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 shadeavoidance responses.

SUMMARYLong days repeatedly enhance the expression of the FLOWERING LOCUS T (FT) gene during the evening and early night. This signal induces flowering despite low FT expression the rest of the day. To investigate whether this temporal behaviour transmits information, plants of Arabidopsis thaliana were exposed to different day-night cycles, including combinations that induced FT expression out of normal hours. Flowering time best correlated with the integral of FT expression over several days, corrected for a higher evening and early night sensitivity to FT. We generated a system to induce FT expression in a leaf removed 8-12 h later. The expression of flowering genes in the apex and flowering required cycles of induction repeated over several days. Evening and early night FT induction was the most effective. The temporal pattern of FT expression encodes information that discriminates long days from other inputs.