Transcriptome Analysis Reveals New Insights into the Bacterial Wilt Resistance Mechanism Mediated by Silicon in Tomato

Abstract

Bacterial wilt is a devastating disease of tomato caused by soilborne pathogenic bacterium Ralstonia solanacearum. Previous studies found that silicon (Si) can increase tomato resistance against R. solanacearum, but the exact molecular mechanism remains unclear. RNA sequencing (RNA-Seq) technology was used to investigate the dynamic changes of root transcriptome profiles between Si-treated (+Si) and untreated (-Si) tomato plants at 1, 3, and 7 days post-inoculation with R. solanacearum. The contents of salicylic acid (SA), ethylene (ET), and jasmonic acid (JA) and the activity of defense-related enzymes in roots of tomato in different treatments were also determined. The burst of ET production in roots was delayed, and SA and JA contents were altered in Si treatment. The transcriptional response to R. solanacearum infection of the +Si plants was quicker than that of the untreated plants. The expression levels of differentially-expressed genes involved in pathogen-associated molecular pattern-triggered immunity (PTI), oxidation resistance, and water-deficit stress tolerance were upregulated in the Si-treated plants. Multiple hormone-related genes were differentially expressed in the Si-treated plants. Si-mediated resistance involves mechanisms other than SA- and JA/ET-mediated stress responses. We propose that Si-mediated tomato resistance to R. solanacearum is associated with activated PTI-related responses and enhanced disease resistance and tolerance via several signaling pathways. Such pathways are mediated by multiple hormones (e.g., SA, JA, ET, and auxin), leading to diminished adverse effects (e.g., senescence, water-deficit, salinity and oxidative stress) normally caused by R. solanacearum infection. This finding will provide an important basis to further characterize the role of Si in enhancing plant resistance against biotic stress.

Keywords: Ralstonia solanacearum; induced resistance; silicon; tomato; transcriptomics.

Figure 1

Responses of silicon (Si)-treated (+Si) and non-Si-treated (−Si) tomato plants to R. solanacearum infection. (A) Disease symptoms. (B) Disease index. (C) Bacterial population. FW: fresh weight. (D) Si content. DW: dry weight. Data presented are means ± standard error (SE) of three replicates. Asterisks denote a significant difference between treatments at the same time-point (Student’s t-test, p < 0.05).

Figure 2

Hormone measurements of silicon (Si)-treated (+Si) and non-Si-treated (−Si) tomato plants after infection. (A) ET production. (B) SA content. (C) JA content. FW: fresh weight. Data presented are means ± standard error (SE) of three replicates. Asterisks denote a significant difference between treatments at the same time-point (Student’s t-test, p < 0.05).

Figure 3

Differentially-expressed genes (DEGs) in different paired-comparisons. (A) The numbers of DEGs identified from the three comparisons. (B,C) Venn diagram for DEGs identified in different comparisons. +Si1, +Si3, and +Si7 represents silicon (Si)-treated (+Si) samples obtained at 1, 3, and 7dpi, respectively; −Si1, −Si3 and −Si7 represents non-Si-treated (−Si) samples obtained at 1, 3, and 7dpi, respectively.

Figure 4

Coefficient analysis of gene expression levels obtained from RNA-Seq and qRT-PCR data. Log₂ fold change: log₂ fold-change in gene expression between Si-treated and non-Si-treated samples.

Figure 5

Expression profiles of DEGs in the four main clusters. The top left-hand corner indicates the number of DEGs belonging to the profile. The lower left-hand corner contains the p-value of the profile. The gray lines represent the DEGs, and the bold black line represents the expression tendency of all these DEGs. The x-axis represents days after R. solanacearum inoculation (dpi). The Y-axes represents log₂ fold change in gene expression between treatments.

Figure 6

Heat map of DEGs potentially associated with silicon (Si)-mediated tomato resistance against R. solanacearum. The columns represent the pairwise comparisons of Si-treated samples (+Si) and their respective non-Si-treated samples (−Si) at three time points post-inoculation. +Si1, +Si3, and +Si7 represent Si-treated samples obtained at 1, 3, and 7dpi, respectively; −Si1, −Si3, and −Si7 represent non-Si-treated samples obtained at 1, 3, and 7dpi, respectively. Relative transcript level was indicated on a color scale from magenta (high) to green (low). DEGs names are on the right side of the figure. Details of the genes shown in heat maps are available in Table S10.

Figure 7

Hypothetical schematic model showing mechanisms involved in silicon (Si)-mediated tomato resistance against R. solanacearum. Upregulated genes are marked in red italics, and downregulated genes are marked in blue italics. Black dotted lines with arrows denote uncertain regulation; red lines with arrows denote positive regulation; and blue lines with bars indicate negative regulation. Question marks indicate unclear events. Several crosstalk and feedback mechanisms between multiple pathways are not presented in the model.