Differences in correlations between traits within an inbred population are determined at each genetic marker. Phenotypes are assigned to genotype groups and a single phenotype is used to scan all other phenotypes for a loss or gain of correlation. The likelihood profiles (~ QTL profiles) of this 'loss of correlation' measurement shows a very high degree of overlap with classical QTL profiles. However additional information is available from the phenotype x phenotype interactions. With the right dataset (ideally a combination of: classical phenotypes, protein abundance and gene expression) CTL shows the genetic wiring of the classical phenotypes and identify key players in the genetic / protein network underlying classical phenotypes using QTL and CTL information.
For more information on CTL and their interaction with QTLs, or how-to calculate CTLs on N-genotypes, please see Chapter 4 of my Doctoral Thesis