Genomic Science Program
U.S. Department of Energy | Office of Science | Biological and Environmental Research Program

Phenotypic and Molecular Characterization of Nitrogen-Responsive Genes in Sorghum

Authors:

Jinliang Yang1* (jinliang.yang@unl.edu), Zhen Wang1, Thomas Clemente1, Yufeng Ge1, James Schnable1, Sanzhen Liu2, Kankshita Swaminathan3, Jane Grimwood3, Avinash Sreedasyam3

Institutions:

1University of Nebraska–Lincoln; 2Kansas State University; 3HudsonAlpha Institute for Biotechnology

Goals

This project will phenotypically and molecularly characterize the 33 existing CRISPR-Cas9-edited N-responsive genes. Subsequently, the research team will conduct gene editing for the three glutamate-like receptor (GLR) genes in a cluster and GLR-related genes in the N network and generate a population-scale RNA-seq dataset to cross-validate edited genes and identify new gene candidates for further characterization.

Abstract

The inefficient use of inorganic nitrogen (N) fertilizer in crop production increases ecological burdens including biodiversity loss, N leaching into groundwater, and greenhouse gas emissions (e.g., nitrous oxide) that contribute to global warming. Moreover, inorganic N fertilizer stands out as one of the most expensive and energy-intensive agricultural inputs, particularly for sorghum cultivation.

Enhancing sorghum’s nitrogen use efficiency (NUE) will not only boost its profitability as an energy crop but also alleviate the environmental burdens associated with its cultivation. To understand the biological basis of this essential macronutrient and ultimately enhance NUE, extensive research has been conducted to reveal processes for N assimilation, transport, and reallocation. Studies in model plant species have identified specialized nitrate transporters, enabling N mobilization processes to be well characterized. However, N sensing, signaling, and downstream regulatory pathways in crop species remain largely unclear.

Previously, this research team has generated resources and accumulated extensive experiences in N-related research on sorghum. The team conducted transcriptomic analysis using data collected from sorghum genotype Tx430 grown in different N levels and edited 33 N-responsive genes using CRISPR-Cas9. The current project has developed a high-throughput phenotyping pipeline to extract N-related phenotypes from the state-of-the-art LemnaTec Greenhouse.

During the summer of 2023, the team collected a variety of manually measured and imagery-based data on the Sorghum Association Panel (SAP; n=330) under both high N and low N field conditions. Data included traits related to root morphology and root-associated microbial characteristics. Additionally, the team conducted RNA-seq on three-week-old seedlings from SAP grown in high N and low N greenhouse conditions. Currently, the research team is developing statistical models and conducting empirical analyses to integrate multi-omics data and provide valuable biological insights. Notably, population genetics and comparative genomics analyses have suggested that a cluster of glutamate-like receptor (GLR) genes may function as cellular N sensors, activating Ca2+-dependent N signaling—an essential step in the N pathway.

Funding Information

This project is supported by the DOE under award no. DE-SC0023138.