Genetics Selection Evolution 2009, 41:36 http://www.gsejournal.org/content/41/1/36 Results Genotype and allele frequencies A total of 443 animals were genotyped at all eight SNP, however, successful genotype assignment was not possi- ble for all animals, in particular for the leptin SNP UASMS1 where 17 animals were missing genotypes (Table 4). The frequencies of genotypes at all eight SNP were in agreement with Hardy-Weinberg equilibrium [22]. The two SNP in the CAPN1 gene and the three SNP in the leptin gene were found to be in LD with D' above 0.62 for each SNP pair combination. R2 values between each pair of leptin SNP were above 0.18 whilst the value between the two CAPN1 SNP was 0.07. Phenotypic trait data An analysis of the phenotypic trait data is presented in full in: Gill, Matika, Williams, Worton, Wiener, and Bishop: Consistency statistics and genetic parameters for taste panel assessed meat quality traits in a commercial popu- lation of Angus-sired beef cattle (submitted), including consideration of the reliability of taste panel measure- ments and genetic parameters for traits of interest. In brief, a total of 27 traits were measured, seven of which are taste panel assessed sensory traits, one a mechanical measure of tenderness with the remaining 19 being carcass and sir- loin measurements. Trait means, coefficients of variation and heritability estimates are given in Tables 1 and 2. Table 4: Genotypic and allelic frequencies for SNP Genotype effects Genotypes for four of the eight SNP tested did not signif- icantly influence any of the 27 traits measured and 20 of the traits were not affected by the genotypes of any of the SNP tested. Tenderometer score, sirloin weight after mat- uration, sirloin fat depth, hindquarter weight, odour, overall liking and tenderness showed significant additive effects of at least one of the remaining four SNP. At the CAPN1 gene SNP, CAPN316, the C allele was asso- ciated with reduced tenderometer values, increased hind- quarter weight and an increase in taste panel assessed tenderness compared to the G allele (Table 5). The esti- mated differences between the homozygous genotypes CC and GG were 2.93 kPa, 3.83 kg and 0.37 taste panel units for shear force, hindquarter weight and taste panel tenderness respectively. There were no significant domi- nance effects seen for CAPN316. The T allele of the leptin SNP, UASMS2, was significantly associated with an increase in overall liking, with the esti- mated difference between the homozygous genotypes TT and CC equal to 0.21 taste panel units (Table 5). There was a significant dominance effect (P = 0.01) such that the C allele was dominant to the T allele. For DGAT1, the A allele was associated with an increase in sirloin weight after maturation and an increase in sirloin fat depth when compared to the G allele (Table 5). The Genotype frequency Allele Allele frequency SNP CAPN4751 CAPN316 Exon2FB UASMS2 UASMS1 DGAT1 GHR UoGCAST1 Genotype CC (n = 182) CT (n = 209) TT (n = 48) CC (n = 20) CG (n = 152) GG (n = 268) CC (n = 130) CT (n = 222) TT (n = 90) CC (n = 166) CT (n = 219) TT (n = 54) CC (n = 77) CT (n = 205) TT (n = 144) AA (n = 22) AG (n = 176) GG (n = 243) AA (n = 12) AT (n = 93) TT (n = 333) CC (n = 181) CG (n = 207) GG (n = 54) 0.41 0.48 0.11 0.05 0.35 0.61 0.29 0.50 0.20 0.38 0.50 0.12 0.18 0.48 0.34 0.05 0.40 0.55 0.03 0.21 0.76 0.41 0.47 0.12 C T - C G - C T - C T - C T - A G - A T - C G - 0.65 0.35 - 0.22 0.78 - 0.55 0.45 - 0.63 0.37 - 0.42 0.58 - 0.25 0.75 - 0.13 0.87 - 0.64 0.36 - Page 6 of 12 (page number not for citation purposes)