Optimizing the use of shed feathers for genetic analysis
Optimizing the use of shed feathers for genetic analysis
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优化使用脱落的羽毛进行遗传分析
DOI：
10.1111/j.1471-8286.2007.02044.x
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发表时间：
2008
影响因子：
7.7
通讯作者：
Janette A. Norman
中科院分区：
文献类型：
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作者：
F. Hogan;R. Cooke;C. Burridge;Janette A. Norman
通过非侵入性遗传采样(NGS)获得的羽毛是鸟类遗传研究的宝贵DNA来源。它们可以在很大的地理范围内收集，并促进对否则将极难研究的物种的研究。这种方法的局限性在于提取的DNA的质量存在不确定性。在这里，我们研究羽毛类型、羽毛条件和DNA质量(扩增成功)之间的关系，以便为在遗传分析之前筛选样本提供一种简单、经济有效的方法。我们在澳大利亚东南部采集了637只强大的猫头鹰(Ninox Strenua)的羽毛。用聚合酶链式反应扩增线粒体DNA、ND3和核DNA、简单重复序列(Nst02)和部分CHD-1基因(P2/P8)。我们发现，羽毛状况对所有三个座位的扩增成功率都有显著影响，其中‘好’的羽毛扩增成功率更高。羽毛类型的重要性较低，所有类型的优质羽毛在所有三个座位上的成功率都很高。我们还发现，多位点基因的成功扩增依赖于起始材料的条件，并且与性连锁CHD-1基因座的成功扩增高度相关。DNA质量低的样本扩增失败的可能性更高，并且更有可能产生错误的基因类型；因此，识别DNA质量高的样本可以节省与NGS基因分析相关的大量时间和成本。因此，我们提出了一种筛选脱落羽毛的方法，以提供一个子集的样本，该样本子集将具有更大的概率包含适合于多位点基因型扩增的高质量DNA。
Shed feathers obtained by noninvasive genetic sampling (NGS) are a valuable source of DNA for genetic studies of birds. They can be collected across a large geographical range and facilitate research on species that would otherwise be extremely difficult to study. A limitation of this approach is uncertainty concerning the quality of the extracted DNA. Here we investigate the relationship between feather type, feather condition and DNA quality (amplification success) in order to provide a simple, cost‐effective method for screening samples prior to genetic analysis. We obtained 637 shed feathers of the powerful owl (Ninox strenua) from across its range in southeastern Australia. The extracted DNA was amplified using polymerase chain reaction for a range of markers including mitochondrial DNA, ND3 and nuclear DNA, a simple sequence repeat (Nst02) and a portion of the CHD‐1 gene (P2/P8). We found that feather condition significantly influenced the amplification success of all three loci, with feathers characterized as ‘good’ having greater success. Feather type was found to be of lower importance, with good quality feathers of all types consistently producing high success for all three loci. We also found that the successful amplification of multilocus genotypes was dependant on the condition of the starting material and was highly correlated with successful amplification of the sex‐linked CHD‐1 locus. Samples with low DNA quality have a higher probability of amplification failure and are more likely to produce incorrect genotypes; therefore, identifying samples with high DNA quality can save substantial time and cost associated with the genetic analysis of NGS. As a result, we propose a method for screening shed feathers in order to provide a subset of samples which will have a greater probability of containing high quality DNA suitable for the amplification of multilocus genotypes.