Cavanagh et al. Genetics Selection Evolution 2010, 42:36 http://www.gsejournal.org/content/42/1/36 Page 7 of 14 Figure 2 QTL map of the entire genome for carcass lean, total lean, eye muscle area and lean percentage. and total percent fat compared to animals from cohort 1. There were significant correlations between the major tissue groups (lean, fat and bone). Fat traits tended to be significantly and negatively correlated with lean traits, as reported by Lambe et al. [55]. Without adjusting for body weight, the correlations would have been strongly positive [55,56], as was also the case here (results not shown). The importance of adjustment for body weight is that properties of body tissue can be investigated free from the effects of body mass. The differences in stage of maturity resulted in different adjustments for body weight, namely a linear effect for cohort 1 and a curvi- linear effect for cohort 2, suggesting a plateau of growth had been reached and animals were in the mature fattening phase of development. QTL analysis Genome-wise error rates were controlled by adjustment of P-values through the use of a chromosome- and experiment-wide permutation test in the case of QTL