Imputation accuracy to whole genome sequence in Nellore beef cattle

• Grant number: 19/12434-1
• Support Opportunities: Scholarships abroad - Research Internship - Post-doctor
• Start date: January 15, 2020
• End date: January 14, 2021
• Field of knowledge: Agronomical Sciences - Animal Husbandry - Genetics and Improvement of Domestic Animals
• Principal Investigator: Henrique Nunes de Oliveira
• Grantee: Gerardo Alves Fernandes Júnior
• Supervisor: Ben Hayes
• Host Institution: Faculdade de Ciências Agrárias e Veterinárias (FCAV). Universidade Estadual Paulista (UNESP). Campus de Jaboticabal. Jaboticabal , SP, Brazil
• Institution abroad: University of Queensland, Brisbane (UQ), Australia
• Associated to the scholarship: 18/10109-3 - Identification and analysis of genetic variants obtained from the whole-genome sequencing of Nellore bulls, BP.PD

Abstract

Advances in next-generation sequencing techniques associated to a drastically decreasing in sequencing costs is favoring the development of strategies to explore the complete DNA sequence in genetic evaluations due to the possibility of using causal mutations. Anyway, it is still cheaper genotyping a large number of animals than sequencing them. An alternative and cost-effective strategy would be to sequence key ancestors of the population, and impute sequence to the remaining reference population of animals genotyped with low density SNP panels. Our research group has a database with more than 10,000 animals, among bulls, dams, and young animals, from different breeding programs and genotyped with Illumina SNP panels with different densities. Using sequence data of influential Nellore bulls, we can carry out the imputation of this reference population to whole genome sequence, which will increase the amount of genomic information per animal. A previous investigation of the imputation accuracy is essential to determine the feasibility of this process. This issue will be investigated in the present research Project, in order to generate information on sequence imputation accuracy in Nellore cattle, in addition to develop a pipeline to impute sequence data to about 10,000 animals of an existing Nellore genotype database. (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)

FERNANDES JUNIOR, GERARDO A.; CARVALHEIRO, ROBERTO; DE OLIVEIRA, HENRIQUE N.; SARGOLZAEI, MEHDI; COSTILLA, ROY; VENTURA, RICARDO V.; FONSECA, LARISSA F. S.; NEVES, HAROLDO H. R.; HAYES, BEN J.; DE ALBUQUERQUE, LUCIA G.. Imputation accuracy to whole-genome sequence in Nellore cattle. GENETICS SELECTION EVOLUTION, v. 53, n. 1, MAR 12 2021. (17/10630-2, 19/12434-1, 09/16118-5, 18/10109-3, 18/20026-8)

FERNANDES JUNIOR, GERARDO ALVES; DE OLIVEIRA, HENRIQUE NUNES; CARVALHEIRO, ROBERTO; CARDOSO, DIERCLES FRANCISCO; FONSECA, LARISSA FERNANDA SIMIELLI; VENTURA, RICARDO VIEIRA; DE ALBUQUERQUE, LUCIA GALVAO. Whole-genome sequencing provides new insights into genetic mechanisms of tropical adaptation in Nellore (Bos primigenius indicus). SCIENTIFIC REPORTS, v. 10, n. 1, JUN 10 2020. (09/16118-5, 19/12434-1, 18/10109-3, 18/20026-8, 17/10630-2)