ESTIMATION OF GENOMIC VARIATION IN CERVIDS USING CROSS-SPECIES APPLICATION OF SNP ARRAYS

• Main Authors: Nina Moravčíková, Róbert Kirchner, Veronika Šidlová, Radovan Kasarda, Anna Trakovická
• Format: Article
• Language: English
• Published: Faculty of Agrobitechnical Sciences Osijek 2015-09-01
• Series: Poljoprivreda
• Subjects: bovineSNP50 chip; fallow deer; genetic differentiation; polymorphism; red deer
• Online Access: http://poljoprivreda.pfos.hr/upload/publications/poljoprivreda-21-1-sup6.pdf
• ISSN: 1330-7142; 1848-8080

The aim of this study was to assess the utility of commercially developed genotyping array for cross-species genotyping in order to estimate the genetic variation across two species from family Cervidae. The genotyping of individuals was carried out using Illumina BovineSNP50 BeadChip. The cross-species application of bovine array was tested overall in 3 farmed and 5 free range Red deer (Cervus elaphus) and 2 free range Fallow deer (Dama dama). After applying data quality control 97.2% of SNPs localized on the chip were removed and only 1,530 autosomal markers showed polymorphism across all analysed individuals. Across all polymorphic SNPs the minor allele frequency reached the average value 0.23±0.16. The analysis based on Bayesian clustering approach clearly showed a partition of deer in two separate clusters in relation to their phylogenetical relationship. Moreover, the PCA analysis indicated that the genetic differences between farmed and free range Red deer caused the division of analysed individuals into the two subpopulations. But the results of cross-species genotyping should be present with caution, because the bovine chip developed primarily for taurine cattle breeds is not fully representative to the evolutionary changes in genome of cervids. Nevertheless, our results suggested that the utility of bovine array alongside microsatellite markers and mtDNA can be very perspective for genetic diversity estimation in deer populations.