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

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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.