Original scientific paper

https://doi.org/10.18047/poljo.21.1.sup.6

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

Nina Moravčíková orcid.org/0000-0003-1898-8718 ; Slovak University of Agriculture, Faculty of Agrobiology and Food Resources, Tr. A. Hlinku 2, 94976 Nitra, the Slovak Republic
Róbert Kirchner ; Slovak University of Agriculture, Faculty of Agrobiology and Food Resources, Tr. A. Hlinku 2, 94976 Nitra, the Slovak Republic
Veronika Šidlová ; Slovak University of Agriculture, Faculty of Agrobiology and Food Resources, Tr. A. Hlinku 2, 94976 Nitra, the Slovak Republic
Radovan Kasarda ; Slovak University of Agriculture, Faculty of Agrobiology and Food Resources, Tr. A. Hlinku 2, 94976 Nitra, the Slovak Republic
Anna Trakovická ; Slovak University of Agriculture, Faculty of Agrobiology and Food Resources, Tr. A. Hlinku 2, 94976 Nitra, the Slovak Republic

Abstract

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.

Keywords

bovineSNP50 chip; fallow deer; genetic differentiation; polymorphism; red deer

Hrčak ID:

150605

URI

https://hrcak.srce.hr/150605

Publication date:

2.9.2015.

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