ArticleFrontiers in genetics2012
Genetical Genomics Reveals Large Scale Genotype-By-Environment Interactions in Arabidopsis thaliana.
Article in Frontiers in genetics, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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Who cites it
23 citing papers in PubMed.
- Article
- Systems genomics of salinity stress response in rice.bioRxiv : the preprint server for biology · 2024Article
- Plasticity of maternal environment-dependent expression-QTLs of tomato seeds.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2023Article
- Prioritizing candidate eQTL causal genes in Arabidopsis using RANDOM FORESTS.G3 (Bethesda, Md.) · 2022Article
- The genetics of gene expression in a Caenorhabditis elegans multiparental recombinant inbred line population.G3 (Bethesda, Md.) · 2021Article
- Transcriptome and physiological analyses provide insights into the leaf epicuticular wax accumulation mechanism in yellowhorn.Horticulture research · 2021Article
- Network Analysis PrioritizesG3 (Bethesda, Md.) · 2020Article
- Dissecting the eQTL Micro-Architecture inFrontiers in genetics · 2020Article
- WormQTL2: an interactive platform for systems genetics in Caenorhabditis elegans.Database : the journal of biological databases and curation · 2020Article
- Ras/MAPK Modifier Loci Revealed by eQTL inG3 (Bethesda, Md.) · 2017Article
- Genetic Dissection of Morphometric Traits Reveals That Phytochrome B Affects Nucleus Size and Heterochromatin Organization inG3 (Bethesda, Md.) · 2017Article
- Contribution of trans regulatory eQTL to cryptic genetic variation in C. elegans.BMC genomics · 2017Article
- Metabolomic analysis of tomato seed germination.Metabolomics : Official journal of the Metabolomic Society · 2017Article
- Construction of a High-Density Genetic Map from RNA-Seq Data for an Arabidopsis Bay-0 × Shahdara RIL Population.Frontiers in genetics · 2017Article
- Leaf Growth Response to Mild Drought: Natural Variation in Arabidopsis Sheds Light on Trait Architecture.The Plant cell · 2016Article
- Natural Genetic Variation Differentially Affects the Proteome and Transcriptome in Caenorhabditis elegans.Molecular & cellular proteomics : MCP · 2016Article
- Transcriptome sequencing reveals the roles of transcription factors in modulating genotype by nitrogen interaction in maize.Plant cell reports · 2015Article
- On predicting regulatory genes by analysis of functional networks in C. elegans.BioData mining · 2015Article
- Widespread genomic incompatibilities in Caenorhabditis elegans.G3 (Bethesda, Md.) · 2014Article
- WormQTLHD--a web database for linking human disease to natural variation data in C. elegans.Nucleic acids research · 2014Article
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5 authors.
Funding
No grant is acknowledged in the PubMed record.
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.
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