Genetics of Vector Populations: Aedes aegypi

病媒种群遗传学：埃及伊蚊

• 批准号: 8479317
• 负责人: Jeffrey R POWELL
• 金额: $ 39.12万
• 依托单位: YALE UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2012
• 资助国家: 美国
• 起止时间: 2012-06-15 至 2017-05-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8479317
• 关键词: Aedes; Africa; Animals; Behavior; Bite; Breeding; Cities; Collection; Culicidae; Data; Data Set; Dengue; Development; Ecology; Event; Exhibits; Fright; Genetic; Genetic Population Study; Genetic Variation; Genetic Vectors; Genome; Genomics; Genotype; Goals; Grant; Hand; Human; Human Genetics; Individual; Laboratories; Length; Linkage Disequilibrium; Literature; Methodology; Methods; Morphologic artifacts; Mutation; Nature; Nuclear; Pattern; Phase; Population; Population Genetics; Population Heterogeneity; Population Sizes; Process; Relative (related person); Repetitive Sequence; Sample Size; Sampling; Single Nucleotide Polymorphism; Source; Techniques; Technology; Testing; Time; Urban Population; Validation; Variant; Virus Diseases; Work; Yellow Fever; arbovirus disease; base; cost; cost effective; design; expectation; forest; genome wide association study; insight; interest; population based; vector

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.

描述（由申请人提供）：我们在来自世界各地的 16 个埃及伊蚊样本及其近亲伊蚊的样本中鉴定出了超过 40,000 个单核苷酸多态性 (SNP)。马斯卡伦西斯。这是使用一种可有效识别 SNP（RAD 标签）的技术来完成的，但该方法不适用于常规基因分型。我们建议基于这些已识别的 SNP 开发一种 SNP 芯片，该芯片可以以时间和成本有效的方式常规应用于可靠的基因分型。我们自己的兴趣在于群体遗传学和血统水平，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；所有数据都将公开。该项目的第一部分是人口芯片的开发。这将分三个步骤进行：(1) 从 >40,000 个可用的 SNP 中，识别出约 5,000 个在物种分布中变异最大的 SNP 以及 SNP 芯片上可靠的基因型。 (2) 从这 5,000 个中，使用理论分析来识别约 750 个捕获完整数据集的种群/祖先信息的样本。 (2)进行杂交以确认这750个的孟德尔(单拷贝、核)性质，预计至少500个将是孟德尔的并构成群体SNP芯片的基础。该项目的第二部分是该芯片的应用。提出了四个项目：（1）进行全球群体遗传学研究，以确定世界各地群体的遗传多样性、模式和相关性；为此，我们已经收集了一些藏品。 (2) 随着时间的推移研究五个生态和地理上不同的种群，以确定伊蚊的遗传稳定性。埃及伊蚊种群数量以及有效种群规模。 (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来自不同实验室的分离株之间的同质性或异质性。 (4) 西非最近殖民城市中心的基因型种群，并将它们与附近可能是“驯化”事件来源的森林种群进行比较；独立的复制案例将使我们能够识别平行的遗传变化，从而深入了解驯化过程的遗传本质。