Population transcriptomics of life-history variation in the genus Salmo

Giger, Thomas; Excoffier, Laurent; Amstutz, Ursula; Day, Philip J R; Champigneulle, Alexis; Hansen, Michael M; Kelso, Janet; Largiadèr, Carlo R (2008). Population transcriptomics of life-history variation in the genus Salmo. Molecular Ecology, 17(13), pp. 3095-3108. Oxford: Wiley-Blackwell 10.1111/j.1365-294X.2008.03820.x

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In this study, we demonstrate the power of applying complementary DNA (cDNA) microarray technology to identifying candidate loci that exhibit subtle differences in expression levels associated with a complex trait in natural populations of a nonmodel organism. Using a highly replicated experimental design involving 180 cDNA microarray experiments, we measured gene-expression levels from 1098 transcript probes in 90 individuals originating from six brown trout (Salmo trutta) and one Atlantic salmon (Salmo salar) population, which follow either a migratory or a sedentary life history. We identified several candidate genes associated with preparatory adaptations to different life histories in salmonids, including genes encoding for transaldolase 1, constitutive heat-shock protein HSC70-1 and endozepine. Some of these genes clustered into functional groups, providing insight into the physiological pathways potentially involved in the expression of life-history related phenotypic differences. Such differences included the down-regulation of genes involved in the respiratory system of future migratory individuals. In addition, we used linear discriminant analysis to identify a set of 12 genes that correctly classified immature individuals as migratory or sedentary with high accuracy. Using the expression levels of these 12 genes, 17 out of 18 individuals used for cross-validation were correctly assigned to their respective life-history phenotype. Finally, we found various candidate genes associated with physiological changes that are likely to be involved in preadaptations to seawater in anadromous populations of the genus Salmo, one of which was identified to encode for nucleophosmin 1. Our findings thus provide new molecular insights into salmonid life-history variation, opening new perspectives in the study of this complex trait.

Item Type:

Journal Article (Original Article)


08 Faculty of Science > Department of Biology > Institute of Ecology and Evolution (IEE) > Population Genetics
04 Faculty of Medicine > Department of Haematology, Oncology, Infectious Diseases, Laboratory Medicine and Hospital Pharmacy (DOLS) > Institute of Clinical Chemistry

UniBE Contributor:

Excoffier, Laurent; Amstutz, Ursula and Largiadèr, Carlo Rodolfo








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Date Deposited:

04 Oct 2013 15:05

Last Modified:

01 Sep 2015 16:12

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https://boris.unibe.ch/id/eprint/28107 (FactScience: 116762)

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