Estimating quantitative genetic parameters in wild populations: a comparison of pedigree and genomic approaches.
Estimating quantitative genetic parameters in wild populations: a comparison of pedigree and genomic approaches.
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DOI：
10.1111/mec.12827
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发表时间：
2014-07
影响因子：
4.9
通讯作者：
Pemberton JM
中科院分区：
文献类型：
--
作者：
Bérénos C;Ellis PA;Pilkington JG;Pemberton JM
野生种群遗传参数的定量估计通常受到现有系谱信息的准确性和完整性的限制。在全基因组标记上使用相关性可以潜在地消除这一限制，并导致更少的偏差和更精确的估计。我们使用三种越来越完整和准确的亲缘关系估计了圣基尔达一个未经管理的长期研究种群的遗传力、母系遗传效应和体型性状的遗传相关性：(i)系谱1，使用观测衍生的母系联系和微卫星衍生的父系联系；谱系2，使用snp衍生的母系和父系分配；（iii） 37037个常染色体snp的全基因组相关性。在最初的分析中，所有三种方法的遗传率估计惊人地相似，而基于系谱2和基因组相关性的分析的标准误差系统地较低。遗传相关性通常很强，三种亲缘关系估计之间的差异很小，随着亲缘关系信息的改善，标准误差仅略有下降。当将母体效应划分为单独的遗传和环境成分时，在三种相关性估计中发现的幼年性状的母体遗传效应显著增加。与只拟合母系环境影响的平行模型相比，遗传率下降了，这表明母系遗传效应与直接遗传效应相混淆，更准确的亲缘关系估计能够更好地将母系遗传效应与直接遗传效应区分开来。我们发现，SNP标记捕获的遗传力在大约一半可用的SNP上渐近化，这表明对于精确和无偏的遗传力估计，不一定需要更密集的标记面板。最后，我们提出了在未来自然种群数量遗传学研究中使用基因组亲缘性的指导方针。
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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影响因子：
3.1
作者：
Hayes, Ben;Goddard, Mike
通讯作者：
Goddard, Mike
影响因子：
9.8
作者：
Kijas JW;Lenstra JA;Hayes B;Boitard S;Porto Neto LR;San Cristobal M;Servin B;McCulloch R;Whan V;Gietzen K;Paiva S;Barendse W;Ciani E;Raadsma H;McEwan J;Dalrymple B;International Sheep Genomics Consortium Members
通讯作者：
International Sheep Genomics Consortium Members
影响因子：
4.1
作者：
Clément, V;Bibé, B;Hanocq, É
通讯作者：
Hanocq, É
影响因子：
2.6
作者：
Haile-Mariam, M.;Nieuwhof, G. J.;Hayes, B. J.
通讯作者：
Hayes, B. J.
影响因子：
1.5
作者：
Hill, W. G.;Weir, B. S.
通讯作者：
Weir, B. S.