Genetic diversity, population structure, and correlations between locally adapted zebu and taurine breeds in Brazil using SNP markers

Abstract

Genetic diversity is one of the most important issues in studies on conservation of cattle breeds and endangered species. The objective of this study was to estimate the levels of genetic differentiation between locally adapted taurine (Bos taurus taurus) and zebu (Bos taurus indicus) breeds in Brazil, which were genotyped for more than 777,000 SNPs. The fixation index (F ), principal component analysis (PCA), and Bayesian clustering were estimated. The F highlighted genetic differentiation between taurine and zebu breeds. The taurine lines, Caracu and Caracu Caldeano, had significant genetic differentiation (F close to 5%) despite their recent selection for different uses (meat and milk). This genetic variability can be used for conservation of locally adapted animals, as well as for breeding programs on zebu breeds. Introgression of zebu in locally adapted breeds was identified, especially in Curraleiro Pé-Duro breed. The Gyr breed, however, had low breed purity at genomic level due to its very heterogeneous mixing pattern.

Genome-wide detection of signatures of selection in indicine and Brazilian locally adapted taurine cattle breeds using whole-genome re-sequencing data

“…Levels of introgression of indicine genes in taurine breeds described herein are consistent with previous studies on Brazilian locally adapted taurine breeds [ 16 , 17 , 19 ]. This gene flow reinforces the concept that the import of exotic breeds at the beginning of the twentieth century [ 3 ] led to the miscegenation of the locally adapted breeds due to crossbreeding practices, resulting nearly in their extinction [ 4 ].…”

“…Further, the divergence within the locally adapted cattle breeds may be a result of artificial selection events over time since the CAR cattle have been selected for milk production for the past 100 years, while CRL and PAN started recently to be artificially selected. Levels of introgression of indicine genes in taurine breeds described herein are consistent with previous studies on Brazilian locally adapted taurine breeds [16,17,19]. This gene flow reinforces the concept that the import of exotic breeds at the beginning of the twentieth century [3] led to the miscegenation of the locally adapted breeds due to crossbreeding practices, resulting nearly in their extinction [4].…”

“…A cytogenetic analysis study on the PAN cattle also revealed absorbing crosses with the indicine cattle [59]. In addition, the absence of admixture patterns in CAR individuals has been previously described by Campos et al [16] and Egito et al [21]. The homogeneity of such population most likely reflects its formation process and the objective of selection for dairy traits since 1893 [60], which may have distinguished them from other locally adapted taurine breeds when taking into consideration the genetic structure integrity.…”

“…However, despite the recent achievements in high-throughput sequencing, studies to detect positive selection in endangered Brazilian locally adapted cattle breeds are incipient. Previous studies on such breeds have mainly focused on population structure and genetic diversity using Random Amplified Polymorphic DNA (RAPD), pedigree data, microsatellite, and Single-Nucleotide Polymorphism (SNP) arrays [15][16][17][18][19].…”

Genetic material from buffalo and cattle: crucial importance in the formalization of bilateral trade between India and Brazil

“…These authors reported the most common problem as the presence of bottlenecks in the pedigree, which occurs mainly due to the intensive use of few animals as parents and the high degree of subdivision in the population. Campos et al (2017) demonstrated that the Gir breed had low racial purity at the genomic level due to its very heterogeneous mixing pattern.…”