原创力文档application of site and haplotype-frequency based approaches for detecting selection signatures in cattle基于应用程序的网站和haplotype-frequency方法检测选择签名牛.pdfVIP
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application of site and haplotype-frequency based approaches for detecting selection signatures in cattle基于应用程序的网站和haplotype-frequency方法检测选择签名牛
Qanbari et al. BMC Genomics 2011, 12:318
/1471-2164/12/318
RESEARCH ARTICLE Open Access
Application of site and haplotype-frequency
based approaches for detecting selection
signatures in cattle
1* 2 3 4 4 5 6
Saber Qanbari , Daniel Gianola , Ben Hayes , Flavio Schenkel , Steve Miller , Stephen Moore , Georg Thaller and
Henner Simianer1
Abstract
Background: ’Selection signatures’ delimit regions of the genome that are, or have been, functionally important
and have therefore been under either natural or artificial selection. In this study, two different and complementary
methods–integrated Haplotype Homozygosity Score (|iHS|) and population differentiation index (FST)–were applied
to identify traces of decades of intensive artificial selection for traits of economic importance in modern cattle.
Results: We scanned the genome of a diverse set of dairy and beef breeds from Germany, Canada and Australia
genotyped with a 50 K SNP panel. Across breeds, a total of 109 extreme |iHS| values exceeded the empirical
threshold level of 5% with 19, 27, 9, 10 and 17 outliers in Holstein, Brown Swiss, Australian Angus, Hereford and
Simmental, respectively. Annotating the regions harboring clustered |iHS| signals revealed a panel of interesting
candidate genes like SPATA17, MGAT1, PGRMC2 and ACTC1, COL23A1, MATN2, respectively, in the context of
reproduction and muscle formation. In a further step, a new Bayesian FST-based approach was applied with a set
of geographically separated populations including Holstein, Brown Swiss, Simmental, North American Angus and
Piedmontese for detecting differentiated loci. In total, 127 regions exceeding the 2.5 per cent threshold of the
empirical posterior
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