How tomatoes cope when nitrogen runs low
image: SlDOF3.4 interacts with SlCDF4 to promote LN tolerance by modulating the expression of genes related to N assimilation and JA biosynthesis in tomato. The expression of SlDOF3.4 and SlCDF4 increases under LN conditions, and SlDOF3.4 physically interacts with SlCDF4. SlDOF3.4 and SlCDF4 directly target and activate the N-assimilation gene SlGS and the JA biosynthesis gene SlLOXD and increase their expression, thereby enhancing LN tolerance.
Credit: Horticulture Research
Nitrogen is essential for crop growth, but the heavy use of nitrogen fertilizers increases production costs and contributes to environmental pollution. A new study in tomato reveals a molecular module that helps seedlings maintain growth when nitrogen is limited. The researchers found that the genes SlDOF3.4 and SlCDF4 work together to activate nitrogen assimilation and jasmonic acid (JA) biosynthesis, two processes that support plant adaptation under low nitrogen (LN) conditions. Tomato seedlings with elevated expression of either gene developed longer roots, accumulated more biomass, and showed stronger expression of nitrogen-related genes, pointing to a promising route for improving crop performance with reduced fertilizer input.
Nitrogen (N) fertilizers are widely used to sustain crop productivity, yet a large share of applied N is not taken up by plants and can be lost to surrounding soil and water systems. Improving nitrogen use efficiency (NUE) is therefore a major goal for sustainable agriculture. Tomato (Solanum lycopersicum) is an important horticultural crop, but the transcriptional networks that help tomato seedlings cope with N limitation remain insufficiently understood. In particular, how nutrient signaling connects with hormone pathways such as jasmonic acid (JA) biosynthesis is still unclear. Based on these challenges, deeper research is needed into the molecular mechanisms that help tomato plants maintain growth under low-nitrogen conditions.
Researchers from the Faculty of Life Science and Technology and the Academy for Cell and Life Health at Kunming University of Science and Technology, together with the Yunnan Key Laboratory of Crop Wild Relatives Omics at the Kunming Institute of Botany, Chinese Academy of Sciences, reported (DOI: 10.1093/hr/uhag020) the study in Horticulture Research on January 20, 2026. The work examines how DNA-binding with one finger (DOF) transcription factors regulate tomato seedling growth under low nitrogen (LN) conditions, with a focus on the cooperative role of SlDOF3.4 and SlCDF4.
The team first showed that SlDOF3.4 expression increased under LN treatment. Tomato seedlings overexpressing SlDOF3.4 produced longer roots and higher fresh weight than wild-type plants under LN conditions. These plants also showed increased nitrate nitrogen content, higher nitrate reductase (NR) and glutamine synthetase (GS) activities, and stronger expression of nitrogen assimilation genes, including SlNR, SlNiR, SlGS, and SlGOGAT. Further experiments showed that the SlDOF3.4 protein directly binds to the promoters of SlGS and SlLOXD, a gene involved in JA biosynthesis. The researchers then identified SlCDF4 as a physical partner of SlDOF3.4 through yeast two-hybrid, luciferase complementation imaging, and co-immunoprecipitation assays. Like SlDOF3.4, SlCDF4 overexpression improved seedling growth under LN stress, while SlCDF4 knockout weakened growth. Co-expression of the two transcription factors further enhanced activation of SlGS and SlLOXD.
The authors said the findings reveal a coordinated mechanism rather than a single-gene response. Under LN conditions, the SlDOF3.4–SlCDF4 module appears to help tomato seedlings use limited nitrogen more efficiently while also strengthening the JA pathway, which supports stress adaptation. They said this connection between nutrient assimilation and hormone biosynthesis offers a clearer view of how tomato seedlings balance growth and environmental pressure. The study also suggests that DOF transcription factors may serve as useful molecular entry points for improving crop resilience under nutrient-limited conditions.
The discovery provides a potential target for breeding or engineering tomato varieties with improved NUE. By activating both nitrogen assimilation and JA-related stress responses, the SlDOF3.4–SlCDF4 module may help reduce dependence on nitrogen fertilizers while supporting early seedling growth. The work also offers a framework for testing similar regulatory modules in other crops. Future studies will be needed to determine whether this mechanism improves field performance across different tomato varieties, developmental stages, and soil nitrogen conditions. If validated beyond seedling experiments, the module could contribute to more fertilizer-efficient and environmentally sustainable horticultural production.
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References
DOI
Original Source URL
https://doi.org/10.1093/hr/uhag020
Funding information
This research was funded by the National Natural Science Foundation of China (grant 32260753, 32370405).
About Horticulture Research
Horticulture Research is an open access journal of Nanjing Agricultural University and ranked number one in the Horticulture category of the Journal Citation Reports ™ from Clarivate, 2023. The journal is committed to publishing original research articles, reviews, perspectives, comments, correspondence articles and letters to the editor related to all major horticultural plants and disciplines, including biotechnology, breeding, cellular and molecular biology, evolution, genetics, inter-species interactions, physiology, and the origination and domestication of crops.