Genetical Genomics Reveals Large Scale Genotype-By-Environment Interactions in Arabidopsis thaliana

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.

Leaf Growth Response to Mild Drought: Natural Variation in Arabidopsis Sheds Light on Trait Architecture

“…This observation is strengthened by the variance component analysis that indicated a clear role for trans-located SNPs for explaining the expression variation. Previous studies on RIL populations identified mainly cis variation to be associated with gene expression in general Keurentjes et al, 2007), whereas the environment-dependent expression showed enrichment in trans regulators (Cubillos et al, 2014;Lowry et al, 2013;Snoek et al, 2013). This general trend corresponds to our results; however, the absence of cis regulators for environmentdependent expression is striking, especially because cis loci typically have stronger effects on gene expression compared with trans (Fusi et al, 2012).…”

Natural Genetic Variation Differentially Affects the Proteome and Transcriptome in Caenorhabditis elegans

“…In total, 47 fractions were collected and pooled into 10 fractions based on the intensity measured by a UV-light detector at 214 nm. The reproducibility of the separation was controlled by running twice a self-mixed standard peptide mixture (adrenocorticotropin(1-16), angiotensinogen (1)(2)(3)(4)(5)(6)(7)(8)(9)(10)(11)(12)(13)(14), bradykinin(2-9), leu-enkephalin, substance P, and vasopressin). Pooled fractions were vacuum-centrifuged until complete dryness and resuspended in 50 l of 5% ACN, 0.1% TFA.…”

“…The broad-sense heritable variation in gene expression has been estimated to be up to 70% in the nematode Caenorhabditis elegans (3,4) and up to 80% in yeast (5). This high heritability and the ability to construct genetically segregating populations facilitate mapping of gene expression regulation and subsequent detection of expression quantitative trait loci (eQTL) 1 (5)(6)(7)(8)(9)(10)(11). eQTLs are genomic regions containing a polymorphism associated with variation in transcript abundance between genotypes (12).…”

“…eQTLs are genomic regions containing a polymorphism associated with variation in transcript abundance between genotypes (12). eQTL analysis provides insight into the underlying genetic architecture of complex traits and is valuable for the identification of pathways and gene networks (10,(13)(14)(15). A key question is whether gene expression variation is translated into variation at the proteome level and whether it affects functionally relevant proteins.…”

Expression Quantitative Trait Locus Mapping across Water Availability Environments Reveals Contrasting Associations with Genomic Features in Arabidopsis

“…Furthermore, gene expression can vary among individuals of a species due to natural genetic variation (G), and some genes may further exhibit genetic variation in their expression in response to the environment (expression GxE interactions). One promising avenue for studying natural variation in gene expression is through expression quantitative trait locus (eQTL) mapping (Li et al, 2006;Smith and Kruglyak, 2008;Keurentjes et al, 2007;Breitling et al, 2008;Fu et al, 2009, Cubillos et al, 2012a, 2012bSnoek et al, 2012). Here, mRNA transcript abundance for each gene in the genome is treated as a trait for genetic mapping.…”