Genetical genomics reveals large scale genotype-by-environment interactions in Arabisopsis thaliana

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-byenvironment
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.