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Originally published as Genetics Published Articles Ahead of Print on July 27, 2008.
Genetics, Vol. 179, 1903-1917, August 2008, Copyright © 2008
doi:10.1534/genetics.107.086306
Pervasive Sex-Linked Effects on Transcription Regulation As Revealed by Expression Quantitative Trait Loci Mapping in Lake Whitefish Species Pairs (Coregonus sp., Salmonidae)
N. Derome*,1,
B. Bougas*,
S. M. Rogers
,
A. R. Whiteley
,
A. Labbe
,
J. Laroche** and
L. Bernatchez*
* Département de Biologie, Département de Mathématiques and ** Centre de Université Bioinformatique et de Biologie Computationnelle, Université Laval, Québec, Québec G1V 0A6, Canada, Department of Zoology, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada and Department of Natural Sciences, University of Alaska Southeast, Juneau, Alaska 99801
1 Corresponding author: Département de Biologie, Université Laval, Québec, QC, G1V 0A6, Canada.
E-mail: nicolas.derome{at}bio.ulaval.ca
Mapping of expression quantitative trait loci (eQTL) is a powerful means for elucidating the genetic architecture of gene regulation. Yet, eQTL mapping has not been applied toward investigating the regulation architecture of genes involved in the process of population divergence, ultimately leading to speciation events. Here, we conducted an eQTL mapping experiment to compare the genetic architecture of transcript regulation in adaptive traits, differentiating the recently evolved limnetic (dwarf) and benthic (normal) species pairs of lake whitefish. The eQTL were mapped in three data sets derived from an F1 hybrid-dwarf backcrossed family: the entire set of 66 genotyped individuals and the two sexes treated separately. We identified strikingly more eQTL in the female data set (174), compared to both male (54) and combined (33) data sets. The majority of these genes were not differentially expressed between male and female progeny of the backcross family, thus providing evidence for a strong pleiotropic sex-linked effect in transcriptomic regulation. The subtelomeric region of a linkage group segregating in females encompassed >50% of all eQTL, which exhibited the most pronounced additive effects. We also conducted a direct comparison of transcriptomic profiles between pure dwarf and normal progeny reared in controlled conditions. We detected 34 differentially expressed transcripts associated with eQTL segregating only in sex-specific data sets and mostly belonging to functional groups that differentiate dwarf and normal whitefish in natural populations. Therefore, these eQTL are not related to interindividual variation, but instead to the adaptive and historical genetic divergence between dwarf and normal whitefish. This study exemplifies how the integration of genetic and transcriptomic data offers a strong means for dissecting the functional genomic response to selection by separating mapping family-specific effects from genetic factors under selection, potentially involved in the phenotypic divergence of natural populations.
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  S. Renaut, A.W. Nolte, and L. Bernatchez Gene Expression Divergence and Hybrid Misexpression between Lake Whitefish Species Pairs (Coregonus spp. Salmonidae) Mol. Biol. Evol., April 1, 2009; 26(4): 925 - 936. [Abstract] [Full Text] [PDF]
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J. Jeukens, D. Bittner, R. Knudsen, and L. Bernatchez Candidate Genes and Adaptive Radiation: Insights from Transcriptional Adaptation to the Limnetic Niche among Coregonine Fishes (Coregonus spp., Salmonidae) Mol. Biol. Evol., January 1, 2009; 26(1): 155 - 166. [Abstract] [Full Text] [PDF]
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