Dissection of genomic correlation matrices of US Holsteins using multivariate factor analysis

The aim of this study was to compare correlation matrices between direct genomic predictions for 31 traits at the genomic and chromosomal levels in US Holstein bulls. Multivariate factor analysis carried out at the genome level identified seven factors associated with conformation, longevity, yield, feet and legs, fat and protein content traits. Some differences were found at the chromosome level; variations in covariance structure on BTA 6, 14, 18 and 20 were interpreted as evidence of segregating QTL for different groups of traits. For example, milk yield and composition tended to join in a single factor on BTA 14, which is known to harbour the DGAT1 locus that affects these traits. Another example was on BTA 18, where a factor strongly correlated with sire calving ease and conformation traits was identified. It is known that in US Holstein, there is a segregating QTL on BTA18 influencing these traits. Moreover, a possible candidate gene for daughter pregnancy rate was suggested for BTA28. The methodology proposed in this study could be used to identify individual chromosomes, which have covariance structures that differ from the overall (whole genome) covariance structure. Such differences can be difficult to detect when a large number of traits are evaluated, and covariances may be affected by QTL that do not have large allele substitution effects.