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

农作物为牲畜提供食物、饲料和其他基本材料。育种者正在不断改进我们的作物;然而，面对气候变化和有限的资源，迫切需要加快作物改良。DNA突变形式的自然遗传变异在作物中广泛存在，是作物改良的起始材料，但这种变异通常没有用，或者对植物生长的影响是不可预测的。控制重要产量性状的基因在植物生长期间以特定水平、位置和时间表达，并且调整这些表达程序可以提高作物生产力。基因表达是由基因周围的DNA区域控制的，这些区域被称为顺式调控元件。尽管它们具有基本的生物学意义，但这些元素的鉴定及其在农业中的应用一直具有挑战性。这项研究项目是冷泉港实验室、马萨诸塞大学阿默斯特分校和耶路撒冷希伯来大学的科学家们的合作，将使用新开发的计算算法Conservatory结合许多植物家族的现有基因组序列来预测调控元件。然后使用CRISPR基因组编辑工具修改这些元件。这些新的变异体将被测试表型的变化，从而导致产量和其他重要农艺性状的改善。该项目将培训各级年轻科学家，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推广和教育。该项目将为来自资源不足的Title I学校和历史上被排除在生命科学之外的人口群体的高中生开发新课程，以探索CRISPR在农业中的应用，包括植物转化和CRISPR编辑的动手实验室。 该项目将测试这一假设，即具有保守功能的基因是由被子植物中高度保守的顺式调控元件（克雷斯）调控的，并且表征这些克雷斯将为基因型与表型之间的联系提供新的理解水平。该项目将利用最近高质量测序基因组的爆炸，使用温室算法确定被子植物多样性的保守调控元件。温室所确定的元素的功能将通过精确的基因组编辑进行测试，重点是发育调节因子和结构特征。功能解剖将在三个不同的植物家族中的每一个中的两个物种中进行，跨越真双子叶植物和单子叶植物，这将允许在浅和深的时间尺度上评估CRE功能进化。确定的保守调控元件目录以及为测试其功能而开发的编辑策略将揭示基因表达控制的基本原则，并将加速微调作物生产力性状的创新方法。重要的是，从这个多学科项目中产生的工具，技术和基本原则将构成一个宝贵的社区资源，使不同系统和表型的工程，如生物和非生物胁迫耐受性，营养质量和共生。所有项目成果将通过长期公共数据和基因库广泛获取。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。

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.