Genome mapping in intensively studied wild vertebrate populations

Slate, Jon; Santure, Anna W.; Feulner, Philine G. D.; Brown, Emily; Ball, Alex D.; Johnston, Susan E.; Gratten, Jacob

doi:10.1016/j.tig.2010.03.005

Cited by 82 publications

(113 citation statements)

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“…Dissecting the genetic architecture of ecologically important traits is key to understanding evolution as well as the mechanisms allowing the maintenance of adaptive genetic variation (Ellegren and Sheldon, 2008;Nadeau and Jiggins, 2010;Slate et al, 2010). While a variety of approaches can be used to identify relevant loci (Stinchcombe and Hoekstra, 2007;Ellegren and Sheldon, 2008), there is growing interest in performing genomic studies using free-living pedigreed populations .…”

Section: Introductionmentioning

confidence: 99%

“…While a variety of approaches can be used to identify relevant loci (Stinchcombe and Hoekstra, 2007;Ellegren and Sheldon, 2008), there is growing interest in performing genomic studies using free-living pedigreed populations . Apart from enabling work on species that may not be amenable to controlled experiments, the study of wild populations is motivated by unparalleled opportunities to address topics requiring fitness estimates that are minimally influenced by experimental conditions (Ellegren and Sheldon, 2008;Clutton-Brock and Sheldon, 2010;Slate et al, 2010). These include the genetic architecture of fitness in natural environments (Ellegren and Sheldon, 2008), the evolutionary dynamics of sexually selected traits (Chenoweth and McGuigan, 2010), evolutionary stasis (for example, Gratten et al, 2008) and sexually antagonistic genetic variation (Bonduriansky and Chenoweth, 2009;Slate et al, 2010).…”

Section: Introductionmentioning

confidence: 99%

“…Apart from enabling work on species that may not be amenable to controlled experiments, the study of wild populations is motivated by unparalleled opportunities to address topics requiring fitness estimates that are minimally influenced by experimental conditions (Ellegren and Sheldon, 2008;Clutton-Brock and Sheldon, 2010;Slate et al, 2010). These include the genetic architecture of fitness in natural environments (Ellegren and Sheldon, 2008), the evolutionary dynamics of sexually selected traits (Chenoweth and McGuigan, 2010), evolutionary stasis (for example, Gratten et al, 2008) and sexually antagonistic genetic variation (Bonduriansky and Chenoweth, 2009;Slate et al, 2010). However, apart from work in humans, studies on the genetic architecture of ecologically important traits in free-living populations remain rare because of difficulties in maintaining multigenerational pedigrees and assembling adequate genotype-phenotype data sets (Slate, 2005;Slate et al, 2010).…”

Section: Introductionmentioning

confidence: 99%

“…These include the genetic architecture of fitness in natural environments (Ellegren and Sheldon, 2008), the evolutionary dynamics of sexually selected traits (Chenoweth and McGuigan, 2010), evolutionary stasis (for example, Gratten et al, 2008) and sexually antagonistic genetic variation (Bonduriansky and Chenoweth, 2009;Slate et al, 2010). However, apart from work in humans, studies on the genetic architecture of ecologically important traits in free-living populations remain rare because of difficulties in maintaining multigenerational pedigrees and assembling adequate genotype-phenotype data sets (Slate, 2005;Slate et al, 2010).…”

Section: Introductionmentioning

confidence: 99%

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QTL mapping for sexually dimorphic fitness-related traits in wild bighorn sheep

et al. 2011

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Dissecting the genetic architecture of fitness-related traits in wild populations is key to understanding evolution and the mechanisms maintaining adaptive genetic variation. We took advantage of a recently developed genetic linkage map and phenotypic information from wild pedigreed individuals from Ram Mountain, Alberta, Canada, to study the genetic architecture of ecologically important traits (horn volume, length, base circumference and body mass) in bighorn sheep. In addition to estimating sex-specific and cross-sex quantitative genetic parameters, we tested for the presence of quantitative trait loci (QTLs), colocalization of QTLs between bighorn sheep and domestic sheep, and sexÂQTL interactions. All traits showed significant additive genetic variance and genetic correlations tended to be positive. Linkage analysis based on 241 microsatellite loci typed in 310 pedigreed animals resulted in no significant and five suggestive QTLs (four for horn dimension on chromosomes 1, 18 and 23, and one for body mass on chromosome 26) using genome-wide significance thresholds (Logarithm of odds (LOD) 43.31 and 41.88, respectively). We also confirmed the presence of a horn dimension QTL in bighorn sheep at the only position known to contain a similar QTL in domestic sheep (on chromosome 10 near the horns locus; nominal Po0.01) and highlighted a number of regions potentially containing weight-related QTLs in both species. As expected for sexually dimorphic traits involved in male-male combat, loci with sex-specific effects were detected. This study lays the foundation for future work on adaptive genetic variation and the evolutionary dynamics of sexually dimorphic traits in bighorn sheep.

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Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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QTL mapping for sexually dimorphic fitness-related traits in wild bighorn sheep

et al. 2011

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“…Only loci identified as outliers by multiple methods are considered for subsequent validation investigations (see for example, . Finally, future approaches using sets of SNPs in target candidate genes, as opposed to genome scans, may be more fruitful in identifying loci associated with specific selection and adaptation scenarios (see the reviews by Slate et al (2010) and Stapley et al (2010)). …”

Section: Asip As a Candidate Gene For White Versus Non-whitementioning

confidence: 99%

A genome-wide scan study identifies a single nucleotide substitution in ASIP associated with white versus non-white coat-colour variation in sheep (Ovis aries)

Tiirikka

Kantanen

2013

Heredity

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In sheep, coat colour (and pattern) is one of the important traits of great biological, economic and social importance. However, the genetics of sheep coat colour has not yet been fully clarified. We conducted a genome-wide association study of sheep coat colours by genotyping 47 303 single-nucleotide polymorphisms (SNPs) in the Finnsheep population in Finland. We identified 35 SNPs associated with all the coat colours studied, which cover genomic regions encompassing three known pigmentation genes (TYRP1, ASIP and MITF) in sheep. Eighteen of these associations were confirmed in further tests between white versus non-white individuals, but none of the 35 associations were significant in the analysis of only non-white colours. Across the tests, the s66432.1 in ASIP showed significant association (P ¼ 4.2 Â 10 À11 for all the colours; P ¼ 2.3 Â 10 À11 for white versus non-white colours) with the variation in coat colours and strong linkage disequilibrium with other significant variants surrounding the ASIP gene. The signals detected around the ASIP gene were explained by differences in white versus non-white alleles. Further, a genome scan for selection for white coat pigmentation identified a strong and striking selection signal spanning ASIP. Our study identified the main candidate gene for the coat colour variation between white and non-white as ASIP, an autosomal gene that has been directly implicated in the pathway regulating melanogenesis. Together with ASIP, the two other newly identified genes (TYRP1 and MITF) in the Finnsheep, bordering associated SNPs, represent a new resource for enriching sheep coat-colour genetics and breeding.

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Genomic Studies of Adaptation in Natural Populations

Martin

Jiggins

2013

Encyclopedia of Life Sciences

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Understanding the genetic basis of adaptive evolution is a problem almost as old as evolutionary biology itself. Recent advances in genome sequencing and the ability to generate genomic samples from natural populations promises to provide answers to many long‐standing questions. The recent surge in genomic studies of adaptation has been accompanied by the development of numerous powerful techniques to analyse these enormous data sets. The state of the field is reviewed in this article, with an emphasis on the various approaches used. This article covers both ‘top‐down’, used to identify the genetic basis of a known trait, and ‘bottom‐up’ approaches, used to identify the footprints of selection on the genome. It shows how recent studies highlight the benefits of combining multiple methods and also discusses important goals for the future of the field. Key Concepts: Association mapping is used to identify genomic loci that control a trait of interest, by identifying molecular markers that display genotype‐by‐phenotype associations. Either offspring from controlled crosses or population samples can be used as the recombinant ‘mapping population’. Numerous loci underlying important adaptive traits have been identified using association mapping; however, this approach is biased towards loci of large effect and may not accurately capture the true genetic architecture of a trait. Genome‐wide scans for the footprints of selection are less sensitive to effect‐size biases but are naive with regard to the trait(s) under selection. Selective sweeps can be identified by the presence of reduced variation, enhanced linkage disequilibrium and a shift in the ‘site frequency spectrum’. Loci under divergent selection between populations can be identified as outliers displaying greater differentiation between populations than expected under neutral evolution. By comparing between‐species divergence with within‐species polymorphism at synonymous and nonsynonymous sites, it has been estimated that a large proportion of the genome is involved in adaptive evolution.

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Genome mapping in intensively studied wild vertebrate populations

Cited by 82 publications

References 68 publications

QTL mapping for sexually dimorphic fitness-related traits in wild bighorn sheep

QTL mapping for sexually dimorphic fitness-related traits in wild bighorn sheep

A genome-wide scan study identifies a single nucleotide substitution in ASIP associated with white versus non-white coat-colour variation in sheep (Ovis aries)

Genomic Studies of Adaptation in Natural Populations

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