IOS EDGE: Expanding the toolkit for functional genetics in threespine stickleback to place genomics into its natural context

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'To learn about human biology, researchers use non-human species as stand-ins, or 'models'. Because no single species is a perfect model of human biology, science benefits from a broad portfolio of model organisms, each with its own relevance to human biology. This project will create new methods to study an emerging model, the threespine stickleback (Gasterosteus aculeatus). This small fish offers an important advantage over traditional lab models. Since the glaciers retreated in the northern hemisphere ~12,000 years ago, many beneficial genetic variants have survived in thousands of distinct natural populations. Unlike laboratory genetic screens, which reveal mutations in genes causing abnormal development or physiology, these natural variants reveal biological innovations: new ways of resisting parasites, for instance. A large community of researchers (100 labs) now studies stickleback to understand behavior, development, and immunology. The research team has identified candidate genes affecting important traits like brain and bone development, but require tools to experimentally alter gene function for confirmation. This grant will support a team of five researchers developing new gene-editing methods for stickleback. Because stickleback are easily studied in the wild as well, this research team can take the unique step of linking laboratory genetics back to gene function in their natural environment. The researchers will train undergraduates, graduate students, and researchers from around the world, via new online communities and in-person courses. The project will also build infrastructure (a stock center) to perpetuate research-useful populations and provide research experiences for Native American students and communities, exposing them to scientific studies of local native animals.Stickleback are a leading model in organismal biology for several reasons: 1. Marine populations independently colonized many diverse coastal watersheds, yielding exceptional phenotypic variation from a massively replicated natural experiment. 2. Ancestral alleles persist in modern oceanic populations, enabling genetic mapping of adaptive traits in known ecological contexts. 3. Stickleback are easy to breed and manipulate in large numbers in the lab and in nature. 4. Published genomes, transcriptomes, and microbiomes provide references for robust candidate gene identification and probe development. Consequently, hundreds of researchers study the genetics of stickleback adaptation. However, this research is largely confined to correlative approaches: QTL mapping, divergence mapping, and association studies. It remains rare for researchers to validate suspected candidate genes using experimental gene manipulation. To enable functional genomic studies of stickleback, this project will refine methods for gene editing. First, the research team will use transcriptomics and ChIP-Seq to improve genome annotation, to better locate candidate genes. Second, they will develop methods for more efficient gene editing with CRISPR-Cas9 delivered via embryo microinjection or cell culture transfection, or using viral-mediated gene transfer. Finally, the team will construct a stock center where natural and transgenic lines can be maintained and shipped to users, enabling studies on standardized genetic backgrounds spanning sticklebacks? natural diversity. The work will be disseminated via webinars, methods blogs, cross training of students, and a large lab course. This will provide research training to undergraduates, graduate students, postdocs, and colleagues around the world, as well as Native American communities in Alaska.