RESEARCH-PGR: Dissecting the Genomic Architecture of Functional Redundancy to Modulate Meristem Homeostasis and Crop Yields

RESEARCH-PGR：剖析功能冗余的基因组结构以调节分生组织稳态和作物产量

• 批准号: 1546837
• 负责人: David Jackson
• 金额: $ 461.68万
• 依托单位: Cold Spring Harbor Laboratory
• 依托单位国家: 美国
• 项目类别: Continuing Grant
• 财政年份: 2016
• 资助国家: 美国
• 起止时间: 2016-09-01 至 2021-08-31
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=1546837&HistoricalAwards=false
• 关键词: RESEARCH; PGR; Dissecting; Genomic; Architecture

Plant genome research over the past 20 years has provided a deep understanding of genetic pathways that underlie economically important processes in crop plants. However, as in most organisms, many plant genes have "backup" copies, or duplicates representing genetic redundancy. Very little is known about the effect of such redundancy on plant improvement efforts. This lack of knowledge complicates the efficient use of genetic resources. This project will focus on a known group of signaling genes to understand the basic principles that underlie genetic redundancy in plants. It will therefore advance knowledge in a fundamental area of plant genome biology. Outcomes from this project will have the potential to bring improvements to US agriculture by providing new knowledge and tools to develop high yielding crops. The project will also train a number of young scientists at various levels, as well as promote outreach and education in plant genomics. Project personnel will develop new teaching modules to highlight the importance of plant genomics in crop domestication, and will present these in schools and workshops that target female students and underrepresented minorities. Outreach activities will also target rural farming communities in the New York, Massachusetts and North Carolina areas, where open house displays and lab visits will be used to educate these groups about the importance of plant genomics research in agriculture.This project asks how redundancy in signaling pathways has evolved across the plant kingdom. It will develop a genome-level understanding to link genes and pathways to complex phenotypes, by testing the hypothesis that genetic redundancy in plants is controlled by Responsive Backup Circuits (RBCs). A second hypothesis to be tested is that signaling network outputs can be modulated and exploited using weak promoter alleles. Three species will be used, the model system Arabidopsis, to rapidly test hypotheses, and tomato and maize, divergent and economically important crop species. Genetic redundancy is a major limitation to the ability to link genes to phenotypes in plants, and this project will use a subset of Leucine Rich Repeat Receptor Like Kinases and their predicted ligands as a model network. Signaling genes selected by phylogenetic analysis will be targeted for knockouts using genome editing technologies (CRISPR/Cas9). Genome-wide transcript profiling will then be used to deduce redundancy mechanisms and reiteratively design new knockouts to address the effect of disrupting redundant paralogs. At each stage, careful phenotyping will be used to understand the effect of multiple gene knockouts at different developmental stages relevant to crop productivity. Redundancy in gene regulatory sequences (promoters) will also be addressed by developing a generalizable CRISPR/Cas9 multiplex knockout strategy to make semi-random mutations across gene regulatory sequence regions. These lines will be screened en masse, and represent a new approach to mutagenesis in plants, with a potential to generate new genetic diversity, and to recover weak alleles with enhanced yield traits.

在过去的20年中，植物基因组研究对作物植物中具有经济重要过程的基础的遗传途径有了深刻的了解。但是，与大多数生物体一样，许多植物基因具有“备份”副本，或代表遗传冗余的重复。关于这种冗余对植物改善工作的影响知之甚少。缺乏知识使有效利用遗传资源复杂化。该项目将集中在已知的一组信号基因上，以了解植物中遗传冗余的基本原理。因此，它将在植物基因组生物学的基本领域提高知识。该项目的成果将有可能通过提供新知识和工具来发展高产作物，从而为美国农业带来改善。该项目还将在各个层面上培训许多年轻科学家，并促进植物基因组学领域的外展和教育。项目人员将开发新的教学模块，以强调植物基因组学在农作物驯化中的重要性，并将在针对女学生和代表性不足的少数民族的学校和讲习班中展示这些模块。外展活动还将针对纽约，马萨诸塞州和北卡​​罗来纳州地区的农村农业社区，在那里开放式展览和实验室就诊将教育这些群体有关植物基因组学研究在农业中的重要性。该项目询问在整个植物王国中，信号途径中的冗余已经发展。它将通过检验以下假设，即植物中的遗传冗余是由响应式备用电路（RBC）控制的，它将发展基因组水平的理解，以将基因和途径与复杂表型联系起来。要测试的第二个假设是，可以使用弱启动子等位基因调制和利用信号网络输出。将使用三种物种，即模型系统拟南芥，快速检验假设，以及番茄和玉米，分歧且经济上重要的农作物物种。遗传冗余是将基因与植物中的表型联系起来的能力的主要限制，该项目将使用富含亮氨酸的重复受体（如激酶）及其预测的配体作为模型网络的子集。通过系统发育分析选择的信号基因将使用基因组编辑技术（CRISPR/CAS9）来敲除。然后，全基因组的转录物分析将用于推断冗余机制，并重复设计新的敲除，以解决破坏冗余旁系同源物的效果。在每个阶段，仔细的表型将用于了解与作物生产力相关的不同发育阶段的多个基因敲除的效果。基因调节序列（启动子）的冗余也将通过开发可推广的CRISPR/CAS9多重敲除策略来解决基因调节序列区域的半随机突变。这些线将被大批筛选，并代表植物中诱变的新方法，具有产生新的遗传多样性，并具有增强的产量特征的弱等位基因。

项目成果

Engineering Quantitative Trait Variation for Crop Improvement by Genome Editing

• DOI: 10.1016/j.cell.2017.08.030
• 发表时间: 2017-10-05
• 期刊: CELL
• 影响因子: 64.5
• 作者: Rodriguez-Leal, Daniel;Lemmon, Zachary H.;Lippman, Zachary B.
• 通讯作者: Lippman, Zachary B.