Revealing the History of Sheep Domestication Using Retrovirus Integrations

Chessa, Bernardo; Pereira, Filipe; Arnaud, Frédérick; Amorim, António; Goyache, F.; Mainland, Ingrid; Kao, Rowland R.; Pemberton, Josephine M.; Beraldi, Dario; Stear, M. J.; Alberti, Alberto; Pittau, Marco; Iannuzzi, L.; Banabazi, Mohammad Hossein; Kazwala, Rudovick; Zhang, Yaping; Arranz, Juan José; Ali, Bahy A.; Wang, Zhiliang; Uzun, Metehan; Dione, Michel; Olsaker, I.; Holm, Lars‐Erik; Saarma, Urmas; Ahmad, Sohail; Марзанов, Н. С.; Eythórsdóttir, Emma; Holland, Martin J.; Ajmone‐Marsan, Paolo; Bruford, Michael William; Kantanen, Juha; Spencer, Thomas E.; Palmarini, Massimo

doi:10.1126/science.1170587

Cited by 396 publications

(410 citation statements)

References 22 publications

(37 reference statements)

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“…The mitogenome of the European mouflon (O. musimon) grouped with other haplogroup HB sequences in line with previous findings that indicate it should not be considered a truly wild sheep (Hiendleder et al, 2002;Pedrosa et al, 2005;Meadows and Kijas, 2008). Rather, the European mouflon likely represents a remnant from early domestication events which have readapted to a feral life (Chessa et al, 2009). The Asian mouflon, O. orientalis, is less well-characterised and thought to be the next closest extant Ovis species to domestic sheep based on cytB sequence (Bunch et al, 2006; Tapio et al, 2006;Meadows et al, 2007).…”

Section: Discussionsupporting

confidence: 66%

Haplogroup relationships between domestic and wild sheep resolved using a mitogenome panel

2010

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Section: Discussionsupporting

confidence: 66%

Haplogroup relationships between domestic and wild sheep resolved using a mitogenome panel

2010

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“…Changes in the genomes of different breeds of domesticated pigs detected by comparing SNP allele frequencies with those of ancestral wild boars are attributed to nearby genes under selection (Ai et al., 2015; Li et al., 2013). Similar studies have been published in cattle (Hayes et al., 2008; The Bovine HapMap Consortium 2009) and sheep (Chessa et al., 2009). …”

Section: Introductionmentioning

confidence: 99%

A genome scan for selection signatures comparing farmed Atlantic salmon with two wild populations: Testing colocalization among outlier markers, candidate genes, and quantitative trait loci for production traits

Liu

Ang

Elliott

et al. 2016

Evolutionary Applications

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Comparative genome scans can be used to identify chromosome regions, but not traits, that are putatively under selection. Identification of targeted traits may be more likely in recently domesticated populations under strong artificial selection for increased production. We used a North American Atlantic salmon 6K SNP dataset to locate genome regions of an aquaculture strain (Saint John River) that were highly diverged from that of its putative wild founder population (Tobique River). First, admixed individuals with partial European ancestry were detected using STRUCTURE and removed from the dataset. Outlier loci were then identified as those showing extreme differentiation between the aquaculture population and the founder population. All Arlequin methods identified an overlapping subset of 17 outlier loci, three of which were also identified by BayeScan. Many outlier loci were near candidate genes and some were near published quantitative trait loci (QTLs) for growth, appetite, maturity, or disease resistance. Parallel comparisons using a wild, nonfounder population (Stewiacke River) yielded only one overlapping outlier locus as well as a known maturity QTL. We conclude that genome scans comparing a recently domesticated strain with its wild founder population can facilitate identification of candidate genes for traits known to have been under strong artificial selection.

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“…To date, o30 copies related to Jaagsiekte retrovirus have been identified in 65 different sheep breeds and in 8 related species: Capra hircus, C. falconeri, O. aries musimon, O. ammon, O. canadensis, O. dalli, Bos taurus and Budorcas taxicolor Mozorov et al, 2007;Wang et al, 2008;Chessa et al, 2009 Traditional methods can only analyze a small sample of the total genetic variability of polymorphic retroelements (Boissinot et al, 2004). Inverse PCR (iPCR) technique has been widely used to identify virus insertion points into the genome or sequences flanking transposable elements; (Ochman et al, 1988) but in 2000, a new technique called PCR suppression was used to detect polymorphic insertions/deletions in the genome of different and unsequenced species, and facilitated the creation of a specific library of these flanking regions (Siebert et al, 1995;Lebedev et al, 2000;Mamedov et al, 2002).…”

Section: Introductionmentioning

confidence: 99%

Evolutionary dynamics of endogenous Jaagsiekte sheep retroviruses proliferation in the domestic sheep, mouflon and Pyrenean chamois

Sistiaga-Poveda

Jugo

2014

Heredity

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The oncogenic exogenous Jaagsiekte sheep retrovirus (JSRV), responsible for ovine pulmonary adenocarcinoma, has several endogenous counterparts termed enJSRVs. Although many of these elements have been inactivated over time by the accumulation of deleterious mutations or internal recombination leading to solo long terminal repeat (LTR) formation, several members of enJSRVs have been identified as nearly intact and probably represent recent integration events. To determine the level of enJSRV polymorphism in the sheep population and related species, we have undertaken a study by characterizing enJSRVs copies and independent integration sites in six domestic sheep and two wild species of the sheep lineage. enJSRVs copies were detected by amplifying the env-LTR region by PCR, and for the detection of the insertion sites, we used two approaches: (1) an in silico approach based on the recently published Sheep Reference Genome Assembly (OARv3.0) and (2) an experimental approach based on PCR suppression and inverse PCR techniques. In total, 103 enJSRV sequences were generated across 10 individuals and enJSRV integrations were found on 11 of the 28 sheep chromosomes. These findings suggest that there are still uncharacterized enJSRVs, and that some of the integration sites are variable among the different species, breeds of the same species, subspecies and geographic locations.

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Revealing the History of Sheep Domestication Using Retrovirus Integrations

Cited by 396 publications

References 22 publications

Haplogroup relationships between domestic and wild sheep resolved using a mitogenome panel

Haplogroup relationships between domestic and wild sheep resolved using a mitogenome panel

A genome scan for selection signatures comparing farmed Atlantic salmon with two wild populations: Testing colocalization among outlier markers, candidate genes, and quantitative trait loci for production traits

Evolutionary dynamics of endogenous Jaagsiekte sheep retroviruses proliferation in the domestic sheep, mouflon and Pyrenean chamois

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