Genome-Wide Association Study for Beef Fatty Acid Profile Using Haplotypes in Nellore Cattle

The aim of this study was to identify genomic regions associated with total amount of saturated (SFA), monounsaturated (MUFA) and polyunsaturated (PUFA) fatty acids in beef of Nellore cattle. The investigated dataset contained records from 963 Nellore bulls, about two years old, finished in feedlot (90 days). Meat samples of Longissimus dorsi muscle, between the 12th and 13th ribs of the left half-carcasses, were taken to measure the fatty acids (FAs). FAs were quantified by gas chromatography (GC-2010 Plus - Shimadzu AOC 20i autoinjector) using SP-2560 capillary column (100 m x 0.25 mm diameter with 0.02 mm thickness, Supelco, Bellefonte, PA). The animals were genotyped using the high-density SNP panel (BovineHD BeadChip assay 777k, Illumina Inc., San Diego, CA). Those SNP markers with minor allele frequency less than 0.05, call rate less than 90%, monomorphic, located on sex chromosomes, and those with unknown position were removed from the analysis. After genomic quality control, 470,007 SNPs and 868 animals were available for the analyses. Missing genotypes were imputed using FImpute software. Genotypes were phased to haplotypes using fastPHASE software and, then, haplotype blocks were defined based on linkage disequilibrium using HaploView software. Genome-wide association analyses were performed considering one haplotype at a time. The model included fixed effects of contemporary group (92 levels), haplotype (linear regression on number of copies), and age at slaughter as a linear covariate. Bonferroni correction was applied at 5% significance to adjust for multiple tests. A total of 83,883 haplotypes were included in the genome-wide association analyses. From those haplotypes, 292, 17 and 31 were significantly associated (p < 0.05) with SFA, MUFA and PUFA, respectively. Most associations were found on BTA17, BTA3, BTA1, BTA8, BTA25 and BTA2. These significant regions harbour genes such as GALNT12, SLC6A7, CAMK2A, SYTL3, EPAS1, PRKCB, EPHA6, MPZL1, UHMK1, KIRREL, FYN, LTBP1, PRKCE, SIK2, TOM1L1, NF1, DNAJA3, SH2B2, AFAP1L2 and AGAP1. These genes are involved in lipid metabolism, reproductive hormone receptors, transport and use of fatty acids and cholesterol, phospholipid and membrane hydrolysis and biosynthesis, energy metabolism and protein kinase synthesis. Thus, the identification of these associated haplotypes may contribute to further studies to validate these regions and prospect candidate genes that would be useful for breeding programs to improve the beef quality of Nellore cattle.