Stem transcriptome reveals mechanisms to reduce the energetic cost of shade-avoidance responses in tomato

Abstract

While the most conspicuous response to low red/far-red ratios (R:FR) of shade light perceived by phytochrome is the promotion of stem growth, additional, less obvious effects may be discovered by studying changes in the stem transcriptome. Here, we report rapid and reversible stem transcriptome responses to R:FR in tomato (Solanum lycopersicum). As expected, low R:FR promoted the expression of growth-related genes, including those involved in the metabolism of cell wall carbohydrates and in auxin responses. In addition, genes involved in flavonoid synthesis, isoprenoid metabolism, and photosynthesis (dark reactions) were overrepresented in clusters showing reduced expression in the stem of low R:FR-treated plants. Consistent with these responses, low R:FR decreased the levels of flavonoids (anthocyanin, quercetin, kaempferol) and selected isoprenoid derivatives (chlorophyll, carotenoids) in the stem and severely reduced the photosynthetic capacity of this organ. However, lignin contents were unaffected. Low R:FR reduced the stem levels of jasmonate, which is a known inducer of flavonoid synthesis. The rate of stem respiration was also reduced in low R:FR-treated plants, indicating that by downsizing the stem photosynthetic apparatus and the levels of photoprotective pigments under low R:FR, tomato plants reduce the energetic cost of shade-avoidance responses.

Figure 1.

Shared and specific responses of the stem and leaves of tomato to low R:FR. A, Tomato plant grown under low R:FR for 4 d compared with the high-R:FR control. B, Clusters of genes with stem and/or leaf expression affected by 4 d of low compared with high R:FR. Clusters A1 to A9 show additive effects of R:FR and organ, and clusters I1 to I11 show interaction between R:FR and organ. C, Clusters of genes with early stem expression responses to low R:FR (S1–S9). In B and C, data are means and se of all the genes represented in the cluster (the number of genes is indicated in parentheses); clusters with less than 30 genes are not included (Supplemental Table S1), and overrepresented GO terms are indicated. D, Number of genes with expression promoted or inhibited by 4 d of low, compared with high, R:FR in the stem and/or leaves (the number of genes with at least 2-fold change is given in parentheses). E, Correlation of the log₁₀ low-R:FR/high-R:FR expression ratio of the genes significantly affected after 4 h and 4 d by low R:FR. [See online article for color version of this figure.]

Figure 2.

Promotion of stem growth by low R:FR. A, Stem length increment as affected by 1 or 4 h of low R:FR and the subsequent transfer back to high R:FR. The growth rate is indicated close to the corresponding regression line. B, Size (length or area) and dry weight of the stem and first pair of leaves in seedlings exposed to 4 d of low R:FR compared with the high-R:FR controls. C, Low R:FR promotes the expression of auxin response genes (IAA7, IAA4, Les. 3702, Les. 4097) and cell wall genes (XTH9, CELL WALL INVERTASE [CWI]). In A and B, data are means ± se of seven plant replicates, and significant effects of low compared with high R:FR are indicated (t test, *** P < 0.001). Data shown in B are from Supplemental Tables S1 and S2. WL, White light.

Figure 3.

Reduced levels of flavonoids in the stem of low-R:FR-treated plants. The chart shows the steps of lignin and flavonoid (anthocyanin, flavonol) biosynthesis catalyzed by enzymes encoded by genes showing significant expression responses to R:FR. The expression in the stem and leaf of plants treated for 4 d with low R:FR compared with their high-R:FR controls and/or in the stem of seedlings exposed for 1 or 4 h to low R:FR and subsequently transferred back to high R:FR is shown when significant differences were observed (data are from Supplemental Tables S1 and S2). The levels of lignin, kaempferol, rutin, quercetin, and anthocyanin in plants treated for 4 d with low R:FR compared with their high-R:FR controls are indicated (data are means ± se of four to 12 plant replicates, and significant effects of low compared with high R:FR are indicated [t test, * P < 0.05, ** P < 0.01]). ANS, Anthocyanin synthase; C4H, transcinnamate 4-monooxygenase; CHI, chalcone isomerase-like protein; CHS, chalcone synthase; DFR, dihydroflavonol 4-reductase; F3H, flavanone 3β-hydroxylase; FLS, flavonol synthase; FW, fresh weight; IFR, isoflavone reductase; HQT, hydroxycinnamoyl-CoA quinate transferase; RT, rhamnosyltransferase; UFGT, flavonoid 3-glucosyltransferase; UGG, UDP-Glc:glucosyltransferase. The chart is based on the BRENDA database (http://www.brenda-enzymes.info; Scheer et al., 2011).

Figure 4.

Low R:FR severely reduces the stem photosynthetic capacity. A, Net carbon dioxide exchange in the leaves of plants treated for 4 d with low R:FR compared with their high-R:FR controls. B, The same in the stem of these plants. C, Internal carbon dioxide concentration for the stems shown in B. D, Low R:FR reduces the expression of Calvin cycle protein genes. E, Chlorophyll content in the stem and leaf of plants treated for 4 d with low R:FR compared with their high-R:FR controls. F, The same for carotenoid content. In A to C, E, and F, data are means ± se of six (A), three (B and C), or seven (E and F) plant replicates, and significant effects of low compared with high R:FR are indicated (t test, * P < 0.05, ** P < 0.01, *** P < 0.001). In A, maximum net carbon dioxide exchange is significantly different if the rates are corrected by using rates at 300 μmol m⁻² s⁻¹ as covariate. Data shown in D are from Supplemental Table S2. WL, White light.

Figure 5.

Low R:FR alters the hormonal balance. JA, ABA, ACC, and IAA in the stem and leaves of plants treated for 4 d with low R:FR compared with their high-R:FR controls. Data are means ± se of five plant replicates, and significant effects of low compared with high R:FR are indicated (t test, * P < 0.05, *** P < 0.001). DW, Dry weight.

Figure 6.

Exogenous JA applied to the stem promotes stem anthocyanin (A) and stem growth (B) in high- but not in low-R:FR-treated plants. The stem was painted with a brush soaked in a water solution containing 450 μm JA and 0.015% (v/v) Silwet, twice during the first day of treatment and daily during the subsequent 3 d of treatment. Controls were painted similarly but without JA. Data are means ± se of three (A) or seven (B) plant replicates, and significant effects of JA are indicated (t test, *** P < 0.001). FW, Fresh weight.