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

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 (vertical bar iHS vertical bar) and population differentiation index (F(ST))-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 vertical bar iHS vertical bar 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 vertical bar iHS vertical bar 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 F(ST)-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 F(ST) 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 F(ST) 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 vertical bar iHS vertical bar and F(ST) 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.