MYB transcription factors in alfalfa (Medicago sativa): genome-wide identification and expression analysis under abiotic stresses

Abstract

Background Alfalfa is the most widely cultivated forage legume and one of the most economically valuable crops in the world. Its survival and production are often hampered by environmental changes. However, there are few studies on stress-resistance genes in alfalfa because of its incomplete genomic information and rare expression profile data. The MYB proteins are characterized by a highly conserved DNA-binding domain, which is large, functionally diverse, and represented in all eukaryotes. The role of MYB proteins in plant development is essential; they function in diverse biological processes, including stress and defense responses, and seed and floral development. Studies on the MYB gene family have been reported in several species, but they have not been comprehensively analyzed in alfalfa. Methods To identify more comprehensive MYB transcription factor family genes, the sequences of 168 Arabidopsis thaliana, 430 Glycine max, 185 Medicago truncatula, and 130 Oryza sativa MYB proteins were downloaded from the Plant Transcription Factor Database. These sequences were used as queries in a BLAST search against the M. sativa proteome sequences provided by the Noble Research Institute. Results In the present study, a total of 265 MsMYB proteins were obtained, including 50 R1-MYB, 186 R2R3-MYB, 26 R1R2R3-MYB, and three atypical-MYB proteins. These predicted MsMYB proteins were divided into 12 subgroups by phylogenetic analysis, and gene ontology (GO) analysis indicated that most of the MsMYB genes are involved in various biological processes. The expression profiles and quantitative real-time PCR analysis indicated that some MsMYB genes might play a crucial role in the response to abiotic stresses. Additionally, a total of 170 and 914 predicted protein–protein and protein-DNA interactions were obtained, respectively. The interactions between MsMYB043 and MSAD320162, MsMYB253 and MSAD320162, and MsMYB253 and MSAD308489 were confirmed by a yeast two-hybrid system. This work provides information on the MYB family in alfalfa that was previously lacking and might promote the cultivation of stress-resistant alfalfa.

Genome-wide characterization of the abscisic acid-, stress- and ripening-induced (ASR) gene family in wheat (Triticum aestivum L.)

“…To explore the possible binding sites of TFs, the 2.0 kb upstream promoter regions of the TaASRs were examined via the online database, PlantRegMap. The results showed that a total of 4511 binding cites for 12 TFs including TEOSINTE BRANCHED1/CYCLOIDEA/PROLIFER-ATING CELL FACTOR1 (TCP) [34,62], NAM/ATAF/ CUC (NAC [63,64]), B3 [65], WRKY [66], Ethylene Response Factor (ERF) [67], Cys2His2 (C2H2) [68,69], DNA binding with one finger (Dof ) [70], basic leucine zipper (bZIP) [71], basic Helix-Loop-Helix (bHLH) [72,73], Lateral Organ Boundaries Domain (LBD) [74], myeloblastosis (MYB) [75] and GATA [76][77][78] were discovered (Fig. 5, Additional file 8: Table S7).…”

“…285, 207 and 115 binding sites of B3, Dof and WRKY were identified spanning 32, 32 and 29 TaASR promoters, which were absent from 1 (TaASR5A), 1 (TaASR2D) and 4 (TaASR1B, TaASR5A, TaASR5B and TaASR7D2) TaASRs, respectively. Most of these TFs, such as NAC [63,64], WRKY [79,66], C2H2 [68], bZIP [71], bHLH [72,73], MYB [75] and GATA [76,77], were involved in regulating plant growth and development, and the responses to multiple abiotic stress, such as drought and salt. All of the ASR genes contained GATA binding sites which were involved in light responsive development [78].…”

A chromosome-scale genome assembly of a diploid alfalfa, the progenitor of autotetraploid alfalfa

“…1a). As one of the most economically valuable crops in the world [1][2][3] , alfalfa has total estimated annual sales ranging from 7.8 to 10.8 billion dollars in the USA 4 . Alfalfa is known as "the queen of forage crops" not only because of its high-protein content and nutritive value as an animal feed but also because of its atmospheric nitrogen (N) fixation capacity.…”

Genome-wide identification of R2R3-MYB family in wheat and functional characteristics of the abiotic stress responsive gene TaMYB344

“…Moreover, the MYB families of other plant species were also identified and studied, such as Glycine max, Vitis vinifera, Zea mays, Solanum tuberosum, Gossypium, Medicago sativa, Solanum lycopersicum, and Brassica napus etc. [12][13][14][15][16][17][18][19].…”