Genetics Selection Evolution 2009, 41:36 http://www.gsejournal.org/content/41/1/36 Table 5: Genotype means, standard errors, P values and estimates of additive and dominance effects for SNP with significant trait associations Genotype means ± se1 Overall P-value2 a ± se1,3 d ± se1,4 Tenderometer score, kPa5 Hindquarter weight, kg Tenderness 22.25 ± 1.16 75.67 ± 1.57 6.00 ± 0.16 24.24 ± 0.7 72.05 ± 0.84 5.79 ± 0.08 25.18 ± 0.67 71.84 ± 0.77 5.63 ± 0.07 1.46 ± 0.52** -1.92 ± 0.76* -0.19 ± 0.08* 0.53 ± 0.61 -1.70 ± 0.92 -0.03 ± 0.09 Overall liking 5.59 ± 0.08 5.55 ± 0.08 5.80 ± 0.10 0.10 ± 0.05* -0.15 ± 0.06* SNP CAPN316 UASMS2 DGAT1 GHR CC CC AA AA CG CT AG AT GG TT GG TT 0.016 0.04 0.016 0.02 0.04 0.05 0.02 Sirloin weight after maturation, kg Sirloin fat depth, mm 8.31 ± 0.46 11.11 ± 1.65 7.17 ± 0.12 6.62 ± 0.4 7.14 ± 0.11 6.53 ± 0.33 -0.59 ± 0.23* -2.29 ± 0.83* -0.55 ± 0.23* -2.20 ± 0.87 * Odour 5.64 ± 0.19 5.24 ± 0.08 5.16 ± 0.06 -0.24 ± 0.09** -0.16 ± 0.11 1 Mean values were adjusted for farm and averaged over sex. Estimate of the effect is expressed in units of the trait 2 P-value for the overall genotype effect 3 Additive effect is estimated as the difference between the 2 homozygous means divided by 2 4 Dominance effect is estimated as the non-additive genetic effects or the deviation of the heterozygote from the mean of the 2 homozygotes ** P < 0.01 and * P < 0.05 5 Units for tenderometer score are kilopascals 6 Associations remain significant following correction for multiple testing (adjusted P-value was 0.01) estimated differences between the homozygous genotypes AA and GG were 1.17 kg and 4.58 mm for sirloin weight after maturation and sirloin fat depth. There were signifi- cant dominance effects for both sirloin weight after matu- ration and sirloin fat depth (P = 0.02 and 0.01, respectively). Animals with the heterozygous genotype had values close to the homozygous GG animals, indicat- ing a strong degree of dominance of the G allele over the A allele. The A allele of the GHR SNP was significantly associated with an increase in taste panel-assessed odour, with the estimated difference between the homozygous genotypes AA and TT equal to 0.48 taste panel units (Table 5). There was no significant dominance effect. To further investigate the observed associations, a number of covariates were added to the fixed model. These included hot carcass weight, age at kill and percentage Aberdeen Angus (50, 75 or 100%, depending on dam breed). Percentage Aberdeen Angus made no difference to the genotypic effects for all of significant traits. As expected, when hot carcass weight was fitted as a covari- ate, the significance of the associations with weight traits was reduced. Age at kill made no difference to the effects of genotype on tenderness, hindquarter weight, overall liking, sirloin fat depth or odour. The only SNP trait asso- ciation affected by age at kill was the association between DGAT1 genotype and sirloin weight after maturation. The p-value increased above 0.05 although animals with the AA genotype were still found to have heavier sirloins after maturation than those animals with either AT or TT geno- types. Most age differences between animals are accounted for in the model as farm effects, hence the small impact of this covariate. Sex × genotype interactions There were significant genotype-by-sex interactions for six of the significant trait SNP genotype pairs (Table 6). These were the CAPN316 association with tenderometer, weight of hindquarter and taste panel tenderness; the GHR asso- ciation with odour; and the DGAT1 association with com- plete sirloin weight and sirloin fat depth. When the genotype means of each sex were assessed using pair wise comparisons it became apparent that the majority of sig- nificant genotype-trait associations mentioned previously were stronger in the female animals. Females with the CC genotype at the CAPN316 SNP had significantly lower tenderometer values, higher hindquarter weights and higher taste panel tenderness scores than CG or GG ani- mals. In contrast, the CC males had higher tenderometer Page 7 of 12 (page number not for citation purposes)