Abstract
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 FST 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.
Highlights
In captive breeding of brown trout (Salmo trutta L.) for conservation, supplemental stocking or farming, wild specimens are captured, gametes striped, and fertilization conducted artificially
A variety of assay tools, analysis techniques and software packages are available for geneticists studying topics related to conservation biology and molecular ecology, with both simple sequence repeats (SSRs) (Balloux & Lugon-Moulin, 2002) and single nucleotide polymorphisms (SNPs) (Thomas & Kejariwal, 2004) representing powerful tools for genetic studies
SNPs are prevalently biallelic in contrast to SSRs; SNP assays are easy to standardize across detection platforms and laboratories and may be developed so that thousands of robust markers are genotyped simultaneously in a single sample
Summary
In captive breeding of brown trout (Salmo trutta L.) for conservation, supplemental stocking or farming, wild specimens are captured, gametes striped, and fertilization conducted artificially. In monitoring populations from a conservation perspective, important population-genetic indices are calculated based on SSRs or SNPs, but to explore the effects of selection, SNPs are better suited than the basically neutral SSRs. This study includes three groups of brown trout, from the same population, of which two groups comprise wild specimens and one is composed of F1-generation individuals reared in a hatchery. The hatchery-reared fish (Figure 1) are used for annual supportive stocking in a downstream lake and are bred from a mixture of two local strains to maintain locally adapted genotypes. One of those is the wild fish strain of the two former groups. The following hypothesis were tested as follows: (1) Genetic differentiation between different age groups of the same cohort and population, is in part affected by selective forces, potentially linked to selective traits such as body size, that is, individual growth. (2) Artificial spawning and breeding in hatchery will, due to the lack of sexual selection and natural selection by the environment, result in a “hatchery genepool” differing from that of their pristine relatives
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
