Regulatory Architecture of Gene Expression Variation in the Threespine Stickleback Gasterosteus aculeatus.
Much adaptive evolutionary change is underlain by mutational variation in regions of the genome that regulate gene expression rather than in the coding regions of the genes themselves. An understanding of the role of gene expression variation in facilitating local adaptation will be aided by an understanding of underlying regulatory networks. Here, we characterize the genetic architecture of gene expression variation in the threespine stickleback (Gasterosteus aculeatus), an important model in the study of adaptive evolution. We collected transcriptomic and genomic data from 60 half-sib families using an expression microarray and genotyping-by-sequencing, and located expression quantitative trait loci (eQTL) underlying the variation in gene expression in liver tissue using an interval mapping approach. We identified eQTL for several thousand expression traits. Expression was influenced by polymorphism in both cis- and trans-regulatory regions. Trans-eQTL clustered into hotspots. We did not identify master transcriptional regulators in hotspot locations: rather, the presence of hotspots may be driven by complex interactions between multiple transcription factors. One observed hotspot colocated with a QTL recently found to underlie salinity tolerance in the threespine stickleback. However, most other observed hotspots did not colocate with regions of the genome known to be involved in adaptive divergence between marine and freshwater habitats.
Division of Genetics and Physiology, Department of Biology, University of Turku, Finland.
Victoria L
0000-0003-0992-7403
VL
Pritchard
Division of Genetics and Physiology, Department of Biology, University of Turku, Finland.|Ecological Genetics Research Unit, Department of Biosciences, University of Helsinki, Finland.
Heidi M
HM
Viitaniemi
Ecological Genetics Research Unit, Department of Biosciences, University of Helsinki, Finland.|Institut Méditerranéen de la Biodiversité et d'Ecologie Marine et Continentale, Marseille, France.
R J Scott
0000-0002-0392-7413
RJ
McCairns
Ecological Genetics Research Unit, Department of Biosciences, University of Helsinki, Finland.
Juha
0000-0001-9614-0072
J
Merilä
Division of Genetics and Physiology, Department of Biology, University of Turku, Finland.
Mikko
0000-0003-0593-1018
M
Nikinmaa
Division of Genetics and Physiology, Department of Biology, University of Turku, Finland.
Craig R
0000-0002-3687-8435
CR
Primmer
Division of Genetics and Physiology, Department of Biology, University of Turku, Finland erica.leder@nhm.uio.no.|Natural History Museum, University of Oslo, 0318, Norway.|Institute of Veterinary Medicine and Animal Sciences, Estonian University of Life Sciences, Tartu, Estonia.
Erica H
0000-0002-7160-2290
EH
Leder
D000222:Adaptation, Physiological / Q000235:genetics*; D000818:Animals; D019143:Evolution, Molecular; D005618:Fresh Water; D005786:Gene Expression Regulation; D014644:Genetic Variation; D016678:Genome; D049750:Genome, Insect; D005838:Genotype; D010641:Phenotype; D040641:Quantitative Trait Loci / Q000235:genetics; D012641:Selection, Genetic / Q000235:genetics*; D023701:Smegmamorpha / Q000235:genetics* / Q000502:physiology
Baltic Sea; eQTL; gene expression; liver; threespine stickleback