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

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

PLOS ONE, 2017, vol. 12, issue 2, 1-16

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.

Date: 2017
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Persistent link: https://EconPapers.repec.org/RePEc:plo:pone00:0171660

DOI: 10.1371/journal.pone.0171660

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