Genetics Selection Evolution 2009, 41:36 http://www.gsejournal.org/content/41/1/36 shown to be significantly associated with milk fat yield and fat percentage where AA animals, with the lysine amino acid, had increased levels for both traits [40]. The present study found that the polymorphism was also asso- ciated with sirloin weight after maturation and sirloin fat depth. In both cases the A allele was associated with the higher value indicating that the increase in sirloin weight is probably due to the increase in the depth of fat sur- rounding the muscle. This is consistent with work done in German Holstein cattle where animals with the lysine allele at DGAT1 were found to have an increase in intra- muscular fat content [30]. In contrast, work done on Brah- man cattle found no association between K232A genotype and carcass fat traits [41]. The GHR polymorphism studied here is an A to T substi- tution in exon eight of the gene which results in a non- conservative replacement of phenylalanine with a tyro- sine residue (F279Y) [42]. Whilst polymorphisms in the GHR gene (BTA 20 [43]) have previously been found to be significantly associated with drip loss [14], body weight [15,16] and USDA marbling score [17], the present study found no associations between F279Y genotype and any of the carcass quality traits. The only trait that was signifi- cantly affected by GHR genotype was meat odour as judged by the taste panel. The panellists assigned higher odour scores for animals with the AA genotype, which corresponds to the phenylanine amino acid, when com- pared to either AT or TT animals. The present study confirmed some well-known associa- tions and identified novel significant trait-genotype asso- ciations. However, there were some traits where associations were expected but not observed. Specifically, associations between carcass and sirloin related traits and the SNP in the leptin gene were expected but were not found. Serum levels of the leptin hormone have previ- ously been found to be significantly associated traits such as marbling, backfat depth and kidney, pelvic and heart fat [44]. Additionally, genotype at the leptin SNP, UASMS2, has been shown to be associated with serum leptin concentration as well as with backfat thickness, marbling score and live weight at slaughter [9], carcass marbling score, Longissimus muscle (LM) area and hot carcass weight [45], although these results were not con- firmed by Schenkel et al., (2005). As discussed above, the present study observed a significant, non-additive associ- ation between sirloin fat depth and UASMS2 genotype but no association was found with carcass or sirloin weight related traits. Previous reports also indicate associ- ations between UASMS1 and fat yield and Exon2FB with fat and lean yield and grade fat [7], however, the current study found no associations between either UASMS1 or Exon2FB genotype and any of the traits tested. These con- trasting results may be due to the different populations studied and indicate the importance of multiple valida- tion studies in different breeds and populations. Sex × genotype interactions The analyses of the mean trait value for each genotype in each sex for those trait-SNP pairs where there were signif- icant sex interactions indicated that, for the majority of associations, the effect was primarily in the female ani- mals. Differences between male and female genotype effects were seen in five traits: taste panel assessed tender- ness, weight of hindquarter, odour, sirloin weight after maturation and sirloin fat depth. The reason for the differ- ence between male and female animals is unknown. Whilst differences in meat quality between male and female cattle have been reported [46,47], there are few that describe differences in genetic effects between sexes such as those seen in the current study. Differences could be partly due to the limited number of females (135) in the analysis when compared to the males (308) although allele frequencies for both sexes were similar (data not shown). Alternatively, trait expression could be strongly correlated with fatness. Means for each sex showed that females tended to have higher fat class scores than males (data not shown). Therefore, it is possible the female ani- mals are more likely to express genetic differences in traits that are correlated with fatness. Haplotype analysis The haplotype analyses tested whether incorporating information on combinations of SNP (for μ-calpain and leptin respectively) led to an improvement over models with only single SNP genotypes. We found that using hap- lotypes in addition to SNP genotypes in the analysis accounted for no extra variation for any of the SNP/trait combinations. This may be explained by the fact that only one of the SNP from each of the genes (CAPN316 from the μ-calpain gene, and UASMS2 from the leptin gene) had a significant effect on any of the traits in the single SNP analyses. Thus incorporating haplotype information would not improve the performance of marker-assisted selection for this population. Conclusion The results presented here confirm some of the previously documented associations, for example, the association between CAPN316 genotype and tenderness, the most important quality trait for consumers. Furthermore, novel associations have been identified which, following valida- tion in other populations, could be incorporated into breeding programmes to improve meat quality. Finally, whilst some previously noted associations were not repli- cated in the current study, it is important to note that val- idation is dependent on the specific nature of the population screened and that genetic background may influence the size of the effect of a polymorphism. Valida- Page 10 of 12 (page number not for citation purposes)