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Identification and analysis of genetic variants obtained from the whole-genome sequencing of Nellore bulls

Grant number: 18/10109-3
Support type:Scholarships in Brazil - Post-Doctorate
Effective date (Start): August 01, 2018
Effective date (End): August 01, 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
Home Institution: Faculdade de Ciências Agrárias e Veterinárias (FCAV). Universidade Estadual Paulista (UNESP). Campus de Jaboticabal. Jaboticabal , SP, Brazil
Associated research grant:17/10630-2 - Genetic aspects of meat production quality, efficiency and sustainability in Nelore breed animals, AP.TEM
Associated scholarship(s):19/12434-1 - Imputation accuracy to whole genome sequence in Nellore beef cattle, BE.EP.PD

Abstract

Strategies to use the complete DNA sequence in animal genetic evaluations of several species have been developed due to advances in next-generation sequencing techniques associated with decreasing in sequencing costs and due to an expected increasing of prediction accuracies by the possibility of using causal mutations. Aligner and variant calling methods are of paramount importance to use sequencing data in genetic analyses. There are differences among methods regarding the number and phase concordance of part of the identified genotypes. These differences can influence the results of analysis performed to genetic evaluations which are directly dependent of variant discovery. Thus, the use of an inadequate method could compromise the results of all subsequent analyses or, at least, to reduce the expected accuracy gain. In the present project, there will be used data from the complete DNA sequence and genotyping by the panel Illumina Bovine HD chip of 150 Nellore bulls selected by their importance for the breed. There will be compared two aligners (BWA e HISAT2) and two variant calling methods (SAMtools e GATK) in a factorial scheme. In this way, there will be tested four combinations to the process of identification of genetic variants (SNPs and indels) in the population (BWA-SAMtools, BWA-GATK, HISAT2-SAMtools e HISAT2-GATK). The platforms will be compared based on the Non-Reference Sensitivity (NRS) and Non-Reference Discrepancy (NRD) statistics. The NRS measures the methodology sensibility degree in which a value of NRS equal to unit means a perfect agreement between the sequencing and genotyping results, while the NRD statistics denotes the false positive rate. With the definition of the better strategy for variant identification, there will be performed the variant annotation as well as the genome linkage disequilibrium characterization. There will be also investigated the imputation accuracy of different SNP panel densities to complete genome sequence with a subsequent imputation of a database with more than 10,000 animals. The developing of this project should contribute to the obtaining and utilization process of genomic data generated from the whole-genome sequencing of beef cattle. (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. Web of Science Citations: 0.
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. Web of Science Citations: 2.

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