Researchers unlock gene-editing for fungi-resistant cacao plants

Scientists in the US have leveraged gene-editing techniques to develop cacao plants (Theobroma cacao L.) resistant to the Phytophthora species — a fungal-like pathogen that causes the black pod disease. 

The innovation could potentially help resolve a significant problem for the global chocolate industry, worth over US$135 billion annually, which the Phytophthora species threatens, note the scientists. 

Nearly 20-40% of the world’s cacao beans are reportedly lost to cacao plant diseases, posing a major problem for the confectionery industry, which depends heavily on chocolate.

Researchers at Penn State used CRISPR-Cas9, a gene-editing technology that acts like “molecular scissors” to precisely modify a specific gene called TcNPR3 in cacao plants, helping the plants fight off disease. When the edited plants were infected with the fungus, the infected spots on their leaves were 42% smaller than in normal, non-edited plants.

The innovation could help cacao farmers, particularly those who have limited economic resources and “struggle to implement expensive disease-control measures,” says team leader Mark Guiltinan, professor of plant molecular biology in the College of Agricultural Sciences and the study’s first author.

“And many genetic modification approaches are met with stigma because foreign DNA is left in the final product. Our approach could solve both of those problems.”

The findings, published in Plant Biotechnology Journal, explain that the “breakthrough” method represents the first demonstration of “genome-edited, transgene-free” cacao plants and offer a promising strategy for sustainable cacao cultivation and improved farmer livelihoods.

Genes as “molecular brakes”

The team edited the TcNPR3 gene, which helps control how cacao plants defend themselves from disease in single plant cells, grew those cells into whole plants, and then crossed the edited plants with normal cacao plants. 

Some new plants (the offspring) retained the beneficial gene change but did not contain any foreign DNA, described as “clean” edits.

Mycelium of Phytophthora palmivora, which can cause cacao black pod disease, grows from an agar plug, infecting a cacao leaf 48 hours after inoculation (Image credit: Mark Guiltinan/Penn State).“Our research team targeted the gene TcNPR3 because we learned from earlier studies that it acts as a molecular ‘brake’ on the plant’s natural defense system,” explains Guiltinan. 

“NPR3 proteins — the family to which TcNPR3 belongs — are negative regulators of plant immunity, essentially preventing plants from mounting robust defenses against pathogens when they’re not immediately under attack.”

NPR3 acts as a security system that is set to “standby mode.” Disrupting the gene turns on its “high alert” mode, increasing the plant’s natural defenses and making the plant less susceptible to pathogen attacks.

Regulatory path

Guiltinan says the method sets an important regulatory example by developing cacao plants with only the desired genetic changes and no foreign DNA.

The USDA has reviewed the study’s data and officially stated that it “does not consider the genome-edited cacao lines to meet the same regulation requirements as genetically modified plants,” notes the study. 

However, the US FDA might still review the plants later, says Guiltinan.

What’s next?

With regulatory clarity removing a major barrier to adoption, the team plans to test the lines outside research stations in tropical areas as the next step.

“We need to assess the plants’ performance outside of our greenhouses. If successful, our hope is that someday soon, farmers and consumers can benefit from these disease-resistant plants to improve their livelihoods and protect the environment.”

The team is examining additional targets to increase disease resistance and exploring new methods of genome editing. In the coming years, it aims to develop a “second generation” of genome-edited cacao lines.

“We’re not just creating better cacao plants — we’re exploring how modern biotechnology can work within existing regulatory frameworks to address real-world agricultural challenges,” underscores Guiltinan.

“Traditional breeding approaches are slow, often taking decades to develop new resistant varieties. For the millions of farmers who depend on cacao cultivation, and the billions who enjoy chocolate, this research offers hope for a more sustainable and secure future — one precise genetic edit at a time.”

Besides cacao, gene-editing technologies have also recently been used to improve raspberries and tomatoes.