Genetics Selection Evolution 2009, 41:36 http://www.gsejournal.org/content/41/1/36 Table 8: F-statistics and degrees of freedom for SNP-by-haplotype interaction term for a nested model of genotype effects Gene Calpain Leptin SNP CAPN316 UASMS2 Trait Tenderometer score, kPa1 Weight of hindquarter, kg Tenderness Overall Liking ** P < 0.01, * P < 0.05 and ns P > 0.05 1Units for tenderometer score are kilopascals derness test [28]. Additionally, SNP in the leptin gene are included in the Igenity OptiGRID test, whilst the SNP in the DGAT1 and GHR genes comprise the Igenity Opti- YIELD test [27]. Allele frequencies The allele frequencies found for the CAPN316, CAPN4751 and UoGCAST SNP are in agreement with previous studies [7,29-31]. Allele frequencies were also estimated for the sire population (purebred Aberdeen Angus). On the whole, frequencies in the sire population were found to be similar to those in the progeny, however, at the CAPN316 SNP, the C allele was found to have a frequency of only 0.10 in the sires (data not shown), as opposed to 0.22 in the offspring. This is due to the absence of sires with the CC genotype at this SNP. Single genotype-trait associations Using single-marker, mixed-model association analysis four of the SNP were found to be associated with one or more of the traits tested in a significantly additive manner. These include the CAPN316 SNP in the CAPN1 gene, the UASMS2 SNP in the leptin gene, the DGAT1 SNP and the GHR SNP. The CAPN1 gene, mapped to BTA 29 [32], encodes a cysteine protease thought to be the primary enzyme in the post mortem tenderisation of meat [33]. It is therefore a prime candidate for association studies involving tender- ness, and, indeed, SNP in the gene have previously been associated with the trait in several studies [10,13,31,34,35]. In the present study the effects of two SNP located in CAPN1 were evaluated; CAPN316, situated in exon 9 of the gene, results in an amino acid substitution from alanine to glycine for the C and G alleles respec- tively; and CAPN4751, situated in the intron between the 17th and 18th exons of the gene. A significant effect of CAPN316 genotype was found on the hindquarter weight; animals with the CC genotype at this locus had signifi- cantly heavier hindquarters (by 3.8 kg) than GG animals (P = 0.04). However, some of this effect could be explained by effects on overall carcass weight. Addition- ally, animals inheriting two copies of the C allele at the CAPN316 SNP had meat that was more tender than ani- mals with one or zero copies, when measured by both the F-Statistic (d.f.: numerator, denominator) 1.16 (8, 79.8)ns 0.88 (8, 32.4)ns 0.85 (8, 120.4)ns 0.95 (11, 197.5)ns tenderometer machine and the taste panel. The associa- tion with mechanical tenderness is consistent with work done in experimental herds of crossbred cattle [12,35]. Previous work has shown an association between geno- types at the other CAPN1 SNP, CAPN4751, and WBSF val- ues in an experimental population and a Bos indicus- influenced crossbred population [13] where CC animals had significantly lower WBSF values, and therefore more tender meat, than TT animals. The current study did not find a significant effect of genotype at the CAPN4751 SNP on the tenderness trait (although the difference between CC and TT means was in the expected direction). Poly- morphisms in CAST, an inhibitor of the CAPN1 protease mapped to BTA 7 [36], have previously been shown to be associated with tenderness [10,11,31]. However, the present study did not find a significant difference in ten- derness, measured by the tenderometer machine, between the genotype groups. Three SNP in the leptin gene, which has been mapped to BTA 4 [37] and produces a hormone that plays a key role in the regulation of appetite and body composition [38], were tested for associations in the present study. In con- trast to previous studies [7,9], only one of these, UASMS2, was found to be significantly associated with any of the traits tested. Panellists gave animals with the TT genotype significantly higher overall liking scores than animals with CC or CT genotypes. A significant, non-additive asso- ciation was also observed between the UASMS2 SNP and sirloin fat thickness, such that animals inheriting the CC genotype had significantly less fat surrounding the sirloin when compared to either CT or TT animals. This is in line with previous reports where UASMS2 was significantly associated with both backfat thickness and marbling score, with TT animals having higher values for both traits [9]. It may be that this association also explains the higher overall liking scores for TT animals as fat composition is known to affect meat flavour. The DGAT1 gene, which has been mapped to BTA 14 [39], plays a key role in triglyceride synthesis [30]. The SNP studied here is an AA/GC dinucleotide substitution caus- ing a K (lysine) to A (alanine) amino acid substitution (K232A) in the protein [40]. This polymorphism was Page 9 of 12 (page number not for citation purposes)