Collaborative Research: RESEARCH-PGR: Development of epigenetic editing for crop improvement

基因组编辑工具已经彻底改变了生物学。科学家们正在使用这些工具将基因与表型联系起来，产生新的表型变异，并用于多种作物改良应用。这个项目扩大了编辑农作物的可能性，包括一种编辑基因表达的方法，即所谓的“表观遗传编辑”。表观遗传学是一个广义的术语，用于描述在不直接改变DNA的情况下改变基因表达的机制。表观遗传变异可以对生物体的表型产生深远的影响，许多重要的农艺性状受到基因表达的影响。该项目的更广泛影响包括广泛传播作物植物和其他物种改良方法，以及通过与长期运行和成功的本科实习计划相结合来培训学生。表观遗传作物改良战略将补充现有的生物技术和育种战略，并可能提供机会，帮助在气候变化的情况下保持作物产量。该项目将通过有效的本科生研究经验（REU）计划直接培训下一代科学家使用这些工具。在这个项目中产生的所有资源都将可供使用。这个项目将扩大作物编辑的可能性，包括表观遗传编辑。最近有研究表明，在重要作物木薯中，通过靶向DNA甲基化MeSWEET10a来影响基因表达是可能的。MeSWEET10a通常不在叶组织中表达，但可由细菌病原体利用转录激活因子样（TAL）效应物异位诱导。MeSWEET10a启动子的从头甲基化阻断了TAL结合并导致疾病症状减轻。尽管有这些令人鼓舞的结果，表观遗传编辑仍然是一项不成熟的技术。该项目的目标是填补与表观遗传编辑的建立、维护和继承相关的特定知识空白，从而降低其他研究人员采用这一强大技术的门槛。具体来说，本提案的目标1是在其他作物物种中开发和推广表观遗传编辑工具。这项工作将利用和调整已知用于木薯的技术，在水稻和番茄上实现类似的疾病结果。目标2将扩展表观遗传编辑在作物中的应用。这包括同时靶向多个基因座、“微调”基因表达和组织特异性编辑的能力。目的3致力于表征新生胚轴的稳定性和遗传力。如果成功，生物技术的其他研究项目和应用将受益。这项工作也将为非模式植物系统表观遗传学的基础工作提供额外的起点。此外，直接编辑表观基因组的能力将赋予更大的表观遗传学领域以力量。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。

Genome editing tools have revolutionized biology. Scientists are using these tools to connect genes to phenotypes, generate novel phenotypic variation, and for diverse crop improvement applications. This project expands the possibilities for editing in crop plants to include a method for editing gene expression, so called “epigenetic editing”. Epigenetics is a broad term used to describe mechanisms that change gene expression without directly changing the DNA. Epigenetic variability can have profound impacts on an organism’s phenotype, and many important agronomic traits are influenced by gene expression. Broader impacts of the project include the wide dissemination of the method for the improvement of crop plants and other species, plus the training of students via integration with a long running and successful undergraduate internship program. Epigenetic crop improvement strategies will complement existing biotechnology and breeding strategies and may offer opportunities to help maintain crop yields in the face of climate change. This project will directly train the next generation of scientists to use these tools through an effective Research Experiences for Undergraduates (REU) program. All resources generated in this project will be made available for use.This project will expand the possibilities for editing in crop plants to include epigenetic editing. It was recently demonstrated that it is possible to affect gene expression through targeted DNA methylation at MeSWEET10a in the important crop, cassava. MeSWEET10a is not normally expressed in leaf tissue but is ectopically induced by a bacterial pathogen using a transcription activator-like (TAL) effector. De novo methylation of the MeSWEET10a promoter blocked TAL binding and led to decreased disease symptoms. Despite these encouraging results, epigenetic editing is still an immature technology. The goal of this project is to fill specific knowledge gaps related to establishment, maintenance, and inheritance of epigenetic edits and in so doing, lower the entry point for other researchers to adopt this powerful technology. Specifically, aim 1 of this proposal is to develop and distribute epigenetic editing tools in other crop species. The work will leverage and adapt the technologies known to work in cassava to accomplish similar disease outcomes in rice and tomato. Aim 2 will expand on the applications of epigenetic editing in crops. This includes the ability to target multiple loci simultaneously, “fine tune” gene expression and tissue specific editing. Aim 3 is dedicated to characterizing stability and heritability of de novo epialleles. If successful, other research projects and applications in biotechnology will benefit. This work will also provide additional jumping off points for fundamental work on epigenetics in non-model plant systems. Further, an ability to directly edit the epigenome will empower the larger field of epigenetics.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.