Genomic selection and metabolic pathways associated with beef fatty acid groups profile using haplotypes in Nellore cattle

Abstract

Currently, there is a continuing and growing concern among the population and public health agencies for excessive consumption of fats, especially animal fats, as well as the type of fat or fatty acid group profile of the meat and its impact on consumer health. The haplotype-based analysis can identify loci that are not captured by a single marker or identify the join effect of two or more loci. The aim of this project is to infer the phase between SNP markers to estimate the haplotypes present in the genome of Nellore cattle, and use these haplotypes as markers in genomic selection study and the identification of genomic regions associated with beef fatty acid groups. Data from 943 Nellore bulls finished in feedlot about two years old, from 8 farms that integrate three breeding programs will be used. The contemporary groups were formed by animals born in the same farm, year and management group at yearling. To determine the fatty acid group, the extraction of lipids was performed by the Folch method and the methylation Kramer method was applied. The animals were genotyped with the BovineHD BeadChip. The haplotypes will be constructed using two alternate software, i.e. Fimpute and Beagle. For genomic selection analysis (GS) the effects of the haplotypes will be estimated in a training population. Cross-validation will be used to evaluate accurary of predicting the direct genomic values (DGV). To estimate the haplotypes effects, the following methods will be evaluated: GBLUP, Bayesian Lasso, BayesCÀ and BayesC. The model will include the haplotype effect, the effect of the GC, and age of the animal at slaughter as a covariate (linear and quadratic). To determine the possible QTL regions segments that explain values equal to or greater than 1% of the additive genetic variance will be selected. Database data will be used in NCBI in the UMD3.1 version of the bovine genome and Ensembl Genome Browser. The results obtained in genomic selection and metabolic pathways analyses based on haplotype information will be compared to the results obtained with individual markers (SNPs). This project will assess the usefulness of haplotype based models to predict breeding values and map QTLs for beef fatty acid groups in Nellore cattle.