Phenotypic differentiation analysis: A case study in hybridizing Çoruh trout (Salmo coruhensis), Rize trout (Salmo rizeensis) and brown trout (Salmo trutta fario)

Kocabaş, Mehmet; Kutluyer, Filiz; Başçınar, Nadir

doi:10.1111/azo.12211

Cited by 2 publications

(1 citation statement)

References 40 publications

(57 reference statements)

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“…Indeed, S. trutta is a highly polytypic species for many traits, including body colour and pigmentation, going from continuous colour (silver, brownish, greenish) to complex spotty, marbled, blotchy and striped patterns (Colihueque, 2010). These patterns are traditionally included for subspecies and lineage description, but also population characterization and the detection of hybrids ( e.g ., Aparicio et al ., 2005; Delling et al ., 2000; Duchi, 2018; Kocabaş et al ., 2018; Lorenzoni et al ., 2019; Mezzera et al ., 1997). Indeed, specific pigmentation patterns ( e.g ., spots) in trout have been shown to be under simple genetic control in controlled‐crosses experiments (Blanc et al ., 1982, 1994; Colihueque, 2010; Skaala & Jørstad, 1988).…”

Section: Introductionmentioning

confidence: 99%

Redundancy analysis, genome‐wide association studies and the pigmentation of brown trout (Salmo trutta L.)

Valette

Leitwein

Lascaux³

et al. 2022

Journal of Fish Biology

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The association of molecular variants with phenotypic variation is a main issue in biology, often tackled with genome-wide association studies (GWAS). GWAS are challenging, with increasing, but still limited, use in evolutionary biology. We used redundancy analysis (RDA) as a complimentary ordination approach to single-and multitrait GWAS to explore the molecular basis of pigmentation variation in brown trout (Salmo trutta) belonging to wild populations impacted by hatchery fish. Based on 75,684 single nucleotide polymorphic (SNP) markers, RDA, single-and multitrait GWAS allowed the extraction of 337 independent colour patterning loci (CPLs) associated with trout pigmentation traits, such as the number of red and black spots on flanks. Collectively, these CPLs (i) mapped onto 35 out of 40 brown trout linkage groups indicating a polygenic genomic architecture of pigmentation, (ii) were found to be associated with 218 candidate genes, including 197 genes formerly mentioned in the literature associated to skin pigmentation, skin patterning, differentiation or structure notably in a close relative, the rainbow trout (Onchorhynchus mykiss), and (iii) related to functions relevant to pigmentation variation (e.g., calcium-and ionbinding, cell adhesion). Annotated CPLs include genes with well-known pigmentation effects (e.g., PMEL, SLC45A2, SOX10), but also markers associated with genes formerly found expressed in rainbow or brown trout skins. RDA was also shown to be useful to investigate management issues, especially the dynamics of trout pigmentation submitted to several generations of hatchery introgression.

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Section: Introductionmentioning

confidence: 99%

Redundancy analysis, genome‐wide association studies and the pigmentation of brown trout (Salmo trutta L.)

Valette

Leitwein

Lascaux³

et al. 2022

Journal of Fish Biology

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Spotting genome-wide pigmentation variation in a brown trout admixture context

Valette¹,

Leitwein

Lascaux³

et al. 2020

Preprint

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Colour and pigmentation variation attracted fish biologists for a while, but high-throughput genomic studies investigating the molecular basis of body pigmentation remain still limited to few species and conservation biology issues ignored. Using 75,684 SNPs, we investigated the genomic basis of pigmentation pattern variation among individuals of the Atlantic and Mediterranean clades of the brown trout (Salmo trutta), a polytypic species in which Atlantic hatchery individuals are commonly used to supplement local wild populations. Using redundancy analyses and genome-wide association studies, a set of 384 “colour patterning loci” (CPL) significantly correlated with pigmentation traits such as the number of red and black spots on flanks, but also the presence of a large black stain on the opercular bone was identified. CPLs map onto 35 out of 40 brown trout linkage groups indicating a polygenic basis to pigmentation patterns. They are mostly located in coding regions (43.4%) of 223 candidate genes, and correspond to GO-terms known to be involved in pigmentation (e.g. calcium and ion-binding, cell adhesion). Annotated genes especially include 24 candidates with known pigmentation effects (e.g. SOX10, PEML, SLC45A2), but also the Gap-junction Δ2 (GJD2) gene that was previously showed be differentially expressed in trout skin. Patterns of admixture were found significantly distinct when using either the full SNP data set or the set of CPLs, indicating that pigmentation patterns accessible to practitioners are not a reliable proxy of genome-wide admixture. Consequences for management are discussed.

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Phenotypic differentiation analysis: A case study in hybridizing Çoruh trout (Salmo coruhensis), Rize trout (Salmo rizeensis) and brown trout (Salmo trutta fario)

Cited by 2 publications

References 40 publications

Redundancy analysis, genome‐wide association studies and the pigmentation of brown trout (Salmo trutta L.)

Redundancy analysis, genome‐wide association studies and the pigmentation of brown trout (Salmo trutta L.)

Spotting genome-wide pigmentation variation in a brown trout admixture context

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