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Genome selection and genome-wide association study for beef fatty acid composition using haplotypes in Nellore cattle

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Author(s):
Fabieli Loise Braga Feitosa
Total Authors: 1
Document type: Doctoral Thesis
Press: Jaboticabal. 2018-10-01.
Institution: Universidade Estadual Paulista (Unesp). Faculdade de Ciências Agrárias e Veterinárias. Jaboticabal
Defense date:
Advisor: Fernando Sebastián Baldi Rey; Gregório Miguel Ferreira de Camargo; Rafael Medeiros de Oliveira Silva
Abstract

The aim of this study were genome-wide association (GWAS) and genomic prediction using haplotypes approach for fatty acid profile of intramuscular fat of longissimus dorsi muscle in Nellore cattle. The investigated dataset contained records from 963 Nellore bulls, finished in feedlot (90 days) and slaughter with about two years old. 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, 469,981 SNPs and 892 animals were available for the analyses. Missing genotypes were imputed and genotypes were phased to haplotypes using FImpute software. Haplotype blocks were defined based on linkage disequilibrium using HaploView software. In chapter 2, statistical analyzes incorporating the haplotype information were performed using ASREML software implementing the REML method. The model included fixed effects of the contemporary group (62 levels), haplotype (linear regression in number of copies) and age at slaughter as a linear covariate. The p values were adjusted by FDR method. Haplotypes significantly associated were selected at 10% significance level. For the prospection of the genes, the NCBI database was used in the UMD3.1 version of the bovine genome, the Ensembl Genome Browser and DAVID. There were significantly (p <0.05), 4, 3, 5, 1, 6, 2 and 7 haplotypes associated with SFA, MUFA, PUFA, PUFA/SFA ratio, n3, n6 and n6/n3 ratio, respectively. These significant haplotypes harboring genes involved in lipid metabolism elongation factors and long-chain fatty acid synthesis, reproductive hormone receptors, transport and use of fatty acids and cholesterol biosynthesis and hydrolysis of phospholipids and constituents membrane, cell membrane constituent , energetic 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 quality of Nellore beef. In chapter 3, the model used to estimate variance components, genetic parameters and predict the genomic values included fixed effects of contemporary group and age at slaughter as a linear covariate, and the additive random genetic effect. The accuracy using haplotype approach ranged from 0.07 to 0.31 and using SNP approach ranged from 0.06 to 0.33. The regression coefficient using haplotype approach ranged from 0.07 to 0.74 and using SNP approach ranged from 0.08 to 1.45. Despite prediction accuracy was not high for both approach we can consider use SNP approach in genomic selection because is more efficient computational. (AU)

FAPESP's process: 15/25304-8 - Genome-wide association and genomic selection study for fatty acid profile using haplotypes in Nellore cattle
Grantee:Fabieli Loise Braga Feitosa
Support Opportunities: Scholarships in Brazil - Doctorate