmental/whole duplication ( Chen et al., 2023 ; Qi et al., 2023 ). For example, four LuARF genes (two gene pairs) underwent tandem duplication events, whereas 27 (81.8%, 18 gene pairs) underwent segmental/whole duplication events in flax ( Qi et al., 2023 ).…”

“…For example, four LuARF genes (two gene pairs) underwent tandem duplication events, whereas 27 (81.8%, 18 gene pairs) underwent segmental/whole duplication events in flax ( Qi et al., 2023 ). In alfalfa, 14 segmental duplications and two sets of tandem repeats were identified ( Chen et al., 2023 ). Similarly, seven CsARF genes (three sets of gene pairs) underwent tandem duplication, and one segmental duplication was identified ( Figures 5 , 6 , 7).…”

Genome-Wide Association Study (GWAS) Identifies Key Candidate Genes Associated with Leaf Size in Alfalfa (Medicago sativa L.)

“…Alfalfa (Medicago sativa L.), known as the "Queen of Forages", is a globally cultivated forage crop valued for its high biomass yield and nutritional quality [16,17]. The change in its growth and development determines its yield and economic benefit [18]. Increasing biomass is a key breeding objective for alfalfa.…”