Abstract
BackgroundThe Tasmanian devil (Sarcophilus harrisii) has undergone a recent, drastic population decline due to the highly contagious devil facial tumor disease. The tumor is one of only two naturally occurring transmissible cancers and is almost inevitably fatal. In 2006 a disease-free insurance population was established to ensure that the Tasmanian devil is protected from extinction. The insurance program is dependent upon preserving as much wild genetic diversity as possible to maximize the success of subsequent reintroductions to the wild. Accurate genotypic data is vital to the success of the program to ensure that loss of genetic diversity does not occur in captivity. Until recently, microsatellite markers have been used to study devil population genetics, however as genetic diversity is low in the devil and potentially decreasing in the captive population, a more sensitive genotyping assay is required.MethodsUtilising the devil reference genome and whole genome re-sequencing data, we have identified polymorphic regions for use in a custom genotyping assay. These regions were amplified using PCR and sequenced on the Illumina MiSeq platform to refine a set a markers to genotype the Tasmanian devil insurance population.ResultsWe have developed a set of single nucleotide polymorphic (SNP) markers, assayed by amplicon sequencing, that provide a high-throughput method for monitoring genetic diversity and assessing familial relationships among devils. To date we have used a total of 267 unique SNPs within both putatively neutral and functional loci to genotype 305 individuals in the Tasmanian devil insurance population. We have used these data to assess genetic diversity in the population as well as resolve the parentage of 21 offspring.ConclusionsOur molecular data has been incorporated with studbook management practices to provide more accurate pedigree information and to inform breeding recommendations. The assay will continue to be used to monitor the genetic diversity of the insurance population of Tasmanian devils with the aim of reducing inbreeding and maximizing success of reintroductions to the wild.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-2020-4) contains supplementary material, which is available to authorized users.
Highlights
The Tasmanian devil (Sarcophilus harrisii) has undergone a recent, drastic population decline due to the highly contagious devil facial tumor disease
The original trial run identified the need for a streamlined normalization and clean up step of Polymerase chain reaction (PCR) product prior to library preparation as there was a large difference in reads produced between samples likely due to amplification bias leading from differences in input DNA (Additional file 1: Fig S1)
single nucleotide polymorphic (SNP)-based genotyping provides an informative and reliable method of assessing genetic diversity within captive breeding programs where large numbers of individuals and relationships must be evaluated and data is to be shared across institutions
Summary
The Tasmanian devil (Sarcophilus harrisii) has undergone a recent, drastic population decline due to the highly contagious devil facial tumor disease. The Tasmanian devil (Sarcophilus harrisii) has recently suffered a severe population decline due to the recently emerged devil facial tumour disease (DFTD) [1]. The devil is listed as endangered due to the disease [9] and a captive breeding program has been established to prevent extinction of the species. This insurance program has the aim of preserving 95 % of founding genetic diversity for a period of 50 years [10]
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