Genotype Imputation and Accuracy Evaluation in Racing Quarter Horses Genotyped Using Different Commercial SNP Panels

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dc.contributor.authorPereira, Guilherme L. [UNESP]
dc.contributor.authorChud, Tatiane C.S. [UNESP]
dc.contributor.authorBernardes, Priscila A. [UNESP]
dc.contributor.authorVenturini, Guilherme C. [UNESP]
dc.contributor.authorChardulo, Luís A.L. [UNESP]
dc.contributor.authorCuri, Rogério A. [UNESP]
dc.contributor.institutionUniversidade Estadual Paulista (Unesp)
dc.date.accessioned2018-12-11T16:49:24Z
dc.date.available2018-12-11T16:49:24Z
dc.date.issued2017-11-01
dc.description.abstractThe availability of large-scale SNP genotyping panels for horses has opened up new possibilities for genetic studies of the species. The first panel version contained around 54,000 SNPs (54k). The current second generation panel possesses approximately 65,000 SNPs (65k), which 19,000 of them are new markers and 45,000 were present in the first panel. The objectives of this study were to perform two-step genotype imputation between individuals in a relatively small population sample of racing Quarter Horses genotyped with the 54k or 65k panel and to evaluate the accuracy of imputation in a practical situation. Genotypes were imputed using 116 horses genotyped with the 54k SNP array and 233 animals genotyped with the 65k array. For the simulations, random samples were chosen to compose the imputed (about 50% samples) and reference populations in two scenarios. Scenario A simulated the genotype imputation in the first step (from 65k to 54k) and the scenario B in the second step (from 54k to 65k). For each scenario, the individuals genotyped with the same panel were considered as the reference population but that were included in the imputed group had their exclusive genotypes masked for subsequent evaluation of imputation accuracy. Thus, after quality control, the 54k and 65k panels contained 7,048 and 16,940 exclusive markers, respectively. The mean concordance rate was 0.9815 and 0.9751 for scenarios A and B, and the mean allelic r2 was 0.9791 and 0.974, respectively. No important influences of the genomic relationship coefficients on imputation accuracy were observed between the imputed and reference samples. Thus, two-step imputation of exclusive genotypes between the 54k and 65k equine panels resulted in a considerable increase of SNPs for all samples (12%–26%) without losses in the quality of information.en
dc.description.affiliationFaculdade de Ciências Agrárias e Veterinárias Universidade Estadual Paulista (Unesp)
dc.description.affiliationFaculdade de Medicina Veterinária e Zootecnia Universidade Estadual Paulista (Unesp)
dc.description.affiliationUnespFaculdade de Ciências Agrárias e Veterinárias Universidade Estadual Paulista (Unesp)
dc.description.affiliationUnespFaculdade de Medicina Veterinária e Zootecnia Universidade Estadual Paulista (Unesp)
dc.description.sponsorshipFundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)
dc.description.sponsorshipIdFAPESP: 2014/20207-1
dc.format.extent89-96
dc.identifierhttp://dx.doi.org/10.1016/j.jevs.2017.07.012
dc.identifier.citationJournal of Equine Veterinary Science, v. 58, p. 89-96.
dc.identifier.doi10.1016/j.jevs.2017.07.012
dc.identifier.file2-s2.0-85029523950.pdf
dc.identifier.issn0737-0806
dc.identifier.lattes3514713413919126
dc.identifier.orcid0000-0001-6289-0406
dc.identifier.scopus2-s2.0-85029523950
dc.identifier.urihttp://hdl.handle.net/11449/170133
dc.language.isoeng
dc.relation.ispartofJournal of Equine Veterinary Science
dc.relation.ispartofsjr0,390
dc.rights.accessRightsAcesso aberto
dc.sourceScopus
dc.subjectChromosome
dc.subjectConcordance rate
dc.subjectIBD
dc.subjectMAF
dc.subjectPopulation structure
dc.titleGenotype Imputation and Accuracy Evaluation in Racing Quarter Horses Genotyped Using Different Commercial SNP Panelsen
dc.typeArtigo
unesp.author.lattes3514713413919126[6]
unesp.author.orcid0000-0001-6289-0406[6]

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