Cavanagh et al. Genetics Selection Evolution 2010, 42:36 http://www.gsejournal.org/content/42/1/36 the animal. This is seen in the correlations of non-unity between traits indicative of fatness at different sites (Table 1). This suggests that different measures of the same tissue reflect different traits with different QTL. This may have implications for QTL detection and application. For instance, QTL used to reduce subcuta- neous fat content may not necessarily result in a reduc- tion of total carcass fat. Despite many QTL reports and a significant associa- tion on chromosome 18, we could not confirm the effects of the important loci such as the Carwell and Callipyge genes with known effects on muscle lean in sheep [20,58,59]. These and other genes on the same chromosomal region are known to be imprinted with paternally expressed protein-coding genes, as well as several maternally expressed non-coding RNA genes [20], which may have prevented their detection in our study, which used only one paternal half-sib family. Sin- gle-marker association analyses revealed significant asso- ciations for markers close these genes (results not shown) but this requires more detailed analysis. In future studies, the use of multi-sire families and linkage disequilibrium among maternal alleles should focus on the identification of these imprinting effects. We considered an interdependency of QTL for body weight on OAR11 and 16. These chromosomes contain the growth hormone (GH) and growth hormone receptor (GHR) genes, with known effects on body weight and carcass composition across species [60-66]. Even though we identified QTL for final body weight on both chromo- somes, we could not detect an interaction between these two QTL and assume that the genes underlying these two QTL act in a simple additive fashion. Although we examined the likely importance of two QTL for all traits and report on five cases with signifi- cant support for QTL pairs, the interpretation of the results warrant caution, especially where the QTL are closely located or no corresponding QTL were detected under the single QTL model. Meta-assembly and comparative analysis A meta-assembly of QTL identified for carcass traits was conducted by collating all known ovine QTL from pub- lic sources for matched traits, as previously described [27]. Additionally, studies in cattle were summarised using the same methodology. A summary of the carcass meta-scores from cattle and sheep that is incorporated into the ovine genome browser http://crcidp.vetsci.usyd. edu.au/cgi-bin/gbrowse/oaries_genome/ is shown in Fig- ure 5. Furthermore, due to the lack of studies based on CT-derived phenotypes, and the different methods, models, and population types used across studies, we considered them to be the same carcass trait if they described the same carcass characteristic. Page 11 of 14 Despite the large number of QTL detected in cattle, relatively few QTL in sheep were found in comparative locations. However, for some traits, especially for muscle and fat, loci were mapped to homologous regions; these QTL may possibly describe the same gene. Among the 11 studies summarised using the meta- assembly in cattle, four reported QTL for body weight on chromosome 14 [39,46,67,68], but no QTL was found in sheep in the homologous position. The highest ovine meta-scores for body weight were derived for chromosomes 1 [13,14,17], 6 [26] and 21 [13,26]. QTL were reported for body weight in cattle on the homolo- gous chromosomes 1 [37,39,67], 6 [40,67,69] and 29 [39,70,71]. Amongst the six ovine and 13 bovine QTL studies reporting linkage regions for muscle related traits, we found one region in common between sheep and cattle, namely OAR2 and BTA2 for carcass weight, eye muscle area and retail product yield [8,16,36-38,67,70,72] (Figure 5). High meta-scores for fat QTL were derived for sheep and cattle on homologous chromosomes OAR2/BTA2 and OAR6/BTA6 [37,38,45,67,68,70,71,73]. However, no QTL for fat traits were identified in sheep, which align to bovine chromosome 14, where the highest meta- score was calculated for corresponding traits in cattle [46,67,69,70,74]. No homologous regions were found between sheep and cattle for bone traits. This is likely due to the lim- ited number of studies conducted and QTL reported for these traits in either species. Conclusion This is the first study using CT-derived carcass mea- sures for a full-genome scan in sheep. To our knowl- edge this is the only study with a focus on carcass fat characteristics in mature sheep. We present evidence for a significant number of new QTL for muscle, fat and bone traits in sheep. We also confirm and support the presence of previously published QTL in breeds other than those studied here. Finally, homology in QTL regions between sheep and cattle for muscle, bone, fat and body weight was demonstrated. Additional material Additional file 1: Summary of linear models for trait pre-correction used in this study. R-square, overall P-value (Model P-value) and P- values for the regression coefficients in the fitted models. Models were adjusted for final body weight (FBW) and cohort allowing for nonlinearity if observed in a scatter plot of the trait versus final body weight Additional file 2: Phenotypic correlation between body weight and carcass weight measures. Phenotypic correlation between body weight and carcass weight measures. Correlations exceeded the P < 0.01 threshold using with n = 160 animals and 1n = 72 animals