Genome-Wide Identification and Expression Analysis of the Trehalose-6-phosphate Synthase and Trehalose-6-phosphate Phosphatase Gene Families in Rose (Rosa hybrida cv 'Carola') under Different Light Conditions

Abstract

Trehalose, trehalose-6-phosphate synthase (TPS),and trehalose-6-phosphatase (TPP) have been reported to play important roles in plant abiotic stress and growth development. However, their functions in the flowering process of Rosa hybrida have not been characterized. In this study we found that, under a short photoperiod or weak light intensity, the content of trehalose in the shoot apical meristem of Rosa hybrida cv 'Carola' significantly decreased, leading to delayed flowering time. A total of nine RhTPSs and seven RhTPPs genes were identified in the genome. Cis-element analysis suggested that RhTPS and RhTPP genes were involved in plant hormones and environmental stress responses. Transcriptome data analysis reveals significant differences in the expression levels of RhTPSs and RhTPPs family genes in different tissues and indicates that RhTPPF and RhTPPJ are potential key genes involved in rose flower bud development under different light environments. The results of quantitative real-time reverse transcription (qRT-PCR) further indicate that under short photoperiod and weak light intensity all RhTPP members were significantly down-regulated. Additionally, RhTPS1a, RhTPS10, and RhTPS11 were up-regulated under a short photoperiod and showed a negative correlation with flowering time and trehalose content decrease. Under weak light intensity, RhTPS11 was up-regulated and negatively regulated flowering, while RhTPS5, RhTPS6, RhTPS7b, RhTPS9, and RhTPS10 were down-regulated and positively regulated flowering. This work lays the foundation for revealing the functions of RhTPS and RhTPP gene families in the regulation of rose trehalose.

Keywords: Rosa hybrida; flowering; photoperiod and light intensity responses; trehalose; trehalose-6-phosphate phosphatase gene; trehalose-6-phosphate synthase gene.

Figure 1

Flowering time and trehalose content data under different lighting treatments. (a) Phenotypic characterization of R. hybrida cv ‘Carola’ under CK, 10 hL/14 hD, 8 hL/16 hD, 80%LI, 60%LI condition. (b) Flowering time of R. hybrida ‘Carola’ under CK, 10 hL/14 hD, 8 hL/16 hD, 80%LI, 60%LI condition. Values are mean ± SEM (n = 6). (c) Flower formation rate of R. hybrida cv ‘Carola’ under CK, 10 hL/14 hD, 8 hL/16 hD, 80%LI, 60%LI condition. Values are mean ± SEM (n = 6). (d) Trehalose content (mg·g⁻¹FW) of R. hybrida cv ‘Carola’ under CK, 10 hL/14 hD, 8 hL/16 hD condition, values are mean ± SEM (n = 3). (e) Trehalose content (mg·g⁻¹FW) of R. hybrida cv ‘Carola’ under CK, 80%LI, 60%LI condition, values are mean ± SEM (n = 3). Different letters indicate significant differences.

Figure 2

Construction of phylogenetic tree proteins for TPS and TPP. (a) Phylogenetic tree of the TPS proteins from seven plant species. The TPS proteins of R. hybrida (RhTPS), P. trichocarpa (PtTPS), A. thaliana (AtTPS), Malus domestica (MdTPS), Fragaria vesca (FvTPS), Rosa rugosa (RrTPS) and Rosa wichruana (RwTPS). (b) Phylogenetic tree of the TPP proteins from seven plant species. The TPP proteins of R. hybrida (RhTPP), P. trichocarpa (PtTPP), A. thaliana (AtTPP), M. domestica (MdTPP), F. vesca (FvTPP), R. rugosa (RrTPP) and R. wichruana (RwTPP).

Figure 3

Phylogenetic relationships and gene structures, domains, and motifs of the RhTPSs and RhTPPs family. (a) Phylogenetic analysis. (b) The conserved trehalose-6-phosphate synthase (TPS) domain (Glyco_transf_20), and the trehalose-6-phosphate phosphatase (TPP) domain (Trehalose_PPase)—the domains are indicated in different color. (c) Light green rectangles represent untranslated regions (UTRs); turquoise rectangles represent coding sequence (CDS) or introns; black lines represent introns. (d) Motif analysis, all motifs were identified by MEME tools, as shown in different bars.

Figure 4

Chromosomal synteny analysis of RhTPS and RhTPP genes. (a) Chromosome distribution and positioning of RhTPSs and RhTPPs across all seven chromosomes of rose. (b) Synteny analysis of RhTPS and RhTPP genes of R. hybrida. Chr1, Chr2, Chr3, Chr4, Chr5, Chr6, and Chr7 represent the seven chromosomes of R. hybrida, respectively.

Figure 5

Composition and number of cis-acting elements in the promoter regions of RhTPS (a) and RhTPP (b) genes. (a) Cis-acting elements found in the promoter region of RhTPSs. (Left): The number and function classification of cis-acting element in each RhTPS genes. (Right): Key cis-acting elements in each RhTPS; elements are represented by the boxes in different colors. (b) Cis-acting elements found in the promoter region of RhTPPs. (Left): The number and function classification of cis-acting element in each RhTPP genes. (Right): Key cis-acting elements in each RhTPP; elements are represented by the boxes in different colors.

Figure 6

Expression profiles of RhTPS and RhTPP genes in different tissues and under diverse light environments. (a) Expression profile of RhTPSs and RhTPPs in different tissues. FPKM values were normalized by log₂(FPKM + 1) transformation to display the heatmap color scores. (b) Expression profiles of RhTPSs and RhTPPs after three days under different light treatments. Different shades of yellow and purple denote the extent of the expression values according to the colour bar provided log₂(FPKM + 1). (c) Expression levels of RhTPS and RhTPP genes under CK, 10 hL/14 hD, 8 hL/16 hD. RhACTIN2 was used as the reference gene. Error bars indicate SD (n = 3). (d) Expression levels of RhTPS and RhTPP genes under CK, 80%LI, 60%LI. RhACTIN2 was used as the reference gene. Error bars indicate SD (n = 3). (e) Correlation analysis of RhTPS and RhTPP gene expression with flowering time, flowering rate, and trehalose content under CK, 10 hL/14 hD, 8 hL/16 hD conditions. Use the Pearson correlation coefficient method for correlation analysis, where orange represents positive correlation and dark blue represents negative correlation. The correlation coefficient is kept within the circle. Values with p < 0.05 are retained. (f) Correlation analysis of RhTPS and RhTPP gene expression with flowering time, flowering rate, and trehalose content under CK, 80%LI, 60%LI conditions. Use the Pearson correlation coefficient method for correlation analysis, where orange represents positive correlation and dark blue represents negative correlation. The correlation coefficient is kept within the circle. Values with p < 0.05 are retained.

Figure 7

Proposed RhTPPs and RhTPPs genes respond to short light periods and weak light intensity through different expression patterns. A solid arrow indicates activation, and a line ending in a bar indicates negative adjustment.