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 FIS values were close to zero, which suggested low SNP variance within them. The value of FIT 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.
Highlights
The families Bovidae and Cervidae belong to the Pecorans, the most important group of large terrestrial herbivorous mammals
The phylogenetic relationships of the majority of groups have been estimated using morphological data from extant and fossil taxa; the use of molecular markers and genomic data provide an unparalleled tool for the evaluation of genetic relationships among organisms and has exploded in recent years (Marcot, 2007; Bibi, 2013)
The number of successfully genotyped single nucleotide polymorphism (SNP) in least 90 % of individuals ranged from 98 % to 53.85 %
Summary
The families Bovidae and Cervidae belong to the Pecorans (higher ruminants, order Artiodactyls), the most important group of large terrestrial herbivorous mammals. The richness in species and geographical spread of ruminants are reasons for the general interest in much phylogenetic and diversity research (Hassanin and Douzery, 2003; Fernández and Vrba, 2005; Decker et al, 2009). Bovidae and Cervidae represent the greatest degree of taxonomic and geographical diversity among the ruminants, with 48 bovid genera in Africa, most of Eurasia, and North America and 16 cervid general from mainly North and South America and Eurasia (Hassanin and Douzery, 2003). The sequencing of complete mitochondrial DNA (mtDNA) of many species enabled the determination of the evolutionary history and phylogenetic relationship in more detail and promotes research on molecular evolution of these animal groups. More than 500 complete mtDNA genomes from vertebrates have been determined, including livestock and free-living
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