Endonuclease V digestion for SNP discovery and marker development in South African white rhinoceros (Ceratotherium simum)

Abstract

Single nucleotide polymorphism (SNP) markers are a promising new tool that can be used to study evolutionary processes, population genetic parameters, forensic cases and parentage. However, application of SNP marker analysis to wildlife has been limited, due to the lack of available sequence data in non‐model organisms. Here, we describe a simple, rapid and cost effective method to isolate candidate SNPs in non‐model organisms using the commercially available Endonuclease V enzyme. In a first application of this method, this SNP isolation strategy resulted in the identification of 12 new SNPs for white rhinoceros (Ceratotherium simum). This species has low reported genetic variability and has suffered severe bottlenecks over the last 150 years. Developed SNP markers in white rhinoceros could be used to define the genetic mating system of this species, for forensic applications and to determine population structure and variability when other markers prove problematic.