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

Citation

Buzanskas, M.E., Ventura, R.V., Chud, T.C.S., Bernardes, P.A., De Abreu Santos, D.J., De Almeida Regitano, L.C., De Alencar, M.M., De Alvarenga Mudadu, M., Zanella, R., Da Silva, M.V.G.B., Li, C., Schenkel, F.S., Munari, D.P. (2017). Study on the introgression of beef breeds in Canchim cattle using single nucleotide polymorphism markers. PLoS ONE, [online] 12(2), http://dx.doi.org/10.1371/journal.pone.0171660

Plain language summary

In beef cattle, different breeds mix or introgress during crossbreeding. For better beef production, it is important to know the breed composition or introgression level of other breeds for each animal in a herd. In this study, we evaluated the level of introgression of breeds in Canchim, a breed type in Braszil from crossbreeding between Charolais and Zebu (mainly Nelore) breeds, and in a MA breed type that were from mating between Charolais bulls and ½ Canchim + ½ Zebu dams. The breed introgression analysis was based on 32,308 SNPs (single nucleotide polymorphism DNA markers). The results showed that the SNP marker estimated and expected breed proportions were similar (i.e. 62.5% Charolais and 37.5% Zebu for Canchim, 65.6% Charolais and 34.4% Zebu for the MA), indicating that the usage of 32,308 SNPs in the analyses was able to determine the breed composition for each animal. The results also suggested that genetic parameter estimation should account for the breed composition information as a source of variation in order to improve the accuracy of genetic models. The findings will also help assemble appropriate reference populations for genomic prediction for Canchim and MA in order to improve prediction accuracy. The information on the level of introgression in each individual could also be useful in crossbreeding design for the beef industry to improve individual heterosis in crossbred cattle.

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 Bovine 50SNP 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.

Publication date

2017-02-01

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