Cavanagh et al. Genetics Selection Evolution 2010, 42:36 http://www.gsejournal.org/content/42/1/36 Page 10 of 14 Figure 5 Comparative genome map of aggregated meta-scores for carcass-related QTL derived from sheep and cattle studies. Express, therefore the number of false positive QTL was assumed to be minimal. For the maximum-likelihood analysis we chose thresholds for a LOD statistic which was deemed to be conservative at LOD of 2 (P ≈ 0.01) and LOD of 3 (P ≈ 0.001). The close agreement between the number of QTL detected in each method suggests that the likelihood of random false positives is expected to be small. For body and carcass weight, QTL were identified on chromosomes 2, 6, 11 and 16. The QTL on chromo- somes 6 and 11 were consistent with those reported in the same study population at earlier time points [26]. The QTL for final and carcass weight on chromosome 2 was the only one that corresponded to a QTL for live weight in Scottish Blackface and Suffolk, Texel sheep [13,17]. A total of eight QTL across seven chromosomal regions were identified for muscle. QTL on chromo- somes 1 and 6 were consistent with other studies in Suf- folk and Texel populations [11,16,17], whereas QTL on chromosomes 7, 9, 10, 16 and 23 can be considered novel. QTL for fat have previously been reported on OAR 1-4, 18 and 20 in different sheep populations [14,16,17,31,33,34]. Within the confidence interval of our QTL, we confirmed QTL on chromosome 1 and 3, and novel QTL were identified on OAR 6, 10, 14, 16 and 23. QTL for fatness have consistently been reported on chromosomes 2, 3 and 18 [14,16,17], but the QTL on OAR18 was only identified using the two-QTL model and no QTL on OAR2 was detected in the cur- rent study despite the emphasis on fat traits. Few reports are available for bone-related traits in sheep, and no QTL study on bone yield in the carcass has been reported. Previous QTL studies have analysed bone density and cross sectional area in Scottish Black- face and Coopworth sheep [13,31,32]. The two QTL detected here for bone yield suggest that the QTL land- scape is rather featureless for this trait. In summary, the first interesting discovery of this paper was the identification of novel QTL with small to moderate effects on body composition and body weight on chromosomes 1, 6, 7, 9, 10, 14, 16 and 23. This may in part be due to an increase in accuracy of phenotyping using CT image analysis. A notable finding of this study was that there were no QTL which exclusively affected multiple measures of the same tissue group, i.e. fat, lean or bone. The effect of measuring fat at individual or a limited number of sites was discussed by Thompson [57], who proposed that individual depots may not reflect total body fat in