Nitrogen, phosphorus, and potassium are fundamental macronutrients required for plant growth, metabolism, and yield formation. In modern agriculture, their inefficient use has led to excessive fertilizer inputs, causing economic losses and environmental pollution. Plants have evolved complex physiological and genetic strategies to cope with nutrient limitation, including altered biomass allocation, changes in photosynthesis, and modified root architecture. While these responses have been extensively studied in model plants and major cereal crops, vegetable crops such as tomato remain less explored at the genomic level. Given the global importance of tomato for nutrition and horticulture, addressing these knowledge gaps is essential. Based on these challenges, there is a clear need to conduct in-depth research on the genetic mechanisms underlying tomato responses to nitrogen, phosphorus, and potassium deficiency.
Researchers from Huazhong Agricultural University report new insights into how tomato plants respond to shortages of nitrogen, phosphorus, and potassium, according to a study published (DOI: 10.1093/hr/uhaf112) on April 24, 2025, in Horticulture Research. By integrating genome-wide association studies with transcriptome profiling across diverse tomato accessions, the team identified genetic loci and key response genes associated with nutrient stress. Their findings illuminate how different plant tissues coordinate physiological and molecular adjustments to maintain growth under limited nutrient availability.
The study evaluated 427 genetically diverse tomato accessions under full nutrition and nitrogen-, phosphorus-, or potassium-deficient conditions. Researchers measured 28 traits, including plant height, above- and below-ground biomass, and leaf pigment composition. Genome-wide association analyses uncovered 116 loci linked to nutrient response traits, many of which were shared across multiple deficiency conditions, indicating common regulatory pathways.
Transcriptome sequencing of shoots and roots revealed pronounced tissue-specific responses. Under nutrient stress, roots showed a greater number of differentially expressed genes than shoots, reflecting their central role in nutrient acquisition. Genes related to ion transport and inorganic nutrient uptake were strongly upregulated in below-ground tissues, while shoots enhanced pathways associated with photosynthesis and energy metabolism.
By integrating genomic and transcriptomic datasets, the researchers narrowed thousands of candidate genes to 28 high-confidence nutrient-responsive genes across 17 loci. Two genes were further validated through haplotype analysis: one associated with changes in carotenoid and chlorophyll accumulation under nitrogen deficiency, and another linked to plant growth responses under phosphorus limitation. Together, these results reveal a coordinated strategy in which tomatoes rebalance growth, metabolism, and resource allocation to cope with nutrient scarcity.
“Our findings show that tomato plants respond to nutrient limitation through a finely tuned coordination between shoots and roots,” said the study’s corresponding author. “By integrating genome-wide association studies with transcriptome analysis, we were able to pinpoint genes that play central roles in nutrient sensing and utilization. These genes not only explain visible traits such as leaf yellowing and biomass shifts, but also provide concrete molecular targets. This work lays a foundation for breeding tomato varieties that maintain productivity while using fertilizers more efficiently.”
The identification of nutrient-responsive genes and loci offers practical opportunities for crop improvement. These genetic resources can be used to breed tomato varieties with enhanced nutrient-use efficiency, reducing fertilizer requirements while maintaining yield and quality. Beyond tomato, the conserved nature of many identified pathways suggests broader relevance to other horticultural and field crops. By supporting more precise fertilizer management and environmentally friendly agricultural practices, this research contributes to sustainable food production and reduced ecological impact. Ultimately, integrating genetic insights into breeding programs could help address the dual challenges of rising food demand and environmental protection.
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References
DOI
10.1093/hr/uhaf112
Original Source URL
https://doi.org/10.1093/hr/uhaf112
Funding information
This work was supported by the National Key Research and Development Plan (2022YFF10030002); Knowledge Innovation Program of Wuhan-Shuguang Project (2022020801020228); Fundamental Research Funds for the Central Universities (2662022YJ014, 2662023PY011); the Key Project of Hubei Hongshan Laboratory (2021hszd007); Young Scientist Fostering Funds for the National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops (11909920008); China Agricultural Research System (CARS-23-A13); and the Natural Science Foundation of Hubei Province (2022CFB153).
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.