Variants of the bovine retinoic acid receptor-related orphan receptor C gene are in linkage disequilibrium with QTL for milk production traits on chromosome 3 in a beef x dairy crossbreed population

The bovine retinoic acid receptor-related orphan receptor C gene (RORC) is located on bovine chromosome 3 in the vicinity of several QTL for milk production traits, and an association of RORC genetic variants with carcass fatness traits had been confirmed by several studies. In a F-2 resource population, a chromosome-wise OIL and association study with 26 genetic markers (microsatellites and SNPs from genes involved in fat metabolism) on BTA3 was performed. In the analysis, 183 first and 152 second lactation records of 183 cows were included. The QTL study revealed five QTL affecting milk yield (MY), fat percentage (FP) and protein percentage (PP) as well as the milk fat/milk protein ratio (FPR), respectively, in the chromosomal region harbouring the RORC gene. The association study displayed a significant association between RORC c.1138+65A>G and MY and also associations between RORC c.934-262T>G and MY, FP and FPR, respectively. A combined QTL association study showed that these SNPs included as fixed effect in the corresponding model resulted in a prominent drop of the OIL test statistic. For the RORC c.934-262T allele, which had been confirmed to increase intramuscular fat deposition, an increasing effect on milk fat content traits was detected. The RORC c.1138+65G allele that had been shown to positively affect rump fat thickness, was associated with increased MY in our study. In conclusion, we found indications that the RORC SNPs, which previously had been highlighted due to their effects on carcass fat deposition, are also associated with milk production traits.