Comparative genetics of selected Southern African Mountain zebra (Equus zebra zebra and Equus zebra hartmannae) populations

Abstract

In recent years, South African conservation officials have noted the appearance of tumour like growths, very similar to equine sarcoids, in some Cape mountain zebra (CMZ) populations. In domestic horses, a genetic predisposition for this bovine papillomavirus-induced tumour is suspected. This investigation studied the levels of heterozygosity and population parameters such as inbreeding, within the tumour-affected populations. In comparison, CMZ populations with few or no tumours and Hartmann’s mountain zebras (HMZ) from Namibia were analysed using similar techniques. This study utilised dinucleotide repeat genetic markers called microsatellites, originally isolated from domestic horse (Equus caballus), to amplify related segments in the mountain zebras. Sixteen such fluorescent-labelled markers were amplified using polymerase chain reactions run in multiplexes. A commercial genetic analyser was used to detect the amplified markers and resulting data was analysed using STRand software. Marker visualisation and genotyping was completed using specialised open-source software. Fifteen loci were repeatedly amplified with clarity within both mountain zebra subspecies. The lowest heterozygosity and allele polymorphism levels were detected in sarcoid-tumour affected populations. All CMZ populations analysed were highly related and substructured. By comparison, Hartmann’s zebras were found to have highest levels of genetic diversity and polymorphism. The highest levels of inbreeding were found within the tumour-affected populations. High levels of heterozygote deficit found in CMZ populations, for the loci investigated, resulted in nonsignificant results when inbreeding values were analysed. This study indicates that the sarcoid tumour has been expressed in populations with the highest levels of consanguinity. The sarcoid tumour is a disease that is considered mutifactorial in aetiology and therefore other parameters such as immune status of tumour-affected populations and associated environmental variables warrant investigation. This study has simplified the archival and genotyping of individual mountain zebras. The study concludes that, among the populations tested, sarcoid tumours have been expressed in CMZ with highest levels of inbreeding. The establishment of a genetic database, incorporating information from polymorphic microsatellite markers, would assist in the conservation management of isolated CMZ populations by providing the information necessary to increase allelic diversity.