Learn more about this 2026 Madison Trust Project.
Developing a Novel Genome Editing Research Program to Study Plant Disease Resistance at JMU
Presenters
Dr. Ning Zhang | zhang6nx@jmu.edu Assistant Professor, Biology, College of Science and Mathematics
Abstract
Bacterial diseases can cause serious losses in crop yields, but boosting a plant’s natural defenses often comes with a cost - such as stunted growth, poor reproduction, or even plant death. This happens because many of the genes that help plants fight disease are also essential for their normal growth and development. To solve this problem, our project takes a new approach to improving plant resistance. Instead of changing the parts of genes that control what they do, we focus on the “switches” that control when and how strongly those genes are turned on - the regulatory regions of the DNA, known as promoters. By using advanced genome editing tools like CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats), we will fine-tune these genetic switches in tomato plants to strengthen their natural defenses against bacterial infections without hurting their growth. This work will not only enhance tomato resilience but also provide valuable insights for future crop improvement efforts, helping farmers grow healthier plants with fewer chemical inputs, supporting agricultural sustainability and food security.
Project
As the global population continues to grow and the climate becomes more unpredictable, developing resilient crops is essential to ensure enough food for everyone. By 2050, the world’s population is expected to reach nearly 9.7 billion, meaning agriculture must produce significantly higher yields to meet demand. Yet an average of 20-40% crop yields is lost annually due to diseases caused by pathogens and pests (Savary et al., 2019). While pesticides can help control these diseases, they often harm the environment and pose risks to human health. Developing crops that can naturally resist diseases offers a safer, more sustainable solution. We are a newly established plant biotechnology lab in the Department of Biology at JMU. Our research focuses on understanding plant disease resistance and developing innovative biotechnological solutions to engineer crops with desirable traits - particularly enhanced resistance to bacterial pathogens. Using plant tissue culture, transformation, and advanced genome editing techniques, we modify the genetic code in tomato plants to study the genes involved in their defense responses and improve their resistance to
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bacterial pathogens.
The gene-editing tool CRISPR allows scientists to make highly precise and targeted changes in plant DNA sequences. In most cases, CRISPR has been used to completely turn off specific genes to study their function or improve traits. However, our previous research found that switching off certain key defense genes can lead to serious problems - such as dwarfism, sterility, or even plant death - making it difficult to study the function of these genes or use these genes to strengthen disease resistance (Zhang et al., 2020). To overcome this, we propose fine-tuning the activity of these important genes instead of completely turning them off. We do this by editing the “switches” that control when and how strongly a gene is activated, known as promoter regions. During my PhD research, I discovered that even a single nucleotide (the basic building block of DNA) change in a promoter, can significantly alter how much of a protein is produced (Zhang et al., 2019). This finding supports a powerful new approach: instead of changing what genes do, we can fine- tune how they are expressed to achieve better plant performance. This allows us to find the right balance between disease resistance and healthy growth. In addition, because these edits are small, precise, and could naturally occur in plants, they may not fall under strict federal regulations, making it easier to apply our findings to real-world agriculture. Our project will proceed in four main steps: 1) Identify key plant defense genes that protect against disease but cause growth issues when completely turned off. Candidate genes will be identified based on my postdoc project and other published papers. 2) Pinpoint the functional parts of promoters that control how and when these genes are activated, using specialized reporter tests and targeted DNA changes. 3) Use CRISPR tools to make precise, single-nucleotide or small-sequence edits in promoter regions that increase or decrease gene activity. Generate a series of tomato mutant plants with slightly adjusted promoter sequences through tomato tissue culture and transformation. 4) Evaluate these tomato mutants for both disease resistance and growth performance by measuring disease symptoms, morphological changes, and yield. Identify lines that show strong resistance without reduced yield or vigor. Through this fine-tuning strategy, we aim to develop tomato plants that balance strong disease resistance with robust growth and productivity, paving the way for more sustainable agriculture. Specifically, two outcomes are listed below. 1) A group of tomato plants with elevated bacterial disease resistance and healthy growth. 2) Generalizable design rules for promoter engineering that can be applied to improve other crop species.
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Benefit to JMU This project has lasting benefits for students, faculty, and the JMU community: 1) Student training and research experience: undergraduate and graduate students will gain hands-on experience in plant tissue culture and transformation, CRISPR genome editing, and other biotechnology research. They will also have opportunities to present their findings at conferences and contribute to peer- viewed publications. These will enhance their career prospects in graduate school or the biotech industry. 2) Integration with JMU courses: I also plan to integrate this project into my plant biotechnology lecture and lab beginning in Spring 2027, exposing a large group of students to real-world applications of gene editing and plant biotechnology. 3) Future funding and institutional growth: This project can potentially bring external research funding to JMU. I will use the preliminary data generated with Madison Trust support to apply for other large grants, such as NSF Career Award, USDA- NIFA, etc. 4) Regional and Global impact: Developing more resilient crops will support local and regional agriculture while contributing to global efforts for sustainable food production.
Projected Budget
Supplies and Materials:
$12,000
Personnel:
$9,000
Travel:
$3,000
Other:
$1,000
Total:
$25,000
• Supplies and Materials: Expendable materials and supplies needed for routine molecular biology, plant tissue culture/transformation, and disease assays. Examples include Gibson Assembly kits for cloning; competent bacterial cells for transformation; Taq polymerase, primers, and DNA purification kits for genotyping; plant hormones, agar, and other chemicals for tomato tissue culture and transformation; plasticware (Petri dishes, pipette tips, tubes, etc.); and Sanger sequencing and amplicon sequencing to detect mutations in the target region of tomato mutants. • Personnel: Summer salary support for one master’s student for two summers (total: 4 months). • Travel: Support for one master’s student to attend national and local conferences (registration, airfare, lodging, and meals, as allowed). • Other: Postage and printing, including shipping materials (seeds and bacterial strains) and conference poster printing.
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With partial funding, this project could achieve: 1) Identification of promoter regions in the genes of interest; 2) Construction of CRISPR vectors used for tomato transformation; 3) Tomato transformation to generate promoter-edited tomato lines; 4) Bacterial infection testing with tomato mutants; 5) Collection of growth and resistance data for wildtype and mutant plants. This support will generate essential preliminary data for high-impact external grant applications and accelerate our lab’s contribution to JMU’s mission of fostering research-driven student learning.
Project Team
Faculty: Dr. Ning Zhang, Assistant Professor, Biology, College of Science and Mathematics. Dr. Zhang has extensive experience in plant genome editing. She has utilized CRISPR/Cas9 technology to study tomato speck disease and has generated hundreds of tomato mutant lines, disrupting more than 150 immunity-associated genes in tomato.
Master’s student: I have a prospective master student for 2026 Fall. This project will serve as the primary research focus for the Master’s student.
Undergraduate students: Maya Burns, Will Royer, Noora Seidou, Gabrielle King, Nathan Koon and Kira Kang are currently working with Dr. Zhang on generating and characterizing tomato CRISPR knockout mutants to study resistance against the bacterial pathogens Pseudomonas syringae pv. tomato.
Supplemental Materials •
Zhang lab website: https://zhang6nx.wixsite.com/plantbiotech • References • Savary, S., Willocquet, L., Pethybridge, S.J., Esker, P., McRoberts, N., and Nelson, A., (2019) The global burden of pathogens and pests on major food crops. Nat Ecol Evol 3, 430-439. • Zhang, N., McHale, L.M., Finer, J.J., (2019). Changes to the core and flanking sequences of G-box elements lead to increases and decreases in gene expression in both native and synthetic soybean promoters. Plant Biotechnology Journal 17(4):724-735. • Zhang, N., Roberts, H.M., Van Eck, J. and Martin, G.B., (2020). Generation and molecular characterization of CRISPR/Cas9-induced mutations in 63 immunity-associated genes in tomato reveals specificity and a range of gene modifications. Frontiers in plant science , 11 , p.10.
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