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Effects and interactions of calpain-system tenderness gene markers on objective meat quality traits of Brahman (Bos indicus) cattle were quantified within 2 concurrent experiments at different locations. Cattle were selected for study from commercial and research herds at weaning based on their genotype for calpastatin (CAST) and calpain 3 (CAPN3) gene markers for beef tenderness. Gene marker status for [mu]-calpain (CAPN1-4751 and CAPN1-316) was also determined for inclusion in statistical analyses. Eighty-two heifer and 82 castrated male cattle with 0 or 2 favorable alleles for CAST and CAPN3 were studied in New South Wales (NSW), and 143 castrated male cattle with 0, 1, or 2 favorable alleles for CAST and CAPN3 were studied in Western Australia (WA). The cattle were backgrounded for 6 to 8 mo and grain-fed for 117 d (NSW) or 80 d (WA) before slaughter. One-half the cattle in each experiment were implanted with a hormortal growth promotant during feedlotting. One side of each carcass was suspended from the Achilles tendon (AT) and the other from the pelvis (tenderstretch). The M. longissimus lumborum from both sides and the M. semitendinosus from the AT side were collected; then samples of each were aged at 1[degrees]C for 1 or 7 d. Favorable alleles for one or more markers reduced shear force, with little effect on other meat quality traits. The size of effects of individual markers varied with site, muscle, method of carcass suspension, and aging period. Individual marker effects were additive as evident in cattle with 4 favorable alleles for CAST and CAPN3 markers, which had shear force reductions of 12.2 N (P < 0.001, NSW) and 9.3 N (P = 0.002, WA) in AT 7 d aged M. longissimus lumborum compared with those with no favorable alleles. There was no evidence (all P > 025) of interactions between the gene markers, or between the hormonal growth promotant and gene markers for any meat quality traits. This study provides further evidence that selection based on the CAST or CAPN3 gene markers improves meat tenderness in Brahman cattle, with little if any detrimental effects on other meat quality traits. The CAPN1-4751 gene marker also improved beef tenderness without affecting other objective meat quality traits in heterozygous cattle compared with homozygotes for the unfavorable allele. Key words: calpain, calpastatin, cattle, genetic marker, meat quality, shear force doi: 10.2527/jas.2009-2679

Experiments were conducted concurrently at 2 locations to quantify effects and interactions of calpain-system tenderness gene markers on growth, efficiency, temperament, and carcass traits of Brahman cattle. Cattle were selected at weaning from commercial and research herds based on their genotype for commercially available calpastatin (CAST) and calpain 3 (CAPN3) gene markers for beef tenderness. Genotypes for [mu]-calpain gene markers (CAPN1-4751 and CAPN1-316) were also determined and included in statistical analyses. The New South Wales (NSW) herd was composed of 82 heifers and 82 castrated male cattle with 0 or 2 favorable alleles for CAST and CAPN3. The Western Australia (WA) herd was composed of 173 castrated male cattle with 0, 1, or 2 favorable alleles for CAST and CAPN3. One-half of the cattle at each site were implanted with a hormonal growth promotant (HGP: Revalor-H) during grain finishing. Cattle were backgrounded at pasture for 6 to 8 mo and grain-fed for 117 d (NSW) or 80 d (WA) before slaughter. Individually, or in combination with each other and with CAPN1-4751 status, CAST and CAPN3 status had no significant (all P > 0.05) effects on BW, growth, feed efficiency, or temperament traits. The only significant effect of CAST or CAPN3 on carcass characteristics was a small increase in rib fat with increasing number of favorable CAST alleles (P = 0.042) in the WA herd. There were no significant interactions (all P > 0.05) between the markers, or between the markers and sex or HGP treatment apart from CAST x HGP for area of the M. longissimus lumborum (P = 0.024) in the NSW experiment. Favorable CAST or CAPN3 alleles appear unlikely to have detrimental effects on growth, efficiency, temperament, or carcass characteristics of Brahman cattle; however, some effects evident for CAPN1 status indicate the need for further production studies on effects of these markers. Overall, the findings of the present study indicate that calpain-system gene markers are suitable for use in marker-assisted selection to improve meat tenderness in Brahman cattle without negative effects on other production and carcass characteristics. Key words: calpain, calpastatin, carcass, cattle, genetic marker, growth doi: 10.2527/jas.2009-2678

Variation at the retinoic acid receptorrelated orphan receptor C (RORC) gene was previously associated with marbling score in a large sample of Australian taurine feedlot cattle of Angus and Shorthorn breeds. The T allele at the SNP RORC:g.3290T > G increased marbling score in Angus and Shorthorn cattle. We genotyped this SNP in an independent sample of 2,741 Australian cattle of Angus, Brahman, and Hereford breeds, and tested the association of this SNP with marbling score in all animals and with intramuscular fat (IMF) measurements in 2,104 animals. We found an allele frequency of the G allele of [p.sub.G] = 0.57 in Angus, [p.sub.G] = 0.09 in Hereford, and [p.sub.G] = 0.64 in Brahman. The regression of marbling score against number of copies of the G allele was significant (P = 0.033) in the combined sample after accounting for ancestry, breed, and the contemporary group structure of the data. All breeds had the same favorable homozygote; the regression on alleles showed a trend in Angus and Brahman cattle (P < 0.1), but not in Hereford cattle (P = 0.912). The regression of IMF against number of copies of the G allele was significant (P = 0.018) after accounting for ancestry, breed, and contemporary group structure. All breeds had the same favorable homozygote and the regression on alleles was significant (P = 0.024) in the Angus breed. In all breeds tested in this study, the T allele increased both marbling score and IMF. This polymorphism explained 0.3% of the phenotypic variance for IMF in this sample. Key words: Bos taurus chromosome 3, cattle, deoxyribonucleic acid, intramuscular fat, quantitative trait loci, retinoic acid receptor-related orphan receptor C gene doi: 10.2527/jas.2009-2178

The calpain gene family and its inhibitors have diverse effects, many related to protein turnover, which appear to affect a range of phenotypes such as diabetes, exercise-induced muscle injury, and pathological events associated with degenerative neural diseases in humans, fertility, longevity, and postmortem effects on meat tenderness in livestock species. The calpains are inhibited by calpastatin, which binds directly to calpain. Here we report the direct measurement of epistatic interactions of causative mutations for quantitative trait loci (QTL) at calpain 1 (CAPN1), located on chromosome 29, with causative mutations for QTL variation at calpastatin (CAST), located on chromosome 7, in cattle. First we identified potential causative mutations at CAST and then genotyped these along with putative causative mutations at CAPN1 in >1500 cattle of seven breeds. The maximum allele substitution effect on the phenotype of the CAPN1:c.947G>C single nucleotide polymorphism (SNP) was 0.14 [[sigma].sub.P] (P = 0.0003) and of the CAST:c.155C> T SNP was also 0.14 [[sigma].sup.P] (P = 0.0011) when measured across breeds. We found significant epistasis between SNPs at CAPN1 and CAST in both taurine and zebu derived breeds. There were more additive x dominance components of epistasis than additive x additive and dominance x dominance components combined. A minority of breed comparisons did not show epistasis, suggesting that genetic variation at other genes may influence the degree of epistasis found in this system.

The genetic factors that contribute to efficient food conversion are largely unknown. Several physiological systems are likely to be important, including basal metabolic rate, the generation of ATE the regulation of growth and development, and the homeostatic control of body mass. Using whole-genome association, we found that DNA variants in or near proteins contributing to the background use of energy of the cell were 10 times as common as those affecting appetite and body-mass homeostasis. In addition, there was a genic contribution from the extracellular matrix and tissue structure, suggesting a trade-off between efficiency and tissue construction. Nevertheless, the largest group consisted of those involved in gene regulation or control of the phenotype. We found that the distribution of micro-RNA motifs was significantly different for the genetic variants associated with residual feed intake than for the genetic variants in total, although the distribution of promoter sequence motifs was not different. This suggests that certain subsets of micro-RNA are more important for the regulation of this trait. Successful validation depended on the sign of the allelic association ill different populations rather than on the strength of the initial association or its size of effect.

Genotypes at the retinoic acid receptor-related orphan receptor C (RORC) gene were associated with fatness in 1750 cattle. Ten SNPs were genotyped in RORC and the adjacent gene leucine-rich repeat neuronal 6D (LRRN6D) to map the QTL, 7 of which are in a 4.2-kb sequence around the ligand-binding domain of the RORC gene. Of the 29 inferred haplotypes for these SNPs, 2 have a combined frequency of 54.6% while the top 5 haplotypes have a combined frequency of 85.3%. The average D' value of linkage disequilibrium was 0.92 although the average [r.sup.2] was a low 0.18. The RORC:g.3290T>G SNP had the strongest association with marbling. The inferred haplotypes were significantly associated with marbling and the difference between the most divergent haplotypes was 0.35 [[sigma].sub.p] of marbling and 0.28 [[sigma].sub.P] of rump fat, explaining the previously reported QTL effect, cDNA for RORC were sequenced and 2 new alternative transcripts were found. Fetal tissue shows 40 times greater transcription of RORC than adult tissue. The highest expression in fetal tissue was found in liver and kidney, but in adults the longissimus muscle had the greatest expression of the tissues tested.

The comparative mapping of genes improves the comprehensiveness of most genetic maps and extends our knowledge of evolutionary history. A new study maps loci from human chromosome 12 in cattle to compare the gene order. It is shown that six cattle loci contain polymorphisms that have previously been mapped in humans. Four loci, LALBA, SYT1, SLC2A3 and TP11, mapped to chromosome 5 in cattle and one, PLA2G1B, mapped to cattle chromosome 17. The study reveals cattle have a lower genetic variation than humans but reveals a potential for the production of millions of single-nucleotide polymorphisms in cattle.