Genes for quantitative traits in domestic animals Leif Andersson Department of Medical Biochemistry and Microbiology, Uppsala University, BMC, Box 597, S-751 24 Uppsala, Sweden A huge number of QTLs have by now been documented in domestic animals. However, as in other species the identification of the genes underlying QTLs is very challenging. Despite considerable efforts, the causal genes for only a handful QTLs have been described so far. The most prominent examples being a single nucleotide substitution in intron 3 of IGF3 affecting postnatal muscle growth in pigs and a single nucleotide substitution in the 3’UTR of MSTN, creating a new target site for two microRNAs, which underlies a QTL for muscularity in sheep. So why is the identification of QTL mutations so difficult? One obvious reason is the difficulty in getting a sufficient map resolution (<1 Mbp) that makes it possible to resequence and evaluate all transcripts in the QTL region as regards their coding sequence and regulatory elements. Another complicating factor is that a good proportion of QTLs have a complex architecture where mutations in two or more closely linked genes and/or two or more mutations in the same gene cause the QTL. Epistatic interaction further complicates the analysis. However, the extensive use of linkage combined with linkage disequilibrium mapping hold the promise to make positional identification of QTL mutations more feasible in the future. My prediction is that a majority of these mutations will constitute tissue-specific regulatory mutations and this notion is supported by our recent identification of mutations underlying monogenic trait loci in dogs, horses and chicken.