Collaborative Research: RESEARCH-PGR: Cis-Regulatory Dynamics of Maize Domestication and Improvement QTL at Single-Cell Resolution

Regulatory regions are essential components of plant genomes that have shaped the domestication and improvement of modern crop species. However, their identity, function and diversity remain poorly characterized, thus limiting our ability to harness their full potential for agricultural advances using induced or natural variation. In large genomes, such as those of most crops, these regions constitute only a tiny fraction of the total genomic content, which together with their variable nature, makes them difficult to detect. Overcoming these obstacles is key to accelerating breeding efforts, including those that leverage recent advances in AI and biotechnology, to enhance the national bioeconomy. This project will also contribute to the development of a biotechnology workforce through the training of a new generation of scientists proficient in the use of rapidly advancing AI, genomics and epigenomics technologies. Mapping accessible chromatin is a cost-effective strategy for capturing regulatory regions in multiple genetic backgrounds, and maize is an ideal system for mining regulatory diversity. Here innovative genomic, epigenomic and computational approaches will be used to provide new insight into cell-type-specific network variation that drives important traits in maize, a major crop species. The ability to capture distinct, empirical transcription factor binding events will provide unprecedented precision to locate the exact sequences that cause phenotypic variation, support the development of AI models that predict regulatory regions in complex crop genomes, and ultimately enable these regulatory sequences to be exploited for breeding gains and novel biotechnological applications. This knowledge will be used to functionally dissect two important QTLs for the domestication and improvement of modern maize. Overall, this collaborative project will identify differential regulatory activity that modulates important traits associated with maize domestication and improvement and will uncover new genotype-to-phenotype connections to guide the generation of novel varieties based on rational trait engineering, an approach that could also be applied to other species. 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.