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Dissection of genomic correlation matrices of US H olsteins using multivariate factor analysis
Author(s) -
Macciotta N.P.P.,
Dimauro C.,
D.J.,
Gaspa G.,
Cellesi M.,
Cole J.B.
Publication year - 2015
Publication title -
journal of animal breeding and genetics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.689
H-Index - 51
eISSN - 1439-0388
pISSN - 0931-2668
DOI - 10.1111/jbg.12113
Subject(s) - quantitative trait locus , biology , genetics , sire , locus (genetics) , covariance , genome wide association study , pleiotropy , multivariate statistics , correlation , single nucleotide polymorphism , gene , statistics , phenotype , mathematics , zoology , genotype , geometry
Summary 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 DGAT 1 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 BTA 18 influencing these traits. Moreover, a possible candidate gene for daughter pregnancy rate was suggested for BTA 28. 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.