The effect of variation at the retinoic acid receptor-related orphan receptor C gene on intramuscular fat percent and marbling

Variation at the retinoic acid receptor- related orphan receptor C (RORC) gene was previously associated with marbling score in a large sample of Australian taurine feedlot cattle of Angus and Short- horn 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 sam- ple 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 intramus- cular fat (IMF) measurements in 2,104 animals. We found an allele frequency of the G allele of pG = 0.57 in Angus, pG = 0.09 in Hereford, and pG = 0.64 in Brah- man. 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 ho- mozygote 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.