Identification of large selective sweeps associated with major genes in cattle
Identification of large selective sweeps associated with major genes in cattle
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DOI：
10.1111/age.12073
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发表时间：
2013-12-01
期刊：
影响因子：
2.4
通讯作者：
Gautier, M.
中科院分区：
文献类型：
--
作者：
Druet, T.;Perez-Pardal, L.;Gautier, M.
对新的有利变种的选择可以导致选择性的扫荡。然而，在不同物种的进化中，这样的扫描可能很少见，因为对不同物种来说，多基因适应或基于标准变异的选择可能更常见。尽管如此，在家养物种中也描述了强烈的选择性扫荡，如鸡系或狗品种。我们研究的目标是使用一组来自12个不同品种的牛的高密度(800K SNPs)基因分型的个体来执行全基因组扫描，选择性扫描的定义是出人意料的长时间杂合性降低。为此，我们开发了一个隐马尔可夫模型，其中一个隐藏状态对应于降低杂合度的区域。发现了一些出人意料的长区域。在这些基因中，有6个含有已知影响简单遗传结构特征的基因，如毛色或角发育。然而，几乎没有证据表明扫描与潜在的生产性状基因有关。
Selection for new favorable variants can lead to selective sweeps. However, such sweeps might be rare in the evolution of different species for which polygenic adaptation or selection on standing variation might be more common. Still, strong selective sweeps have been described in domestic species such as chicken lines or dog breeds. The goal of our study was to use a panel of individuals from 12 different cattle breeds genotyped at high density (800K SNPs) to perform a whole-genome scan for selective sweeps defined as unexpectedly long stretches of reduced heterozygosity. To that end, we developed a hidden Markov model in which one of the hidden states corresponds to regions of reduced heterozygosity. Some unexpectedly long regions were identified. Among those, six contained genes known to affect traits with simple genetic architecture such as coat color or horn development. However, there was little evidence for sweeps associated with genes underlying production traits.