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Genetic differences between wild and hatchery‐bred brown trout (Salmo trutta L.) in single nucleotide polymorphisms linked to selective traits

To study effects from natural selection acting on brown trout in a natural stream habitat compared with a hatchery environment, 3,781 single nucleotide polymorphism (SNP) markers were analyzed in three closely related groups of brown trout (Salmo trutta L.). Autumn (W/0+, n = 48) and consecutive spr...

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Autores principales: Linløkken, Arne N., Haugen, Thrond O., Kent, Matthew P., Lien, Sigbjørn
Formato: Online Artículo Texto
Lenguaje:English
Publicado: John Wiley and Sons Inc. 2017
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5496558/
https://www.ncbi.nlm.nih.gov/pubmed/28690822
http://dx.doi.org/10.1002/ece3.3070
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author Linløkken, Arne N.
Haugen, Thrond O.
Kent, Matthew P.
Lien, Sigbjørn
author_facet Linløkken, Arne N.
Haugen, Thrond O.
Kent, Matthew P.
Lien, Sigbjørn
author_sort Linløkken, Arne N.
collection PubMed
description To study effects from natural selection acting on brown trout in a natural stream habitat compared with a hatchery environment, 3,781 single nucleotide polymorphism (SNP) markers were analyzed in three closely related groups of brown trout (Salmo trutta L.). Autumn (W/0+, n = 48) and consecutive spring (W/1+, n = 47) samples of brown trout individuals belonging to the same cohort and stream were retrieved using electrofishing. A third group (H/1+, n = 48) comprised hatchery‐reared individuals, bred from a mixture of wild parents of the strain of the two former groups and from a neighboring stream. Pairwise analysis of F(ST) outliers and analysis under a hierarchical model by means of ARLEQUIN software detected 421 (10.8%) candidates of selection, before multitest correction. BAYESCAN software detected 10 candidate loci, all of which were included among the ARLEQUIN candidate loci. Body length was significantly different across genotypes at 10 candidate loci in the W/0+, at 34 candidate loci in the W/1+ and at 21 candidate loci in the H/1+ group. The W/1+ sample was tested for genotype‐specific body length at all loci, and significant differences were found in 10.6% of all loci, and of these, 14.2% had higher frequency of the largest genotype in the W/1+ sample than in W/0+. The corresponding proportion among the candidate loci of W/1+ was 22.7% with genotype‐specific body length, and 88.2% of these had increased frequency of the largest genotype from W/0+ to W/1+, indicating a linkage between these loci and traits affecting growth and survival under this stream's environmental conditions. Bayesian structuring of all loci, and of the noncandidate loci suggested two (K = 2), alternatively four clusters (K = 4). This differed from the candidate SNPs, which suggested only two clusters. In both cases, the hatchery fish dominated one cluster, and body length of W/1+ fish was positively correlated with membership of one cluster both from the K = 2 and the K = 4 structure. Our analysis demonstrates profound genetic differentiation that can be linked to differential selection on a fitness‐related trait (individual growth) in brown trout living under natural vs. hatchery conditions. Candidate SNP loci linked to genes affecting individual growth were identified and provide important inputs into future mapping of the genetic basis of brown trout body size selection.
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spelling pubmed-54965582017-07-07 Genetic differences between wild and hatchery‐bred brown trout (Salmo trutta L.) in single nucleotide polymorphisms linked to selective traits Linløkken, Arne N. Haugen, Thrond O. Kent, Matthew P. Lien, Sigbjørn Ecol Evol Original Research To study effects from natural selection acting on brown trout in a natural stream habitat compared with a hatchery environment, 3,781 single nucleotide polymorphism (SNP) markers were analyzed in three closely related groups of brown trout (Salmo trutta L.). Autumn (W/0+, n = 48) and consecutive spring (W/1+, n = 47) samples of brown trout individuals belonging to the same cohort and stream were retrieved using electrofishing. A third group (H/1+, n = 48) comprised hatchery‐reared individuals, bred from a mixture of wild parents of the strain of the two former groups and from a neighboring stream. Pairwise analysis of F(ST) outliers and analysis under a hierarchical model by means of ARLEQUIN software detected 421 (10.8%) candidates of selection, before multitest correction. BAYESCAN software detected 10 candidate loci, all of which were included among the ARLEQUIN candidate loci. Body length was significantly different across genotypes at 10 candidate loci in the W/0+, at 34 candidate loci in the W/1+ and at 21 candidate loci in the H/1+ group. The W/1+ sample was tested for genotype‐specific body length at all loci, and significant differences were found in 10.6% of all loci, and of these, 14.2% had higher frequency of the largest genotype in the W/1+ sample than in W/0+. The corresponding proportion among the candidate loci of W/1+ was 22.7% with genotype‐specific body length, and 88.2% of these had increased frequency of the largest genotype from W/0+ to W/1+, indicating a linkage between these loci and traits affecting growth and survival under this stream's environmental conditions. Bayesian structuring of all loci, and of the noncandidate loci suggested two (K = 2), alternatively four clusters (K = 4). This differed from the candidate SNPs, which suggested only two clusters. In both cases, the hatchery fish dominated one cluster, and body length of W/1+ fish was positively correlated with membership of one cluster both from the K = 2 and the K = 4 structure. Our analysis demonstrates profound genetic differentiation that can be linked to differential selection on a fitness‐related trait (individual growth) in brown trout living under natural vs. hatchery conditions. Candidate SNP loci linked to genes affecting individual growth were identified and provide important inputs into future mapping of the genetic basis of brown trout body size selection. John Wiley and Sons Inc. 2017-05-30 /pmc/articles/PMC5496558/ /pubmed/28690822 http://dx.doi.org/10.1002/ece3.3070 Text en © 2017 The Authors. Ecology and Evolution published by John Wiley & Sons Ltd. This is an open access article under the terms of the Creative Commons Attribution (http://creativecommons.org/licenses/by/4.0/) License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.
spellingShingle Original Research
Linløkken, Arne N.
Haugen, Thrond O.
Kent, Matthew P.
Lien, Sigbjørn
Genetic differences between wild and hatchery‐bred brown trout (Salmo trutta L.) in single nucleotide polymorphisms linked to selective traits
title Genetic differences between wild and hatchery‐bred brown trout (Salmo trutta L.) in single nucleotide polymorphisms linked to selective traits
title_full Genetic differences between wild and hatchery‐bred brown trout (Salmo trutta L.) in single nucleotide polymorphisms linked to selective traits
title_fullStr Genetic differences between wild and hatchery‐bred brown trout (Salmo trutta L.) in single nucleotide polymorphisms linked to selective traits
title_full_unstemmed Genetic differences between wild and hatchery‐bred brown trout (Salmo trutta L.) in single nucleotide polymorphisms linked to selective traits
title_short Genetic differences between wild and hatchery‐bred brown trout (Salmo trutta L.) in single nucleotide polymorphisms linked to selective traits
title_sort genetic differences between wild and hatchery‐bred brown trout (salmo trutta l.) in single nucleotide polymorphisms linked to selective traits
topic Original Research
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5496558/
https://www.ncbi.nlm.nih.gov/pubmed/28690822
http://dx.doi.org/10.1002/ece3.3070
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