RESEARCH-PGR: Enhancer discovery and design in agriculturally important crop plants

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With climate change threatening global food security, this team will use its expertise in technology development, plant gene regulation and genomics to provide essential tools to make crops better able to withstand environmental stresses. Patterns of gene expression that dictate plant responses to the environment and changes during development are directed by DNA sequences called transcriptional enhancers. In plants, fewer than 20 plant enhancers have ever been characterized yet understanding them is crucial for crop engineering and breeding. Using novel, genome-scale technology, this team will discover large numbers of transcriptional enhancers in the cereal crops maize, sorghum, rice and wheat, particularly those driving gene expression in response to heat and cold stress. The team will then compare heat- or cold-specific enhancers among these species and among different varieties of each species, determine what differences among them are associated with differences in plant performance under heat and cold stress, and identify the protein factors that bind to these enhancers to influence gene expression. After validating the function of these enhancer sequences in heat and cold tolerance, beneficial natural variants of them will be identified for crop improvement efforts. In addition, the team will introduce mutations into these candidates to try and improve them and carry out massively parallel functional assays of enhancer fragments to develop a toolkit of synthetic enhancers with defined strengths and specificities for future crop engineering. This project broadly impacts plant research, crop engineering and breeding; it also impacts the education of future plant genome scholars through targeted outreach efforts, including summer research internships for undergraduate students.This project will apply a novel combination of ATAC- and STARR-seq to discover large numbers of regulatory elements that actively drive transcription in maize and sorghum. Limited studies in rice and wheat will allow for species-level comparisons. The team will focus on transcriptional enhancers, in particular enhancers that drive gene regulation in response to heat and cold stress. With enhancer sequences in hand, the team will characterize condition-specific enhancers that are conserved or diverged between maize and sorghum, determine phenotype-associated enhancer variation, and identify the transcription factors binding these enhancers through motif searches. In-depth comparisons of sorghum and maize enhancers will yield insights into genome evolution after genome duplication in addition to insights into sorghum's greater stress tolerance. The team will also carry out mutagenesis and massively parallel functional assays of enhancer fragments in order to computationally derive synthetic enhancers of defined strength and specificity for crop engineering. Securing food supplies through crop engineering holds immense public interest and the pursuit of this goal enables this team to effectively reach out to diverse groups and students. The outreach program, a distributed network of undergraduate plant genomics scholars, builds on the success of existing programs at partner sites by providing additional funding for four students. Participants will be able to join the program for a second year at another site to acquire new skills and to experience a different research environment.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.