MYB Gene Family in Potato (Solanum tuberosum L.): Genome-Wide Identification of Hormone-Responsive Reveals Their Potential Functions in Growth and Development

Abstract

As an important nongrain crop, the growth and yield of potato (Solanum tuberosum L.) is often affected by an unfavorable external environment in the process of cultivation. The MYB family is one of the largest and most important gene families, participating in the regulation of plant growth and development and response to abiotic stresses. Several MYB genes in potato that regulate anthocyanin synthesis and participate in abiotic stress responses have been identified. To identify all Solanum tuberosum L. MYB (StMYB) genes involved in hormone or stress responses to potentially regulate potato growth and development, we identified the MYB gene family at the genome-wide level. In this work, 158 StMYB genes were found in the potato genome. According to the amino acid sequence of the MYB domain and gene structure, the StMYB genes were divided into R2R3-MYB and R1R2R3-MYB families, and the R2R3-MYB family was divided into 20 subgroups (SGs). The expression of 21 StMYB genes from different SGs in roots, stems, leaves, flowers, shoots, stolons, young tubers, and mature tubers was determined by quantitative real-time polymerase chain reaction (qRT-PCR). The expression patterns of StMYB genes in potatoes treated with abscisic acid (ABA), indole-3-acetic acid (IAA), gibberellin acid 3 (GA3), NaCl, mannitol, and heat were also measured. We have identified several potential candidate genes that regulate the synthesis of potato flavonoids or participate in hormone or stress responses. This work provides a comprehensive understanding of the MYB family in potato and will lay a foundation for the future investigation of the potential functions of StMYB genes in the growth and development of potato.

Keywords: StMYB; expression patterns; hormone or stress responses; potato genome.

Figure 1

Unrooted phylogenetic tree representing the relationships among 158 MYB genes of potato and Arabidopsis thaliana (L.) Heynh. with 1000 bootstrap replicates by the maximum likelihood (ML) method. MYB genes from potato and Arabidopsis thaliana (L.) Heynh. are classified into S1, S2, S3, S4, S5, S6, S7, S9, S10, S11, S12, S13, S14, S15, S17, S18, S19, S20, S21, S22, S23, S24, and S25. The genes in potato are marked in red, while those in Arabidopsis thaliana (L.) Heynh. are marked in black.

Figure 2

Phylogenetic relationships, gene structures, architectures of the conserved protein motifs, and cis-acting elements analysis of the MYB genes from potato. (A) The phylogenetic tree was constructed based on the full-length sequences of potato MYB proteins using Geneious R11 software. (B) Exon-intron structures of potato MYB genes. Blue boxes indicate untranslated 5′- and 3′-regions, and black lines indicate introns. The number indicates the phases of the corresponding introns. (C) The motif compositions of the potato MYB proteins. The motifs, numbered 1–10, are displayed in different colored boxes. The sequence information for each motif is provided in Table S2. The protein length can be estimated using the scale at the bottom. (D) The cis-acting elements analysis of StMYB genes promoters. Blocks of different colors represent light responsiveness elements, low temperature responsiveness elements, salicylic acid responsiveness elements, abscisic acid responsiveness elements, MeJA responsiveness elements, auxin responsiveness elements, gibberellin responsiveness elements, and defense and stress responsiveness elements.

Figure 3

The distribution of MYB genes on chromosomes. The chromosome number is indicated to the left of each chromosome.

Figure 4

The interchromosomal relationships of the potato MYB genes. Colored lines indicate all syntenic blocks in the potato genome.

Figure 5

Phylogenetic relationships and motif compositions of the MYB proteins from six different plant species (Solanum tuberosum L., Arabidopsis thaliana (L.) Heynh., Solanum lycopersicum, Vitis vinifera L., Manihot esculenta Crantz, and Oryza sativa L.). MYB genes from multiple species are classified into S 1, S 2, S 3, S 4, S 5, S 6, S 7, S 9, S 11, S 12, S 13, S 14, S 15, S 17, S 18, S 19, S 20, S 21, S 22, S 23, S 24, and S 25. Outer layer: An unrooted ML phylogenetic tree constructed using Mega 7.0. Inner layer: Distribution of the conserved motifs in MYB proteins. The differently colored boxes represent different motifs and their positions in each MYB protein sequence.

Figure 6

Synteny analyses between the MYB genes of potato and seven representative plant species. Gray lines in the background indicate collinear blocks within potato and other plant genomes, while red lines highlight syntenic MYB gene pairs.

Figure 7

Tissue-specific gene expression of 21 potato MYB genes and the correlation between the gene expression patterns of StMYBs. (A) The expression patterns of 21 potato MYB genes in roots, stems, leave, flowers, shoots, stolons, young tuber, and mature tuber were examined by quantitative real-time polymerase chain reaction (qRT-PCR). The expression pattern of each gene was calculated based on the minimum expression of each gene in different tissues. Error bars were obtained from three measurements. Lowercase letter(s) above the bars indicate significant differences (α = 0.05, least significant difference (LSD)) among the treatments. (B) Different colors represent the correlation of StMYB gene expression patterns in different tissues. Different colors in the lower left corner represent the correlation of StMYB gene expression patterns in different tissues, while the different colors in the upper right corner represent the p-value of the correlation.

Figure 8

Gene expression of 19 potato MYB genes under hormones and abiotic stress and the correlation between the gene expression patterns of StMYB genes. (A) The expression patterns of 19 potato MYB genes under hormones and abiotic stress were examined using a qRT-PCR assay. Error bars were obtained from three measurements. Lowercase letter(s) above the bars indicate significant differences (α = 0.05, LSD) among the treatments. (B) Different colors represent the correlation of StMYB gene expression patterns under different hormone and abiotic stress treatments. Different colors in the lower left corner represent the correlation of StMYB gene expression patterns under different hormone and abiotic stress treatments, while the different colors in the upper right corner represent the p-value of the correlation.

Figure 9

Subcellular localization of StMYB6 and StMYB19 in Arabidopsis thaliana (L.) Heynh. protoplasts. Enhanced green fluorescent protein (eGFP), StMYB6-eGFP, and StMYB19-eGFP under the control of the CaMV35S promoter separately transiently expressed in Arabidopsis thaliana (L.) Heynh. protoplasts. eGFP fluorescence signal was observed by Olympus confocal microscope. Scale bars = 10 µm.