Global gene expression analysis in etiolated and de-etiolated seedlings in conifers

Abstract

Plant life cycle begins with germination of seed below the ground. This is followed by seedling’s development in the dark: skotomorphogenesis; and then a light-mediated growth: photomorphogenesis. After germination, hypocotyl grows rapidly to reach the sun, which involves elongation of shoot at the expense of root and cotyledons. Upon reaching ground level, seedling gets exposed to sunlight following a switch from the etiolated (skotomorphogenesis) to the de-etiolated (photomorphogenesis) stage, involving a series of molecular and physiological changes. Gymnosperms have evolved very differently and adopted diverse strategies as compared to angiosperms; with regards to response to light quality, conifers display a very mild high-irradiance response as compared to angiosperms. Absence of apical hook and synthesis of chlorophyll during skotomorphogenesis are two typical features in gymnosperms which differentiate them from angiosperms (dicots). Information regarding etiolation and de-etiolation processes are well understood in angiosperms, but these mechanisms are less explored in conifer species. It is, therefore, interesting to know how similar these processes are in conifers as compared to angiosperms. We performed a global expression analysis (RNA sequencing) on etiolated and de-etiolated seedlings of two economically important conifer species in Sweden to review the differentially expressed genes associated with the two processes. Based on the results, we propose that high levels of HY5 in conifers under DARK condition coupled with expression of few other genes associated with de-etiolation in angiosperms e.g. SPA , DET1 (lower expression under DARK) and CRY1 (higher expression under DARK), leads to partial expression of photomorphogenic genes in the DARK phenotype in conifers as displayed by absence of apical hook, opening of cotyledons and synthesis of chlorophyll.

Comparative Transcriptomic Analysis Provides Novel Insights into the Blanched Stem of Oenanthe javanica

“…We also found several downregulated genes in the post-blanched samples that encode AUX1, ARR-B, and SAUR. IAA1 is induced by auxin under light stress and helps in the elongation of coleoptile in rice [22]. We also found IAA1 upregulation in blanched samples, and IAA1 downregulated in the control samples.…”

“…Plants with repressed Lhcb1 and Lhcb2 genes are pale green and have low chlorophyll content [18,20]. The low chlorophyll content and pale color of water dropwort could be due to the downregulation of these Lhc genes [21,22].…”

“…Auxin is used to stimulate organogenesis and patterning in plants [22]. PIN and PILS show a significant role in auxin accumulation in developing organs, and the upregulation of these genes are positively associated with IAA accumulation [27,28].…”

Influence of Light of Different Spectral Compositions on the Growth, Photosynthesis, and Expression of Light-Dependent Genes of Scots Pine Seedlings

“…Gymnosperms have the ability to synthesize chlorophyll in the dark due to the presence of the three genes of light-independent protochlorophyllide oxidoreductase L, N, and B ( ChlL , ChlN , and ChlB ) involved in the light-independent reduction of protochlorophyllide to chlorophyllide [ 30 ]. This also confirms the presence of special light regulation in conifers, which makes them a unique object of research.…”

“…The features of development and metabolism in plants induced by light of different spectral composition are primarily mediated by changes in the expression of light-dependent genes [ 20 , 30 ], including those encoding chloroplast proteins, photoreceptor apoproteins, transcription factors, and enzymes involved in the biosynthesis of secondary metabolites [ 31 ] and phytohormone signaling. In our work, we showed that several genes involved in the response to RL or BL are expressed in different ways.…”