TY - JOUR
T1 - Combining evidence of selection with association analysis increases power to detect regions influencing complex traits in dairy cattle
AU - Schwarzenbacher, Hermann
AU - Dolezal, Marlies
AU - Flisikowski, Krzysztof
AU - Seefried, Franz
AU - Wurmser, Christine
AU - Schlötterer, Christian
AU - Fries, Ruedi
N1 - Funding Information:
These studies were internally funded by the Technische Universität München. We thank the following artificial insemination stations for providing us with semen samples: Besamungstation J. Bauer GmbH & Co. KG, Besamungsverein Neustadt a. d. Aisch e. V. Meggle Besamungsstation Rottmoos GmbH, Niederbayerische Besamungsgenossenschaft Landshut-Pocking e. G., Prüf-und Besamungsstation München-Grub e. V., Rinderbesamungsgenossenschaft Memmingen e. G., Besamungsstation Birkenberg, Besamungsanstalt Gleisdorf, Oberösterreichische Besamungsstation, NÖ-Genetik Wieselburg. We thank T. Meitinger and P. Lichtner from Institute of Human Genetics from Helmholtz Zentrum München for generating and validating genotypes. MD was supported by Austrian Science Fund (FWF): project number L403-B11 to CS. We thank three anonymous reviewers for helpful comments and criticisms on earlier versions of this manuscript.
PY - 2012/1/30
Y1 - 2012/1/30
N2 - Background: Hitchhiking mapping and association studies are two popular approaches to map genotypes to phenotypes. In this study we combine both approaches to complement their specific strengths and weaknesses, resulting in a method with higher statistical power and fewer false positive signals. We applied our approach to dairy cattle as they underwent extremely successful selection for milk production traits and since an excellent phenotypic record is available. We performed whole genome association tests with a new mixed model approach to account for stratification, which we validated via Monte Carlo simulations. Selection signatures were inferred with the integrated haplotype score and a locus specific permutation based integrated haplotype score that works with a folded frequency spectrum and provides a formal test of signifance to identify selection signatures.Results: About 1,600 out of 34,851 SNPs showed signatures of selection and the locus specific permutation based integrated haplotype score showed overall good accordance with the whole genome association study. Each approach provides distinct information about the genomic regions that influence complex traits. Combining whole genome association with hitchhiking mapping yielded two significant loci for the trait protein yield. These regions agree well with previous results from other selection signature scans and whole genome association studies in cattle.Conclusion: We show that the combination of whole genome association and selection signature mapping based on the same SNPs increases the power to detect loci influencing complex traits. The locus specific permutation based integrated haplotype score provides a formal test of significance in selection signature mapping. Importantly it does not rely on knowledge of ancestral and derived allele states.
AB - Background: Hitchhiking mapping and association studies are two popular approaches to map genotypes to phenotypes. In this study we combine both approaches to complement their specific strengths and weaknesses, resulting in a method with higher statistical power and fewer false positive signals. We applied our approach to dairy cattle as they underwent extremely successful selection for milk production traits and since an excellent phenotypic record is available. We performed whole genome association tests with a new mixed model approach to account for stratification, which we validated via Monte Carlo simulations. Selection signatures were inferred with the integrated haplotype score and a locus specific permutation based integrated haplotype score that works with a folded frequency spectrum and provides a formal test of signifance to identify selection signatures.Results: About 1,600 out of 34,851 SNPs showed signatures of selection and the locus specific permutation based integrated haplotype score showed overall good accordance with the whole genome association study. Each approach provides distinct information about the genomic regions that influence complex traits. Combining whole genome association with hitchhiking mapping yielded two significant loci for the trait protein yield. These regions agree well with previous results from other selection signature scans and whole genome association studies in cattle.Conclusion: We show that the combination of whole genome association and selection signature mapping based on the same SNPs increases the power to detect loci influencing complex traits. The locus specific permutation based integrated haplotype score provides a formal test of significance in selection signature mapping. Importantly it does not rely on knowledge of ancestral and derived allele states.
KW - Cattle
KW - Complex trait
KW - Selection signature
KW - Whole genome association
UR - http://www.scopus.com/inward/record.url?scp=84856265264&partnerID=8YFLogxK
U2 - 10.1186/1471-2164-13-48
DO - 10.1186/1471-2164-13-48
M3 - Article
C2 - 22289501
AN - SCOPUS:84856265264
SN - 1471-2164
VL - 13
JO - BMC Genomics
JF - BMC Genomics
IS - 1
M1 - 48
ER -