Development and characterization of 21 SNP markers in Manis javanica based on high-throughput sequencing

Abstract

The Sunda pangolin (Manis javanica) is a quite remarkable and distinctive mammal species with its diet specialization of ants and termites, so it plays an important role in forest protection and maintaining ecological balance. But now the wild population of M. javanica has become declining dramatically due to over hunting and it has been listed as a critically endangered species by IUCN. In order to aid the conservation of this species, we report the development of 21 novel single nucleotide polymorphism (SNP) markers based on high-throughput sequencing in this study. The results show that observed heterozygosity and expected heterozygosity varied from 0.0333 to 0.9000 and from 0.0333 to 0.5172, respectively. The polymorphic information content and the minor allele frequency ranged from 0.0320 to 0.3750 and from 0.0168 to 0.5000, respectively. Only two loci showed significant deviation from Hardy–Weinberg equilibrium, but no significant linkage disequilibrium existed after Bonferroni correction. These SNP markers may provide a valuable tool for population genetic analysis, natural resource conservation and captive breeding of M. javanica.