RT Journal Article SR Electronic T1 Regulatory architecture of gene expression variation in the threespine stickleback, Gasterosteus aculeatus JF bioRxiv FD Cold Spring Harbor Laboratory SP 055061 DO 10.1101/055061 A1 Victoria L. Pritchard A1 Heidi M. Viitaniemi A1 R.J. Scott McCairns A1 Juha Merilä A1 Mikko Nikinmaa A1 Craig R. Primmer A1 Erica H. Leder YR 2016 UL http://biorxiv.org/content/early/2016/11/04/055061.abstract AB 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 QTL underlying the variation in gene expression (eQTL) 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 co-located with a QTL recently found to underlie salinity tolerance in the threespine stickleback. However, most other observed hotspots did not co-locate with regions of the genome known to be involved in adaptive divergence between marine and freshwater habitats.