Systematic Analysis of MYB Family Genes in Potato and Their Multiple Roles in Development and Stress Responses

Abstract

The MYB proteins represent a large family of transcription factors and play important roles in development, senescence, and stress responses in plants. In the current study, 233 MYB transcription factor-encoding genes were identified and analyzed in the potato genome, including 119 R1-MYB, 112 R2R3-MYB, and two R1R2R3-MYB members. R2R3-MYB is the most abundant MYB subclass and potato R2R3-MYB members together with their Arabidopsis homologs were divided into 35 well-supported subgroups as the result of phylogenetic analyses. Analyses on gene structure and protein motif revealed that members from the same subgroup shared similar exon/intron and motif organization, further supporting the results of phylogenetic analyses. Evolution of the potato MYB family was studied via syntenic analysis. Forty-one pairs of StMYB genes were predicted to have arisen from tandem or segmental duplication events, which played important roles in the expansion of the StMYB family. Expression profiling revealed that the StMYB genes were expressed in various tissues and several StMYB genes were identified to be induced by different stress conditions. Notably, StMYB030 was found to act as the homolog of AtMYB44 and was significantly up-regulated by salt and drought stress treatments. Furthermore, overexpression of StMYB030 in Arabidopsis enhanced salt stress tolerance of transgenic plants. The results from this study provided information for further functional analysis and for crop improvements through genetic manipulation of these StMYB genes.

Keywords: MYB; abiotic stress; biotic stress; leaf senescence; potato.

Figure 1

Sequence logos of the R2 and R3 MYB repeats of MYB members from potato (A) and Arabidopsis (B). The results were generated by multiple alignment analysis of Arabidopsis and potato R2R3-MYB members and visualized by Texshade. The asterisks indicate the typical conserved Trp residues in the MYB domain.

Figure 2

Phylogenetic analysis of potato R2R3-MYB family members. The phylogenetic tree was generated from the alignment of potato and Arabidopsis R2R3-MYB proteins with 1000 bootstrap replicates using the neighbor-joining (NJ) method. The potato R2R3-MYB members together with their Arabidopsis homologs were classified into 34 subgroups.

Figure 3

Synteny analysis of MYB genes between potato and five other representative species. (A) The gray line in the background represented the collinear blocks between potato and five other representative species, while the red line exhibited the syntenic MYB gene pairs. (B) The MYB genes formed the syntenic pairs between potato and all the other five selected species, which was visualized by the Venn plot.

Figure 4

Distribution of StMYB genes on potato chromosomes. In potato, 230 StMYB genes were successfully mapped to 12 potato chromosomes. The red box indicated the gene cluster, while the tandem duplication pair was featured by red color.

Figure 5

Segmental duplication events and inter-chromosomal relationships between StMYB genes. The 31 putative segmental duplication pairs of StMYB genes were investigated with MCScanX and linked by the colored lines, respectively. The gray lines indicate all putative segmental duplication pairs in the potato genome.

Figure 6

Regulatory elements in the promoter regions of StMYB genes.

Figure 7

The expression patterns of the StMYB genes in the tested tissues. The expression pattern data were retrieved from transcriptome data and visualized by R Programming Language. Y Tuber, young tuber; M Tuber, mature tuber.

Figure 8

The expression patterns of StMYB genes under abiotic and biotic stress treatments. (A) The relative expression ratios of abiotic stress treatments; (B) the relative expression ratios of biotic stress treatments; (C) the summarized information of the stress-induced StMYB genes. The relative expression ratios of abiotic and biotic stress treatments were calculated relative to the untreated control, respectively, and then the significantly induced gene was defined to possess a log2 relative expression ratio ≥1 under one of the stress treatments. The red color, white color, and blue color represent the up-regulated, unaltered, and down-regulated expression, respectively.

Figure 9

The expression patterns of selected StMYB genes detected by qRT-PCR. (A) To confirm the tissue specificity, the expression pattern of the selected StMYB genes was calculated as folds relative to the expression level of the root. (B) The expression pattern of selected StMYB genes in response to salt stress treatments, which was calculated as folds relative to the untreated control.

Figure 10

The subcellular localization of StMYB030 in tobacco epidermal cells. The StMYB030-GFP fusion construct and GFP gene driven by the CaMV-35S promoter were transiently expressed into tobacco, respectively. DAPI (dye 4,6-diamidino-2-phenylindole) staining indicted the nucleus.

Figure 11

The Effects of salt stress treatment on root growth of StMYB030 gene overexpressing lines in transgenic Arabidopsis. (A) The primary root length of wildtype and StMYB030 gene overexpression lines under salt treatments in transgenic Arabidopsis. (B) The quantification of primary root length under normal condition and 100 mM NaCl treatments. The data were retrieved from three biological replicates. WT, wildtype. The data were means ± SD of three biological repeats. * p < 0.05 (t-tests).