Genetics Selection Evolution 2009, 41:36 http://www.gsejournal.org/content/41/1/36 including animal ID and steak ID (A or B) was added for analysis of taste panel traits to allow a distinction to be made between the A and B steaks of those animals that had repeat steaks tested. The general model used for carcass traits was as follows: Yijklmno = μ + F j + G k + Sl + (G × S)kl + K m + M jn + e ijklmno where: Yijklmn is the trait measured on the individual i μ is the overall mean for the trait Fj is the fixed effect of farm j (14 levels) Gk is the fixed effect of SNP genotype k (3 levels) Sl is the fixed effect of sex l (2 levels) (G × S)kl is the interaction between the k-th SNP genotype and the l-th sex Km is the random effect of kill-date m Mjn is the random effect of the n-th sire on the j-th farm ejklmno is the residual term associated with the observation Additional interaction terms between sire, kill-date, geno- type and sex groupings were fitted as random effects. Var- iance components were constrained to be non-negative, i.e. where effects were estimated to be negative they were set to zero. For the taste panel traits the general model was as follows: Yijklmnop = μ + Fj + G k + Sl + (G × S)kl + Pm + M jn + Tio+e ijklmnop where additional terms are: Pm is the random effect of taste panel date m Tio is the random effect of the o-th steak (A or B) for the i- th animal eijklmnop is the residual error associated with the observa- tion. Again, additional interaction terms between sire, taste panel date, genotype and sex groupings were fitted as ran- dom effects, and variance components were constrained to be non-negative. The effects of several covariates (percentage Aberdeen Angus, hot carcass weight and age at kill) were also exam- ined in separate analyses. The percentage Aberdeen Angus (% AA) was based on dam breed so that each animal was assigned a value of 100% (if the dam was AA), 75% (if the dam was AA-cross) or 50% (if the dam was neither). Sta- tistical significance for the fixed effects was determined using approximate F-statistics with denominator degrees of freedom [25] estimated in the Genstat REML proce- dure. Additive effects and dominance deviation were also calcu- lated using a re-parameterized model. The additive effect was estimated as the difference between the mean of the two homozygotes divided by two, and dominance was estimated as the deviation of the heterozygote from the mean of the two homozygotes [22]. Correction for multiple testing To allow correction for the fact that a large number of traits were analysed with a large number of SNP, and hence a high probability of false positive results, a Bonfer- roni correction was applied. The three leptin SNP and the two μ-calpain SNP were found to be in partial or strong LD so that the effective number of SNP tested was esti- mated as five. The correction for multiple SNP testing resulted in an adjusted P value of 0.01 for the 5% signifi- cance level. Haplotype reconstruction and analysis Haplotypes were reconstructed for the genes that con- tained more than one SNP using software that determines the gametic haplotypes for each animal where phase is known with certainty [26] based on sire and sibling geno- type information. Haplotype pairs were unambiguously reconstructed for 258 individuals for SNP in the leptin gene and 291 individuals for SNP in the CAPN1 gene out of the 443 genotyped animals. In order to determine whether the haplotype information accounted for addi- tional variation beyond the SNP genotype analysis, we nested the haplotype group (a combination of the two haplotypes) within a SNP model i.e. the model was the same as the genotype model but with additional fixed terms accounting for the variation between the haplotype groups within the SNP groups in the fixed model. This analysis was carried out for each of the traits found to be significantly affected by either the μ-calpain or leptin SNP, i.e. tenderometer, weight of hindquarter and tenderness for the μ-calpain markers and overall liking for the leptin markers. Statistical significance of the extra variation accounted for by the presence of the haplotype groups in the model was determined using approximate F-statistics derived from Wald statistics with denominator degrees of freedom estimated in the Genstat REML procedure [25]. Page 5 of 12 (page number not for citation purposes)