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使用非侵入性粪便拭子对野马进行全基因组靶向单核苷酸多态性基因分型。

Targeted genome-wide SNP genotyping in feral horses using non-invasive fecal swabs.

作者信息

Gavriliuc Stefan, Reza Salman, Jeong Chanwoori, Getachew Fitsum, McLoughlin Philip D, Poissant Jocelyn

机构信息

Department of Ecosystem and Public Health, University of Calgary, 3280 Hospital Drive, Calgary, AB T2N 4Z6 Canada.

Faculty of Veterinary Medicine, University of Calgary, Calgary, AB T2N 4Z6 Canada.

出版信息

Conserv Genet Resour. 2022;14(2):203-213. doi: 10.1007/s12686-022-01259-2. Epub 2022 Mar 16.

Abstract

UNLABELLED

The development of high-throughput sequencing has prompted a transition in wildlife genetics from using microsatellites toward sets of single nucleotide polymorphisms (SNPs). However, genotyping large numbers of targeted SNPs using non-invasive samples remains challenging due to relatively large DNA input requirements. Recently, target enrichment has emerged as a promising approach requiring little template DNA. We assessed the efficacy of Tecan Genomics' Allegro Targeted Genotyping (ATG) for generating genome-wide SNP data in feral horses using DNA isolated from fecal swabs. Total and host-specific DNA were quantified for 989 samples collected as part of a long-term individual-based study of feral horses on Sable Island, Nova Scotia, Canada, using dsDNA fluorescence and a host-specific qPCR assay, respectively. Forty-eight samples representing 44 individuals containing at least 10 ng of host DNA (ATG's recommended minimum input) were genotyped using a custom multiplex panel targeting 279 SNPs. Genotyping accuracy and consistency were assessed by contrasting ATG genotypes with those obtained from the same individuals with SNP microarrays, and from multiple samples from the same horse, respectively. 62% of swabs yielded the minimum recommended amount of host DNA for ATG. Ignoring samples that failed to amplify, ATG recovered an average of 88.8% targeted sites per sample, while genotype concordance between ATG and SNP microarrays was 98.5%. The repeatability of genotypes from the same individual approached unity with an average of 99.9%. This study demonstrates the suitability of ATG for genome-wide, non-invasive targeted SNP genotyping, and will facilitate further ecological and conservation genetics research in equids and related species.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s12686-022-01259-2.

摘要

未标注

高通量测序的发展促使野生动物遗传学从使用微卫星向单核苷酸多态性(SNP)组转变。然而,由于相对较大的DNA输入要求,使用非侵入性样本对大量靶向SNP进行基因分型仍然具有挑战性。最近,目标富集已成为一种有前景的方法,所需模板DNA很少。我们评估了帝肯基因组学公司的Allegro靶向基因分型(ATG)在使用从粪便拭子中分离的DNA对野马进行全基因组SNP数据生成方面的功效。作为对加拿大新斯科舍省黑貂岛野马进行的一项基于个体的长期研究的一部分,分别使用双链DNA荧光法和宿主特异性定量PCR测定法对收集的989个样本中的总DNA和宿主特异性DNA进行了定量。使用针对279个SNP的定制多重面板对代表44个个体的48个样本进行基因分型,这些样本含有至少10 ng的宿主DNA(ATG推荐的最低输入量)。分别通过将ATG基因型与从相同个体的SNP微阵列获得的基因型以及同一匹马的多个样本获得的基因型进行对比,评估基因分型的准确性和一致性。62%的拭子产生了ATG推荐的最低宿主DNA量。忽略未能扩增的样本,ATG每个样本平均回收88.8%的靶向位点,而ATG与SNP微阵列之间的基因型一致性为98.5%。来自同一个体的基因型重复性接近统一,平均为99.9%。这项研究证明了ATG适用于全基因组、非侵入性靶向SNP基因分型,并将促进马科动物及相关物种的进一步生态和保护遗传学研究。

补充信息

在线版本包含可在10.1007/s12686-022-01259-2获取的补充材料。

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