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Estimating quantitative genetic parameters in wild populations: a comparison of pedigree and genomic approaches

The estimation of quantitative genetic parameters in wild populations is generally limited by the accuracy and completeness of the available pedigree information. Using relatedness at genomewide markers can potentially remove this limitation and lead to less biased and more precise estimates. We est...

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Autores principales: Bérénos, Camillo, Ellis, Philip A, Pilkington, Jill G, Pemberton, Josephine M
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Blackwell Publishing Ltd 2014
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4149785/
https://www.ncbi.nlm.nih.gov/pubmed/24917482
http://dx.doi.org/10.1111/mec.12827
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author Bérénos, Camillo
Ellis, Philip A
Pilkington, Jill G
Pemberton, Josephine M
author_facet Bérénos, Camillo
Ellis, Philip A
Pilkington, Jill G
Pemberton, Josephine M
author_sort Bérénos, Camillo
collection PubMed
description The estimation of quantitative genetic parameters in wild populations is generally limited by the accuracy and completeness of the available pedigree information. Using relatedness at genomewide markers can potentially remove this limitation and lead to less biased and more precise estimates. We estimated heritability, maternal genetic effects and genetic correlations for body size traits in an unmanaged long-term study population of Soay sheep on St Kilda using three increasingly complete and accurate estimates of relatedness: (i) Pedigree 1, using observation-derived maternal links and microsatellite-derived paternal links; (ii) Pedigree 2, using SNP-derived assignment of both maternity and paternity; and (iii) whole-genome relatedness at 37 037 autosomal SNPs. In initial analyses, heritability estimates were strikingly similar for all three methods, while standard errors were systematically lower in analyses based on Pedigree 2 and genomic relatedness. Genetic correlations were generally strong, differed little between the three estimates of relatedness and the standard errors declined only very slightly with improved relatedness information. When partitioning maternal effects into separate genetic and environmental components, maternal genetic effects found in juvenile traits increased substantially across the three relatedness estimates. Heritability declined compared to parallel models where only a maternal environment effect was fitted, suggesting that maternal genetic effects are confounded with direct genetic effects and that more accurate estimates of relatedness were better able to separate maternal genetic effects from direct genetic effects. We found that the heritability captured by SNP markers asymptoted at about half the SNPs available, suggesting that denser marker panels are not necessarily required for precise and unbiased heritability estimates. Finally, we present guidelines for the use of genomic relatedness in future quantitative genetics studies in natural populations.
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spelling pubmed-41497852014-09-17 Estimating quantitative genetic parameters in wild populations: a comparison of pedigree and genomic approaches Bérénos, Camillo Ellis, Philip A Pilkington, Jill G Pemberton, Josephine M Mol Ecol Original Articles The estimation of quantitative genetic parameters in wild populations is generally limited by the accuracy and completeness of the available pedigree information. Using relatedness at genomewide markers can potentially remove this limitation and lead to less biased and more precise estimates. We estimated heritability, maternal genetic effects and genetic correlations for body size traits in an unmanaged long-term study population of Soay sheep on St Kilda using three increasingly complete and accurate estimates of relatedness: (i) Pedigree 1, using observation-derived maternal links and microsatellite-derived paternal links; (ii) Pedigree 2, using SNP-derived assignment of both maternity and paternity; and (iii) whole-genome relatedness at 37 037 autosomal SNPs. In initial analyses, heritability estimates were strikingly similar for all three methods, while standard errors were systematically lower in analyses based on Pedigree 2 and genomic relatedness. Genetic correlations were generally strong, differed little between the three estimates of relatedness and the standard errors declined only very slightly with improved relatedness information. When partitioning maternal effects into separate genetic and environmental components, maternal genetic effects found in juvenile traits increased substantially across the three relatedness estimates. Heritability declined compared to parallel models where only a maternal environment effect was fitted, suggesting that maternal genetic effects are confounded with direct genetic effects and that more accurate estimates of relatedness were better able to separate maternal genetic effects from direct genetic effects. We found that the heritability captured by SNP markers asymptoted at about half the SNPs available, suggesting that denser marker panels are not necessarily required for precise and unbiased heritability estimates. Finally, we present guidelines for the use of genomic relatedness in future quantitative genetics studies in natural populations. Blackwell Publishing Ltd 2014-07 2014-06-26 /pmc/articles/PMC4149785/ /pubmed/24917482 http://dx.doi.org/10.1111/mec.12827 Text en © 2014 The Authors. Molecular Ecology Published by John Wiley & Sons Ltd. http://creativecommons.org/licenses/by/3.0/ This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.
spellingShingle Original Articles
Bérénos, Camillo
Ellis, Philip A
Pilkington, Jill G
Pemberton, Josephine M
Estimating quantitative genetic parameters in wild populations: a comparison of pedigree and genomic approaches
title Estimating quantitative genetic parameters in wild populations: a comparison of pedigree and genomic approaches
title_full Estimating quantitative genetic parameters in wild populations: a comparison of pedigree and genomic approaches
title_fullStr Estimating quantitative genetic parameters in wild populations: a comparison of pedigree and genomic approaches
title_full_unstemmed Estimating quantitative genetic parameters in wild populations: a comparison of pedigree and genomic approaches
title_short Estimating quantitative genetic parameters in wild populations: a comparison of pedigree and genomic approaches
title_sort estimating quantitative genetic parameters in wild populations: a comparison of pedigree and genomic approaches
topic Original Articles
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4149785/
https://www.ncbi.nlm.nih.gov/pubmed/24917482
http://dx.doi.org/10.1111/mec.12827
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