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Genome-wide association and genomic selection study for fatty acid profile using haplotypes in Nellore cattle

Grant number: 15/25304-8
Support type:Scholarships in Brazil - Doctorate
Effective date (Start): November 01, 2016
Effective date (End): July 31, 2018
Field of knowledge:Agronomical Sciences - Animal Husbandry
Principal Investigator:Fernando Sebastián Baldi Rey
Grantee:Fabieli Loise Braga Feitosa
Home Institution: Faculdade de Ciências Agrárias e Veterinárias (FCAV). Universidade Estadual Paulista (UNESP). Campus de Jaboticabal. Jaboticabal , SP, Brazil
Associated research grant:09/16118-5 - Genomic tools to genetic improvement of direct economic important traits in Nelore cattle, AP.TEM
Associated scholarship(s):16/24085-3 - Genomic selection and metabolic pathways associated with beef fatty acid groups profile using haplotypes in Nellore cattle, BE.EP.DR

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 profile of the meat and its impact on consumer health. As much as the individual markers can lead to significant results, the haplotype-based analysis can identify loci that are not captured by a single marker or reveal the combinatorial effect between loci. The objective of this project was to infer linkage phase between SNP markers to estimate the haplotypes present in the genome of Nellore, and use these haplotypes as markers in genome-wide association and genomic selection studies for the beef fatty acid profile. Data from meat fatty acid profile of 943 animals of Nellore breed finished on feedlot, around the age of two years, from three farms that are part of breeding programs were used. The contemporary group was formed by animals born on the same farm and harvest, and the same management group at yearling. For determining the fatty acid profile was used for the extraction of lipids the Folch method and methylation Kramer method. For genotyping of animals we used a panel of more than 777,000 SNPs BovineHD BeadChip (High-Density Bovine BeadChip). The haplotypes are constructed using fastPHASE software. The linkage phase between the SNP markers will be determined for the haplotypes using (EM) algorithm present in the Haploview program. The models to be used for the estimation of variance components include the genetic random effect direct, the fixed effect of the GC, and age of the animal at slaughter as a covariate (linear and quadratic). The variance components and genetic parameters are estimated implementing Bayesian inference using the single step method (ssGBLUP), using the GIBBS2F90 computer programs. The effects of haplotypes and weightings for the association analysis will be derived using the postGSf90 program. To determine the possible QTL regions of the segments that explain values equal to or higher than 1% of the additive genetic variance will be selected. Data from database available at NCBI used in UMD3.1 version of the bovine genome and Ensembl Genome Browser. For genomic selection analysis (GS) the effects of the haplotypes will be estimated in a population of training. To predict the GEBV (genomic value) will be used cross-validation methodology. The GS3 software will be used for the GEBV with 500,000 iterations. For the purposes of haplotypes are considered different prior distributions (GBLUP, Bayesian Lasso, BayesCÀ and BayesC). This project provides an opportunity to study the genome-wide association and genomic selection based on haplotypes for the fatty acid profile beef of Nellore cattle.

Academic Publications
(References retrieved automatically from State of São Paulo Research Institutions)
FEITOSA, Fabieli Loise Braga. Associação e seleção genômica para perfil de ácidos graxos utilizando haplótipos como marcadores em bovinos Nelore. 2018. Doctoral Thesis - Universidade Estadual Paulista "Júlio de Mesquita Filho" Faculdade de Ciências Agrárias e Veterinárias..

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