Open Access Highly Accessed Methodology article

Combining evidence of selection with association analysis increases power to detect regions influencing complex traits in dairy cattle

Hermann Schwarzenbacher13, Marlies Dolezal2*, Krzysztof Flisikowski1, Franz Seefried1, Christine Wurmser1, Christian Schlötterer2 and Ruedi Fries1

Author Affiliations

1 Lehrstuhl für Tierzucht, Technische Universität München, Hochfeldweg 1, 85376 Freising-Weihenstephan, Germany

2 Institut für Populationsgenetik, Veterinärmedizinische Universität Wien, Veterinärplatz 1, 1210 Vienna, Austria

3 ZuchtData EDV Dienstleistungen Ges.m.b.H. Dresdner Sraße 89/19 1200 Vienna, Austria

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BMC Genomics 2012, 13:48  doi:10.1186/1471-2164-13-48

Published: 30 January 2012

Additional files

Additional file 1:

Supplementary Figures S1-S5. The PDF contains Figure S1: Histogram of means of 1000 permuted uIHS test statistics per locus; Figure S2: Histogram of derived allele frequencies for 34,851 SNPs in the study; Figure S3: Histogram of minor allele frequencies for 34,851 SNPs in the study; Figure S4: Histogram of P - Values of iHSVoight test statistics; Figure S5: Histogram of P - Values of iHS test statistics.

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Additional file 2:

Supplementary Figures S6-S33. The PDF shows Manhattan plots of bovine autosomes 1-5, 7-29; Capital letters denote QTLs reported from whole genome association studies (WGA) in cattle QTLdb at animalgenome.org, summarized as QTL trait ontology classes: B.. meat traits, E... exterior traits, H.. health traits, M.. milk traits, P.. production traits, R.. reproduction traits; o annotates a top 5% iHSVoight test statistic as reported in by [Quanbari et al. (2011)] in windows of 500 kb in Brown Swiss, x in any of the other breeds investigated; Plot A: iHSVoight test statistics, blue line: threshold identifying the top 5%; B: iHS test statistics, blue line: threshold identifying the top 5%; C: combined iHSVoight and WGA results with model MIXstrat, D: combined iHS and WGA results with model MIXstrat; blue line is a at 10% false discovery rate threshold.

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Additional file 3:

Supplementary Figures S34-S36. The PDF shows Figure S34: Histogram of allele substitution effects from whole genome association study employing model MIXstrat in kilogram protein yield; Figure S35: Histogram of Stouffer's P - Values of combined model MIXstrat and iHSVoight test statistics; Figure S36: Histogram of Stouffer's P - Values of combined model MIXstrat and iHS test statistics.

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