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

• Grant number: 16/22940-3
• Support Opportunities: Scholarships abroad - Research Internship - Doctorate
• Start date: March 22, 2017
• End date: 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: Cedric Gondro
• Host Institution: Faculdade de Ciências Agrárias e Veterinárias (FCAV). Universidade Estadual Paulista (UNESP). Campus de Jaboticabal. Jaboticabal , SP, Brazil
• Institution abroad: 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)

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. (16/22940-3, 15/25096-6)

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. (13/20091-0, 12/23638-8, 16/22940-3, 15/25096-6, 13/19335-2)

WATANABE, RAFAEL NAKAMURA; DO NASCIMENTO, GUILHERME BATISTA; BERNARDES, PRISCILA ARRIGUCCI; DA COSTA, REBEKA MAGALHAES; LOBO, RAYSILDO BARBOSA; BALDI, FERNANDO; MUNARI, DANISIO PRADO. Inclusion of genomic information in estimation of genetic parameters for body weights and visual scores in Nelore cattle. REVISTA BRASILEIRA DE ZOOTECNIA-BRAZILIAN JOURNAL OF ANIMAL SCIENCE, v. 50, 2021. (16/22940-3, 15/25096-6)