Cavanagh et al. Genetics Selection Evolution 2010, 42:36 http://www.gsejournal.org/content/42/1/36 predicted carcass weight from the scan were highly corre- lated (r = 0.90, P < 0.01) and both traits were also highly correlated with final body weight (r = 0.92 and 0.89, for both cohorts respectively, P < 0.01) (Additional file 2). Across both cohorts, the average body weight at scanning was 51 kg, with an average carcass weight of 28 kg (dres- sing percentage 55%). Animals from cohort 2 were signif- icantly (P < 0.01) heavier, with a higher mass of total bone, fat and lean compared to cohort 1. However, they had a significantly (P < 0.01) lower percentage bone in the carcass (Additional file 3). Within tissue groups, lean, fat (except internal fat and subcutaneous fat depth) and bone parameters were significantly correlated (r = 0.27 to 0.81, all P < 0.01) (Additional file 4). Significant correla- tions (P < 0.05) were also detected between many traits among fat and lean tissue groups, with the highest corre- lation between percentage lean and fat (r = -0.97, P < 0.01). No significant correlations were detected between carcass bone, total bone and eye muscle area and most of the other traits (Additional file 4). Putative QTL identified In total, three highly significant (LOD ≥ 3.0), 15 signifi- cant (LOD ≥ 2.0) and 12 suggestive (1.7 < LOD < 2.0) QTL were detected on chromosomes 1 to 3, 6, 7, 9-11, 14, 16 and 23 across the 13 traits using QTL-MLE. A summary of the suggestive and significant QTL posi- tions, effect sizes, and 1-LOD support intervals is shown in Table 2. The genome-wide LOD score profiles for all traits are shown in Figures 1, 2, 3 and 4. With the exception of one suggestive QTL on chromosome 6, all QTL detected by QTL-MLE were confirmed by the QTL regression analysis of QTL Express. A total of five highly significant (experiment-wide P < 0.05), six signifi- cant (chromosome-wide P < 0.01) and 34 suggestive (chromosome-wide P < 0.05) QTL were identified on chromosomes 1-3, 6, 7, 9, 10, 11, 14, 16, 19, 23 and 26 using QTL Express (Additional file 5). Among these, two significant (chromosome-wide P < 0.01) and 16 sug- gestive (chromosome-wide P < 0.05) QTL on chromo- somes 6, 8-14, 16, 23 and 26 were not detected using QTL-MLE. Confidence intervals and 1-LOD support intervals for QTL locations extended across a large pro- portion of each of the chromosomes (Table 2, additional file 5). Common QTL for body and carcass weight were iden- tified on chromosomes 2, 6 and 11 using both QTL analysis methods, in addition to the QTL for body weight on chromosome 16 and for dressing percentage on chromosome 14. For muscle traits, eight QTL were detected on seven chromosomes, for fat traits ten QTL on seven chromosomes and for bone traits only two QTL. There were no QTL which solely contributed to traits related to a single tissue i.e. QTL just for muscle, Page 4 of 14 fat or bone. For chromosomes 1, 6, 10, 14, 16 and 23, the QTL for different tissue groups acted pleiotropically, with the same QTL describing traits for different tissue groups. Among the six QTL identified on chromosome 6, two were for weight and three for fat parameters, although the peak positions of the QTL for these two traits groups differed. Similarly, the QTL regions for final body weight, percent lean and subcutaneous fat area were all on chromosome 16, but the peak positions varied. The effect sizes of the QTL ranged from 0.73 to 0.99 SD (Table 2) and accounted for 3.8 to 9.4% of the phenotypic variance (Additional file 5). Three of the QTL identified here were deemed cryptic QTL, with an effect opposite to what was expected based on breed of origin. The two-QTL model implemented in QTL Express showed four pairs of QTL which were separated by at least one marker; carcass lean (OAR1), percent bone (OAR1), percent fat (OAR18) and internal fat (OAR19). QTL for carcass lean on chromosome 1 were in cou- pling phase, whereas all other QTL pairs were in repul- sion phase. The QTL in repulsion phase were not identified using the single QTL model since the opposite sign of the QTL effects may have prevented detection under the single QTL model. Details describing QTL positions and effect sizes, and comparisons with single and no QTL models are in Table 3. Meta-assembly Published QTL reports for carcass traits in sheep, com- prising four genome-wide linkage studies [26,31-33] and 13 partial genome scans [8,11,13-18,34-36] were used for the meta-assembly. QTL for a wide range of carcass traits, including traits not measured in our study (muscle growth, muscle depth, and meat colour), were reported on chromosomes 1-6, 8, 11, 18, 20, 21, 23, 24 and 26 in various sheep populations [8,13,15-18,31-33,35,36]. For two of the studies, the locations of the QTL were not given [11,34]. No QTL were reported on chromosomes 7, 9, 10, 12-17, 19, 22, and 25, but these results might be biased due to partial genome scans, favouring chromo- somes with known QTL or candidate genes. The meta- scores showed consistency on six regions of interest across multiple studies for fat, muscle and weight traits, specifically for fat on OAR2 (BTA2) and OAR6 (BTA6), for muscle QTL on OAR2 (BTA2) and for weight on OAR1 (BTA1), 6 (BTA6) and 21 (BTA29) (Figure 5). The results of the ovine and bovine meta-assembly are shown as a comparative meta-score plot against the ovine genome in Figure 5 and are visualised on the ovine genome browser http://crcidp.vetsci.usyd.edu.au/ cgi-bin/gbrowse/oaries_genome/. The very broad range of traits describing carcass and body composition in cat- tle resulted in QTL being reported on all chromosomes.