Table 1.
Crossing schemes to obtain animals from the Canchim breed (CA) and other genetic groups through crossings between Charolais (CH) and Zebu (ZB) animals.
Table 2.
Summary of the number of single nucleotide polymorphisms for the original dataset (50K), after genotype quality control (30K), and after linkage disequilibrium pruning (15K, 7K, and 1K).
Table 3.
Mean, standard deviation (SD), and median of the expected and observed heterozygosities in the full genotype data (30K) and in the pruned data according to linkage disequilibrium (15K, 7K, and 1K).
Table 4.
Average linkage disequilibrium for Canchim, Nelore, and Charolais animals genomic distance (Megabase pairs—Mb).
Table 5.
Genome-wide estimates of effective population size from 1 to 200 generations in the past based on estimates of linkage disequilibrium.
Fig 1.
Plot of the first 2 principal components (PC) obtained for the studied breeds.
Canchim (C1, C2, C3, and CA), MA genetic group (MA), Charolais (CH), Nelore (NE), and Indubrasil (IB) using 32,308 SNP (A), 15,286 SNP (B), 7,652 SNP (C), and 1,582 SNP (D).
Fig 2.
Plot of the first two principal components (PC) obtained for Canchim and MA animals.
The plot considered the sire origin.
Fig 3.
Breed composition per animal considering the number of populations of two (k = 2).
Analyses were carried out using ADMIXTURE (A) and STRUCTURE (B) software and Single Regression method (C) and considered 32,308 (1), 15,286 (2), 7,652 (3), and 1,582 (4) SNPs. Orange and blue represents the Bos primigenius indicus (cluster 1) and Bos primigenius taurus (cluster 2) proportions, respectively. The breeds analyzed were Canchim and MA genetic group together as one breed (CAN), Nelore (NE), Charolais (CH), and Indubrasil (IB).
Fig 4.
Breed composition per animal considering the number of populations of three (k = 3).
Analyses were carried out using ADMIXTURE (A) and STRUCTURE (B) software and Single Regression method (C) and considered 32,308 (1), 15,286 (2), 7,652 (3), and 1,582 (4) SNPs. Blue, orange, and purple represent the Nelore (cluster 1), Charolais (cluster 2), and Indubrasil (cluster 3) proportions, respectively. The breeds analyzed were Canchim and MA genetic group together as one breed (CAN), Nelore (NE), Charolais (CH), and Indubrasil (IB).
Table 6.
Comparison between the levels of introgression of breeds present in Canchim-MA animals based on pedigree and prediction methods (ADMIXTURE, STRUCTURE, and Regression).
The second cluster of each prediction method was used as a reference for the Bos primigenius taurus (Charolais) contribution. The highlighted values in bold were considered highly similar.
Table 7.
Estimates of the pairwise genetic differentiation statistic (Fst statistics) between breeds for SNPa densities of 30K, 15K, 7K, and 1K.