Application of a canonical transformation to detection of quantitative trait loci with the aid of genetic markers in a multi-trait experiment.

Effects of individual quantitative trait loci (QTLs) can be isolated with the aid of linked genetic markers. Most studies have analyzed each marker or pair of linked markers separately for each trait included in the analysis. Thus, the number of contrasts tested can be quite large. The experimentwise type-I error can be readily derived from the nominal type-I error if all contrasts are statistically independent, but different traits are generally correlated. A new set of uncorrelated traits can be derived by application of a canonical transformation. The total number of effective traits will generally be less than the original set. An example is presented for DNA microsatellite D21S4, which is used as a marker for milk production traits of Israeli dairy cattle. This locus had significant effects on milk and protein production but not on fat. It had a significant effect on only one of the canonical variables that was highly correlated with both milk and protein, and this variable explained 82% of the total variance. Thus, it can be concluded that a single QTL is affecting both traits. The effects on the original traits could be derived by a reverse transformation of the effects on the canonical variable.