Horn type and horn length genes map to the same chromosomal region in Soay sheep

Johnston, Susan E.; Beraldi, Dario; McRae, Allan F.; Pemberton, J. M.; Slate, Jon

doi:10.1038/hdy.2009.109

Cited by 54 publications

(67 citation statements)

References 55 publications

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“…Relaxin/insulin-like family peptide receptor 2 ( RXFP2 ) gene on ovine autosome 10 (OAR-10: 29491481 – 29538132 bp) is located in a known selected genomic region linked to the horn morphology in sheep [11,56,57]. …”

Section: Methodsmentioning

confidence: 99%

Composite selection signals can localize the trait specific genomic regions in multi-breed populations of cattle and sheep

et al. 2014

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BackgroundDiscerning the traits evolving under neutral conditions from those traits evolving rapidly because of various selection pressures is a great challenge. We propose a new method, composite selection signals (CSS), which unifies the multiple pieces of selection evidence from the rank distribution of its diverse constituent tests. The extreme CSS scores capture highly differentiated loci and underlying common variants hauling excess haplotype homozygosity in the samples of a target population.ResultsThe data on high-density genotypes were analyzed for evidence of an association with either polledness or double muscling in various cohorts of cattle and sheep. In cattle, extreme CSS scores were found in the candidate regions on autosome BTA-1 and BTA-2, flanking the POLL locus and MSTN gene, for polledness and double muscling, respectively. In sheep, the regions with extreme scores were localized on autosome OAR-2 harbouring the MSTN gene for double muscling and on OAR-10 harbouring the RXFP2 gene for polledness. In comparison to the constituent tests, there was a partial agreement between the signals at the four candidate loci; however, they consistently identified additional genomic regions harbouring no known genes. Persuasively, our list of all the additional significant CSS regions contains genes that have been successfully implicated to secondary phenotypic diversity among several subpopulations in our data. For example, the method identified a strong selection signature for stature in cattle capturing selective sweeps harbouring UQCC-GDF5 and PLAG1-CHCHD7 gene regions on BTA-13 and BTA-14, respectively. Both gene pairs have been previously associated with height in humans, while PLAG1-CHCHD7 has also been reported for stature in cattle. In the additional analysis, CSS identified significant regions harbouring multiple genes for various traits under selection in European cattle including polledness, adaptation, metabolism, growth rate, stature, immunity, reproduction traits and some other candidate genes for dairy and beef production.ConclusionsCSS successfully localized the candidate regions in validation datasets as well as identified previously known and novel regions for various traits experiencing selection pressure. Together, the results demonstrate the utility of CSS by its improved power, reduced false positives and high-resolution of selection signals as compared to individual constituent tests.

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Section: Methodsmentioning

confidence: 99%

Composite selection signals can localize the trait specific genomic regions in multi-breed populations of cattle and sheep

et al. 2014

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“…As linkage maps of bighorn sheep and domestic sheep are very similar (Poissant et al, 2010b), we adopted significance thresholds previously calculated for domestic sheep by Johnston et al (2010) based on the formula from Lander and Kruglyak (1995). QTL were therefore considered suggestive and significant when LOD scores were 41.88 and 3.31, respectively.…”

Section: Qtl Mappingmentioning

confidence: 99%

“…More specifically, a QTL was considered to be colocalized between species when a position with LOD 41.175 in bighorn sheep was located within the 95% confidence interval of a significant domestic sheep QTL. This approach is valid for horn size because only one QTL has been mapped for this trait in domestic sheep to date (that is, on chromosome 10 near the horns locus, Johnston et al, 2010). On the other hand, it is anticonservative for body mass because of the large number of QTLs that have been mapped in domestic sheep for this trait.…”

Section: Qtl Mappingmentioning

confidence: 99%

“…In bighorn sheep, data interpretation could be facilitated by previous research in domestic sheep (Ovis aries, B3 million years divergence, Bunch et al, 2006). Indeed, one QTL has already been mapped for horn size in domestic sheep (that is, on chromosome 10 near the horns locus, Johnston et al 2010). A large number of QTLs have also been identified for weight-related traits (reviewed in Cavanagh 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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“…Thus, many empirical studies have successfully utilised pedigree information derived from physical tagging, genetic data or a combination of both approaches, to test a wide range of evolutionary and ecological hypotheses in the wild for various taxa [2,6]. Such studies have provided insights on the long term response of populations to environmental change [7], the effect of inbreeding depression in small or introduced populations [8,9], the elucidation of mating systems [10,11], the estimation of the variance components of life history traits [12,13], and the detection of QTLs [14,15]. However, in species with external fertilisation and limited post-hatching parental care, the construction of pedigrees through observational means is limited by the inability to physically mark individuals and/or monitor parent-offspring associations.…”

Section: Introductionmentioning

confidence: 99%

Molecular pedigree reconstruction and estimation of evolutionary parameters in a wild Atlantic salmon river system with incomplete sampling: a power analysis

et al. 2014

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BackgroundPedigree reconstruction using genetic analysis provides a useful means to estimate fundamental population biology parameters relating to population demography, trait heritability and individual fitness when combined with other sources of data. However, there remain limitations to pedigree reconstruction in wild populations, particularly in systems where parent-offspring relationships cannot be directly observed, there is incomplete sampling of individuals, or molecular parentage inference relies on low quality DNA from archived material. While much can still be inferred from incomplete or sparse pedigrees, it is crucial to evaluate the quality and power of available genetic information a priori to testing specific biological hypotheses. Here, we used microsatellite markers to reconstruct a multi-generation pedigree of wild Atlantic salmon (Salmo salar L.) using archived scale samples collected with a total trapping system within a river over a 10 year period. Using a simulation-based approach, we determined the optimal microsatellite marker number for accurate parentage assignment, and evaluated the power of the resulting partial pedigree to investigate important evolutionary and quantitative genetic characteristics of salmon in the system.ResultsWe show that at least 20 microsatellites (ave. 12 alleles/locus) are required to maximise parentage assignment and to improve the power to estimate reproductive success and heritability in this study system. We also show that 1.5 fold differences can be detected between groups simulated to have differing reproductive success, and that it is possible to detect moderate heritability values for continuous traits (h2 ~ 0.40) with more than 80% power when using 28 moderately to highly polymorphic markers.ConclusionThe methodologies and work flow described provide a robust approach for evaluating archived samples for pedigree-based research, even where only a proportion of the total population is sampled. The results demonstrate the feasibility of pedigree-based studies to address challenging ecological and evolutionary questions in free-living populations, where genealogies can be traced only using molecular tools, and that significant increases in pedigree assignment power can be achieved by using higher numbers of markers.

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Horn type and horn length genes map to the same chromosomal region in Soay sheep

Cited by 54 publications

References 55 publications

Composite selection signals can localize the trait specific genomic regions in multi-breed populations of cattle and sheep

Composite selection signals can localize the trait specific genomic regions in multi-breed populations of cattle and sheep

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

Molecular pedigree reconstruction and estimation of evolutionary parameters in a wild Atlantic salmon river system with incomplete sampling: a power analysis

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