A targeted gene approach to SNP discovery in the White Rhino ( Ceratotherium simum )
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TECHNICAL NOTE
A targeted gene approach to SNP discovery in the White Rhino (Ceratotherium simum) Christiaan Labuschagne • Antoinette Kotze´ J. Paul Grobler • Desire´ L. Dalton
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Received: 6 September 2012 / Accepted: 28 September 2012 / Published online: 9 October 2012 Ó Springer Science+Business Media Dordrecht 2012
Abstract We report the characterization of 10 single nucleotide polymorphism (SNP) markers for the White Rhino (Ceratotherium simum), based on a targeted gene approach. The polymorphisms of these SNP loci were assessed using a captive population comprising 30 individuals. The minor allele frequency ranged from 0.256 to 0.413 and the observed and expected heterozygosity ranged from 0.05 to 0.37 and from 0.05 to 0.49, respectively. An understanding of genetic population structure is required to effectively formulate strategies for conservation and/or management. These SNP markers could be employed to provide estimates of parameters such as population structure, relatedness and current and historical gene flow. Keywords
SNP White Rhino Ceratotherium simum
The African White Rhino population has suffered a decline over the past 150 years as a result of overhunting, habitat destruction and poaching (Seror et al. 2002; Florescu et al. 2003). Currently the estimated population of white rhinos comprises 20,170 individuals (Emslie 2011). The trade in rhinoceros horns is a problem in many parts of the world C. Labuschagne A. Kotze´ J. Paul Grobler D. L. Dalton Department of Genetics, University of the Free State, P.O. Box 339, Bloemfontein 9300, South Africa e-mail: [email protected] C. Labuschagne Inqaba Biotechnical Industries (Pty) Ltd, P.O. Box 14356, Hatfield 0028, South Africa A. Kotze´ D. L. Dalton (&) National Zoological Gardens of South Africa, P.O. Box 754, Pretoria 0001, South Africa e-mail: [email protected]
especially in parts of Asia where the rhinoceros horns are used traditionally as material in sculptures or as drug products for medicinal purposes (Hsieh et al. 2003) adding constant pressure on remaining populations. There is thus a real need for markers that can identify the region of origin of rhino products. Genetic diversity and relatedness data for both captive and wild populations also form an important tool in successful reproductive management, population viability assessments and diversity conservation with regards to translocation of animals and establishing breeding programmes (Seror et al. 2002; Harley et al. 2005). The approach described here made use of currently available conserved primer sets designed to amplify from exons across an intervening intron. These CATS primers were designed from other vertebrate genomes to amplify mammalian genes and have been used successfully by Morin et al. (2007) to characterize 18 SNPs for the sperm whale (Physeter macrocephalus) and by Li et al. (2009) to describe 51 SNPs in the finless porpoise (Neophocaena phocaenoides). The current study is the first to present SNP markers for the white rhino. Fifteen CA
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