Effect of founder breeds on genotype imputation accuracy in Canchim cattle.

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dc.contributorRONEY TEIXEIRA DA SILVA, UNIVERSIDADE ESTADUAL PAULISTA JÚLIO DE MESQUITA FILHO
dc.contributorMARIA VICTÓRIA HENRIQUE GENUÍNO, UNIVERSIDADE FEDERAL DA PARAÍBA
dc.contributorAYRTON FERNANDES DE OLIVEIRA BESSA, UNIVERSIDADE FEDERAL DA PARAÍBA
dc.contributorGIOVANNA MARIA DOS SANTOS CÂMARA, UNIVERSIDADE ESTADUAL PAULISTA JÚLIO DE MESQUITA FILHO
dc.contributorANA CAROLINA DE JESUS OLIVEIRA, UNIVERSIDADE ESTADUAL PAULISTA JÚLIO DE MESQUITA FILHO
dc.contributorJOSINEUDSON AUGUSTO II DE VASCONCELOS SILVA, UNIVERSIDADE ESTADUAL PAULISTA JÚLIO DE MESQUITA FILHO
dc.contributorLUCIO FLAVIO MACEDO MOTA, UNIVERSIDADE ESTADUAL PAULISTA JÚLIO DE MESQUITA FILHO
dc.contributorFERNANDO SEBASTIÁN BALDI REY, UNIVERSIDADE DE SÃO PAULO
dc.contributorLUCIANA CORREIA DE ALMEIDA REGITANO, CPPSE
dc.contributorCINTIA RIGHETTI MARCONDES, CPPSE
dc.contributorPRISCILA ARRIGUCCI BERNARDES, UNIVERSIDADE FEDERAL DE SANTA CATARINA
dc.contributorDONAGH PEARSE BERRY, THE AGRICULTURE AND FOOD DEVELOPMENT AUTHORITY
dc.contributorDANÍSIO PRADO MUNARI, UNIVERSIDADE ESTADUAL PAULISTA JÚLIO DE MESQUITA FILHO
dc.contributorMARCOS ELI BUZANSKAS, UNIVERSIDADE ESTADUAL PAULISTA JÚLIO DE MESQUITA FILHO.
dc.creatorSILVA, R. T. da
dc.creatorGENUÍNO, M. V. H.
dc.creatorBESSA, A. F. O.
dc.creatorCÂMARA, G. M. S.
dc.creatorOLIVEIRA, A. C. J.
dc.creatorSILVA, J. A. II V.
dc.creatorMOTA, L. F. M.
dc.creatorREY, F. S. B.
dc.creatorREGITANO, L. C. de A.
dc.creatorMARCONDES, C. R.
dc.creatorBERNARDES, P. A.
dc.creatorBERRY, D. P.
dc.creatorMUNARI, D. P.
dc.creatorBUZANSKAS, M. E.
dc.date2026-04-22T20:48:39Z
dc.date2026-04-22T20:48:39Z
dc.date2026-04-22
dc.date2026
dc.date.accessioned2026-07-07T05:35:05Z
dc.descriptionGenotype imputation is a technique used to infer unobserved genotypes based on reference panels, allowing increased marker density and cost-effective optimization for genomic selection. This study aimed to evaluate whether the inclusion of genotypes from the founder breeds Nelore (NE) and Charolais (CH) improves the imputation accuracy in the composite beef cattle breed Canchim (CA). The populations studied consisted of 804 NE, 897 CH, and 392 CA animals, all genotyped using high-density panels (777,962 SNP – single nucleotide polymorphisms). CA animals had their genotypes masked to simulate a medium-density panel (54,609 SNP). Fourteen imputation scenarios were evaluated, varying according to breed, sex, year of birth, and lineage. Imputation accuracy was determined based on the percentage of correctly imputed genotypes (PERC) and the squared Pearson’s correlation between observed and imputed genotypes (R2). PERC values ranged from 66.52% to 97.39% and R² from 0.6352 to 0.9780. The scenarios that included NE, CH, and CA (males or animals born before 2004) as the reference population for imputing CA females or CA animals born after 2004 showed the highest imputation accuracies. Therefore, the use of founder breeds in the reference population improves the accuracy of genotype imputation in CA cattle. The results indicate that a multibreed reference population, incorporating founder breeds, could provide a more robust and informative genetic basis for imputing composite cattle.
dc.descriptionFirst online. Na publicação os autores saíram: Roney Teixeira; Fernando Baldi. Projeto com apoio FAPESP (22/11852-7)
dc.identifierJournal of Applied Genetics, 2026.
dc.identifier2190-3883
dc.identifierhttp://www.alice.cnptia.embrapa.br/alice/handle/doc/1186337
dc.identifierhttps://doi.org/10.1007/s13353-026-01060-z
dc.identifier.urihttp://hdl.handle.net/123456789/495783
dc.languageeng
dc.rightsopenAccess
dc.subjectAnimal breeding
dc.subjectCrossbreds
dc.subjectGenotype
dc.subjectQuantitative traits
dc.titleEffect of founder breeds on genotype imputation accuracy in Canchim cattle.
dc.typeArtigo de periódico

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