当前位置: X-MOL 学术BMC Genet. › 论文详情
Our official English website, www.x-mol.net, welcomes your feedback! (Note: you will need to create a separate account there.)
Identification and evaluation of a core microsatellite panel for use in white-tailed deer (Odocoileus virginianus).
BMC Genetics Pub Date : 2019-06-06 , DOI: 10.1186/s12863-019-0750-z
William L Miller 1, 2 , Jessie Edson 3 , Peter Pietrandrea 4 , Cassandra Miller-Butterworth 4 , W David Walter 5
Affiliation  

BACKGROUND Microsatellite loci have been used extensively over the past two decades to study the genetic characteristics of non-model species. The ease of microsatellite development and ability to adapt markers from related species has led to the proliferation of available markers for many commonly studied species. Because it is often infeasible to genotype individuals across all available loci, researchers generally rely on subsets of markers. Marker choice can bias inferences made using disparate suites of loci. This has been a primary motivation for efforts to identify uniform marker panels. Here, we use the geographic distribution of previous studies to identify microsatellite loci for white-tailed deer (Odocoileus virginianus) with the potential for widespread use, and we evaluate the effectiveness of this panel in a portion of the range where few previous studies have been conducted. The purpose was to consolidate the numerous genetic resources for this species into a manageable panel and to provide a uniform methodology that improves comparisons between past and future studies. RESULTS We reviewed microsatellite panels from 58 previous or ongoing projects and identified 106 candidate loci. We developed a multiplex protocol and evaluated the efficacy of 17 of the most commonly used loci using 720 DNA samples collected from the Mid-Atlantic region of the United States of America. Amplification errors were detected in six of these loci. The 11 remaining loci were highly polymorphic, exhibited low frequencies of null alleles, and were easy to interpret with the aid of allele binning software. CONCLUSIONS The development of broadly-applicable, core microsatellite panels has the potential to improve repeatability and comparative ability for commonly studied species. The properties of the consolidated 11 microsatellite panel suggest that they are applicable for many common research objectives for white-tailed deer. The geographic distribution of previous studies using these markers provides a greater degree of confidence regarding the robustness to common sources of error related to amplification anomalies, such as null alleles, relative to loci with more limited use. While this does not replace further evaluation of genotyping errors, it does provide a common platform that benefits future research studies.

中文翻译:

鉴定和评估用于白尾鹿(Odocoileus virginianus)的核心微卫星面板。

背景技术在过去的二十年中,微卫星基因座已被广泛用于研究非模式物种的遗传特征。微卫星发展的容易程度和适应相关物种标记的能力导致许多常用物种的可用标记激增。由于在所有可用基因座上对个体进行基因分型通常是不可行的,因此研究人员通常依赖于标记子集。标记的选择可能会使使用不同基因座套件的推论产生偏差。这一直是识别统一标记面板的主要动机。在这里,我们使用先前研究的地理分布来确定白尾鹿(Odocoileus virginianus)的微卫星基因座,并具有广泛使用的潜力,并且我们在以前很少进行研究的部分范围内评估了该小组的有效性。目的是将该物种的众多遗传资源整合到一个易于管理的小组中,并提供一种统一的方法,以改进过去和未来研究之间的比较。结果我们审查了来自58个先前或正在进行的项目的微卫星研究小组,确定了106个候选基因座。我们开发了一种多重协议,并使用了从美国中大西洋地区收集的720个DNA样品评估了17个最常用基因座的功效。在这些基因座中的六个中检测到扩增错误。剩下的11个位点是高度多态的,表现出无效等位基因的频率较低,并且易于通过等位基因分箱软件进行解释。结论广泛应用的核心微卫星面板的发展具有改善常见物种的可重复性和比较能力的潜力。合并的11个微卫星面板的属性表明,它们可用于白尾鹿的许多常见研究目标。相对于使用有限的基因座,先前使用这些标记物进行的研究的地理分布提供了与扩增异常(例如无效等位基因)相关的常见错误源的鲁棒性更高的置信度。尽管这不能代替对基因分型错误的进一步评估,但它确实提供了有益于未来研究的通用平台。核心微卫星面板有可能提高通常研究物种的可重复性和比较能力。合并的11个微卫星面板的属性表明,它们可用于白尾鹿的许多常见研究目标。相对于使用较为有限的基因座,使用这些标记的先前研究的地理分布对于与扩增异常(例如无效等位基因)有关的常见错误源的鲁棒性提供了更高的可信度。尽管这不能代替对基因分型错误的进一步评估,但它确实提供了有益于未来研究的通用平台。核心微卫星面板有可能提高通常研究物种的可重复性和比较能力。合并的11个微卫星面板的属性表明,它们可用于白尾鹿的许多常见研究目标。相对于使用有限的基因座,先前使用这些标记物进行的研究的地理分布提供了与扩增异常(例如无效等位基因)相关的常见错误源的鲁棒性更高的置信度。尽管这不能代替对基因分型错误的进一步评估,但它确实提供了有益于未来研究的通用平台。相对于使用有限的基因座,先前使用这些标记物进行的研究的地理分布提供了与扩增异常(例如无效等位基因)相关的常见错误源的鲁棒性更高的置信度。尽管这不能代替对基因分型错误的进一步评估,但它确实提供了有益于未来研究的通用平台。相对于使用较为有限的基因座,使用这些标记的先前研究的地理分布对于与扩增异常(例如无效等位基因)有关的常见错误源的鲁棒性提供了更高的可信度。尽管这不能代替对基因分型错误的进一步评估,但它确实提供了有益于未来研究的通用平台。
更新日期:2019-06-06
down
wechat
bug