RESEARCH-PGR: Enhancer discovery and design in agriculturally important crop plants

随着气候变化威胁全球粮食安全，该团队将利用其在技术开发、植物基因调控和基因组学方面的专业知识，提供必要的工具，使作物能够更好地承受环境压力。决定植物对环境的反应和发育过程中的变化的基因表达模式由称为转录增强子的DNA序列指导。在植物中，只有不到20种植物增强子被表征，但了解它们对于作物工程和育种至关重要。利用新的基因组规模技术，该团队将在玉米、高粱、水稻和小麦等谷类作物中发现大量的转录增强子，特别是那些驱动基因表达以应对高温和低温胁迫的增强子。然后，研究小组将比较这些物种之间以及每个物种的不同品种之间的热或冷特异性增强子，确定它们之间的差异与热和冷胁迫下植物性能的差异有关，并确定与这些增强子结合以影响基因表达的蛋白质因子。在验证这些增强子序列在耐热性和耐寒性中的功能之后，将鉴定它们的有益的天然变体用于作物改良工作。此外，该团队将向这些候选者中引入突变，以尝试和改进它们，并对增强子片段进行大规模并行功能测定，以开发具有明确优势和特异性的合成增强子工具包，用于未来的作物工程。该项目将广泛影响植物研究、作物工程和育种;通过有针对性的外展工作，包括本科生暑期研究实习，也将影响未来植物基因组学者的教育。该项目将应用ATAC-和STARR-seq的新组合，发现大量活跃驱动玉米和高粱转录的调控元件。对水稻和小麦的有限研究将允许进行物种一级的比较。该团队将专注于转录增强子，特别是驱动基因调节以应对热和冷应激的增强子。有了增强子序列，研究小组将表征玉米和高粱之间保守或分歧的条件特异性增强子，确定表型相关的增强子变异，并通过基序搜索识别结合这些增强子的转录因子。高粱和玉米增强子的深入比较将产生对基因组复制后基因组进化的见解，以及对高粱更强的胁迫耐受性的见解。该团队还将对增强子片段进行诱变和大规模并行功能测定，以便通过计算获得具有确定强度和特异性的合成增强子，用于作物工程。通过作物工程确保粮食供应具有巨大的公众利益，追求这一目标使该团队能够有效地接触到不同的群体和学生。该推广计划是一个由本科植物基因组学学者组成的分布式网络，通过为四名学生提供额外资金，建立在合作伙伴网站现有计划的成功基础上。参与者将能够在另一个地点参加该计划的第二年，以获得新的技能并体验不同的研究环境。该奖项反映了NSF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。

With climate change threatening global food security, this team will use its expertise in technology development, plant gene regulation and genomics to provide essential tools to make crops better able to withstand environmental stresses. Patterns of gene expression that dictate plant responses to the environment and changes during development are directed by DNA sequences called transcriptional enhancers. In plants, fewer than 20 plant enhancers have ever been characterized yet understanding them is crucial for crop engineering and breeding. Using novel, genome-scale technology, this team will discover large numbers of transcriptional enhancers in the cereal crops maize, sorghum, rice and wheat, particularly those driving gene expression in response to heat and cold stress. The team will then compare heat- or cold-specific enhancers among these species and among different varieties of each species, determine what differences among them are associated with differences in plant performance under heat and cold stress, and identify the protein factors that bind to these enhancers to influence gene expression. After validating the function of these enhancer sequences in heat and cold tolerance, beneficial natural variants of them will be identified for crop improvement efforts. In addition, the team will introduce mutations into these candidates to try and improve them and carry out massively parallel functional assays of enhancer fragments to develop a toolkit of synthetic enhancers with defined strengths and specificities for future crop engineering. This project broadly impacts plant research, crop engineering and breeding; it also impacts the education of future plant genome scholars through targeted outreach efforts, including summer research internships for undergraduate students.This project will apply a novel combination of ATAC- and STARR-seq to discover large numbers of regulatory elements that actively drive transcription in maize and sorghum. Limited studies in rice and wheat will allow for species-level comparisons. The team will focus on transcriptional enhancers, in particular enhancers that drive gene regulation in response to heat and cold stress. With enhancer sequences in hand, the team will characterize condition-specific enhancers that are conserved or diverged between maize and sorghum, determine phenotype-associated enhancer variation, and identify the transcription factors binding these enhancers through motif searches. In-depth comparisons of sorghum and maize enhancers will yield insights into genome evolution after genome duplication in addition to insights into sorghum's greater stress tolerance. The team will also carry out mutagenesis and massively parallel functional assays of enhancer fragments in order to computationally derive synthetic enhancers of defined strength and specificity for crop engineering. Securing food supplies through crop engineering holds immense public interest and the pursuit of this goal enables this team to effectively reach out to diverse groups and students. The outreach program, a distributed network of undergraduate plant genomics scholars, builds on the success of existing programs at partner sites by providing additional funding for four students. Participants will be able to join the program for a second year at another site to acquire new skills and to experience a different research environment.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.