How tomatoes team up with fungi: Scientists decode a genetic switch for smarter nutrient use
image: A proposed model showing SlDELLA-SlPIF4-SLs/PTs signaling pathway regulates AMS and phosphate uptake in tomato.
Credit: Horticulture Research
Tomato plants rely on a hidden partnership with soil fungi to absorb phosphate, an essential yet elusive nutrient in many farmlands. In a new study, scientists uncovered a genetic tug-of-war between two key proteins—SlPIF4 and SlDELLA—that controls this partnership. SlPIF4 acts as a gatekeeper, dampening the plant's ability to attract helpful fungi and absorb phosphate, while SlDELLA steps in to restrain this repression, enabling the symbiosis to flourish. The research reveals a fine-tuned genetic mechanism that could inspire new strategies to improve nutrient efficiency in crops.
Phosphorus is vital for plant growth, but in most soils, it exists in forms that are not readily accessible to crops. To cope, plants form arbuscular mycorrhizal symbiosis (AMS)—a mutually beneficial relationship with soil fungi that helps scavenge phosphate. This interaction is driven by plant-produced strigolactones (SLs), which stimulate fungal colonization, and by specific phosphate transporter genes. Despite its importance, the underlying transcriptional regulation of AMS remains poorly understood, especially how light and hormone signals converge to control this process. Due to these challenges, it is essential to investigate the molecular players orchestrating AMS in crops like tomato.
In a study (DOI: 10.1093/hr/uhae195) published on July 21, 2024, in Horticulture Research, researchers from Zhejiang University and the Chinese Academy of Agricultural Sciences revealed how the transcription factors SlPIF4 and SlDELLA coordinate AMS and phosphate uptake in tomato. Using gene editing, protein interaction assays, and chromatin analyses, the team showed that SlPIF4 represses genes critical to symbiosis, while SlDELLA counteracts its activity, facilitating root-fungal collaboration. The findings shed light on a finely balanced signaling network with major implications for sustainable agriculture.
The study began by profiling gene expression in tomato roots under phosphate-deficient conditions. They found that SlPIF4 expression and protein levels dropped significantly during fungal colonization, hinting at a suppressive role. Indeed, SlPIF4 knockout mutants showed greater fungal colonization, more developed arbuscules, and elevated phosphate transporter gene expression. In contrast, overexpressing SlPIF4 curtailed symbiosis and nutrient uptake. Protein interaction assays confirmed that SlDELLA physically binds SlPIF4, weakening its stability and transcriptional repression. Further experiments revealed that SlPIF4 directly binds the promoters of SL biosynthesis genes (SlCCD7, SlCCD8, SlMAX1) and phosphate transporters (PT4, PT5) to inhibit their expression. Application of a synthetic SL analog restored fungal colonization in SlPIF4-overexpressing plants, confirming the functional importance of this pathway. The study concludes that SlDELLA lifts the brake imposed by SlPIF4, promoting fungal alliance and phosphate acquisition.
“This study uncovers a beautifully orchestrated mechanism at the root-fungus interface,” said Dr. Yanhong Zhou, corresponding author of the paper. “We now understand that SlPIF4 acts as a repressor, while SlDELLA steps in as a molecular safeguard to ensure the plant can fully benefit from symbiosis. This balance between repression and release could be key to improving how crops use nutrients, especially under stress conditions.”
The discovery opens new doors for breeding crops with enhanced nutrient-use efficiency. By fine-tuning the SlDELLA–SlPIF4 interaction, it may be possible to engineer tomato varieties that form stronger partnerships with soil fungi and absorb phosphorus more effectively—reducing reliance on chemical fertilizers. This strategy holds particular promise for low-input or organic farming systems. Future studies could explore whether similar regulatory modules operate in other staple crops, and how environmental cues like light and drought influence the SlDELLA–SlPIF4–SLs/PTs pathway across plant species.
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References
DOI
Original Source URL
https://doi.org/10.1093/hr/uhae195
Funding information
This work was supported by the National Natural Science Foundation of China (U21A20233), the National Key Research and Development Program of China (2023YFD2300701), and the Starry Night Science Fund of Zhejiang University Shanghai Institute for Advanced Study (SN-ZJU-SIAS-0011).
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.