EDGE: Expanding the functional genetics toolkit to link genes to phenotypes in cichlid fish

基因组是如何为身体的正常发育和功能编码信息的？这个重要的问题在技术上和伦理上都难以在人类中解决，并且需要额外的动物模型来支持获得这一基本理解。慈鲷是一个很好的系统，因为这些物种在解剖、生理和行为上有很大的差异。由于最近对它们的基因组进行了测序，因此可以确定动物特征与基因序列之间的相关性。然而，基因序列和功能之间的因果关系必须直接测试，以获得有意义的理解。对这些联系进行因果测试需要开发和部署新技术。该基金支持的工作开发了获取慈鲷胚胎和修改基因序列的工具，使研究人员能够了解特定基因如何控制身体的形状和功能。鉴于慈鲷和人类拥有大部分相同的基因，这项工作应该能让我们对基因在健康和疾病中的作用有新的认识。这项工作还为来自不同背景的本科生研究提供了许多直接参与研究事业的机会，它包括为来自其他机构的研究人员举办的讲习班，使他们能够在自己的研究项目中采用新的协议和工具。2000种慈鲷鱼在形态、生理和行为上表现出惊人的各种表型。全基因组扫描已将这些特征映射到候选遗传位点。然而，基因功能的直接测试需要功能性基因操作，而此类实验的技术落后。CRISPR/Cas已经成为一种强有力的基因编辑工具，并且已经在两个鲷鱼物种中进行了原理验证实验。这项拨款的工作包括开发实验管道，以便在更广泛的慈鲷物种中进行基因编辑实验。具体来说，已经确定了支持慈鲷生殖周期和受精卵衍生的激素治疗方案，并开发了允许通过创建功能丧失突变和将物种特异性序列变体插入其他物种来修改各种物种基因的方案。通过这些努力获得的见解和知识通过研讨会、网站和出版物与更广泛的社区分享。总之，新开发的方法将支持遗传变异及其对形式和功能的影响的研究。该奖项反映了美国国家科学基金会的法定使命，并通过使用基金会的知识价值和更广泛的影响审查标准进行评估，被认为值得支持。

How does the genome encode the information for proper development and function of the body? This important question is technically and ethically difficult to address in humans, and there is a need for additional animal models that can support gaining this foundational understanding. The cichlid fish are an excellent system to use because these species have wide variation in anatomy, physiology, and behavior. Because their genomes have been sequenced recently, correlations between animal features and gene sequences can be determined. However, the causal links between gene sequence and function must be tested directly to gain meaningful understanding. Causal testing of the links requires the development and deployment of new technologies. The work supported by this grant develops the tools to obtain cichlid embryos and modify gene sequences, enabling researchers to understand how specific genes control the form and function of the body. Given that cichlids and humans share most of the same genes, this work should allow new insights into how genes function in health and disease. The work also allows many opportunities for undergraduate researches from diverse backgrounds to participate directly in the research enterprise, and it includes workshops for investigators from other institutions to enable them to adopt the new protocols and tools in their own research programs.The 2000 species of cichlid fish exhibit a stunning variety of phenotypes in morphology, physiology, and behavior. Genome-wide scans have mapped these traits to candidate genetic loci. However, functional genetic manipulations are required for direct tests of gene function, and technology for such experiments has lagged behind. CRISPR/Cas has emerged as a potent gene editing tool, and proof-of-principle experiments have been performed in two cichlid species. The work of this grant involves development of experimental pipelines that enable gene editing experiments in a wider variety of cichlid species. Specifically, hormonal treatment regimens that support the reproductive cycle of cichlids and derivation of fertilized eggs are identified, and protocols that permit the modification of genes in a variety of species, through creation of loss-of-function mutations and the insertion of species-specific sequence variants into other species, are developed. Insights and knowledge obtained through these efforts are shared with the broader community through workshops, websites, and publications. Together, the newly developed approaches will support the study of genetic variation and its effects on form and function.This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.