TRTech-PGR: Comprehensive identification and functional characterization of cis-regulatory elements in legumes

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This project will produce a large, high-quality and uniform dataset that includes several, complementary types of data to address a number of outstanding questions in the economically important legume family of plants, which includes soybean, common bean and peanut. These data are highly valuable for studying diverse developmental pathways such as leaf, root and seed development, as well as the formation and function of root nodules, specialized plant structures that fix atmospheric nitrogen. The datasets will also lead to the identification of critical DNA sequences that control gene expression and will allow their more accurate characterization as well as lead to engineering of these sequences for crop improvement. The datasets and genomic resources generated here will be released publicly and immediately following quality control through an interactive website and federal data repositories. In addition to the scientific and agricultural impact, the project continues a partnership with primarily Hispanic and Native American tribal colleges in the Southwest. A workshop that presents modern-day computational biology approaches to explore DNA sequences will be hosted at Santa Fe Community College. This event serves as a conduit to engage the public and interested undergraduates in research activities and also serves as a means to recruit interns and their faculty mentors for summer training at our research institutions annually. Significant progress has been made in recent years in plant genome assembly and gene annotation. However, the systematic identification and functional characterization of plant cis-regulatory DNA elements remain a challenge, as methods that are highly effective in animals have not translated to plants. A comprehensive and well-curated data set of plant cis-regulatory DNA elements is instrumental to understanding transcriptional regulation during development and/or in response to external stimuli. In addition, cis-regulatory DNA elements are hotspots for genetic variations underlying agronomically and evolutionarily important traits. The research team has recently optimized several high-throughput methods to identify cis-regulatory elements by chromatin signatures, their bound transcription factors, their target genes by direct physical chromatin interactions, and their regulatory activities in high-throughput reporter assays. The goal of this project is to use these methods to systematically identify, analyze and functionally validate cis-regulatory elements in important legume species including Glycine max (soybean), Phaseolus vulgaris (common bean), Phaseolus coccineus (runner bean), Arachis ipaensis, Arachis duranensis and Arachis hypogea (peanut). The results will be used to address a number of mechanistic, developmental and evolutionary questions.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.