Multivariate analysis of a genome-wide association study in dairy cattle

Bolormaa, S., Pryce, J. E., Hayes, B. J. and Goddard, M. E. (2010) Multivariate analysis of a genome-wide association study in dairy cattle. Journal of Dairy Science, 93 8: 3818-3833. doi:10.3168/jds.2009-2980


Author Bolormaa, S.
Pryce, J. E.
Hayes, B. J.
Goddard, M. E.
Title Multivariate analysis of a genome-wide association study in dairy cattle
Journal name Journal of Dairy Science   Check publisher's open access policy
ISSN 0022-0302
1525-3198
Publication date 2010-08
Sub-type Article (original research)
DOI 10.3168/jds.2009-2980
Open Access Status DOI
Volume 93
Issue 8
Start page 3818
End page 3833
Total pages 16
Place of publication New York, NY, United States
Publisher Elsevier
Language eng
Abstract Multiple-trait genome-wide association study (GWAS) analyses were compared with single-trait GWAS for power to discover and subsequently validate genetic markers (single nucleotide polymorphisms; SNP) associated with dairy traits. The SNP associations were discovered in 1 Holstein population and validated in both a Holstein population consisting of bulls younger than those in the discovery population and a Jersey population. The multivariate methods used were a principal component analysis and a series of bivariate analyses. The statistical power of detecting associations using multiple-trait GWAS was as good as or better than that of the best single-trait GWAS. Additional SNP associations were found with the multivariate methods that had not been discovered in the single-trait analyses; this was achieved without an increase in the false discovery rate. From the multivariate analysis, 4 common pleiotropic patterns were identified among the putative quantitative trait loci (QTL) affecting the Australian selection index. These patterns could be interpreted as a primary effect of the putative QTL on 1 or more milk components and secondary effects on other components. The multivariate analysis did not appear to increase the precision with which putative QTL were mapped.
Keyword Multivariate genome-wide association study
Pleiotropy
Principal component
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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