Selection of dairy cattle based on genetic evaluations has been effective at increasing production, yet improvement could be accelerated for yield and other economically important traits by directly selecting on genetic differences affecting phenotypes. Producers can reliably select animals in this manner if loci in the bovine genome containing important differences have been identified, and more importantly, if the efficacy of selection for these economic trait loci (ETL) has been demonstrated in commercial population. In most cases, application of these tools will only supplement and not replace traditional progeny test schemes for evaluating young bulls. In an effort to maximize efficiency and acceptance of marker-assisted selection (MAS), we have focused our efforts on ETL with potential for industry use, milk protein and dairy form. In extension of preliminary studies, our investigation now includes an ongoing collection of related sire lines, so that ETL inheritance can be traced from older prominent sire families to recent bulls relevant to dairy producers. Analysis of these complex pedigrees will further refine genetic intervals containing ETL. Reducing genetic distances between selection markers minimizes the occurrence of marker-ETL recombinations that decrease accuracy of selection. Finally, allele frequency and contribution to phenotype will need to be determined before identified ETL can be used. The ultimate endpoint of ETL interval refinement is to identify the causative genetic variation in gene(s). This outcome is ideal, because then selection on the gene level can be effectively implemented even in unrelated families. Gene discovery also identifies important biochemical pathways for further research. To augment ETL mapping efforts, genes expressed in the mammary gland are being characterized and mapped. This sequence data serves as a valuable resource for gene expression profiling that can be used to identify candidate genes near ETL.