Wright Belinda, Morris Katrina, Grueber Catherine E, Willet Cali E, Gooley Rebecca, Hogg Carolyn J, O'Meally Denis, Hamede Rodrigo, Jones Menna, Wade Claire, Belov Katherine
University of Sydney, Faculty of Veterinary Science, Rm 303, RMC Gunn Building, Sydney, NSW, 2006, Australia.
San Diego Zoo Global, San Diego, CA, USA.
BMC Genomics. 2015 Oct 14;16:791. doi: 10.1186/s12864-015-2020-4.
The 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.
Utilising 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.
We 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.
Our 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.
袋獾（袋獾属哈里斯袋獾种）由于极具传染性的袋獾面部肿瘤疾病，近期种群数量急剧下降。该肿瘤是仅有的两种自然发生的可传播癌症之一，几乎不可避免地会导致死亡。2006年建立了一个无病保险种群，以确保袋獾不会灭绝。该保险计划依赖于尽可能多地保存野生遗传多样性，以最大限度地提高后续放归野外的成功率。准确的基因型数据对于该计划的成功至关重要，以确保圈养过程中不会发生遗传多样性的丧失。直到最近，微卫星标记一直用于研究袋獾种群遗传学，然而由于袋獾的遗传多样性较低且圈养种群中可能正在减少，因此需要一种更灵敏的基因分型检测方法。
利用袋獾参考基因组和全基因组重测序数据，我们确定了多态性区域，用于定制基因分型检测。使用聚合酶链反应（PCR）扩增这些区域，并在Illumina MiSeq平台上进行测序，以优化一组用于袋獾保险种群基因分型的标记。
我们开发了一组通过扩增子测序检测的单核苷酸多态性（SNP）标记，为监测袋獾的遗传多样性和评估其家族关系提供了一种高通量方法。迄今为止，我们在假定的中性和功能位点内总共使用了267个独特的SNP，对袋獾保险种群中的305个个体进行基因分型。我们利用这些数据评估了种群中的遗传多样性，并确定了21只后代的亲本。
我们的分子数据已与种畜登记簿管理实践相结合，以提供更准确的谱系信息并为育种建议提供参考。该检测将继续用于监测袋獾保险种群的遗传多样性，目的是减少近亲繁殖并最大限度地提高放归野外的成功率。
