The Effect of Genetic Variation of the Retinoic Acid Receptor-Related Orphan Receptor C Gene on Fatness in Cattle

Abstract

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 D9 value of linkage disequilibrium was 0.92 although the average r 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 s p of marbling and 0.28 s 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.

A Validated Whole-Genome Association Study of Efficient Food Conversion in Cattle

“…Tag SNP pairs (Chapman et al 2003) did show associations to RFI of a similar level of significance, but no tag SNP pairs were found at distances .30 kbp, for the SNP associated with RFI. This lower level of LD across breeds is consistent with previous studies of livestock that show that when highly diverse groups of animals are used, involving several breeds, that the estimates of LD are low even at very small genetic distances (Barendse et al 2007). Similar results of the effect of estimating LD within and across breeds have been reported for a sample of 224 dogs (Lindblad-Toh et al 2005).…”

“…As few as 3000 evenly spaced single nucleotide polymorphisms (SNPs) could therefore be sufficient for WGA to cover the genome. However, estimates of LD calculated across breeds in beef cattle show much lower LD (Barendse et al 2007); to reduce LD and therefore improve the precision of gene mapping, seven breeds were used in this study.…”

“…In this study, the initial associations were made on animals of extreme phenotype so that a small sample will have a large power to detect associations, but using regression methods, albeit with permutation tests, will cause the allele effects to be overestimated (Lander and Botstein 1989), and so it would be important to validate the significance and size of effects in the full sample. We validated 44 of the SNPs from the WGA on the whole sample, using the SNPlex method (ABI 3130XL, ABI, Foster City, CA) in our laboratories or the Taqman assay as reported previously (Barendse et al 2006(Barendse et al , 2007 to determine whether the WGA had identified valid associations, whether the effects were similar in different breeds, and to more accurately measure the size of effect associated with each SNP. The estimates of the allele effects obtained in the WGA were compared to those in the validation sample using linear regression to determine the amount of deflation in the estimates of the additive effects.…”

Epistasis Between Calpain 1 and Its Inhibitor Calpastatin Within Breeds of Cattle

“…Associations between genotypes and meat tenderness were tested using statistical methods described previously (Gilmour et al 1995;Lynch and Walsh 1998;Barendse et al 2007). In brief, mean residual trait values for each genotype were compared using F-tests and the most divergent genotypes were compared with a t-test, with the significance determined using 100,000 permutations.…”

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 × dairy crossbreed population

“…Meissburger et al (2011) found that RORC affects the size of adipocytes, modulates insulin sensitivity in obesity, and is involved in the control of adipogenesis. When Barendse et al (2007) analysed genetic variation in the RORC gene, the strongest association was found between the RORC c.934-262T>G mutation and marbling score, whereas the RORC c.1138+65A>G mutation was highly associated with rump fat in Angus and Shorthorn cattle. RORC haplotypes were shown to explain most of the QTL effect on body fat deposition on BTA3 (Barendse et al 2007).…”