Multivariate analysis of a genome-wide association study in dairy cattle.
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.
Bolormaa
S
S
Biosciences Research Division, Department of Primary Industries Victoria, 1 Park Drive, Bundoora 3083, Australia. bolormaa.sunduimijid@dpi.vic.gov.au
Pryce
J E
JE
Hayes
B J
BJ
Goddard
M E
ME
D000818:Animals; D001315:Australia; D002417:Cattle / Q000235:genetics*; D005260:Female; D005819:Genetic Markers; D005828:Genetics, Population; D055106:Genome-Wide Association Study / Q000379:methods / Q000662:veterinary*; D008297:Male; D015999:Multivariate Analysis; D020641:Polymorphism, Single Nucleotide; D040641:Quantitative Trait Loci
D005819:Genetic Markers