Phenotypic distances

Phenotypical distances are not so widely distributed in Animal Science. It is the big shortage I think. To fill it up I have tried to use cluster discriminant analysis to find such distances and to assess the standardized coefficients of canonical functions.
I am working with biochemical and immunogenetic data collected on pigs. And concerning the results of my research I can underline that it was evident that pig breed bred in West Siberia differ from each other by biochemical indices. It was depended on the genetic contribution. Usually it is impossible to find markers that can be the same at different environment conditions, they should be not the same. It is epigenetics. It means we should bear in mind the continuous traits affected by a numerous genetic interrelationship.
In the near future I am going to put methodological base to extract such indexes and try to explain some effects. The canonical correlation coefficients will be the distance coefficients for multivariate input data. Mahalanobis distance is another way to assess, but with slightly other aim. I will try to compare ones. The work is under way at the initial steps :)