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Imputation, linkage desequilibrium, haplotype blocks and inbreeding in Nelore cattle

Grant number: 16/22940-3
Support type:Scholarships abroad - Research Internship - Doctorate
Effective date (Start): March 22, 2017
Effective date (End): February 06, 2018
Field of knowledge:Agronomical Sciences - Animal Husbandry - Genetics and Improvement of Domestic Animals
Principal Investigator:Danísio Prado Munari
Grantee:Priscila Arrigucci Bernardes
Supervisor abroad: Cedric Gondro
Home Institution: Faculdade de Ciências Agrárias e Veterinárias (FCAV). Universidade Estadual Paulista (UNESP). Campus de Jaboticabal. Jaboticabal , SP, Brazil
Local de pesquisa : University of New England, Armidale (UNE), Australia  
Associated to the scholarship:15/25096-6 - Imputation, linkage desequilibrium, haplotype blocks and inbreeding in Nelore cattle, BP.DR

Abstract

The knowledge of runs of homozygosity (ROH) and linkage disequilibrium (LD) have allowed applied studies with genomic information and have contributed to understand population structure, which improve the animal breedingpractices. However, due to historical and structural differences between populations,it was reported that even in short distances, Bos taurus indicus showed lower LD compared to Bos taurus taurus and crossbred, suggesting the use of higher density of SNPs to improve performance in genomic approaches for this subspecies. Studies of imputation are used to define unknown markers as to reduce costs in genomic selection and are applied to obtain genotypes for ungenotyped animals. Imputation is also important to combine genotyped data with different arrays which allow higherdensity of SNPs with high LD for Bos taurus indicus. The combination of high densityarrays enables improved genome cover when compared to the use of each arrayindependently. Therefore, the present study aims to identify runs of homozygosity(ROH), evaluates imputation using high density arrays (Illumina and Affymetrix) andcustomized array in Nelore beef cattle, estimates linkage disequilibrium (LD), andhaplotype blocks to high density arrays individuality and after imputation. (AU)

Scientific publications
(References retrieved automatically from Web of Science and SciELO through information on FAPESP grants and their corresponding numbers as mentioned in the publications by the authors)
BERNARDES, PRISCILA ARRIGUCCI; DO NASCIMENTO, GUILHERME BATISTA; SAVEGNAGO, RODRIGO PELICIONI; BUZANSKAS, MARCOS ELI; WATANABE, RAFAEL NAKAMURA; DE ALMEIDA REGITANO, LUCIANA CORREIA; COUTINHO, LUIZ LEHMANN; GONDRO, CEDRIC; MUNARI, DANISIO PRADO. Evaluation of imputation accuracy using the combination of two high-density panels in Nelore beef cattle. SCIENTIFIC REPORTS, v. 9, NOV 29 2019. Web of Science Citations: 0.
SBARDELLA, A. P.; WELLER, M. M. D. C. A.; FONSECA, I; STAFUZZA, N. B.; BERNARDES, P. A.; SILVA, F. F. E.; DA SILVA, M. V. G. B.; MARTINS, M. F.; MUNARI, D. P. RNA sequencing differential gene expression analysis of isolated perfused bovine udders experimentally inoculated with Streptococcus agalactiae. JOURNAL OF DAIRY SCIENCE, v. 102, n. 2, p. 1761-1767, FEB 2019. Web of Science Citations: 1.

Please report errors in scientific publications list by writing to: cdi@fapesp.br.