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Estimates of heterozygosity and genetic composition of Braford cattle and their application in a Genome-Wide Association Study of characteristic levels of Babesia bigemina infection

Grant number: 19/00412-3
Support type:Scholarships abroad - Research Internship - Doctorate
Effective date (Start): March 25, 2019
Effective date (End): March 24, 2020
Field of knowledge:Agronomical Sciences - Animal Husbandry
Principal Investigator:Henrique Nunes de Oliveira
Grantee:Andrea Renata da Silva Romero
Supervisor abroad: Cedric Gondro Msu
Home Institution: Faculdade de Ciências Agrárias e Veterinárias (FCAV). Universidade Estadual Paulista (UNESP). Campus de Jaboticabal. Jaboticabal , SP, Brazil
Local de pesquisa : Michigan State University (MSU), United States  
Associated to the scholarship:17/21000-0 - Genomics studies of resistance to bovine Anaplasmosis in Braford animals, BP.DR

Abstract

A constant challenge in tropical animal husbandry is the control of parasites, such as the tick Rhipicephalus (Boophilus) microplus and the hemoparasites transmitted by it, especially Babesia bigemina, a protozoan that causes severe losses in herds. Therefore, the objective of this proposed research will be to carry out a broad genome-wide association study (GWAS) to determine the characteristic B. bigemina infection levels in Braford cattle. The sample group will consist of 1600 animals of the Braford breed. One hundred animals of the Hereford breed and 1000 animals of the Nellore breed will also be used, but only for analyses of the genetic composition of the Braford breed and its heterozygosity. These animals will be genotyped with an Illumina BovineSNP50 BeadChip panel, the results of which will undergo quality control to exclude problematic markers and samples. The phenotype quantified will be the estimated blood levels of B. bigemina infection determined using a quantitative polymerase chain reaction (qPCR) technique. The estimates of genetic composition and heterozygosity to be used in GWAS model analyses will be obtained from the genotypes using the LAMP software suite. The phenotypes will be corrected for any systematic effects using the AIREMLF90 program, and then later GWAS analyses will be performed using the software GEMMA. The regions indicated to be associated with the trait studied by the GWAS analyses will be searched for in the Ensembl and CattleQTLdb databases to identify genes and quantitative trait loci close to the trait-associated single-nucleotide polymorphisms. Searches for genetic interactions involving the genes identified by our GWAS analyses and clusters reported in the literature will be performed through the STRING program. The characteristics of the resulting genes will then be reviewed based on information in the published scientific literature.