Development of a SNP-based assay for measuring genetic diversity in the Tasmanian devil insurance population

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.

From microsatellites to single nucleotide polymorphisms for the genetic monitoring of a critically endangered sturgeon

“…In most cases, the novel sets of SNPs outperform STRs to assess identity, parentage (Tokarska et al, 2009;Wright et al, 2015), or population structure (Glover et al, 2010;Senn et al, 2013).…”

Conservation implications of limited genetic diversity and population structure in Tasmanian devils (Sarcophilus harrisii)

“…Previous characterizations of genetic diversity and population structure in devils have focused on relatively few (<12) microsatellite loci (Jones et al 2004; Brüniche-Olsen et al 2014), MHC loci (Siddle et al 2010), mitochondrial genomes (Miller et al 2011), SNPs (Miller et al 2011; Wright et al 2015; Morris et al 2015), or whole-genome sequencing of two individuals (Miller et al 2011). Here we use Restriction-site-Associated DNA sequencing (RADseq) (Andrews et al 2016) to identify and genotype a large number of polymorphic nuclear loci at 38 localities across the species range to assess genome-wide patterns of genetic diversity and population structure.…”

Metapopulation management of an Endangered species with limited genetic diversity in the presence of disease: the Tasmanian devil Sarcophilus harrisii

“…Furthermore, these markers did not provide enough resolution for the determination of parentage in the large free‐range enclosures that house up to 20 individuals. Since 2012, work has commenced to develop new markers (data in development) and a new single nucleotide polymorphism (SNP)‐based assay to assist with determining founder relationships and to allocate parentage in the managed environmental enclosures and free‐ranging enclosures (Morris et al ., ; Wright et al ., ). Preliminary analysis has shown that some founding individuals exhibit higher relationships than others, which will have knock‐on consequences for the pedigree analysis into the future (B. Wright, pers.…”

“…Recent studies have shown there to be limited genetic diversity in populations across the State (Miller, W., et al ., ), as well as a limited diversity in the immune genes (Morris et al ., ), and that the cancer has the ability to hide from the immune system (Woods et al ., ; Siddle et al ., ). The sequencing of the complete Tasmanian devil genome in 2010 has greatly assisted in the understanding of DFTD as well as with the development of new genetic markers and genomic technologies (Murchison et al ., ; Morris et al ., ; Wright et al ., ).…”