The Animal QTL Database (QTLdb; http://www.animalgenome.org/QTLdb/) has been developed to provide a centralized resource tool to link traits to respective genome locations using curated data in the public domain. To date, it is housing more than 15,000 QTL in 5 animal species (cattle, chicken, pig, sheep and rainbow trout). The Animal QTLdb was built not only to house QTL data for within- and between-species comparisons, but also to facilitate comparative alignment with genome features such as genes, transcripts, RH markers, SNPs, etc. Rapid progress in genome-wide association studies (GWAS) and construction of the Vertebrate Trait Ontology have presented new opportunities for further development of the Animal QTLdb. We report here our recent efforts on the QTLdb developments which have made it possible to accommodate and combine the GWAS study results, and to link out from the QTLdb to the newly constructed Vertebrate Trait, Livestock Product Trait, Clinical Measurement, and livestock breed ontologies. We consider these developments important steps to standardize the ways in which various databases can directly “talk” to each other and exchange information. Our continued efforts to develop the QTLdb are to ensure it is up-to-date in terms of both data contents and functions, and also to make it a central hub bridging between genotypes and phenotypes for all livestock species, which will further facilitate comparative studies across species.