BrphyB is critical for rapid recovery to darkness in mature Brassica rapa leaves

Here, we examine the transcriptomic response of adult wild-type and BrphyB leaves to darkening and recovery in light. Three days of dark was sufficient to elicit a response in wild type leaves suggesting a shift from carbon fixation and nutrient acquisition to active redistribution of cellular resources. Upon a return to light, wild-type leaves appeared to transcriptionally return to a pre-darkness state restoring a focus on nutrient acquisition. BrphyB mutant plants have a similar response with key differences in genes involved in photosynthesis and light response which deviate from the wild type transcriptional dynamics. Genes targeted to the chloroplast are especially affected. Adult plants had fewer, larger chloroplasts suggesting a link between phytochromes, chloroplast development, photosynthetic deficiencies and resource allocation. Overall design: Two developmentally matched leaves from each wild-type and BrphyB-3 plant were tagged that corresponded to the first and second true leaves. Samples were collected at 5 ZT using a standard whole punch (28 mm2 of leaf tissue) with symmetrical harvest for chlorophyll assay, chloroplast measurements and transcriptome analysis. Tissue from 3 plants was combined to make one biological replicate. At 3 weeks of age the “Pre” sample was collected from the first leaf while the second one was covered with tinfoil. 24 hours later the “24hr” sample were harvested from the uncovered leaf, the same leaf that provided the “Pre” sample. Then, 48 hours later the tinfoil was removed from the covered leaf and the “dark” samples were similarly collected. Finally, 24 hours later the “recovery” samples were collected from this same leaf. RNA-seq data from 4 biological replicates of wild-type (WT_3 to WT_6), and 3 of BrphyB-3 (phyB_3 to phyB_5) plants were used in this study.