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.
Highlights
Breeding methods using different genetic groups or breeds are very common in animal production, which aims to explore the maximum heterosis on the crossbred individuals as well as for producing composite breeds [1]
As the introgression analyses assumes that loci are independent within populations and that the heterozygosity estimates are sensitive to various ascertainment biases when loci discovered in one breed are used to genotype other breeds [20], we considered pruning the genotypes according to the level of linkage disequilibrium to minimize the effects of these biases [21]
Canchim and MA, as well as Charolais, presented high heterozygosity for all single nucleotide polymorphism (SNP) panels when compared to Nelore and Indubrasil
Summary
Breeding methods using different genetic groups or breeds are very common in animal production, which aims to explore the maximum heterosis on the crossbred individuals as well as for producing composite breeds [1]. The genetic group called MA (resulting from mating between Charolais bulls and 1⁄2 Canchim + 1⁄2 Zebu dams) has an expected genetic makeup of 65.6% Charolais and 34.4% Zebu and is widely used by breeders in order to expand the genetic basis of Canchim [5] Several studies in this breed have considered different strategies to use the genetic groups for genetic parameter estimation [6], single-marker association [7], genotype imputation [8], and genome-wide association analyses [9]. Other composite breeds, such as Brangus and Girolando, were developed in the South and Southeast of the country, in order to increase meat and milk productivity [1,10]
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