SNP discovery and characterisation in White Rhino (Ceratotherium simum) with application to parentage assignment.

Christiaan Labuschagne,Desiré L Dalton,Antoinette Kotzé,J Paul Grobler

doi:10.1590/1678-4685-gmb-2016-0058

Abstract

The white rhino is one of the great success stories of modern wildlife conservation, growing from as few as 50-100 animals in the 1880s, to approximately 20,000 white rhinoceros remaining today. However, illegal trade in conservational rhinoceros horns is adding constant pressure on remaining populations. Captive management of ex situ populations of endangered species using molecular methods can contribute to improving the management of the species. Here we compare for the first time the utility of 33 Single Nucleotide Polymorphisms (SNPs) and nine microsatellites (MS) in isolation and in combination for assigning parentage in captive White Rhinoceros. We found that a combined dataset of SNPs and microsatellites was most informative with the highest confidence level. This study thus provided us with a useful set of SNP and MS markers for parentage and relatedness testing. Further assessment of the utility of these markers over multiple (> three) generations and the incorporation of a larger variety of relationships among individuals (e.g. half-siblings or cousins) is strongly suggested.

Highlights

Due to intensive protection and conservation efforts, the Southern white rhinoceros (Ceratotherium simum simum) have increased from a population of less than 100 at the end of the 19th century, to an estimated population of over 20,000 (Emslie, 2012)
Together with the 12 new Single Nucleotide Polymorphisms (SNPs) identified in this study, 33 SNPs are available for white rhino (Labuschagne et al, 2013, 2015)
Ascertainment bias is often a concern when using SNPs in population studies, with bias introduced by heterogeneity in the SNP discovery process, varying sample sizes or differences in sample composition leading to underestimation or overestimation of the frequency of SNPs (Nielsen and Signorovitch, 2003; Clark et al, 2005)

Summary

Introduction

Due to intensive protection and conservation efforts, the Southern white rhinoceros (Ceratotherium simum simum) have increased from a population of less than 100 at the end of the 19th century, to an estimated population of over 20,000 (Emslie, 2012). The remaining white rhino populations are being intensively managed as small isolated groups monitoring and maintaining genetic diversity is a key concern for long term survival of this species (Emslie and Brooks, 1999). Potential consequences of a reduction in genetic variability include (1) the inability of the species to adapt to changes in their environment and (2) inbreeding, whereby the expression of rare deleterious alleles may contribute to developmental, reproductive and immunological impairments (Pertoldi et al, 2007; Väli et al, 2008). In order to maintain genetic diversity and the species’ evolutionary potential, a recovery strategy can be.

Methods

Results

Conclusion