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

BMC Genomics

Research Article

Katrina Morris¹  Belinda Wright¹  Denis O’Meally¹  Cali E. Willet¹  Claire Wade¹  Katherine Belov¹  Rebecca Gooley¹  Catherine E. Grueber²  Menna Jones³  Rodrigo Hamede³  Carolyn J. Hogg⁴ 

[1] University of Sydney, Faculty of Veterinary Science, Rm 303, RMC Gunn Building, 2006, Sydney, NSW, Australia;University of Sydney, Faculty of Veterinary Science, Rm 303, RMC Gunn Building, 2006, Sydney, NSW, Australia;San Diego Zoo Global, San Diego, CA, USA;University of Tasmania, School of Biological Sciences, 7001, Hobart, Tas, Australia;Zoo and Aquarium Association, 2088, Mosman, NSW, Australia;

关键词: Next-generation sequencing;    Single nucleotide polymorphism;    Captive breeding;    Population management;    Pedigree assessment;   

DOI  :  10.1186/s12864-015-2020-4

 received in 2015-05-05, accepted in 2015-10-07,  发布年份 2015

来源: Springer

【 摘 要 】

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.

【 授权许可】

CC BY   
© Wright et al. 2015