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

J Dairy Sci. 2010 Aug;93(8):3818-33. doi: 10.3168/jds.2009-2980.


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.

Publication types

  • Comparative Study

MeSH terms

  • Animals
  • Australia
  • Cattle / genetics*
  • Female
  • Genetic Markers
  • Genetics, Population
  • Genome-Wide Association Study / methods
  • Genome-Wide Association Study / veterinary*
  • Male
  • Multivariate Analysis
  • Polymorphism, Single Nucleotide
  • Quantitative Trait Loci


  • Genetic Markers