Detection of selection signatures in the genome of a farmed population of anadromous rainbow trout (Oncorhynchus mykiss)

Genomics applied to livestock and aquaculture breeding

“…History of domestication and artificial selection in aquaculture species is much more recent, and in some cases very incipient (López et al, 2015 ). Selection signatures, generated during the early domestication and recent selective breeding, have been assessed at a genome‐wide scale in important farmed fish species, including Atlantic salmon (Gutierrez et al, 2016 ; López, Benestan, et al, 2019 ; López, Linderoth, et al, 2019 ; Naval‐Sanchez et al, 2020 ), rainbow trout (Cádiz et al, 2021 ), coho salmon (López et al, 2021 ), Nile tilapia ( Oreochromis niloticus ; Cádiz et al, 2020 ; Hong Xia et al, 2015 ), channel catfish (Sun et al, 2014 ), common carp ( Cyprinus carpio ; Xu et al, 2019 ), turbot ( Scophthalmus maximus ; Aramburu et al, 2020 ), Australasian snapper ( Chrysophrys auratus ; Baesjou & Wellenreuther, 2021 ), gilthead seabream ( Sparus aurata ; Gkagkavouzis et al, 2021 ) tambaqui ( Colossoma macropomum ; Agudelo et al, 2022 ), as well as in shellfish farmed populations, including bay scallop ( Argopecten irradians ; Wang et al, 2021 ), Yesso scallop ( Mizuhopecten yessoensis ; Lv et al, 2022 ), European flat oyster ( Ostrea edulis ; Vera et al, 2019 ) and Pacific oyster ( Crassostrea gigas ; Hu et al, 2021 ; Jiao et al, 2021 ). These studies have used dense genome‐wide genotypes to identify genomic regions harboring genes affecting important phenotypes in farmed fish and shellfish.…”

“…ture species is much more recent, and in some cases very incipient (López et al, 2015). Selection signatures, generated during the early domestication and recent selective breeding, have been assessed at a genome-wide scale in important farmed fish species, including Atlantic salmon (Gutierrez et al, 2016;López, Benestan, et al, 2019;López, Linderoth, et al, 2019;Naval-Sanchez et al, 2020), rainbow trout (Cádiz et al, 2021), coho salmon (López et al, 2021), Nile tilapia (Oreochromis niloticus; Cádiz et al, 2020;Hong Xia et al, 2015), channel catfish (Sun et al, 2014)…”

Genome-wide detection of positive and balancing selection signatures shared by four domesticated rainbow trout populations (Oncorhynchus mykiss)

“…The first study in domesticated rainbow trout was performed on a single Chilean population (Cádiz et al, 2021) genotyped with a 57K SNP array; identified signatures of selection were associated with early development, growth, reproduction and immune system. Recently, a highdensity array (665K SNPs) was developed for rainbow trout (Bernard et al, 2022), allowing us to potentially more accurately detect signatures of selection and to compare them across various domesticated rainbow trout populations.…”

“…Numerous studies have been carried out over the last ten years to detect signatures of selection in farmed fish species (Channel Catfish: Sun et al, 2014; Atlantic salmon: Mäkinen et al, 2015; Gutierrez et al, 2016; Liu et al, 2016; Pritchard et al, 2018; López et al, 2019; Carp: Su et al, 2018; Nile Tilapia: Hong et al, 2015; Cádiz et al 2020; Yu et al, 2022; Rainbow trout: Cádiz et al, 2021; Coho salmon : López et al, 2021; Australasian snapper: Baesjou & Wellenreuther, 2021; Brown trout: Magris et al, 2022) in order to identify genomic regions involved in recent adaptation or domestication processes (Smith & Haigh, 1974; Pennings & Hermisson, 2006). In this study, we were interested in farmed rainbow trout populations as it is one of the oldest farmed fish and the analysis of genes under either positive or balancing subsequent selection in.…”

“…Three of them only focused on wild populations and showed signatures of selection linked to life-history variation, egg development, spawning time (Martínez et al, 2011), immune response (Limborg et al, 2012), and smoltification (Weinstein et al, 2019). The first study in domesticated rainbow trout was performed on a single Chilean population (Cádiz et al, 2021) genotyped with a 57K SNP array; identified signatures of selection were associated with early development, growth, reproduction and immune system. Recently, a high-density array (665K SNPs) was developed for rainbow trout (Bernard et al, 2022), allowing us to potentially more accurately detect signatures of selection and to compare them across various domesticated rainbow trout populations.…”