Genetics of Vector Populations: Aedes aegypi

描述（由申请人提供）：我们已经在来自世界各地的16个埃及伊蚊样本中鉴定了超过40，000个单核苷酸多态性（SNP），以及其最近亲属Ae的样本。马斯卡伦西斯这是使用一种在识别SNP（RAD标签）方面有效的技术完成的，但这种方法不适用于常规基因分型。我们建议开发一个SNP芯片的基础上，这些确定的SNP，可以应用于可靠的基因分型，在时间和成本效益的方式。我们自己的兴趣是在群体遗传学和祖先水平上，我们将专注于专门为我们的研究设计的芯片。这项工作的副产品将是更广泛的数据，其他小组可以根据这些数据设计用于全基因组关联研究的芯片;所有数据都将是可利用的。该项目的第一部分是开发人口芯片。这将通过三个步骤进行：（1）从> 40，000个可用的SNP中，鉴定约5，000个在物种分布中具有最大变异的SNP，并在SNP芯片上可靠地进行基因型分析。(2)从这5，000个数据中，使用理论分析确定约750个数据，这些数据捕获了完整数据集的人口/祖先信息。(2)进行杂交以确认这750个基因的孟德尔（单拷贝，核）性质，并期望至少500个基因是孟德尔的，并形成群体SNP芯片的基础。第二部分是该芯片的应用。提出了四个项目：（1）进行全球人口遗传学研究，以确定来自世界各地的人口的遗传多样性，模式和相关性;收集已经在手。(2)研究五个生态和地理上不同的种群，通过时间来确定Ae的遗传稳定性。埃及人口以及有效人口规模。(3)对常见实验室菌株进行基因分型，以确定它们在物种遗传多样性中的位置，以及它们在不同实验室分离株中的同质性或异质性。(4)在西非的基因型人口最近殖民城市中心，并将它们与附近的森林人口的“驯化”事件的可能来源进行比较;独立的复制的情况下，将使我们能够确定平行的遗传变化，这将使我们深入了解驯化过程的遗传性质。

DESCRIPTION (provided by applicant): We have identified more than 40,000 single nucleotide polymorphisms (SNPs) in 16 samples of Aedes aegypti from around the world, as well as a sample of its closest relative, Ae. mascarensis. This was done using a technique that is efficient in identifying SNPs (RAD-tags), but this methodology is not applicable for routine genotyping. We propose to develop a SNP chip based on these identified SNPs that can be applied routinely for reliable genotyping in a time- and cost-effective manner. Our own interests are on the population genetics and ancestry level and we will focus on a chip designed specifically for our studies. A by-product of the work will be more extensive data upon which other groups could design a chip for genome wide association studies; all data will be publically available. The first part of the project is development of the population chip. This will proceed i three steps: (1) From the >40,000 available SNPs, identify ~5,000 that have the most variation across the species' distribution and reliably genotype on SNP chips. (2) From these 5,000, use theoretical analyses to identify ~750 that capture the population/ancestry information of the complete data set. (2) Perform crosses to confirm the Mendelian (single-copy, nuclear) nature of these 750, with the expectation that at least 500 will be Mendelian and form the basis of the population SNP chip. The second part of the project is application of this chip. Four projects are proposed: (1) Perform a global population genetics study to determine the genetic diversity, patterns, and relatedness of populations from around the world; collections are already in hand for this. (2) Study five ecologically and geographically diverse populations through time to determine the genetic stability of Ae. aegypti populations as well as effective population sizes. (3) Genotype common lab strains to determine where they fit into the genetic diversity of the species and how homogeneous or heterogeneous they are among isolates from different laboratories. (4) Genotype populations in West Africa that have recently colonized urban centers and compare them to nearby sylvan populations that are the likely source of the "domestication" event; independent replicate cases will allow us to identify parallel genetic changes that would give insight into the genetic nature of the domestication process.