Transcriptome responses to temperature, water availability and photoperiod are conserved among mature trees of two divergent Douglas-fir provenances from a coastal and an interior habitat

Abstract

BackgroundLocal adaptation and phenotypic plasticity are important components of plant responses to variations in environmental conditions. While local adaptation has been widely studied in trees, little is known about plasticity of gene expression in adult trees in response to ever changing environmental conditions in natural habitats. Here we investigate plasticity of gene expression in needle tissue between two Douglas-fir provenances represented by 25 adult trees using deep RNA sequencing (RNA-Seq).ResultsUsing linear mixed models we investigated the effect of temperature, soil water availability and photoperiod on the abundance of 59189 detected transcripts. Expression of more than 80 % of all identified transcripts revealed a response to variations in environmental conditions in the field. GO term overrepresentation analysis revealed gene expression responses to temperature, soil water availability and photoperiod that are highly conserved among many plant taxa. However, expression differences between the two Douglas-fir provenances were rather small compared to the expression differences observed between individual trees. Although the effect of environment on global transcript expression was high, the observed genotype by environment (GxE) interaction of gene expression was surprisingly low, since only 21 of all detected transcripts showed a GxE interaction.ConclusionsThe majority of the transcriptome responses in plant leaf tissue is driven by variations in environmental conditions. The small variation between individuals and populations suggests strong conservation of this response within Douglas-fir. Therefore we conclude that plastic transcriptome responses to variations in environmental conditions are only weakly affected by local adaptation in Douglas-fir.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-3022-6) contains supplementary material, which is available to authorized users.

Grapevine field experiments reveal the contribution of genotype, the influence of environment and the effect of their interaction (G×E) on the berry transcriptome

“…G×E studies in woody perennial plants are rare because a precise definition of the E component is often challenging in field studies (Brosché et al ., ; Holliday et al ., ; Travers et al ., ; Richards et al ., ; Dal Santo et al ., , 2016b; Hess et al ., ). We have addressed the lack of a temporal G×E component (Grishkevich and Yanai, ) by providing a time‐based approach for both G (fruit development) and E (vintage), given that both aspects are important in an environmentally sensitive crop such as grapevine, particularly in the context of global climate change.…”

“…The stability of crop growth and yields must be maintained over diverse and dynamic environments, and an understanding of how the genotype responds to and interacts with the environment is necessary to predict the effects of climate change on ecology and modern agriculture (Fournier‐Level et al ., ; Sasaki et al ., ). However, the environmental component of this complex interaction is often expensive or impossible to define with any precision in natural environments, and studies based on variation of gene expression in open‐field‐grown plants do not tend to address G×E interactions in detail (Brosché et al ., ; Holliday et al ., ; Travers et al ., ; Richards et al ., ; Dal Santo et al ., , ; Hess et al ., ).…”

RNA-Seq analysis of Clerodendrum inerme (L.) roots in response to salt stress

“…In recent years, RNA-seq, as an important strategy in the investigation of the expression of a large number genes in a given tissue at a given time point, has been widely used to research the responses of plants to abiotic stress [36,37], particularly salt stress [38,39]. And de novo assembly makes it possible for a detailed genetic analysis to be performed on any organism [40] and has been applied to a number of halophytes to uncover their mechanisms of salt tolerance.…”

Advances in ecological genomics in forest trees and applications to genetic resources conservation and breeding

“…; Hess et al . ), but our understanding of the potential for this and related (e.g. epigenomic) resilience mechanisms to buffer the effects of climate change is still limited.…”