Genomic approach to understanding variation in bovine fat colour.

Abstract

Subcutaneous fat is important not only in the live animal but also in the carcass, as it prevents the rapid chilling of the underlying muscle tissues, thereby reducing weight loss during chilling. However, beef with yellow fat is considered undesirable by consumers in most European and Asian markets. Beta-carotene is the major carotenoid deposited in adipose tissue, which results in the yellowness. Genes involved in the metabolism of β-carotene in the cattle are likely to regulate beef fat colour. Therefore, DNA variants in candidate genes related to β-carotene metabolism were examined for association with beef fat colour. Based on their location in fat colour quantitative trait loci (QTL) and function in the metabolism of β-carotene, ALDH8A1, APOM, BCMO1, BCO2, RARA, RDHE2, PPARGC1A and SCARB1 were chosen as candidate genes. One hundred eleven (111) DNA variants were identified from the direct sequencing of 3 F1 sires for these eight genes, of which, 27 DNA single nucleotide polymorphisms (SNPs) were selected for association studies (3-5 SNPs per gene). Most of these genotyped SNPs and their interactions were associated with fat colour related traits (biopsy fat colour (Fc-bio), carcass fat colour (Fc-car), beta-carotene concentration (Bc-bio)), although the size of the effects was relatively low for many of the variants. However, among the DNA variants, a nonsense mutation in the BCO2 gene (BCO2 W80X) accounted for a large proportion (12-16%) of the total SNP variation in fat colour related traits in Jersey-Limousin backcross progeny. Validation of this SNP in other independent herds (Group 2-7) confirmed the BCO2 W80X genotype has a large effect on beef fat colour and milk colour. The individual genotypic effects of RDHE2 SNP2 and SNP3 were also large. However, these effects were greater in the New Zealand abattoir samples than from pedigreed Jersey-Limousin backcross progeny, amounting to 8-17% of the variance in one population. There was a significant interaction between the BCO2 W80X and the RDHE2 SNP2, which accounted for 1.8% of the total SNP variance in milk fat colour in a New Zealand Holstein cow population, and 4.0% of the total SNP variance in carcass fat colour in New Zealand Jersey-Limousin backcross progeny. In addition to the individual SNP effects, the effects of the haplotypes formed for each gene were also investigated. Only haplotypes of BCMO1, PPARGC1A, RDHE2 and SCARB1 genes had effects on beef fat colour. The most likely pathways involved in the beef fat colour were clarified. The association studies showed that the BCMO1, BCO2, RARA, RDHE2, PPARGC1A and ALDH8A1 genes and their interactions account for a large proportion of the variation in beef fat colour. These genes have roles involving retinol or retinoic acid synthesis. Therefore, the retinol/retinoic acid synthesis pathway appears to be the most important in terms of the contribution to the β-carotene concentration in adipose tissue. The effects of APOM and SCARB1 indicate that transportation of β-carotene is also important in the regulation of the β-carotene concentration in fat. Differences in the expression of BCMO1, BCO2 and RDHE2 genes were investigated. The RDHE2 gene mRNA transcript level was significantly different between yellow fat and white fat samples. The gene expression of BCO2 was highly correlated with β-carotene concentration. The results further support the role of BCO2 in cleaving β-carotene eccentrically and the association of RDHE2 with β-carotene concentration. The results also indicate that the control of the retinol/retinoic acid pathway at the gene expression level is important for the β-carotene concentration in subcutaneous adipose tissue and consequently, for beef fat colour. The study conducted herein contributes to the understanding of the metabolism of carotenoids and their numerous derivatives. BCO2-mediated conversion of β-carotene to vitamin A is confirmed in cattle. Epistatic effects accounted for much of the beef fat colour and β-carotene concentration variation. DNA variants that have a large influence on fat colour, such as the BCO2 W80X, can be used in marker selection systems to rapidly reduce the incidence of yellow fat colour in beef.