Empowering functional genomics of An. gambiae through inversion genotyping

在非洲，冈比亚按蚊是主要媒介，其传播和传播的强度 寄生虫和媒介种群的耐药性对疟疾控制构成了重大挑战。新杀虫剂和 迫切需要新的矢量控制策略来补充现有的矢量控制策略。基础基因组学 基于矢量的新策略的资源最近可用于AN。冈比亚亚目。合在一起，它们使 详细的种群基因组学和全基因组关联研究(GWAS)旨在了解 流行病学重要性状的遗传基础。然而，一个。冈比亚亚纲具有高度多态 染色体倒置。未能解释倒置可能会误导整个群体的遗传和基因组 反转和流行病学相关特征之间的关联研究和模糊的关系。还没有 尽管基因组技术发展迅速，但细胞遗传学确定倒位状态是唯一的方法 目前可用。从基因组重新测序数据中，倒置状态并不明显，因为等位基因被映射到 它们在参考基因组上的位置，而不是它们的实际物理位置。不幸的是，细胞遗传学 分析是不切实际的，甚至是令人望而却步的。为了解决这一差距，R01的中心目标是开发和 验证计算和分子倒置基因分型方法，使现代评估 反转与流行病学相关特征之间的关联。为此，我们提出三点建议。 具体目标：(1)建立一种适用于SNP基因数据的计算核型分析方法。我们的 基于现有ag1000G序列的两个倒置的初步数据表明，存在 可以作为替代方向的替代标记。利用野外采集的已知蚊子 在ag1000g的测序支持下，我们将在更广泛的地理范围内验证这些结果。 采样并将其扩展到其他反转。(2)发展一种适用的分子核型分析方法 没有测序。利用现有的核型样本电池，我们将开发出简单而快速的 分子检测消除了在可变断点区域进行聚合酶链式反应的需要，并且 任何实验室都可以访问。(3)评估染色体组型与疟疾重要参数之间的关系。 利用现有的AN。冈比亚样本，我们将应用我们的计算和分子核型方法 测试核型、室内休息行为和寄生虫率之间的关系。总而言之，这些工具 将使绘制和监测病媒种群的流行病学重要特征的努力成为可能。

In Africa, where Anopheles gambiae is the primary vector, the intensity of transmission and the spread of resistance in parasite and vector populations pose major challenges to malaria control. New insecticides and novel vector control strategies complementary to existing ones are badly needed. Foundational genomic resources for novel vector-based strategies are newly available for An. gambiae. Together, they enable detailed population genomics and genome-wide association studies (GWAS) aimed at understanding the genetic basis of epidemiologically important traits. However, An. gambiae is highly polymorphic for chromosomal inversions. Failing to account for inversions can mislead population genetic and genome-wide association studies and obscure relationships between inversions and epidemiologically relevant traits. Yet despite rapid advances in genome technology, cytogenetic determination of inversion status is the only method currently available. Inversion status is not obvious from genome re-sequencing data, as alleles are mapped to their position on a reference genome and not to their actual physical locations. Unfortunately, cytogenetic analysis is impractical or even prohibitive. Addressing this gap, the central goal of this R01 is to develop and validate computational and molecular inversion genotyping approaches, enabling a modern assessment of the association between inversions and epidemiologically relevant traits. Toward this end, we propose three specific Aims: (1) Develop a computational karyotyping approach applicable to SNP genotype data. Our preliminary data for two inversions, based on existing Ag1000G sequences, indicates that there are SNPs that can serve as surrogate markers for alternative orientations. Using field-collected mosquitoes of known karyotype and with sequencing support from Ag1000G, we will validate these results on wider geographic samples and extend them to additional inversions. (2) Develop a molecular karyotyping approach applicable without sequencing. Using an existing battery of karyotyped samples, we will develop simple and rapid molecular assays that eliminate the need to PCR amplify across variable breakpoint regions, and are accessible to any lab. (3) Assess the association between karyotype and malariologically important parameters. Leveraging existing An. gambiae samples, we will apply our computational and molecular karyotyping methods to test for a relationship between karyotype, indoor resting behavior, and parasite rate. Together, these tools will empower efforts to map and monitor epidemiologically important traits in vector populations.