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

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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.