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

• Grant number: 15/25096-6
• Support Opportunities: Scholarships in Brazil - Doctorate
• Effective date (Start): March 01, 2016
• Effective date (End): June 16, 2018
• Field of knowledge: Agronomical Sciences - Animal Husbandry - Genetics and Improvement of Domestic Animals
• Principal Investigator: Danísio Prado Munari
• Grantee: Priscila Arrigucci Bernardes
• Host Institution: Faculdade de Ciências Agrárias e Veterinárias (FCAV). Universidade Estadual Paulista (UNESP). Campus de Jaboticabal. Jaboticabal , SP, Brazil
• Associated scholarship(s): 16/22940-3 - Imputation, linkage desequilibrium, haplotype blocks and inbreeding in Nelore cattle, BE.EP.DR

Abstract

Knowledge on runs of homozygosity (ROH) and linkage disequilibrium (LD) has contributed to the application of studies with genomic information and to understand population structure, which improve the animal breeding practices. However, due to historical and structural differences between populations, studies have reported that even in short distances, Bos taurus indicus showed lower LD compared to Bos taurus taurus and crossbreds. These findings suggest the use of higher density SNP panels improves the performance of genomic approaches for this subspecies. Studies of imputation are used to fill in the gaps left by unknown markers to reduce costs in genomic selection and they are applied to obtain genotypes for ungenotyped animals. Imputation is also an important tool to combine data from different SNP panels which allows to increase the density of SNPs with high LD for Bos taurus indicus. The combination of different high density arrays may improve the genome coverage when compared to the use of each array independently. Therefore, the present study aims to identify runs of homozygosity (ROH), evaluate imputation using high density arrays (Illumina and Affymetrix) and customized array in Nelore beef cattle; estimate linkage disequilibrium (LD) and haplotype blocks conformation of high density arrays both individuality and after imputation.

Scientific publications

(6)

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

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)

BUZANSKAS, MARCOS ELI; VENTURA, RICARDO VIEIRA; SELEGUIM CHUD, TATIANE CRISTINA; BERNARDES, PRISCILA ARRIGUCCI; DE ABREU SANTOS, DANIEL JORDAN; DE ALMEIDA REGITANO, LUCIANA CORREIA; DE ALENCAR, MAURICIO MELLO; MUDADU, MAURICIO DE ALVARENGA; ZANELLA, RICARDO; GUALBERTO BARBOSA DA SILVA, MARCOS VINICIUS; et al. Study on the introgression of beef breeds in Canchim cattle using single nucleotide polymorphism markers. PLoS One, v. 12, n. 2, FEB 9 2017. (12/23638-8, 15/12396-1, 15/08939-0, 13/19335-2, 15/25096-6)

BUZANSKAS, M. E.; PIRES, P. S.; CHUD, T. C. S.; BERNARDES, P. A.; ROLA, L. D.; SAVEGNAGO, R. P.; LOBO, R. B.; MUNARI, D. P.. Parameter estimates for reproductive and carcass traits in Nelore beef cattle. Theriogenology, v. 92, p. 204-209, APR 1 2017. (13/20091-0, 15/08939-0, 13/13972-0, 13/19335-2, 15/25096-6)

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)

RAMOS, S. B.; CAETANO, S. L.; ROSA, G. J. M.; SAVEGNAGO, R. P.; KERN, E. L.; BERNANRDES, P. A.; LOBO, R. B.; MUNARI, D. P.. Estimation of genetic parameters for cow age at last calving under different censorship criteria. LIVESTOCK SCIENCE, v. 208, p. 40-43, FEB 2018. (15/25096-6, 13/20091-0, 10/05903-0)

Academic Publications

(References retrieved automatically from State of São Paulo Research Institutions)

BERNARDES, Priscila Arrigucci. Imputation and genomic studies in bovine Nelore. 2018. Doctoral Thesis - Universidade Estadual Paulista (Unesp). Faculdade de Ciências Agrárias e Veterinárias. Jaboticabal Jaboticabal.