A bioinformatic pipeline for identifying informative SNP panels for parentage assignment from RADseq data.
A bioinformatic pipeline for identifying informative SNP panels for parentage assignment from RADseq data.
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DOI：
10.1111/1755-0998.12910
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发表时间：
2018-11
影响因子：
7.7
通讯作者：
Waits LP
中科院分区：
文献类型：
--
作者：
Andrews KR;Adams JR;Cassirer EF;Plowright RK;Gardner C;Dwire M;Hohenlohe PA;Waits LP
高通量测序技术的发展极大地增加了单核苷酸多态性（SNPs）在遗传学领域的应用，但大多数野生种群的亲本研究仍然依赖于微卫星。我们开发了一个生物信息学管道，用于从限制性内切位点相关DNA测序（RADseq）数据中识别SNP面板，为亲子分析提供信息。该管道包括有或没有参考基因组的分析选项，并提供了最大化基因分型准确性和选择具有高统计能力的非连锁位点集的方法。我们在墨西哥灰狼和大角羊的小种群上测试了这一管道，由于遗传多样性低，并且存在许多密切相关的个体，因此亲子分析预计将具有挑战性。我们比较了使用或不使用参考基因组生成的SNP面板之间以及SNP和微卫星之间的亲本分析结果。对于墨西哥灰狼，我们对来自单一队列的30只幼崽进行了亲子分析，其中来自64%可能的母亲和53%可能的父亲的样本可用，并且可以估计亲子分配的准确性，因为根据现场数据先验地知道父母的真实身份。对于大角羊，我们对来自五个队列的39只羔羊进行了母性分析，其中77%的可能母亲被抽样，但父母的真实身份未知。有参考基因组和没有参考基因组的分析产生的SNP面板对墨西哥灰狼的亲子鉴定准确率为约95%，优于微卫星的78%准确率。大角羊的所有SNP面板的母性分配完全一致，与微卫星分配的74.4%一致。当墨西哥灰狼和大角羊分别使用284个SNP和142个SNP时，亲本分析的准确性和一致性没有降低，表明我们的管道可以用于相对较少位点的亲本分析的SNP基因分型分析。
The development of high-throughput sequencing technologies is dramatically increasing the use of single nucleotide polymorphisms (SNPs) across the field of genetics, but most parentage studies of wild populations still rely on microsatellites. We developed a bioinformatic pipeline for identifying SNP panels that are informative for parentage analysis from restriction site-associated DNA sequencing (RADseq) data. This pipeline includes options for analysis with or without a reference genome, and provides methods to maximize genotyping accuracy and select sets of unlinked loci that have high statistical power. We test this pipeline on small populations of Mexican gray wolf and bighorn sheep, for which parentage analyses are expected to be challenging due to low genetic diversity and the presence of many closely related individuals. We compare the results of parentage analysis across SNP panels generated with or without the use of a reference genome, and between SNPs and microsatellites. For Mexican gray wolf, we conducted parentage analyses for 30 pups from a single cohort where samples were available from 64% of possible mothers and 53% of possible fathers, and the accuracy of parentage assignments could be estimated because true identities of parents were known a priori based on field data. For bighorn sheep, we conducted maternity analyses for 39 lambs from five cohorts where 77% of possible mothers were sampled, but true identities of parents were unknown. Analyses with and without a reference genome produced SNP panels with >95% parentage assignment accuracy for Mexican gray wolf, outperforming microsatellites at 78% accuracy. Maternity assignments were completely consistent across all SNP panels for the bighorn sheep, and were 74.4% consistent with assignments from microsatellites. Accuracy and consistency of parentage analysis were not reduced when using as few as 284 SNPs for Mexican gray wolf and 142 SNPs for bighorn sheep, indicating our pipeline can be used to develop SNP genotyping assays for parentage analysis with relatively small numbers of loci.
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影响因子：
3.7
作者：
Baird NA;Etter PD;Atwood TS;Currey MC;Shiver AL;Lewis ZA;Selker EU;Cresko WA;Johnson EA
通讯作者：
Johnson EA
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4.9
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通讯作者：
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影响因子：
4.1
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通讯作者：
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影响因子：
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作者：
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通讯作者：
Pusey, AE
影响因子：
3.3
作者：
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通讯作者：
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