Strain Specific Genotype−Environment Interactions and Evolutionary Potential for Body Mass in Brook Charr (<i>Salvelinus fontinalis</i>)

Crespel, Amélie; Bernatchez, Louis; Audet, Céline; Garant, Dany

doi:10.1534/g3.112.005017

Cited by 21 publications

(26 citation statements)

References 59 publications

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“…2011). Often heritability depended on strain, for example heritability of body mass showed mean (± standard error) for domestic, Laval and Rupert strains of 0.61 (± 0.07), 0.37 (± 0.06), and 0.30 (± 0.08), respectively (Crespel et al . 2013a).…”

Section: Discussionmentioning

confidence: 99%

Sex chromosome evolution, heterochiasmy and physiological QTL in the salmonid Brook CharrSalvelinus fontinalis

Sutherland

Rico

Audet

et al. 2017

Preprint

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Whole genome duplication can have large impacts on genome evolution, and much remains unknown about these impacts. This includes the mechanisms of coping with a duplicated sex determination system and whether this has an impact on increasing the diversity of sex determination mechanisms. Other impacts include sexual conflict, where alleles having different optimums in each sex can result in sequestration of genes into non-recombining sex chromosomes. Sex chromosome development itself may involve sex-specific recombination rate (i.e. heterochiasmy), which is also poorly understood. Family Salmonidae is a model system for these phenomena, having undergone autotetraploidization and subsequent rediploidization in most of the genome at the base of the lineage. The salmonid master sex determining gene is known, and many species have non-homologous sex chromosomes, putatively due to transposition of this gene. In this study, we identify the sex chromosome of Brook Charr Salvelinus fontinalis and compare sex chromosome identities across the lineage (eight species, four genera). Although non-homology is frequent, homologous sex chromosomes and other consistencies are present in distantly related species, indicating probable convergence on specific sex and neo-sex chromosomes. We also characterize strong heterochiasmy with 2.7-fold more crossovers in maternal than paternal haplotypes with paternal crossovers biased to chromosome ends. When considering only rediploidized chromosomes, the overall heterochiasmy trend remains, although with only 1.9-fold more recombination in the female than the male. Y chromosome crossovers are restricted to a single end of the chromosome, and this chromosome contains a large interspecific inversion, although its status between males and females remains unknown. Finally, we identify QTL for 21 unique growth, reproductive and stress-related phenotypes to improve knowledge of the genetic architecture of these traits important to aquaculture and evolution.

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Section: Discussionmentioning

confidence: 99%

Sex chromosome evolution, heterochiasmy and physiological QTL in the salmonid Brook CharrSalvelinus fontinalis

Sutherland

Rico

Audet

et al. 2017

Preprint

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“…In eastern North America, native Brook Trout demonstrate substantial genetic differentiation even among geographically close populations as well as across major regions of their distribution, which is probably associated with the geography of glacial refugia and postglacial colonization patterns (Angers and Bernatchez 1998;Danzmann et al 1998;Castric et al 2001). Recent studies also showed genetically based differences in terms of growth, gene expression, and energy mobilization among Brook Trout populations from different geographic regions (Bougas et al 2010;Crespel et al 2013aCrespel et al , 2013b. In our study, the broad geographic origins of the four known hatchery sources introduced to Idaho were reflected in significant differentiation from each other with high pairwise F ST values among the four hatchery samples.…”

Section: Discussionmentioning

confidence: 99%

Coding Gene Single Nucleotide Polymorphism Population Genetics of Nonnative Brook Trout: The Ghost of Introductions Past

Neville

Bernatchez²

2013

Trans Am Fish Soc

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Fish have been translocated throughout the world, and introductions often have been executed repeatedly and have used mixtures of different strains from the native range. This history might have contributed to their invasive potential by allowing introduced and invading populations to circumvent expected reductions in genetic diversity from founder effects in a scenario termed the "genetic paradox" of invasions. We characterize patterns of genetic diversity in nonnative Brook Trout Salvelinus fontinalis, which have been introduced across the western United States for over a century but have also invaded broadly and pose a primary threat to native trout. We analyzed 155 coding gene single nucleotide polymorphisms (SNPs) in 34 nonnative Brook Trout populations sampled across eight large river systems as well as samples from the only four hatchery strains with documented use in Idaho. We uncovered similar within-population genetic diversity and large effective population sizes in naturalized populations compared with hatchery samples. Naturalized populations also showed substantial genetic structuring (maximum pairwise F ST = 0.23) across and even within watersheds and indicated suggestions of admixture in certain regions. Assignment probabilities confirmed two main hatcheries as the origin of most fish collected in the field; however, the four hatcheries were excluded as being the origin for 8% of individuals, mirroring results from clustering analyses and suggesting the influence of an additional unsampled hatchery source or sources. Simulated admixtures of hatchery samples produced genetic patterns similar to those observed in field samples, further supporting an influence of multiple historic hatchery stocks on the contemporary genetic structure of Brook Trout in Idaho. Our study highlights the potential contribution of historic hatchery and introduction practices in creating genetically variable and structured naturalized Brook Trout populations across Idaho, which may have allowed these fish to defy the "genetic paradox" early on in their nonnative history and set the stage for successful establishment and subsequent invasion.

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“…; Crespel et al . ) due to the low number of families used (10–36). In total, there were 352 genetic correlation estimates.…”

Section: The Gxe Studies Published During 1964–2013mentioning

confidence: 99%

A review of genotype‐by‐environment interaction and micro‐environmental sensitivity in aquaculture species

Sae-Lim

Gjerde

Nielsen

et al. 2015

Reviews in Aquaculture

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Generating breeding programmes that effectively improve farmed fish performance across multiple environments and make fish more uniform within production environments would aid farmers to produce food under diverse environments. We review genotype-by-environment interaction leading to re-ranking of genotypes across environments, that is non-unity genetic correlation between traits measured in different environments, and micro-environmental sensitivity leading to a change in environmental variance of a trait. A quantitative review across 38 species showed that (i) genotype-by-environment interaction studies are lacking for many economically important traits. (ii) Re-ranking is moderate for growth (average genetic correlation = 0.72) and survival (average genetic correlation = 0.54). Significant re-ranking is of concern because selection in a nucleus leads to lower genetic responses in commercial environments compared to a case when re-ranking does not exist. (iii) Re-ranking is weak for age-at-sexual-maturity and fish appearance (average genetic correlation = 0.86), implying that genetic improvement in one environment is expected to be effective in the other environments. Future research should provide guidelines for how to account for genotype-by-environment interaction when collecting data, estimating breeding values and optimising the structure of the breeding programme. (iv) Coefficient of genetic variation for sensitivity against unknown micro-environmental factors within a single environment for body weight is high. Hence, genetic improvement towards less sensitive fish, resulting in more uniform production, is possible, but a large number of relatives with phenotypes is needed for obtaining moderate accuracy of selection. This review elucidates needs for further research on genotype-by-environment interaction and micro-environmental sensitivity in economically important traits and species.

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Strain Specific Genotype−Environment Interactions and Evolutionary Potential for Body Mass in Brook Charr (Salvelinus fontinalis)

Cited by 21 publications

References 59 publications

Sex chromosome evolution, heterochiasmy and physiological QTL in the salmonid Brook CharrSalvelinus fontinalis

Sex chromosome evolution, heterochiasmy and physiological QTL in the salmonid Brook CharrSalvelinus fontinalis

Coding Gene Single Nucleotide Polymorphism Population Genetics of Nonnative Brook Trout: The Ghost of Introductions Past

A review of genotype‐by‐environment interaction and micro‐environmental sensitivity in aquaculture species

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