Selective breeding programmes start with collection of genetic material from different sources, which could be different wild populations or domesticated stocks / strains. It is important to assess the genetic diversity of these different samples, to ensure that adequate variation is present in the base breeding population being constructed. Molecular analysis is useful in providing a quick assessment, but it is important to assess the actual performance for the trait of interest (in this case growth) of the different samples undertaken to assist decisions on which fish are included ultimately in the base population. This may mean exclusion of particularly poor performers or preferential inclusion of high performers, and assessing presence of any positive or negative interactions between fish from different sources. Strain comparison aims at testing performance of specific strains for production under specific environment(s), and ultimately to establish a foundation, called ‘base population’, for a selective breeding programme using a synthetic strain.