A novel analytical method, Birth Date Selection Mapping, detects response of the Angus (Bos taurus) genome to selection on complex traits
A novel analytical method, Birth Date Selection Mapping, detects response of the Angus (Bos taurus) genome to selection on complex traits
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DOI：
10.1186/1471-2164-13-606
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发表时间：
2012-11-09
期刊：
影响因子：
4.4
通讯作者：
Taylor, Jeremy F.
中科院分区：
文献类型：
--
作者：
Decker, Jared E.;Vasco, Daniel A.;Taylor, Jeremy F.
背景：最近开发了几种方法来识别基因组中遭受强选择的区域。然而，最近的理论和实证工作表明，需要多基因模型来识别对复杂性状的持续选择反应更为温和的基因组区域。我们研究了多性状选择对美国注册安格斯肉牛群体基因组的影响，这些肉牛出生时间超过 50 年，代表大约 10 代选择。我们展示了应用称为出生日期选择图谱的定量遗传模型的结果，以识别最近正在进行的选择的特征。结果：我们表明，美国安格斯牛已被系统地选择，以改变其育种者常规记录的 16 种生产性状中的大多数的平均加性遗传价值。使用出生日期选择映射，我们使用基因组最佳线性无偏预测、广义最小二乘法和 BayesCp 分析来估计 44,817 个 SNP 位点的等位基因频率的时间依赖性。最后，我们重建了历史上经历过对 16 个生产性状的全基因组分析和基因本体富集分析进行选择的主要表型。 结论：我们证明，利用混合模型的出生日期选择图谱可以纠正导致虚假 SNP 关联的时间依赖性谱系抽样效应，并揭示复杂性状持续选择的基因组特征。由于历史上多个性状是一致选择的，并且大多数数量性状基因座的影响很小，因此选择逐渐改变了整个基因组的等位基因频率。两个大效应数量性状基因座不是最强选择的基因座，因为它们对强选择表型具有拮抗多效性作用。出生日期选择映射可以很容易地扩展到时间分层的人类或模型生物群体。
Background: Several methods have recently been developed to identify regions of the genome that have been exposed to strong selection. However, recent theoretical and empirical work suggests that polygenic models are required to identify the genomic regions that are more moderately responding to ongoing selection on complex traits. We examine the effects of multi-trait selection on the genome of a population of US registered Angus beef cattle born over a 50-year period representing approximately 10 generations of selection. We present results from the application of a quantitative genetic model, called Birth Date Selection Mapping, to identify signatures of recent ongoing selection.Results: We show that US Angus cattle have been systematically selected to alter their mean additive genetic merit for most of the 16 production traits routinely recorded by breeders. Using Birth Date Selection Mapping, we estimate the time-dependency of allele frequency for 44,817 SNP loci using genomic best linear unbiased prediction, generalized least squares, and BayesCp analyses. Finally, we reconstruct the primary phenotypes that have historically been exposed to selection from a genome-wide analysis of the 16 production traits and gene ontology enrichment analysis.Conclusions: We demonstrate that Birth Date Selection Mapping utilizing mixed models corrects for time-dependent pedigree sampling effects that lead to spurious SNP associations and reveals genomic signatures of ongoing selection on complex traits. Because multiple traits have historically been selected in concert and most quantitative trait loci have small effects, selection has incrementally altered allele frequencies throughout the genome. Two quantitative trait loci of large effect were not the most strongly selected of the loci due to their antagonistic pleiotropic effects on strongly selected phenotypes. Birth Date Selection Mapping may readily be extended to temporally-stratified human or model organism populations.