Twenty-eight clonal trials of radiata pine planted across Australia and New Zealand were used to investigate genetic variation and genotype by environment (G×E) interaction for diameter-at-breast-height (DBH), height and Dothistroma resistance (DO_R). The average narrow-sense heritabilities were 0.11, 0.21 and 0.30 while the average broad-sense heritabilities were 0.27, 0.34 and 0.40 for DBH, height and Dothistroma resistance, respectively. Dothistroma resistance was assessed as the percentage of needles that were not affected by Dothistroma needle blight. G×E interactions were analysed using an approximate reduced factor analytic model. Apparent G×E interactions were estimated for DBH, height and Dothistroma resistance. Estimates of G×E interactions and their standard errors were strongly influenced by the level of connectivity between trials, in terms of common clones and common parents. When there was sufficient connectivity between trials (more than 30% common clones between trials), a high level of G×E interaction was found for DBH and height but not for Dothistroma resistance. In two simulated clonal trials planted in two environments, low connectivity between environments resulted in a lower estimated genetic correlation between environments with an increased standard error. These results suggest that the number of clones in common between clonal trials is a key factor for inclusion in future experimental designs for estimating G×E interaction. When designing clonal trials for use in multiple environments for accurately estimating the level of G×E, if the resource for creating connectivity between environments is limited, at least 30% of the clones need to be in common between environments.