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

Author(s):Show less -

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

• Document type: Journal article
• Source: PLoS One; v. 12, n. 2 FEB 9 2017.
• Web of Science Citations: 2

Abstract

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)

• FAPESP's process: 12/23638-8 - Molecular basis of meat quality in Nelore beef cattle
• Grantee: Luciana Correia de Almeida Regitano
• Support Opportunities: Research Projects - Thematic Grants
• FAPESP's process: 15/12396-1 - IMPUTATION OF MARKER GENOTYPES IN BUFFALO GENOME AND ITS IMPACT ON GENOMIC EVALUATION OF MILK YIELD AND CONTENT
• Grantee: Daniel Jordan de Abreu Santos
• Support Opportunities: Scholarships in Brazil - Post-Doctoral
• FAPESP's process: 15/08939-0 - Identification of copy number variations in Girolando cattle
• Grantee: Tatiane Cristina Seleguim Chud
• Support Opportunities: Scholarships in Brazil - Doctorate
• FAPESP's process: 13/19335-2 - Study of admixture level in Canchim breed and ma genetic group animals using high density single nucleotide polymorphism markers
• Grantee: Marcos Eli Buzanskas
• Support Opportunities: Scholarships in Brazil - Post-Doctoral
• FAPESP's process: 15/25096-6 - Imputation, linkage desequilibrium, haplotype blocks and inbreeding in Nelore cattle
• Grantee: Priscila Arrigucci Bernardes
• Support Opportunities: Scholarships in Brazil - Doctorate