Atlantic salmon (<i>Salmo salar</i> L.) genetics in the 21st century: taking leaps forward in aquaculture and biological understanding

Houston, Ross D.; Macqueen, Dan

doi:10.1111/age.12748

Cited by 63 publications

(55 citation statements)

References 131 publications

(154 reference statements)

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“…Full results are shown in Supplementary Data 4 (with examples in Supplementary Figs. [12][13][14]. In summary, SV-plaudit curation vastly reduced the FDR to maintain predominantly true SV calls (provided in Supplementary Data 5).…”

Section: Resultsmentioning

confidence: 85%

“…Salmonids have the highest combined economic, ecological and scientific importance among all fish lineages, and have consequently been subject to hundreds of genetics studies employing SNPs and other molecular markers 11 , 12 . In common with most non-model fish species, the SV landscape remains extremely poorly characterized in salmonids, apart from recent work informed by SNPs that revealed multi-megabase inversions in rainbow trout ( Oncorhynchus mykiss Walbaum) influencing migration 13 , 14 , and a chromosomal fusion under selection in Atlantic salmon 15 , consistent with roles in adaptation.…”

Section: Introductionmentioning

confidence: 99%

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The structural variation landscape in 492 Atlantic salmon genomes

et al. 2020

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Structural variants (SVs) are a major source of genetic and phenotypic variation, but remain challenging to accurately type and are hence poorly characterized in most species. We present an approach for reliable SV discovery in non-model species using whole genome sequencing and report 15,483 high-confidence SVs in 492 Atlantic salmon (Salmo salar L.) sampled from a broad phylogeographic distribution. These SVs recover population genetic structure with high resolution, include an active DNA transposon, widely affect functional features, and overlap more duplicated genes retained from an ancestral salmonid autotetraploidization event than expected. Changes in SV allele frequency between wild and farmed fish indicate polygenic selection on behavioural traits during domestication, targeting brain-expressed synaptic networks linked to neurological disorders in humans. This study offers novel insights into the role of SVs in genome evolution and the genetic architecture of domestication traits, along with resources supporting reliable SV discovery in non-model species.

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Section: Resultsmentioning

confidence: 85%

Section: Introductionmentioning

confidence: 99%

The structural variation landscape in 492 Atlantic salmon genomes

et al. 2020

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“…Contrary to mammals/birds, there has been a trend towards evolutionary expansion in the MTR repertoire of teleosts, as observed in many gene families with paralogues retained from Ts3R (Glasauer and Neuhauss, 2014) and Ss4R (Houston and Macqueen, 2019). Interestingly, not all MTR family members were affected equally.…”

Section: Discussionmentioning

confidence: 99%

Phylogenetic reclassification of vertebrate melatonin receptors to include Mel1d

Macqueen

Ebbesson

Hazlerigg

et al. 2019

Preprint

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30The circadian and seasonal actions of melatonin are mediated by high affinity G-31 protein coupled receptors (melatonin receptors, MTRs), classified into 32 phylogenetically distinct subtypes based on sequence divergence and 33 pharmacological characteristics. Three vertebrate MTR subtypes are currently 34 described: MT1 (MTNR1A), MT2 (MTNR1B), and Mel1c (MTNR1C / GPR50), which 35 exhibit distinct affinities, tissue distributions and signaling properties. We present 36 phylogenetic and comparative genomic analyses supporting a revised classification 37 of the vertebrate MTR family. We demonstrate four ancestral vertebrate MTRs, 38including a novel molecule hereafter named Mel1d. We reconstructed the evolution 39 of each vertebrate MTR, detailing genetic losses in addition to gains resulting from 40 whole genome duplication events in teleost fishes. We show that Mel1d was lost 41 separately in mammals and birds and has been previously mistaken for an MT1 42 paralogue. The genetic and functional diversity of vertebrate MTRs is more complex 43 than appreciated, with implications for our understanding of melatonin actions in 44 different taxa. The significance of our findings, including the existence of Mel1d, are 45 discussed in an evolutionary and functional context accommodating a robust 46 phylogenetic assignment of MTR gene family structure. 47 50 51Melatonin is an ancient eukaryotic signalling molecule that regulates diverse 52 biological functions. While best known as a regulator of biological rhythms in 53 humans, this hormone also regulates energy balance, temperature, behavior, blood 54 pressure, and seasonal reproduction. Melatonin is secreted by the pineal gland and 55 targets the brain as well as peripheral tissues (Hardeland et al. 2011, Slominski et 56 al. 2012), but is also produced by several tissues, eliciting paracrine effects (Weaver 57 and Reppert 1990). The actions of melatonin depend on the spatiotemporal 58 expression of high-affinity melatonin receptors (MTR), representing a specific class of 59 G protein-coupled receptor (GPCR). 60 61

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“…Houston and Macqueen () argue that the discovery of a major QTL for IPN resistance in Atlantic salmon (Gheyas et al, ; Houston et al, , ; Moen et al, ), that is not correlated with weight (Flores‐Mara et al, ), has caused a genomics transition in salmonid aquaculture. The development of molecular marker‐based genetic tests to predict IPN resistance of salmon without performing annual disease challenges on their relatives has been ground‐breaking (Houston et al, ; Moen et al, ).…”

Section: Discussionmentioning

confidence: 99%

Mapping quantitative trait loci for infectious salmon anaemia resistance in a North American strain of Atlantic salmon

et al. 2019

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Infectious salmon anaemia (ISA) is a highly virulent viral disease of Atlantic salmon that causes massive economic losses to infected aquaculture operations. Our goal was to detect and map quantitative trait loci (QTL) that confer resistance to ISA in an admixed commercial strain of Atlantic salmon that was largely founded from the Saint John River (SJR) in North America. Full‐sibling families were challenged with a virulent strain of ISA virus. Mortality was tracked during two annual trials with individual fish that survived to the end of the trial being classified as ‘resistant’, and those that died were classified as ‘susceptible’. Ten families with intermediate levels of mortality and an average size of 54.2 individuals were chosen for genotyping with a 50K SNP array designed for the SJR strain. Single nucleotide polymorphisms that were segregating within families were first used to make a composite 11K female linkage map that was then used to find the positions of QTL for ISA resistance using a half‐sib model. The dam‐based HS model detected a total of three QTL for ISA resistance including an experiment‐wide significant QTL on Ssa25 that accounted for 8.3% of the phenotypic variance and chromosome‐wide significant QTL on Ssa03 and on Ssa04 that accounted for 6.0% and 6.6% respectively. We conclude that classic linkage mapping within families continues to be an important method of detecting QTL for oligogenic traits in strains founded from multiple populations. Single nucleotide polymorphisms with moderate trait effects are being used to select within families for more ISA‐resistant strains of Atlantic salmon.

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Atlantic salmon (Salmo salar L.) genetics in the 21st century: taking leaps forward in aquaculture and biological understanding

Cited by 63 publications

References 131 publications

The structural variation landscape in 492 Atlantic salmon genomes

The structural variation landscape in 492 Atlantic salmon genomes

Phylogenetic reclassification of vertebrate melatonin receptors to include Mel1d

Mapping quantitative trait loci for infectious salmon anaemia resistance in a North American strain of Atlantic salmon

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