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

在过去的20年里，植物基因组研究提供了对作物遗传途径的深刻理解，这些遗传途径是作物重要经济过程的基础。然而，就像在大多数生物体中一样，许多植物基因都有“备份”副本，即代表遗传冗余的副本。人们对这种裁员对工厂改进工作的影响知之甚少。这种知识的缺乏使遗传资源的有效利用复杂化。这个项目将集中在一组已知的信号基因上，以了解植物遗传冗余的基本原理。因此，它将促进植物基因组生物学的一个基本领域的知识。该项目的成果将有可能通过提供新的知识和工具来发展高产作物，从而改善美国的农业。该项目还将培训不同层次的一些年轻科学家，并促进植物基因组学的宣传和教育。项目人员将开发新的教学模块，以突出植物基因组学在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群体的学校和研讨会上介绍这些模块。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，在那里将利用开放参观和实验室访问来教育这些群体关于植物基因组研究在农业中的重要性。该项目询问整个植物界信号通路的冗余是如何演变的。它将通过测试植物中的遗传冗余由响应性备份电路(RBC)控制的假设，建立基因组水平的理解，将基因和途径与复杂的表型联系起来。需要检验的第二个假设是，可以使用弱启动子等位基因来调节和利用信号网络输出。将使用三个物种，模型系统拟南芥，以快速检验假设，以及番茄和玉米，不同的和重要的经济作物物种。遗传冗余是将基因与植物表型联系起来的一个主要限制因素，该项目将使用富含亮氨酸重复序列的受体的一个子集，如激酶及其预测的配体作为模型网络。通过系统发育分析选择的信号基因将被用于基因组编辑技术的敲除(CRISPR/Cas9)。然后，全基因组转录图谱将被用来推断冗余机制，并反复设计新的基因敲除，以解决干扰冗余并列基因的影响。在每个阶段，将使用仔细的表型分析来了解不同发育阶段的多个基因敲除对作物生产力的影响。基因调控序列(启动子)中的冗余也将通过开发一种可推广的CRISPR/Cas9多重敲除策略来解决，以在基因调控序列区域进行半随机突变。这些品系将被集体筛选，并代表了一种新的植物诱变方法，有可能产生新的遗传多样性，并恢复具有增强产量性状的弱等位基因。

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.