Genotype imputation in a tropical crossbred dairy cattle population

dc.contributor.authorOliveira Júnior, Gerson A.
dc.contributor.authorChud, Tatiane C.S. [UNESP]
dc.contributor.authorVentura, Ricardo V.
dc.contributor.authorGarrick, Dorian J.
dc.contributor.authorCole, John B.
dc.contributor.authorMunari, Danísio P. [UNESP]
dc.contributor.authorFerraz, José B.S.
dc.contributor.authorMullart, Erik
dc.contributor.authorDeNise, Sue
dc.contributor.authorSmith, Shannon
dc.contributor.authorda Silva, Marcos Vinícius G.B.
dc.contributor.institutionUniversidade de São Paulo (USP)
dc.contributor.institutionUniversidade Estadual Paulista (Unesp)
dc.contributor.institutionBeef Improvement Opportunities
dc.contributor.institutionUniversity of Guelph
dc.contributor.institutionIowa State University
dc.contributor.institutionUnited States Department of Agriculture
dc.contributor.institutionCRV Holding B.V.
dc.contributor.institutionEmpresa Brasileira de Pesquisa Agropecuária (EMBRAPA)
dc.description.abstractThe objective of this study was to investigate different strategies for genotype imputation in a population of crossbred Girolando (Gyr × Holstein) dairy cattle. The data set consisted of 478 Girolando, 583 Gyr, and 1,198 Holstein sires genotyped at high density with the Illumina BovineHD (Illumina, San Diego, CA) panel, which includes ∼777K markers. The accuracy of imputation from low (20K) and medium densities (50K and 70K) to the HD panel density and from low to 50K density were investigated. Seven scenarios using different reference populations (RPop) considering Girolando, Gyr, and Holstein breeds separately or combinations of animals of these breeds were tested for imputing genotypes of 166 randomly chosen Girolando animals. The population genotype imputation were performed using FImpute. Imputation accuracy was measured as the correlation between observed and imputed genotypes (CORR) and also as the proportion of genotypes that were imputed correctly (CR). This is the first paper on imputation accuracy in a Girolando population. The sample-specific imputation accuracies ranged from 0.38 to 0.97 (CORR) and from 0.49 to 0.96 (CR) imputing from low and medium densities to HD, and 0.41 to 0.95 (CORR) and from 0.50 to 0.94 (CR) for imputation from 20K to 50K. The CORRanim exceeded 0.96 (for 50K and 70K panels) when only Girolando animals were included in RPop (S1). We found smaller CORRanim when Gyr (S2) was used instead of Holstein (S3) as RPop. The same behavior was observed between S4 (Gyr + Girolando) and S5 (Holstein + Girolando) because the target animals were more related to the Holstein population than to the Gyr population. The highest imputation accuracies were observed for scenarios including Girolando animals in the reference population, whereas using only Gyr animals resulted in low imputation accuracies, suggesting that the haplotypes segregating in the Girolando population had a greater effect on accuracy than the purebred haplotypes. All chromosomes had similar imputation accuracies (CORRsnp) within each scenario. Crossbred animals (Girolando) must be included in the reference population to provide the best imputation accuracies.en
dc.description.affiliationDepartamento de Medicina Veterinária Universidade de São Paulo (USP) Faculdade de Zootecnia e Engenharia de Alimentos
dc.description.affiliationDepartamento de Ciências Exatas Universidade Estadual Paulista (Unesp) Faculdade de Ciências Agrárias e Veterinárias
dc.description.affiliationBeef Improvement Opportunities
dc.description.affiliationCentre for Genetic Improvement of Livestock University of Guelph
dc.description.affiliationDepartment of Animal Science Iowa State University
dc.description.affiliationAnimal Genomics and Improvement Laboratory Agricultural Research Service United States Department of Agriculture
dc.description.affiliationCRV Holding B.V.
dc.description.affiliationEmbrapa Dairy Cattle Brazilian Corporation of Agricultural Research
dc.description.affiliationUnespDepartamento de Ciências Exatas Universidade Estadual Paulista (Unesp) Faculdade de Ciências Agrárias e Veterinárias
dc.identifier.citationJournal of Dairy Science, v. 100, n. 12, p. 9623-9634, 2017.
dc.relation.ispartofJournal of Dairy Science
dc.rights.accessRightsAcesso restrito
dc.subjectsingle nucleotide polymorphism
dc.titleGenotype imputation in a tropical crossbred dairy cattle populationen
unesp.departmentCiências Exatas - FCAVpt