QTL regions associated with lactation persistency and protein yield in sheep have been identified on OAR3 and OAR20. Genotyping of 8 out of 15 existing microsatellite markers on OAR3, and 5 out of 9 on OAR20, in the QTL region of interest, over additional backcross and double backcross daughters, resulted in high resolution mapping of these two QTL regions to 10 cM and 20cM intervals respectively using Linkage Analysis (LA). An additional 28 informative markers (12 on OAR3 and 16 on OAR20) have been genotyped and combined Linkage Analysis/ Linkage Disequilibrium analysis (LA/LD) will be used to obtain further resolution in these regions so that positional candidate genes can be identified. From standard QTL analyses animals with contrasting genotypes ‘Q-’ and ‘q-’ for desired QTLs have been identified for use in functional (transcriptome) studies to obtain a list of differentially expressed genes. The transect of both positional and functional (differentially expressed) genes should lead to a short list of positional functional candidate genes for further analyses and comparative mapping to dairy cows.