The high yields typical of modern agriculture rely upon nitrogen fertilizer, yet the manufacture of synthetic nitrogen fertilizer is extremely energy intensive and represents a major cost for farmers. Additionally, fertilizer runoff produces many secondary problems such as aquatic dead zones with low oxygen contents, and reduced water quality, increasing the costs of providing safe drinking water in agricultural regions of the country. Genetic gains in nitrogen use efficiency (NUE) by plants will aid in protecting yield while mitigating both costs and negative environmental impacts associated with high rates of fertilizer application in agriculture. Through this Track-2 Focused EPSCoR Collaborations (RII Track-2 FEC) project, researchers at the HudsonAlpha Institute for Biotechnology in Alabama and the University of Nebraska will partner to conduct cutting-edge plant genomics research to better understand how nitrogen affects plant growth and development. HudsonAlpha Institute for Biotechnology will bring its biotechnology education and agricultural genomics research expertise to the collaborative project while the University of Nebraska-Lincoln will contribute its expertise in plant transformation and automated phenotyping with their state-of-the-art automated greenhouse system for imaging large plants. Researchers will collect information of how plants respond to nitrogen levels through a variety of genetic, biotechnological, and observational methods in the widely-used grain crop sorghum. Sorghum thrives in climates where many food crops struggle and is more efficient at utilizing resources such as water and nitrogen. It is an ideal crop to target for improvement to meet the predicted doubling of global food demand by 2050. In addition, the project will include an educational component, which will train and inspire students to pursue genetic and biotechnology-based research for agriculture. To accomplish this, HudsonAlpha will develop a three-week summer course for advanced high school students called the "AgriGenomics Academy." Additional activities include the recruitment of three undergraduate students who will complete summer internships at both HudsonAlpha and University of Nebraska-Lincoln to learn advanced techniques, and support for the Launching Aspiring Biotechnology Students (LABS) program, which introduces low and moderate-income students to biotechnology. The project will also mentor four early career faculty. In addition to nitrogen use efficacy, the combined efforts of these two institutions will make significant progress toward understanding the biology of other complex agronomic crop traits.
The goal of this project is to understand the role of genes in nitrogen (N) responsive co-expression networks in sorghum using a combination of genomics, biotechnology and automated phenotyping by combining the expertise at the Hudson Alpha Institute of Biotechnology and the University of Nebraska, Lincoln. We will achieve this goal through three main objectives: (i) Generate transcriptomic and phenotypic data to characterize the molecular responses of sorghum to N availability; (ii) perturb the N response by combinatorial CRISPR/Cas9 genome editing and overexpression of key genes in N network modules; and (iii) characterize plants with targeted changes in components of the N network. Genomic and transcriptomic data will be used to identify key regulatory sequences controlling genes predicted to affect nitrogen use efficiency (NUE), through effects on component traits of NUE from nitrogen assimilation through in planta metabolism. These predicted target regulatory sequences and genes will be validated in sorghum using innovative protocols for CRISPR/Cas9 genome editing to manipulate the promoters of high-priority gene targets, resulting in expression changes of these genes. Lines confirmed to carry misexpressing alleles will be characterized across development under different levels of nitrogen deficit stress using nondestructive, high throughput phenotyping techniques. Plants exhibiting phenomic changes under N deficit stress will be analyzed for variation in their gene expression networks to understand their roles in regulating sorghum's responses to N deficit stress. The outcome of this program holds great potential to expand our knowledge on N responsive gene regulatory networks and associated gene function in sorghum and closely related C4 grasses. It can also serve as a model for understanding other complex agronomic traits through gene network manipulation. This project will contribute to research infrastructure capacity building by cross-training and motivating students and post-docs to explore strategies to improve the rate of genetic gains in crops by understanding how genomic and phenomic approaches can be integrated using cutting edge genomic, molecular, and whole-plant tools.
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.
