Transcriptome analysis of shade avoidance and shade tolerance in conifers

Abstract

Main conclusion Gymnosperms respond differently to light intensity and R:FR; although some aspects of shade response appear conserved, yet underlying mechanisms seem to be diverse in gymnosperms as compared to angiosperms. Shade avoidance syndrome (SAS) is well-characterized in the shade intolerant model species Arabidopsis thaliana whereas much less is known about shade tolerance response (STR), yet regulation of SAS and STR with reference to conifers remains poorly understood. We conducted a comparative study of two conifer species with contrasting responses to shade, Scots pine (shade-intolerant) and Norway spruce (shade-tolerant), with the aim to understand mechanisms behind SAS and STR in conifers. Pine and spruce seedlings were grown under controlled light and shade conditions, and hypocotyl and seedling elongation following different light treatments were determined in both species as indicators of shade responses. Red to farred light ratio (R:FR) was shown to trigger the shade response in Norway spruce. In Scots pine, we observed an interaction between R:FR and light intensity. RNA sequencing (RNA-Seq) data revealed that SAS and STR responses included changes in expression of genes involved primarily in hormone signalling and pigment biosynthesis. From the RNA-Seq analysis, we propose that although some aspects of shade response appear to be conserved in angiosperms and gymnosperms, yet the underlying mechanisms may be different in gymnosperms that warrants further research.

Molecular signatures of local adaptation to light in Norway Spruce: role of lignin mediated immunity

“…Norway spruce is a shade tolerant conifer species. It is interesting that in our earlier work we reported that SCRM2, NAC036 and FLZ6 were responsible for the shade tolerant response in Norway spruce (Ranade et al , 2019) and our current finding suggest that missense polymorphisms in these genes show a latitudinal cline in response to shade. DRA2 and PAR2 are the shade responsive genes that were up-regulated under SHADE, in the northern population.…”

“…Overexpression of NAC036 resulted in a dwarf phenotype in A. thaliana (Kato et al , 2010). This gene was found to be associated with the shade tolerant response in Norway spruce were it was reported to be up-regulated under SHADE conditions (Ranade et al , 2019). In the current work, NAC036 was up-regulated in response to SHADE in the northern trees as compared to the southern ones.…”

“…increased sensitivity to detect genes that were differentially expressed between conditions). Isolation of total RNA, RNA-Seq and pre-processing of RNA-Seq data was carried as described in our previous work (Ranade et al , 2019). The RNA-Seq data was deposited to the ENA and is accessible under the accession number RJEB19683.…”

“…In the current study, we aimed to identify the genomic signals of local adaptation in response to low Red:Far-red (R:FR) ratio (SHADE) in this species which is shade tolerant. R:FR ratio is considered as a reliable indicator of the degree of shade and low values of it can activate shade-avoidance and shade-tolerance responses (Ranade et al , 2019). In this species, such variation is characterized by an increase in requirement of FR (lower R:FR) with latitude in order to maintain growth (Clapham et al , 1998, Mølmann et al , 2006).…”

Transcriptional analyses reveal the molecular mechanism governing shade tolerance in the invasive plant Solidago canadensis

“…The expression of genes related to photosystem I and photosystem II could be affected by various light conditions (Rogowski et al, 2019). Shade avoidance and tolerance responses in plants could be reflected in the alteration of expressed genes, such as those involved in hormone signaling and pigment biosynthesis (Ranade, Delhomme, & García‐Gil, 2019).…”