Genetics of Vector Populations: Aedes aegypi

描述(申请人提供)：我们已经在来自世界各地的16个埃及伊蚊样本中发现了40,000多个单核苷酸多态(SNPs)，以及它的近亲Ae。睫毛膏。这是使用一种有效地识别SNPs(RAD标签)的技术来完成的，但这种方法不适用于常规的基因分型。我们建议开发一种基于这些已识别的SNPs的SNP芯片，可以以一种既省时又经济的方式常规应用于可靠的基因分型。我们自己的兴趣在于种群、遗传学和祖先水平，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，其他团队可以根据这些数据设计用于全基因组关联研究的芯片；所有数据都将公开。该项目的第一部分是人口芯片的开发。这将通过三个步骤进行：(1)从40,000个可用的SNP中，识别出约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分型。(2)从这5,000人中，使用理论分析确定~750人，这些人捕捉了完整数据集的人口/祖先信息。(2)进行交叉，以确认这750个人的孟德尔(单拷贝，核)性质，预计至少有500人是孟德尔人，并形成种群SNP芯片的基础。项目的第二部分是该芯片的应用。提出了四个项目：(1)进行全球种群遗传学研究，以确定来自世界各地的种群的遗传多样性、模式和亲缘关系；为此，已有收集工作。(2)通过对5个生态地理不同的种群进行研究，确定Ae的遗传稳定性。埃及伊蚊种群以及有效种群数量。(3)常见实验室菌株的基因分型，以确定它们在物种遗传多样性中的位置，以及来自不同实验室的菌株之间的同质性或异质性。(4)最近在城市中心殖民的西非的基因型种群，并将它们与附近的森林种群进行比较，后者可能是“驯化”事件的来源；独立的重复病例将使我们能够识别平行的基因变化，这将使我们深入了解驯化过程的遗传本质。

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.