New genetic pathway discovered for boosting tomato yield without affecting quality

Tomato fruit size results from coordinated cell division, cell expansion, and tissue differentiation, influenced by hormones, transcription factors, and classical QTLs such as fw2.2, lc, and fas. While transcriptional regulators have been extensively characterized, mechanisms acting at the post-transcriptional and translational levels remain largely unknown. RNA-binding proteins are key regulators in animals and crops, yet their roles in fruit development are still insufficiently understood. The known function of SlRBP1 in leaf growth prompted questions about its function in fruit tissues. Due to these challenges, deeper research is needed to elucidate how post-transcriptional pathways, including RNA-binding proteins, regulate fruit size.

Researchers from the College of Food Science and Nutritional Engineering at China Agricultural University published new findings (DOI: 10.1093/hr/uhaf089) on 18 March 2025 in Horticulture Research, revealing a translational regulatory module controlling tomato fruit size. The team demonstrates that the RNA-binding protein SlRBP1 directly governs the translation of two key genes, SlFBA7 and SlGPIMT, which drive pericarp cell division and expansion. This work provides a mechanistic framework for understanding fruit growth at the post-transcriptional level.

The researchers began by analyzing SlRBP1 expression and observed consistently high transcript levels during early and mid-fruit development, peaking around 20 days after anthesis. To dissect its fruit-specific function without affecting vegetative tissues, they generated overexpression and artificial-miRNA silencing lines using a PPC2 promoter. Silencing SlRBP1 led to significantly smaller fruits beginning at 20 days post-anthesis, whereas overexpression did not alter size relative to wild type.

Microscopic analyses revealed that SlRBP1 suppression reduced both the number of pericarp cell layers and individual cell size, resulting in thinner fruit walls and reduced firmness. RNA-seq analysis showed downregulation of multiple genes related to cell wall organization, expansion, and division, including SlEXPA5, SlMYC2, and SlPhIP1.

Using native RNA immunoprecipitation and pull-down assays, the team identified six direct RNA targets of SlRBP1. Among these, SlFBA7 (a fructose-bisphosphate aldolase gene) and SlGPIMT (a GPI-mannosyltransferase gene) were highly expressed in developing fruits and positively correlated with fruit enlargement. Silencing either gene produced fruit size reductions indistinguishable from SlRBP1-silenced lines. Further experiments demonstrated that SlRBP1 interacts physically with the translation factor SleIF4A2, confirming that it modulates fruit growth predominantly through translational rather than transcriptional regulation.

“Our study reveals a previously unrecognized module—SlRBP1–SlFBA7/SlGPIMT—that operates at the translational level to fine-tune tomato fruit size,” noted the study’s senior author. “Fruit development has long been viewed through transcriptional and hormonal frameworks, but our findings show that translational control is equally vital. By targeting RNA-binding steps, breeders may be able to adjust fruit size with heightened precision and fewer pleiotropic effects.”

This research introduces a promising strategy for improving tomato yield by manipulating translational regulation rather than altering hormone pathways or major developmental genes. Because fruit-specific silencing of SlRBP1, SlFBA7, or SlGPIMT affects fruit size without impairing ripening, nutritional quality, or vegetative growth, the module offers a high-specificity target for breeding programs. It also demonstrates the value of tissue-specific promoters to avoid unintended whole-plant effects. The insights from this SlRBP1 module may serve as a framework for exploring similar translational pathways in other horticultural crops, expanding opportunities for precision breeding and yield optimization.

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References

DOI

10.1093/hr/uhaf089

Original Source URl

https://doi.org/10.1093/hr/uhaf089

Funding information

This work was supported by the National Key R&D Program of China (2022YFD2100100) and the National Natural Science Foundation of China (32472803).

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.