Genome-wide identification of R2R3-MYB transcription factor subfamily genes involved in salt stress in rice (Oryza sativa L.)

Abstract

Background: R2R3-MYB transcription factors belong to one of the largest gene subfamilies in plants, and they are involved in diverse biological processes. However, the role of R2R3-MYB transcription factor subfamily genes in the response of rice (Oryza sativa L.) to salt stress has been rarely reported.

Results: In this study, we performed a genome-wide characterization and expression identification of rice R2R3-MYB transcription factor subfamily genes. We identified a total of 117 R2R3-MYB genes in rice and characterized their gene structure, chromosomal location, and cis-regulatory elements. According to the phylogenetic relationships and amino acid sequence homologies, the R2R3-MYB genes were divided into four groups. qRT-PCR of the R2R3-MYB genes showed that the expression levels of 10 genes significantly increased after 3 days of 0.8% NaCl treatment. We selected a high expression gene OsMYB2-115 for further analysis. OsMYB2-115 was highly expressed in the roots, stem, leaf, and leaf sheath. OsMYB2-115 was found to be localized in the nucleus, and the yeast hybrid assay showed that OsMYB2-115 has transcriptional activation activity.

Conclusion: This result provides important information for the functional analyses of rice R2R3-MYB transcription factor subfamily genes related to the salt stress response and reveals that OsMYB2-115 may be an important gene associated with salt tolerance in rice.

Keywords: Gene expression; R2R3-MYB; Rice (Oryza sativa L.); Salt stress; Transcription factor.

Fig. 1

Distribution of R2R3-MYB transcription factor subfamily genes on rice chromosomes. Chromosome numbers are showed at the top of each chromosome. The name of each R2R3-OsMYB genes are shown on the right side of the chromosome. The scale represents 50 Mb chromosomal distance. The bars indicate the positions of the R2R3-OsMYB genes on the chromosomes

Fig. 2

Conserved motifs and gene structure analyses of rice R2R3-MYB genes. A. The conserved motif distribution of rice R2R3-MYB proteins; Different conserved motifs were represented by seven different colors. B. Exon-intron structures of rice R2R3-MYB genes. The green boxes, yellow boxes and black lines indicate untranslated regions, exons, and introns, respectively

Fig. 3

Phylogenetic analysis of R2R3-MYB proteins in rice and Arabidopsis. The neighbor-joining method were used to constructed phylogenetic tree of rice (117) and Arabidopsis (125) MYB proteins by Mega X software with a bootstrap. The MYB proteins were classified into four subfamilies: Group 1, 2, 3 and 4 depicted by red, green, pink, and blue, respectively

Fig. 4

The number of putative regulatory cis-regulatory elements in the promoters of R2R3-MYB genes. The predicted cis-regulatory elements in the promoters of R2R3-MYB gene were classified into four broad categories, including hormone responsive elements (orange), stress responsive elements (green), metabolism responsive elements (brown), and growth and biological process responsive elements (blue)

Fig. 5

Expression patterns of R2R3-MYB subfamily genes after NaCl treatment. A. The expression pattern of R2R3-MYB subfamily genes after 0.8% NaCl treatment for 3 days in rice; B. The expression patterns of OsMYB2-115 genes after 0.8% NaCl treatment for 0 h, 6 h, 1 d, 3 d and 5 d in rice. Data are means ± SD of three biological replicates

Fig. 6

Expression pattern, subcellular localization, and transcriptional activity analyses. A. OsMYB2-115 expression in different tissues was detected by qRT-PCR. Data are means ± SD of three biological replicates; B. Subcellular localization of the OsMYB2-115 protein. GFP alone, mCherry and OsMYB2-115-GFP recombinant vector were transformed into rice protoplasts. The corresponding GFP alone was used as a positive control. mCherry fused with the nuclear localization signal as a nuclear localization control; C. Transcriptional activity using yeast-one-hbrid assay. pGBKT7, pGBKT7-53 and pGBKT7-Lam as negative, negative and positive controls, respectively