Título:	Effect of founder breeds on genotype imputation accuracy in Canchim cattle.
Autoria:	SILVA, R. T. da GENUÍNO, M. V. H. BESSA, A. F. O. CÂMARA, G. M. S. OLIVEIRA, A. C. J. SILVA, J. A. II V. MOTA, L. F. M. REY, F. S. B. REGITANO, L. C. de A. MARCONDES, C. R. BERNARDES, P. A. BERRY, D. P. MUNARI, D. P. BUZANSKAS, M. E.
Afiliação:	RONEY TEIXEIRA DA SILVA, UNIVERSIDADE ESTADUAL PAULISTA JÚLIO DE MESQUITA FILHO MARIA VICTÓRIA HENRIQUE GENUÍNO, UNIVERSIDADE FEDERAL DA PARAÍBA AYRTON FERNANDES DE OLIVEIRA BESSA, UNIVERSIDADE FEDERAL DA PARAÍBA GIOVANNA MARIA DOS SANTOS CÂMARA, UNIVERSIDADE ESTADUAL PAULISTA JÚLIO DE MESQUITA FILHO ANA CAROLINA DE JESUS OLIVEIRA, UNIVERSIDADE ESTADUAL PAULISTA JÚLIO DE MESQUITA FILHO JOSINEUDSON AUGUSTO II DE VASCONCELOS SILVA, UNIVERSIDADE ESTADUAL PAULISTA JÚLIO DE MESQUITA FILHO LUCIO FLAVIO MACEDO MOTA, UNIVERSIDADE ESTADUAL PAULISTA JÚLIO DE MESQUITA FILHO FERNANDO SEBASTIÁN BALDI REY, UNIVERSIDADE DE SÃO PAULO LUCIANA CORREIA DE ALMEIDA REGITANO, CPPSE CINTIA RIGHETTI MARCONDES, CPPSE PRISCILA ARRIGUCCI BERNARDES, UNIVERSIDADE FEDERAL DE SANTA CATARINA DONAGH PEARSE BERRY, THE AGRICULTURE AND FOOD DEVELOPMENT AUTHORITY DANÍSIO PRADO MUNARI, UNIVERSIDADE ESTADUAL PAULISTA JÚLIO DE MESQUITA FILHO MARCOS ELI BUZANSKAS, UNIVERSIDADE ESTADUAL PAULISTA JÚLIO DE MESQUITA FILHO.
Ano de publicação:	2026
Referência:	Journal of Applied Genetics, 2026.
Conteúdo:	Genotype 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.
NAL Thesaurus:	Animal breeding Crossbreds Genotype Quantitative traits
ISSN:	2190-3883
Digital Object Identifier:	https://doi.org/10.1007/s13353-026-01060-z
Notas:	First online. Na publicação os autores saíram: Roney Teixeira; Fernando Baldi. Projeto com apoio FAPESP (22/11852-7)
Tipo do material:	Artigo de periódico
Acesso:	openAccess
Aparece nas coleções:	Artigo em periódico indexado (CPPSE)