Genetics and Habitat Management

Verspoor, Eric; Leániz, Carlos García de; McGinnity, P.

doi:10.1002/9780470995846.ch13

Cited by 17 publications

(28 citation statements)

References 62 publications

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“…The Canadian populations included two generations from four independent year classes (hereafter “populations”) of the SJR aquaculture strain (AQUA). It also included 98 hatchery‐spawned adults captured as wild smolts from the Tobique River (TOB_WILD), which is an upper tributary of the SJR, and 100 hatchery‐spawned “wild” adults from the Stewiacke River (STW_WILD) as part of the live gene‐banking program (O'Reilly & Doyle, 2007). …”

Section: Methodsmentioning

confidence: 99%

“…The founder fish for the Mowi strain were collected from the Voss River, Norway, and surrounding areas in 1964 (Ferguson et al., 2007). …”

Section: Methodsmentioning

confidence: 99%

“…We chose TOB_WILD as a putative founder population of AQUA; however, we acknowledge that salmon from any tributary of the SJR above the Mactaquac dam (http://atlanticsalmonfederation.org/rivers/newbrunswick.html) could potentially have contributed to AQUA (Farmer, 1991). The iBoF—STW_WILD population was chosen as a putative outgroup because it is not thought to have contributed to the SJR aquaculture strain (O'Reilly & Doyle, 2007) and because it is known to grow more slowly than the oBoF—TOB_WILD population (Culling et al., 2013). Finally, to identify individuals from AQUA populations with partial European ancestry, we genotyped a purebred, full‐sibling family of fish from the Mowi aquaculture strain (MOWI_EU) founded from the Voss River region in Norway (Ferguson et al., 2007) as well as some hybrids from documented F1 and backcrosses between MOWI_EU and AQUA (Boulding et al., 2008).…”

Section: Methodsmentioning

confidence: 99%

“…The iBoF—STW_WILD population was chosen as a putative outgroup because it is not thought to have contributed to the SJR aquaculture strain (O'Reilly & Doyle, 2007) and because it is known to grow more slowly than the oBoF—TOB_WILD population (Culling et al., 2013). Finally, to identify individuals from AQUA populations with partial European ancestry, we genotyped a purebred, full‐sibling family of fish from the Mowi aquaculture strain (MOWI_EU) founded from the Voss River region in Norway (Ferguson et al., 2007) as well as some hybrids from documented F1 and backcrosses between MOWI_EU and AQUA (Boulding et al., 2008). This was necessary because AQUA had been reported to have some residual European ancestry due to the importation of the European subspecies into Maine (Glebe, 1998; O'Reilly, Carr, Whoriskey, & Verspoor, 2006).…”

Section: Methodsmentioning

confidence: 99%

“…This was necessary because AQUA had been reported to have some residual European ancestry due to the importation of the European subspecies into Maine (Glebe, 1998; O'Reilly, Carr, Whoriskey, & Verspoor, 2006). Atlantic salmon ( Salmo salar L.) can be characterized as two subspecies, the “North American” and the “European” (King et al., 2007), which differ in the number of chromosomes (Brenna‐Hansen et al., 2012). …”

Section: Methodsmentioning

confidence: 99%

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A genome scan for selection signatures comparing farmed Atlantic salmon with two wild populations: Testing colocalization among outlier markers, candidate genes, and quantitative trait loci for production traits

Liu

Ang

Elliott

et al. 2016

Evolutionary Applications

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Comparative genome scans can be used to identify chromosome regions, but not traits, that are putatively under selection. Identification of targeted traits may be more likely in recently domesticated populations under strong artificial selection for increased production. We used a North American Atlantic salmon 6K SNP dataset to locate genome regions of an aquaculture strain (Saint John River) that were highly diverged from that of its putative wild founder population (Tobique River). First, admixed individuals with partial European ancestry were detected using STRUCTURE and removed from the dataset. Outlier loci were then identified as those showing extreme differentiation between the aquaculture population and the founder population. All Arlequin methods identified an overlapping subset of 17 outlier loci, three of which were also identified by BayeScan. Many outlier loci were near candidate genes and some were near published quantitative trait loci (QTLs) for growth, appetite, maturity, or disease resistance. Parallel comparisons using a wild, nonfounder population (Stewiacke River) yielded only one overlapping outlier locus as well as a known maturity QTL. We conclude that genome scans comparing a recently domesticated strain with its wild founder population can facilitate identification of candidate genes for traits known to have been under strong artificial selection.

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Section: Methodsmentioning

confidence: 99%

“…The founder fish for the Mowi strain were collected from the Voss River, Norway, and surrounding areas in 1964 (Ferguson et al., 2007). …”

Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

See 3 more Smart Citations

A genome scan for selection signatures comparing farmed Atlantic salmon with two wild populations: Testing colocalization among outlier markers, candidate genes, and quantitative trait loci for production traits

Liu

Ang

Elliott

et al. 2016

Evolutionary Applications

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show abstract

Fishes

Planellas,

de Leaniz

2024

The UFAW Handbook on the Care and Management of Laboratory and Other Research Animals

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Characterization of natural variation in North American Atlantic Salmon populations (Salmonidae: Salmo salar) at a locus with a major effect on sea age

Kusche

Côté

Hernández

et al. 2017

Ecology and Evolution

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Age at maturity is a key life‐history trait of most organisms. In anadromous salmonid fishes such as Atlantic Salmon (Salmo salar), age at sexual maturity is associated with sea age, the number of years spent at sea before the spawning migration. For the first time, we investigated the presence of two nonsynonymous vgll3 polymorphisms in North American Atlantic Salmon populations that relate to sea age in European salmon and quantified the natural variation at these and two additional candidate SNPs from two other genes. A targeted resequencing assay was developed and 1,505 returning adult individuals of size‐inferred sea age and sex from four populations were genotyped. Across three of four populations sampled in Québec, Canada, the late‐maturing component (MSW) of the population of a given sex exhibited higher proportions of SNP genotypes 54Thrvgll3 and 323Lysvgll3 compared to early‐maturing fish (1SW), for example, 85% versus 53% of females from Trinité River carried 323Lysvgll3 (n MSW = 205 vs. n 1SW = 30; p < .001). However, the association between vgll3 polymorphism and sea age was more pronounced in females than in males in the rivers we studied. Logistic regression analysis of vgll3 SNP genotypes revealed increased probabilities of exhibiting higher sea age for 54Thrvgll3 and 323Lysvgll3 genotypes compared to alternative genotypes, depending on population and sex. Moreover, individuals carrying the heterozygous vgll3 SNP genotypes were more likely (>66%) to be female. In summary, two nonsynonymous vgll3 polymorphisms were confirmed in North American populations of Atlantic Salmon and our results suggest that variation at those loci correlates with sea age and sex. Our results also suggest that this correlation varies among populations. Future work would benefit from a more balanced sampling and from adding data on juvenile riverine life stages to contrast our data.

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Genetics and Habitat Management

Cited by 17 publications

References 62 publications

A genome scan for selection signatures comparing farmed Atlantic salmon with two wild populations: Testing colocalization among outlier markers, candidate genes, and quantitative trait loci for production traits

A genome scan for selection signatures comparing farmed Atlantic salmon with two wild populations: Testing colocalization among outlier markers, candidate genes, and quantitative trait loci for production traits

Fishes

Characterization of natural variation in North American Atlantic Salmon populations (Salmonidae: Salmo salar) at a locus with a major effect on sea age

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