Study on the introgression of beef breeds in Canchim cattle using single nucleotide polymorphism markers

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Buzanskas, Marcos Eli ; Ventura, Ricardo Vieira ; Seleguim Chud, Tatiane Cristina ; Bernardes, Priscila Arrigucci ; de Abreu Santos, Daniel Jordan ; de Almeida Regitano, Luciana Correia ; de Alencar, Mauricio Mello ; Mudadu, Mauricio de Alvarenga ; Zanella, Ricardo ; Gualberto Barbosa da Silva, Marcos Vinicius ; Li, Changxi ; Schenkel, Flavio Schramm ; Munari, Danisio Prado

• Tipo de documento: Artigo Científico
• Fonte: PLoS One; v. 12, n. 2 FEB 9 2017.
• Citações Web of Science: 2

Resumo

The aim of this study was to evaluate the level of introgression of breeds in the Canchim (CA: 62.5% Charolais-37.5% Zebu) and MA genetic group (MA: 65.6% Charolais-34.4% Zebu) cattle using genomic information on Charolais (CH), Nelore (NE), and Indubrasil (IB) breeds. The number of animals used was 395 (CA and MA), 763 (NE), 338 (CH), and 37 (IB). The Bovine50SNP BeadChip from Illumina panel was used to estimate the levels of introgression of breeds considering the Maximum likelihood, Bayesian, and Single Regression method. After genotype quality control, 32,308 SNPs were considered in the analysis. Furthermore, three thresholds to prune out SNPs in linkage disequilibrium higher than 0.10, 0.05, and 0.01 were considered, resulting in 15,286, 7,652, and 1,582 SNPs, respectively. For k = 2, the proportion of taurine and indicine varied from the expected proportion based on pedigree for all methods studied. For k = 3, the Regression method was able to differentiate the animals in three main clusters assigned to each purebred breed, showing more reasonable according to its biological viewpoint. Analyzing the data considering k = 2 seems to be more appropriate for Canchim-MA animals due to its biological interpretation. The usage of 32,308 SNPs in the analyses resulted in similar findings between the estimated and expected breed proportions. Using the Regression approach, a contribution of Indubrasil was observed in Canchim-MA when k = 3 was considered. Genetic parameter estimation could account for this breed composition information as a source of variation in order to improve the accuracy of genetic models. Our findings may help assemble appropriate reference populations for genomic prediction for Canchim-MA in order to improve prediction accuracy. Using the information on the level of introgression in each individual could also be useful in breeding or crossing design to improve individual heterosis in crossbred cattle. (AU)

• Processo FAPESP: 12/23638-8 - Bases moleculares da qualidade da carne em bovinos da raça Nelore
• Beneficiário: Luciana Correia de Almeida Regitano
• Modalidade de apoio: Auxílio à Pesquisa - Temático
• Processo FAPESP: 15/12396-1 - Imputação de genótipos de marcadores no genoma bubalino e seu impacto nas avaliações genômicas da produção de leite e seus constituintes
• Beneficiário: Daniel Jordan de Abreu Santos
• Modalidade de apoio: Bolsas no Brasil - Pós-Doutorado
• Processo FAPESP: 15/08939-0 - Identificação de regiões com variações no número de cópias dos segmentos de DNA em bovinos da raça Girolando
• Beneficiário: Tatiane Cristina Seleguim Chud
• Modalidade de apoio: Bolsas no Brasil - Doutorado
• Processo FAPESP: 13/19335-2 - Estudo do nível de mistura em animais da raça Canchim e grupo genético ma utilizando painel de polimorfismos de nucleotídeo único de alta densidade
• Beneficiário: Marcos Eli Buzanskas
• Modalidade de apoio: Bolsas no Brasil - Pós-Doutorado
• Processo FAPESP: 15/25096-6 - Imputação, desequilíbrio de ligação, blocos de haplótipos e endogamia em bovinos Nelore
• Beneficiário: Priscila Arrigucci Bernardes
• Modalidade de apoio: Bolsas no Brasil - Doutorado