Changed Patterns of Genomic Variation Following Recent Domestication: Selection Sweeps in Farmed Atlantic Salmon

Naval-Sánchez, Marina; McWilliam, Sean; Evans, Bradley S.; Yáñez, José M.; Houston, Ross D.; Kijas, James W.

doi:10.3389/fgene.2020.00264

Cited by 24 publications

(26 citation statements)

References 77 publications

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“…To detect genomic regions under selection, we used SAMTools v0.1.19 40 to collect summary information from the input BAM (Binary Alignment Map) files and calculated the probability of the data given for each possible genotype and stored the probabilities in the BCF (Binary Variant Call Format) file. BCF tools was applied to the prior data for SNP calling and to convert the data to VCF (Variant Call Format) files, which can be used in subsequent analysis 58 .…”

Section: Resultsmentioning

confidence: 99%

“…Candidate genes contributing to environmental adaptation have been identified in humans 12 – 15 , yaks 16 , Tibetan antelopes 17 , gray wolves 18 , dogs 19 – 21 , cattle 22 – 25 , pigs 26 , 27 , chickens 28 , sheep 19 , 29 , 30 , goats 31 , 32 and Tibetan mastiffs 33 . Similar methodologies have been used to identified genes associated to production traits and the impact of domestication in livestock chickens 34 , 35 , cattle 36 , goats 32 , 37 , dogs 38 , rabbits 39 , salmon 40 and sheep 25 , 37 , 41 , 42 . In sheep, several studies on selective signatures have identified genes linked to domestication and productive traits.…”

Section: Introductionmentioning

confidence: 99%

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Genome-wide comparative analyses reveal selection signatures underlying adaptation and production in Tibetan and Poll Dorset sheep

Zhang

Xue

Liu

et al. 2021

Sci Rep

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The identification of genome-wide selection signatures can provide insights on the mechanisms of natural and/or artificial selection and uncover genes related to biological functions and/or phenotypes. Tibetan sheep are an important livestock in Tibet, providing meat and wool for Tibetans who are renown for breeding livestock that adapt well to high altitudes. Using whole-genome sequences with an effective sequencing depth of 5×, we investigated the genomic diversity and structure and, identified selection signatures of White Tibetan, Oula and Poll Dorset sheep. We obtained 30,163,679 Single Nucleotide Polymorphisms (SNPs) and 5,388,372 indels benchmarked against the ovine Oar_v4.0 genome assembly. Next, using FST, ZHp and XP-EHH approaches, we identified selection signatures spanning a set of candidate genes, including HIF1A, CAPN3, PRKAA1, RXFP2, TRHR and HOXA10 that are associated with pathways and GO categories putatively related to hypoxia responses, meat traits and disease resistance. Candidate genes and GO terms associated with coat color were also identified. Finally, quantification of blood physiological parameters, revealed higher levels of mean corpuscular hemoglobin measurement and mean corpuscular hemoglobin concentration in Tibetan sheep compared with Poll Dorset, suggesting a greater oxygen-carrying capacity in the Tibetan sheep and thus better adaptation to high-altitude hypoxia. In conclusion, this study provides a greater understanding of genome diversity and variations associated with adaptive and production traits in sheep.

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Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Genome-wide comparative analyses reveal selection signatures underlying adaptation and production in Tibetan and Poll Dorset sheep

Zhang

Xue

Liu

et al. 2021

Sci Rep

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“…Genomic scans for detecting selection signatures have been successfully applied to several domestic animals, including aquaculture species. For instance, selection signature scans have been carried out for Atlantic salmon (Mäkinen et al, 2014;Gutierrez et al, 2016;Liu et al, 2016;López et al, 2018;López et al, 2019;Naval-Sanchez et al, 2020), Nile tilapia (Xia et al, 2015;Cadiz et al, 2019); and channel catfish (Nam et al, 2019). To date, there are no studies focusing on the identification of selection signatures in coho salmon populations.…”

Section: Introductionmentioning

confidence: 99%

Detection of selection signatures in farmed coho salmon (Oncorhynchus kisutch) using dense genome-wide information

López

Cádiz

Rondeau

et al. 2020

Preprint

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Animal domestication and artificial selection give rise to gradual changes at the genomic level in populations. Subsequent footprints of selection known as selection signatures or selective sweeps have been traced in the genomes of many animal livestock species by exploiting variations in linkage disequilibrium patterns and/or reduction of genetic diversity.Domestication of most aquatic species is recent in comparison with land animals, and salmonids are one of the most important fish species in aquaculture. Coho salmon (Oncorhynchus kisutch), cultivated primarily in Chile, has been subject to breeding programs to improve growth, disease resistance traits, and flesh color. This study aimed to identify selection signatures that may be involved in adaptation to culture conditions and traits of productive interest. To do so, individuals of two domestic populations cultured in Chile were genotyped with 200 thousand SNPs, and analyses were conducted using iHS, XP-EHH and CLR. Several signatures of selection on different chromosomal regions were detected across both populations. Some of the identified regions under selection contained genes such anapc2, alad, chp2 and myn that have been previously associated with body weight in Atlantic salmon or sec24d and robo1 that have been associated with disease resistance to Piscirickettsia salmonis in coho salmon. Findings in our study can contribute to an integrated genome-wide map of selection signatures, to help identify the genetic mechanisms of phenotypic diversity in coho salmon.

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“…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.…”

Section: Domestication and Artificial Selectionmentioning

confidence: 99%

Genomics applied to livestock and aquaculture breeding

Yáñez

Carvalheiro

et al. 2022

Evolutionary Applications

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The increasing global demand for food, due to the continuous growth of human population, requires improvements in the efficiency and sustainability of animal production systems. In addition, several challenges facing farming of aquatic and terrestrial organisms need to be overcome to ensure food security in the upcoming decades, e.g. adaptation to climate change, reduced availability of conventional animal feed ingredients, emerging infectious and parasitic diseases, among others. Genomic technologies such as massive parallel sequencing, high‐throughput genotyping, genome selection and gene editing, combined with highly efficient computational methods can accelerate the rate of genetic progress in animal breeding. Thus, such technologies can help us meet the needs for protein sources for human consumption in the upcoming years. This Special Issue aims at presenting current advancements in the field of genomic tools applied to aquatic and terrestrial farmed animal populations.

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Changed Patterns of Genomic Variation Following Recent Domestication: Selection Sweeps in Farmed Atlantic Salmon

Cited by 24 publications

References 77 publications

Genome-wide comparative analyses reveal selection signatures underlying adaptation and production in Tibetan and Poll Dorset sheep

Genome-wide comparative analyses reveal selection signatures underlying adaptation and production in Tibetan and Poll Dorset sheep

Detection of selection signatures in farmed coho salmon (Oncorhynchus kisutch) using dense genome-wide information

Genomics applied to livestock and aquaculture breeding

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