Application of site and haplotype-frequency based approaches for detecting selection signatures in cattle

Qanbari, Saber, Gianola, Daniel, Hayes, Ben, Schenkel, Flavio, Miller, Steve, Moore, Stephen, Thaller, Georg and Simianer, Henner (2011) Application of site and haplotype-frequency based approaches for detecting selection signatures in cattle. BMC Genomics, 12 . doi:10.1186/1471-2164-12-318


Author Qanbari, Saber
Gianola, Daniel
Hayes, Ben
Schenkel, Flavio
Miller, Steve
Moore, Stephen
Thaller, Georg
Simianer, Henner
Title Application of site and haplotype-frequency based approaches for detecting selection signatures in cattle
Journal name BMC Genomics   Check publisher's open access policy
ISSN 1471-2164
Publication date 2011-06-16
Sub-type Article (original research)
DOI 10.1186/1471-2164-12-318
Open Access Status DOI
Volume 12
Total pages 12
Place of publication London, United Kingdom
Publisher BioMed Central
Language eng
Formatted 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 distribution were identified as extremely differentiated. In a substantial number (56 out of 127 cases) the extreme FST values were found to be positioned in poor gene content regions which deviated significantly (p < 0.05) from the expectation assuming a random distribution. However, significant FST values were found in regions of some relevant genes such as SMCP and FGF1.
Conclusions: Overall, 236 regions putatively subject to recent positive selection in the cattle genome were detected. Both |iHS| and FST suggested selection in the vicinity of the Sialic acid binding Ig-like lectin 5 gene on BTA18. This region was recently reported to be a major QTL with strong effects on productive life and fertility traits in Holstein cattle. We conclude that high-resolution genome scans of selection signatures can be used to identify genomic regions contributing to within- and inter-breed phenotypic variation.
Q-Index Code C1
Q-Index Status Provisional Code
Institutional Status Non-UQ

Document type: Journal Article
Sub-type: Article (original research)
Collection: Queensland Alliance for Agriculture and Food Innovation
 
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