Investigation of the genetic distances of bovids and cervids using BovineSNP50k BeadChip

Abstract

Abstract. This study presents the application of BovineSNP50 BeadChip for genome-wide screening of two taurine breeds (Bos primigenius taurus) and Zebu (Bos primigenius indicus), and two species from the family Cervidae: red deer (Cervus elaphus) and fallow deer (Dama dama). The aim of the paper was to evaluate the use of bovine array for cross-species genotyping and analyse single nucleotide polymorphism (SNP) distribution, diversity within groups of animals and genetic distance among analysed species. The number of polymorphic SNPs decreased with the increase of phylogenetic distance between species, which also reflected a decrease in call rate (from 99.54 to 61.19 %). The minor allele frequency (MAF) values were significantly different between species and ranged from 0.18 ± 15 (Zebu) to 0.26 ± 0.14 (Pinzgau). The subsequent analyses of genetic diversity were based on the polymorphic loci detected in cervids. Differences in the expected heterozygosity was low (0.06), on average 0.34. In analysed groups the F IS values were close to zero, which suggested low SNP variance within them. The value of F IT indicated homozygote excess in evaluated individuals. Analysis of molecular variance revealed that most of the variability was distributed within all individuals. Observed genetic distances within and across groups of animals suggested that taurine cattle and cervids were more distant. The study results showed that genotyping array prepared for model species can be applied not only to organisms for which was developed, but can be also successfully used in closely related and more phylogenetically divergent species.

Population-Genetic Characteristics of Domestic Reindeer of Yakutia Based on Whole-Genome SNP Analysis

“…They found that 38.7 % of loci could be genotyped, of which 5 % (n = 1068) were polymorphic. R. Kasarda et al [37] performed the study of two species from the family Cervidae: red deer (Cervus elaphus) and fallow deer (Dama dama). In total, 94.76 % SNPs were successfully genotyped and 5.24 % (1542) of them were polymorphic.…”

“…For non-model species (including reindeer), due to the lack of information about the complete genomes, the development of such kind of an SNP matrix remains unachievable [31]. However, a number of authors have demonstrated the possibility of using such commercial DNA chip (designed for domestic animals) for obtaining information about the genetic diversity and population structure of non-model species [32][33][34][35][36][37]. In 2015, we published the first evidence of the successful application of DNA chips developed for cattle (Illumina Bo-vineSNP50 BeadChip) and domestic sheep (Illumina OvineSNP50 BeadChip) to study the reindeer [38].…”

“…In total, 22807 SNPs passed through the quality control and 512 of them were polymorphic and were used for further analysis. The small number of polymorphic markers is due to the fact that with increasing phylogenetic distances between Bovidae and Cervidae families, the number of polymorphic SNPs decreases, which was also revealed by a drop in the total number of genotyped SNPs (call rate) from 99.54 to 61.19% (37).…”

Insight into the Current Genetic Diversity and Population Structure of Domestic Reindeer (Rangifer tarandus) in Russia

“…The final data set comprised 8357 SNPs for domestic and 8145 SNPs for wild individuals. Kasarda et al [30], using 5.3% polymorphic SNPs from the BovineSNP50 BeadChip, successfully evaluated genetic diversity and genetic relatedness among three groups of cervids. Genetic differences between farmed and free-range Red deer originating from Slovakia were observed based on 1530 polymorphic markers [48].…”

“…Despite the abundance of scientific work on the genetic biodiversity of the Cervidae family members through commercial SNP genotyping arrays [4,[29][30][31][32]-including our previous study, which attempted to determine the differences among the domestic reindeer groups within the Nenets Autonomous district, the Murmansk region, and Yakutia, as well as among wild tundra and taiga forms inhabiting Yakutia and western Taymyr-information on the genetic structure and diversity of all domestic reindeer breeds inhabiting the Russian Far North is still lacking.…”