Detecting loci under recent positive selection in dairy and beef cattle by combining different genome-wide scan methods.
Detecting loci under recent positive selection in dairy and beef cattle by combining different genome-wide scan methods.
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DOI：
10.1371/journal.pone.0064280
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发表时间：
2013
期刊：
影响因子：
3.7
通讯作者：
Garcia JF
中科院分区：
文献类型：
--
作者：
Utsunomiya YT;Pérez O'Brien AM;Sonstegard TS;Van Tassell CP;do Carmo AS;Mészáros G;Sölkner J;Garcia JF
由于可用于从基因组数据中检测正选择的方法在假设和执行方面有所不同，预计它们之间存在弱相关性。然而，如果有任何给定的信号在不同的方法中得到一致的支持，这就是该基因座过去一直处于选择之下的有力证据。本文描述了一种基于Stouffer方法的直接频率分析方法，该方法将不同测试中的P值组合起来，以寻找最近在常见变异中进行正选择的证据，以及从检测到的信号中提取生物信息的策略，并将其应用于奶牛和肉牛(牛磺酸和吲哚)产生的高密度单核苷酸多态(SNP)数据。还报道了超过440,000个SNP的祖先牛科等位基因状态。利用这一组合方法，确定了高度显著的(P<；3.17×10−7)群体特异性扫描，指出了可能参与牛肉和乳制品生产的候选基因和途径。最显著的信号出现在棕色瑞士猪的Cornichon Homolog 3基因(P = 3.82×10−12)上，可能参与了排卵前黄体生成素高峰的调节。选择的其他可能途径包括：Angus的糖解/糖异生、转录机制和趋化因子/细胞因子的活性；Brown Swiss的calain-calastatin系统和核糖体的生物发生；以及Gyr的神经节苷脂在乳脂球中的沉积。这种复合方法与用于检索功能信息的策略相结合，可能是调查全基因组选择性扫描和提供对选择来源的洞察的有用工具。
As the methodologies available for the detection of positive selection from genomic data vary in terms of assumptions and execution, weak correlations are expected among them. However, if there is any given signal that is consistently supported across different methodologies, it is strong evidence that the locus has been under past selection. In this paper, a straightforward frequentist approach based on the Stouffer Method to combine P-values across different tests for evidence of recent positive selection in common variations, as well as strategies for extracting biological information from the detected signals, were described and applied to high density single nucleotide polymorphism (SNP) data generated from dairy and beef cattle (taurine and indicine). The ancestral Bovinae allele state of over 440,000 SNP is also reported. Using this combination of methods, highly significant (P<3.17×10−7) population-specific sweeps pointing out to candidate genes and pathways that may be involved in beef and dairy production were identified. The most significant signal was found in the Cornichon homolog 3 gene (CNIH3) in Brown Swiss (P = 3.82×10−12), and may be involved in the regulation of pre-ovulatory luteinizing hormone surge. Other putative pathways under selection are the glucolysis/gluconeogenesis, transcription machinery and chemokine/cytokine activity in Angus; calpain-calpastatin system and ribosome biogenesis in Brown Swiss; and gangliosides deposition in milk fat globules in Gyr. The composite method, combined with the strategies applied to retrieve functional information, may be a useful tool for surveying genome-wide selective sweeps and providing insights in to the source of selection.
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DOI：
10.1098/rstb.2010.0103
发表时间：
2010-08-27
影响因子：
6.3
作者：
Murray, Caitriona;Huerta-Sanchez, Emilia;Bradley, Daniel G.
通讯作者：
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影响因子：
3.7
作者：
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通讯作者：
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DOI：
10.1098/rstb.2011.0299
发表时间：
2012-03-19
影响因子：
6.3
作者：
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通讯作者：
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影响因子：
3.7
作者：
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通讯作者：
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影响因子：
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作者：
Grossman, Sharon R.;Shylakhter, Ilya;Sabeti, Pardis C.
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