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Strategies of imputation of genotypes of SNPs markers for association studies genomic selection of Nellore breed

Grant number: 12/03508-2
Support type:Scholarships abroad - Research Internship - Doctorate
Effective date (Start): June 01, 2012
Effective date (End): May 31, 2013
Field of knowledge:Agronomical Sciences - Animal Husbandry - Genetics and Improvement of Domestic Animals
Principal researcher:Gerson Barreto Mourão
Grantee:Fabiane de Lima Silva
Supervisor abroad: Guilherme J. M. Rosa
Home Institution: Escola Superior de Agricultura Luiz de Queiroz (ESALQ). Universidade de São Paulo (USP). Piracicaba , SP, Brazil
Research place: University of Wisconsin-Madison (UW-Madison), United States  
Associated to the scholarship:10/20432-4 - Strategies of imputation of genotypes of SNPs markers for association studies of Nellore breed, BP.DR

Abstract

The availability of genotyping technologies for high density platforms of single nucleotide polymorphism (SNP)markers for cattle, there was an increased area of research focused on selection and genomic association,however, due to the high cost of genotyping large scale features in is generally impractical to genotype for allcandidates for selection, but there is the possibility of combining panels of low density SNP markers and infergenotypes for high density platforms. As a result, this project aims to investigate the efficiency of differentmethods of imputation of genotypes of SNP markers from panels of low density in Nellore, and then use theseimputed genotypes in genetic association studies and genomic selection. Will be used approximately 800 malecalves produced in three seasons, born in 2007, 2008 and 2009, descendants of 32 registered bulls Nellore,families that make up half - sib produced through artificial insemination. The animals are being created atEmbrapa, located in Campo Grande and São Carlos. The animals were genotyped in the Illumina GenotypingBeadChip BovineHD, in which data will be obtained approximately 770,000 SNPs distributed evenly throughout thegenome. To carry the allocation will be simulated in a situation that genotyping of certain animals were performedon panels of low density and other panel with high density. The association study will be conducted between thegenotypes of SNP markers with high and low trait heritability by regression analysis using the software ASReml,and analysis to estimate the genome will be achieved through Lasso Bayesian. The analysis of genetic associationand genomic selection will be at the University of Wisconsin, USA, in collaboration with Professor Dr. GuilhermeJordão de Magalhães Rosa. (AU)

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