Genetics Selection Evolution 2009, 41:36 http://www.gsejournal.org/content/41/1/36 Table 6: Genotype means and standard errors for each genotype by sex group Sex Genotype CAPN31 6 GHR DGAT1 F M F M F M CC CG GG CC CG GG AA AT TT AA AT TT AA AG GG AA AG GG Tenderometer score, kPa2 19.51 ± 1.60a 25.14 ± 0.84b 25.74 ± 0.77b 24.99 ± 1.38a, b 23.34 ± 0.78a 24.60 ± 0.73b --- --- --- --- --- --- --- --- --- --- --- --- Weight of hindquarter, kg 73.17 ± 2.24a 66.04 ± 1.12b 67.27 ± 1.0b 78.17 ± 1.91a 78.06 ± 0.95a 76.4 ± 0.86a --- --- --- --- --- --- --- --- --- --- --- --- Genotype means ± se1 Tenderness Odour 6.43 ± 0.23a 5.75 ± 0.1b 5.58 ± 0.09b 5.57 ± 0.19a 5.82 ± 0.09a 5.68 ± 0.08a --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- 6.13 ± 0.34a 5.34 ± 0.11b 5.11 ± 0.07b 5.15 ± 0.16a 5.14 ± 0.08a 5.21 ± 0.07a --- --- --- --- --- --- 1 Mean values were adjusted for farm. Estimate of the effect is expressed in units of the trait a, b, Within a trait and sex, genotype means without a common superscript letter are statistically significantly different (P < 0.05) 2 Units for tenderometer score are kilopascals values than the other genotypes although this difference was not significant. tional variation compared to a model with only genotype information. Additionally there was a significant difference in odour score assigned to female animals with the AA, AT and TT genotypes at the GHR SNP. Here, AA animals had signifi- cantly higher scores than either AT or TT animals. For the male animals, those with the TT genotype received the highest score for odour, although again, the differences between genotypes were not significant. Finally, female animals with the AA genotype at the DGAT1 SNP had sig- nificantly heavier sirloins after maturation and sirloin fat depths than AG or GG animals. For males the AA animals also had heavier sirloins although the GG animals had higher values of fat depth, however, differences between genotypes were not significant. Haplotype analysis Haplotypes with a frequency of ≤ 0.01 were excluded from the analysis; this left four haplotypes for SNP in the CAPN1 gene (CC, CG, TC and TG (CAPN4751, CAPN316)), and four haplotype possibilities for SNP in the leptin gene (CCT, CTT, TCC and TTT (Exon2FB, UASMS2, UASMS1)) (Table 7). Results from the nested haplotype model for each of the significant μ-calpain and leptin traits are shown in Table 8. In all cases F-statistics were not significant and, in fact, close to unity, showing that haplotype information does not account for addi- Sirloin weight after maturation, kg Sirloin fat depth, mm --- --- --- --- --- --- --- --- --- --- --- --- 15.7 ± 3.22a 6.66 ± 0.53b 6.46 ± 0.43b 6.56 ± 0.8a 6.58 ± 0.46a 6.60 ± 0.42a 0.16 0.52 0.02 0.30 0.19 0.35 0.44 0.02 --- --- --- --- --- --- --- --- --- --- --- --- 9.02 ± 0.88a 6.85 ± 0.16b 6.73 ± 0.13b 7.59 ± 0.22a 7.5 ± 0.13a 7.54 ± 0.13a CC CG TC TG CCT CTT TCC TTT Discussion The primary objective of this study was to test previously identified associations between SNP from five genes and economically important meat quality traits. The SNP tested are located in the CAPN1, CAST, DGAT1, leptin and GHR genes and have been incorporated into commer- cially available genetic tests based on previously reported associations with meat quality or carcass traits. The two CAPN1 SNP, (CAPN316 and CAPN4751) and the CAST SNP make up the Igenity TenderGENE panel [27], with the two CAPN1 SNP forming the basis of the GeneSTAR ten- Table 7: Haplotype frequencies for calpain and leptin Haplotype Frequency Gene Calpain1 Leptin2 1 Calpain haplotype: CAPN4751, CAPN316 2 Leptin haplotype: Exon2FB, UASMS2, UASMS1 Page 8 of 12 (page number not for citation purposes)