The RNA trio that arms pear trees against fungal attacks

In recent years, scientists have uncovered the remarkable regulatory power of long non-coding RNAs (lncRNAs) — RNA molecules once dismissed as “genetic dark matter.” These silent transcripts orchestrate gene expression and stress responses, yet their role in woody fruit trees remains largely mysterious. Pears, a vital fruit crop cultivated worldwide, face devastating losses from Botryosphaeria dothidea, the pathogen responsible for pear ring rot. Traditional breeding has struggled to provide lasting resistance due to limited molecular insight. Amid these challenges, researchers have turned their attention to the lncRNA world, aiming to uncover how these invisible regulators link nutrient dynamics to disease defense.

WUHAN, China, April 1, 2025 — In a study (DOI: 10.1093/hr/uhae359) published in Horticulture Research, a joint team from Huazhong Agricultural University and Nanjing Agricultural University revealed how a three-part RNA network empowers pear trees to fight fungal infection. The researchers identified the MSTRG.32189–PcmiR399b–PcUBC24 module as a molecular switch that governs both phosphate homeostasis and resistance to Botryosphaeria dothidea. Using transcriptome analysis, genetic transformation, and CRISPR/Cas9 editing, they demonstrated that this RNA-based system activates immune responses by tuning the plant’s phosphate metabolism and reactive oxygen species (ROS) production.

Through large-scale RNA sequencing of infected pear stems, the researchers identified 3,555 lncRNAs, including 286 that changed markedly during infection. Among them, MSTRG.32189 stood out for its dramatic downregulation in diseased tissues. Functional analyses revealed that it acts as an endogenous target mimic (eTM) — a molecular decoy that binds PcmiR399b to prevent it from silencing PcUBC24, a gene involved in phosphate regulation. When MSTRG.32189 was overexpressed in pear callus or Arabidopsis, plants became more vulnerable to fungal invasion, with lower phosphate levels and weaker ROS bursts. Conversely, boosting PcmiR399b expression had the opposite effect, enhancing phosphate uptake, ROS generation, and disease resistance. Further, PcUBC24 knockout lines showed stronger immunity and higher phosphate accumulation, confirming its negative regulatory role. Together, these experiments unveiled a sophisticated nutrient-defense circuit where MSTRG.32189 controls the balance between growth and protection — a vital trade-off for survival under pathogen stress.

“Our study reveals that non-coding RNAs are far more than passive bystanders — they are key strategists in plant defense,” said Prof. Liping Wang, corresponding author of the study. “By acting as a decoy for PcmiR399b, MSTRG.32189 helps the pear tree fine-tune its phosphate metabolism and immune activity. This discovery sheds light on how plants integrate nutrient signaling with pathogen response, providing an important framework for developing RNA-guided approaches to crop protection and resilience.”

The discovery of the MSTRG.32189–PcmiR399b–PcUBC24 module opens a new frontier in precision breeding for fruit trees. By manipulating this RNA regulatory circuit, breeders may develop pear varieties that are both nutrient-efficient and disease-resistant, reducing dependence on fertilizers and fungicides. Beyond pear cultivation, similar RNA-based mechanisms could operate in other crops, offering universal strategies for enhancing plant resilience. Future work will focus on applying genome editing and molecular breeding tools to harness this mechanism, paving the way toward sustainable orchard systems that merge nutrient management with natural immunity.

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References

DOI

10.1093/hr/uhae359

Original Source URL

https://doi.org/10.1093/hr/uhae359

Funding information

This work was financially supported by grants from the National Natural Science Foundation of China (grant 31972321) and the Earmarked Fund for China Agriculture Research System (grant CARS-28).

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, 2024. 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.