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

• Published in: Genetics and molecular biology 2017-01, Vol.40 (1), p.84-92
• Main Authors: Labuschagne, Christiaan, Dalton, Desiré L, Grobler, J Paul, Kotzé, Antoinette
• Format: Article
• Language: English
• Subjects: Animal Genetics; BIOCHEMISTRY & MOLECULAR BIOLOGY; Ceratotherium simum; GENETICS & HEREDITY; microsatellite markers; Single nucleotide polymorphisms; White Rhinoceros
• ISSN: 1415-4757; 1678-4685; 1678-4685
• DOI: 10.1590/1678-4685-GMB-2016-0058

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.