Transcriptomic Study Identifies lncRNAs in Kiwifruit Defense Against Botrytis cinerea

Kiwifruit, a popular and nutritious fruit grown worldwide, faces a serious threat from a fungus called Botrytis cinerea, which causes gray mold disease. Botrytis cinerea is a necrotrophic pathogen, meaning it kills plant cells before feeding on the dead tissue.

This destructive pathogen rots the fruit during storage, leading to significant economic losses for farmers and exporters, with studies estimating up to 50% yield loss in severe cases.

Traditional methods like chemical fungicides are becoming less effective because the fungus is developing resistance, a phenomenon where repeated chemical use makes pathogens less responsive to treatment. As a result, scientists are urgently searching new ways to protect crops.

A groundbreaking study published in 2025 in BMC Plant Biology offers hope by uncovering how hidden parts of the kiwifruit’s genetic code—specifically, long non-coding RNAs (lncRNAs)—help the plant fight back against this deadly fungus.

The Role of LncRNAs in Kiwifruit Disease Resistance

To understand the research, it’s important to first know what lncRNAs are. Long non-coding RNAs (lncRNAs) are RNA molecules longer than 200 nucleotides that do not produce proteins.

Unlike messenger RNA (mRNA), which carries instructions for building proteins, lncRNAs act as managers inside cells, controlling how other genes are used.

For example, they can turn genes on or off, help cells respond to stress, or even strengthen the plant’s physical barriers against invaders.

In recent years, scientists have discovered that lncRNAs play critical roles in helping plants survive droughts, infections, and other challenges. However, their role in kiwifruit’s defense against gray mold was unknown until this study.

Genetic Pathways Behind Kiwifruit’s Botrytis Cinerea Resistance

The research team focused on a kiwifruit variety called ‘Hongyang,’ which is commonly grown in China. They infected healthy fruits with Botrytis cinerea spores and monitored changes in the fruit’s genetic activity over three days.

By analyzing thousands of RNA molecules through RNA sequencing a technique that reads the order of nucleotides in RNA to study gene expression they identified 126 key lncRNAs that became more or less active during the infection.

These lncRNAs were found to control important processes like hormone signaling, sugar metabolism, and the plant’s ability to detect pathogens.

The study’s detailed methods included advanced RNA sequencing, rigorous data filtering, and validation through lab experiments like quantitative reverse transcription PCR (qRT-PCR), a method that measures RNA levels to confirm gene activity, ensuring the results were accurate and reliable.

LncRNAs and Hormone Signaling in Kiwifruit Immunity

One of the most important findings was how lncRNAs influence phytohormones, which are plant-produced chemicals that regulate growth and stress responses.

For instance, the study showed that certain lncRNAs reduce the activity of auxin, a hormone that usually promotes cell growth and development.

By slowing down auxin signaling, the plant might redirect energy from growth to defense.

Similarly, lncRNAs suppressed abscisic acid (ABA), another stress-related hormone involved in closing stomata (tiny pores on leaves) during drought. The downregulation of ABA suggests the plant prioritizes other defense strategies during fungal attack.

On the other hand, ethylene—a hormone known to boost disease resistance and fruit ripening—was strongly activated by lncRNAs. Ethylene helps thicken cell walls and produce antimicrobial compounds, creating a stronger barrier against the fungus.

Kiwifruit’s Hidden Genetic Defense Against Botrytis Cinerea

The study also revealed how lncRNAs affect the MAPK (Mitogen-Activated Protein Kinase) signaling pathway, a system plants use to detect threats like pathogens and trigger immune responses. When Botrytis cinerea attacks, this pathway activates genes that fight the pathogen.

However, the researchers found that lncRNAs fine-tune this response to prevent overreaction. For example, some lncRNAs dialed down genes like 

MEKK1/7 and MPK3/6, which encode enzymes involved in detecting invaders.

This careful balancing act ensures the plant doesn’t waste resources or harm itself with excessive inflammation. Additionally, lncRNAs helped manage reactive oxygen species (ROS)—highly reactive molecules like hydrogen peroxide that kill pathogens.

But can damage the plant’s own cells if levels become too high. By controlling genes like RbohD (Respiratory Burst Oxidase Homolog D) and OXI1 (Oxidative Signal-Inducible 1), lncRNAs kept ROS in check, protecting the plant’s cells.

Kiwifruit’s Metabolic Shifts During Botrytis Cinerea Attack

Another critical discovery involved changes in the kiwifruit’s carbohydrate metabolism, the process by which the plant converts sugars and starches into energy. When infected, the fruit altered how it processes these molecules.

• lncRNAs increased the production of ADP-glucose, a molecule used to build starch, which serves as an energy reserve.
• At the same time, they reduced enzymes like α-amylase and β-amylase, which break starch into simpler sugars.

This shift likely helps the plant store energy for defense rather than using it for immediate growth. Additionally, lncRNAs slowed down enzymes such as endoglucanase and β-glucosidase, which degrade cellulose and 1,3-β-glucan—key components of plant cell walls.

By inhibiting these enzymes, the plant strengthened its cell walls, acting like a physical shield against fungal invasion.

How Kiwifruit Uses LncRNAs to Strengthen Cell Walls

The researchers also explored how lncRNAs interact with genes in two ways: cis-regulation and trans-regulation. In cis-regulation, lncRNAs control genes located nearby on the same chromosome, often within 100,000 base pairs.

For example, lncRNAs near genes involved in cell wall construction boosted processes like lignin deposition, making cells tougher.

In trans-regulation, lncRNAs influence genes far away on different chromosomes, affecting broader functions like protein synthesis and energy production.

These dual mechanisms show how lncRNAs coordinate multiple defense strategies simultaneously, acting as both local managers and global coordinators.

Future of Crop Protection Using Kiwifruit LncRNAs

The implications of this research are vast. For farmers, identifying these lncRNAs could lead to new tools for breeding disease-resistant kiwifruit.

By selecting plants with naturally active defense-related lncRNAs—a process called marker-assisted selection—breeders could develop varieties that withstand gray mold without chemicals.

Scientists might also create sprays containing synthetic lncRNAs to boost immunity in vulnerable crops, similar to how vaccines work in humans.

Beyond kiwifruit, similar mechanisms could protect other fruits like strawberries, grapes, and tomatoes, which face fungal threats like Botrytis and powdery mildew.