Abstract
One of the major goals of quantitative genetics is to unravel the complex interactions between molecular genetic factors and the environment. The effects of these genotype-by-environment interactions also affect and cause variation in gene expression. The regulatory loci responsible for this variation can be found by genetical genomics that involves the mapping of quantitative trait loci (QTLs) for gene expression traits also called expression-QTL (eQTLs). Most genetical genomics experiments published so far, are performed in a single environment and hence do not allow investigation of the role of genotype-by-environment interactions. Furthermore, most studies have been done in a steady state environment leading to acclimated expression patterns. However a response to the environment or change therein can be highly plastic and possibly lead to more and larger differences between genotypes. Here we present a genetical genomics study on 120 Arabidopsis thaliana, Landsberg erecta × Cape Verde Islands, recombinant inbred lines (RILs) in active response to the environment by treating them with 3 h of shade. The results of this experiment are compared to a previous study on seedlings of the same RILs from a steady state environment. The combination of two highly different conditions but exactly the same RILs with a fixed genetic variation showed the large role of genotype-by-environment interactions on gene expression levels. We found environment-dependent hotspots of transcript regulation. The major hotspot was confirmed by the expression profile of a near isogenic line. Our combined analysis leads us to propose CSN5A, a COP9 signalosome component, as a candidate regulator for the gene expression response to shade.
Highlights
Developmental processes and the responses of organisms to their environment are largely genetically determined
NATURAL VARIATION IN TRANSCRIPT ABUNDANCE UNDER LOW LIGHT CONDITIONS The recombinant inbred lines (RILs) generated from the parental Arabidopsis accessions Landsberg erecta (Ler) and Cape Verde Islands (Cvi) show a high level of phenotypic variation in response to low light, indicating there is a strong influence of genotype on the shade avoidance syndrome (SAS)-related responses (Van Zanten et al, 2010)
To assess the effect of genotype on the transcriptional response to low light, genome wide transcript levels were measured in 120 Ler/Cvi RILs and their parental lines
Summary
Developmental processes and the responses of organisms to their environment are largely genetically determined. Regulatory loci that affect the expression of many genes are called Hotspots for transcript regulation (HTRs) These genomic regions, enriched in eQTLs, are identified in most genetical genomics experiments (Brem et al, 2002; Schadt et al, 2003; Bystrykh et al, 2005; Li et al, 2006; Keurentjes et al, 2007; West et al, 2007; Zhang et al, 2011; Snoek et al, 2012) and point to, so called, master regulators. Regulatory genes do not always exert their effect on target gene expression by changing their www.frontiersin.org
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