Correlating naively EBVs for trait A and B is wrong, because EBVs are not TBVs and they’re regressed towards 0. So the correlation is underestimated. Thus, Calo’s method is typically used. The references are:
- Calo, L. L., McDowell, R. E., VanVleck, L. D., & Miller, P. D. (1973). Genetic aspects of beef production among Holstein-Friesians pedigree selected for milk production. Journal of Animal Science, 37(3), 676-682.
- Blanchard, P. J., Everett, R. W., & Searle, S. R. (1983). Estimation of genetic trends and correlations for Jersey cattle. Journal of Dairy Science, 66(9), 1947-1954)
Equation [2] in Blanchard et al. to obtain the genetic correlation between traits A and B from the correlation of EBVs and respective reliabilities Rel is:
$latex r_{A,B} =\frac{\sqrt{(\sum(Rel_A) \sum(Rel_B))}}{\sum(Rel_A Rel_B)} r(EBV_A,EBV_B) $latex
Reading these papers is hard. In Blanchard’s paper b’s are reliabilities because defined as $latex b=\frac{var(EBV)}{var(TBV))} $latex. From Henderson we know that var(EBV) = cov(EBV, TBV) and
$latex Rel=\frac{cov(EBV,TBV)^2}{( Var(EBV)*Var(TBV))} $latex
which simplifies to
$latex Rel=\frac{cov(EBV,TBV)}{var(TBV)} = \frac{var(EBV)}{var(TBV)} $latex
which is equal to these b’s in Blanchard’s paper
For instance assume that all bulls have the same Rel for trait A of 0.3 and average Rel for trait B is 0.9, then rA, B ≈ 1.9 × r(EBVA, EBVB).
so the correlation of EBVs can severely underestimate the genetic correlation.