Single nucleotide polymorphic (SNP) chips enable us to account for variation within genomes very well. It is possible to associate this variation with variation in phenotypes and so predict genetic merit of young individuals better than ancestral indexes. This has significant implications for livestock industries as to accuracy and timing of selection decisions. and how resources are allocated to maximize the returns from investments in genotypic and phenotypic data collection. High density genotyping platforms will exacerbate the problem of the joint analysis of individuals with heterogeneous amounts of genotypic information.