PI: Aaron P. Smith (Louisiana State University & Agricultural and Mechanical College) Co-PI: Niranjan Baisakh (Louisiana State University Agricultural Center)
Rice is a staple crop that feeds more than two billion people worldwide. Agricultural lands used for growing rice frequently contain sub-optimal nutrient levels. Low availability of two important nutrients, phosphorus (P) and iron (Fe), commonly limits crop productivity, whereas excess Fe can cause toxicity in rice grown under flooding conditions. Because of these growth restraints, plants modulate complex responses to fluctuating P and Fe levels via genome-wide transcriptional regulatory networks that involve numerous genes. DNA is found in the nucleus wrapped around histone proteins into structures known as nucleosomes. Nucleosomes are the basic unit of chromatin, which is a fluid, higher-order assembly that is modified by many remodeling complexes. Although chromatin structure plays a substantial role in controlling gene expression, the chromatin-level mechanisms involved in regulating nutrient homeostasis in plants are not well understood. Previous work has shown that the interaction between P and Fe influences the onset of deficiency-induced stress responses. The goal of this project is to identify chromatin-level mechanisms that regulate the uptake, assimilation, and utilization of P and Fe in rice. The four specific aims of the project are to: 1) determine the physiological and transcriptional changes in rice seedlings under P and/or Fe deficiency; 2) identify nutrient deficiency-dependent changes in nucleosome positioning across the rice genome; 3) examine the role of the H2A.Z histone variant in regulating gene expression in rice genome-wide; and 4) characterize the histone post-translational modifications present at rice P and Fe homeostasis genes during nutrient deficiency. By correlating three key components of chromatin structure (i.e. nucleosome positioning, histone variant localization, and histone modifications) with gene expression profiles, the regulatory mechanisms that modulate P and Fe deficiency responses will be revealed. Identifying these chromatin-level mechanisms will provide opportunities for developing crops with improved nutrient use-efficiency, significantly improving U.S. and global agriculture. All sequence data generated during this project will be made available to the public through the Gene Expression Omnibus database (GEO:www.ncbi.nlm.nih.gov/geo/).
This project will contribute to the education of graduate and undergraduate students. The investigators have research groups diverse in ethnicity and gender, and will continue to foster involvement of underrepresented groups in research by mentoring students through programs available through LSU, including the Pre-doctoral Scholars Institute and Noyce Tigers Research Internship. Other planned activities include K-12 outreach through the annual Super Science Saturday event, and training of student-teacher pairs from area high schools in hands-on research for two weeks during the summer.