RESEARCH-PGR/NSF-BSF: Identification and Functional Dissection of Shared Cis-Regulatory Elements Controlling Quantitative Trait Variation Across Angiosperms

RESEARCH-PGR/NSF-BSF：控制被子植物数量性状变异的共享顺式调控元件的识别和功能剖析

• 批准号: 2129189
• 负责人: David Jackson
• 金额: $ 400万
• 依托单位: Cold Spring Harbor Laboratory
• 依托单位国家: 美国
• 项目类别: Standard Grant
• 财政年份: 2021
• 资助国家: 美国
• 起止时间: 2021-09-01 至 2025-08-31
• 项目状态: 未结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=2129189&HistoricalAwards=false
• 关键词: RESEARCH; PGR; NSF; BSF; Identification

Crop plants provide food, feed for livestock, and other essential materials. Breeders are continuously improving our crops; however, there is an urgent need to accelerate crop improvement in the face of climate change and limited resources. Natural genetic variation in the form of DNA mutations is widespread in crops, and is the starting material for their improvement, but such variation is often not useful or is unpredictable in its effect on plant growth. Genes that control important yield traits are expressed at specific levels, locations and times during plant growth, and tuning these expression programs may enhance crop productivity. Gene expression is controlled by regions of DNA surrounding genes known as cis-regulatory elements. Despite their fundamental biological significance, the identification of such elements and their use in agriculture has been challenging. This research project, a collaborative effort between scientists at Cold Spring Harbor Laboratory, the University of Massachusetts-Amherst, and the Hebrew University of Jerusalem, will predict regulatory elements using a newly developed computational algorithm, Conservatory, combined with existing genome sequences from many plant families. These elements will then be modified using CRISPR genome editing tools. These new variants will be tested for changes in phenotype that lead to improvements in yield and other important agronomic traits. The project will train young scientists at various levels, as well as promote outreach and education in plant genomics in partnership with Genspace, a Community Biology lab in Brooklyn, NY. The project will develop a new curriculum for high school students from under-resourced Title I schools and demographic groups historically excluded from the life sciences to explore applications of CRISPR in agriculture, including hands-on labs in plant transformation and CRISPR editing. This project will test the hypothesis that genes with conserved functions are regulated by deeply conserved cis-regulatory elements (CREs) across angiosperms, and that characterizing these CREs will provide a new level of understanding in linking genotype to phenotype. The project will exploit the recent explosion in high-quality sequenced genomes to identify conserved regulatory elements across angiosperm diversity using the Conservatory algorithm. The functions of the elements identified by Conservatory will be tested by precise genome editing, with a focus on developmental regulators and architectural traits. Functional dissections will be performed in two species in each of three diverse plant families, spanning eudicots and monocots, which will allow the assessment of CRE functional evolution over shallow and deep timescales. The catalog of conserved regulatory elements identified, and the editing strategies developed to test their functions, will reveal fundamental principles governing gene expression control and will accelerate innovative approaches to fine-tune crop productivity traits. Critically, the tools, techniques and fundamental principles emerging from this multi-disciplinary project will comprise a valuable community resource, enabling the engineering of diverse systems and phenotypes, such as biotic and abiotic stress tolerance, nutritional quality, and symbiosis. All project outcomes will be widely accessible through long-term public data and genetic repositories.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.

作物工厂提供食物，用于牲畜的饲料和其他必要材料。育种者不断改善我们的农作物。但是，面对气候变化和有限的资源，迫切需要加快作物改善。 DNA突变形式的自然遗传变异在农作物中普遍存在，并且是其改善的起始材料，但是这种变异通常没有用或对其对植物生长的影响不可预测。控制重要产量特征的基因在植物生长过程中的特定水平，位置和时间表达，并调整这些表达程序可能会提高作物生产力。基因表达受周围基因的DNA区域的控制，称为顺式调节元件。尽管它们具有基本的生物学意义，但这种元素及其在农业中的使用仍然具有挑战性。这项研究项目是冷泉港实验室，马萨诸塞州 - 阿默斯特大学和耶路撒冷希伯来大学的科学家之间的合作努力，将使用新开发的计算算法（音乐学院）与许多植物家族的现有基因组序列相结合来预测监管元素。然后，将使用CRISPR基因组编辑工具对这些元素进行修改。这些新变体将测试表型的变化，从而改善产量和其他重要的农艺性状。该项目将在各个层面培训年轻科学家，并与纽约布鲁克林的社区生物学实验室Genspace合作促进植物基因组学的外展和教育。该项目将为来自资源不足的I学校和人口群体的高中生开发新的课程，历史上排除了生命科学，以探索CRISPR在农业中的应用，包括在植物转型和CRISPR编辑中的动手实验室。 该项目将检验以下假设：具有保守功能的基因受被子植物的深度保守的顺式调节元件（CRE）调节，并且表征这些CRE的基因将在将基因型与表型联系起来时提供新的理解水平。该项目将利用高质量测序基因组中最近的爆炸式爆炸，以使用温室算法识别跨被子植物多样性的保守调节元素。音乐学院确定的元素的功能将通过精确的基因组编辑来测试，重点是发展调节剂和建筑特征。功能解剖将在三个不同的植物家族中的两个物种中进行，跨越了Eudicot和Monocots，这将允许评估CRE功能进化，超过浅层和深度时间标准。确定的保守监管元素的目录以及为测试其功能而开发的编辑策略将揭示有关基因表达控制的基本原理，并将加速创新方法来微调作物生产力特征。至关重要的是，这个多学科项目中出现的工具，技术和基本原则将包括有价值的社区资源，从而使各种系统和表型的工程（例如生物和非生物压力耐受性，营养质量和共生型）能够构成。所有项目成果将通过长期的公共数据和遗传存储库都广泛访问。该奖项反映了NSF的法定任务，并且使用基金会的知识分子优点和更广泛的影响审查标准，被认为值得通过评估来获得支持。

项目成果

Convergent selection of a WD40 protein that enhances grain yield in maize and rice

• DOI: 10.1126/science.abg7985
• 发表时间: 2022-03-25
• 期刊: SCIENCE
• 影响因子: 56.9
• 作者: Chen, Wenkang;Chen, Lu;Yang, Xiaohong
• 通讯作者: Yang, Xiaohong

The Impact of Fasciation on Maize Inflorescence Architecture

• DOI: 10.1007/s12374-021-09342-1
• 发表时间: 2022-01-04
• 期刊: JOURNAL OF PLANT BIOLOGY
• 影响因子: 2.9
• 作者: Kim, Da Eun;Jeong, Jin-hee;Je, Byoung Il
• 通讯作者: Je, Byoung Il