Protecting peppers from devastating viral diseases through gene pyramiding

Even with today’s advanced agricultural technologies, plant diseases can still be extremely devastating to crops, causing billions of dollars in losses worldwide every year. Begomoviruses represent a prominent example of this threat—these whitefly-transmitted pathogens cause yellow leaf curl disease in peppers and can destroy up to 100% of fruit yield in affected fields across Asia, Africa, and the Americas.

Breeding crops that are resistant to begomoviruses has long been the most effective and widely used strategy for preventing such massive losses. Though usually effective, this approach has serious limitations, especially when dealing with mixed infections. Scientists have successfully identified resistance genes against specific begomovirus species, but developing broad-spectrum protection for the complex mixtures of viruses commonly found in agricultural settings has proven far more difficult.

Fortunately, a research team led by Associate Professor Sota Koeda from the Graduate School of Agriculture at Kindai University, Japan, has recently made an important breakthrough in addressing this challenge. Their latest study, published online in the journal Plant Disease on June 2, 2025, demonstrates how combining two different resistance genes can provide robust protection against even the most virulent begomovirus combinations. This work was co-authored by Ms. Mika Onouchi, Ms. Namiko Mori, and Ms. Nadya Syafira Pohan, all from Kindai University.

The team focused on two previously identified resistance genes: recessive pepy-1, which encodes a protein called Pelota involved in cellular quality control mechanisms, and dominant Pepy-2, which encodes an RNA-dependent RNA polymerase that helps plants silence viral genes. Using sophisticated inoculation techniques, the researchers tested pepper plants carrying these genes against single virus infections and mixed infections with highly virulent begomoviruses from different regions of the world.

Their experiments revealed that while individual resistance genes provided some protection, they were often overwhelmed by mixed infections—particularly when plants faced simultaneous attack by New World begomoviruses like the pepper huasteco yellow vein virus and the pepper golden mosaic virus. However, when both resistance genes were combined in their most potent form (the homozygous state), the resulting plants showed remarkable resilience.

Through careful analysis and further experimentation, the team delved deeper into the different resistance mechanisms at play. While pepy-1 showed effectiveness against Old World begomoviruses, it struggled with New World species. Pepy-2, on the other hand, provided broader protection. Most importantly, their combination created a synergistic effect known as ‘gene pyramiding’ that overcame the limitations of each gene. This drastically reduced disease symptoms and kept viral DNA accumulation at low levels, leading to plants achieving low disease severity scores.

For pepper growers, this research offers hope for more stable production in regions where begomovirus diseases have been economically devastating.  “Our study provides a framework for breeding peppers with durable resistance to evolving begomoviruses, filling a critical gap in sustainable crop protection,” explains Dr. Koeda, “Both pepy-1 and Pepy-2 will be used widely in commercial pepper cultivars in the near future, enabling farmers to produce pepper fruits even under begomovirus-infected conditions.”

This breakthrough comes at a critical time, as global pepper production faces increasing pressure from viral diseases. With over 42 million tons of peppers produced annually worldwide, protecting this valuable crop from devastating losses is essential for food security and economic stability in major producing regions, such as Mexico, Indonesia, Turkey, and India. The development of durable, multi-pathogen resistance strategies represents a significant step forward in sustainable agriculture.

Worth noting, the implications of this study extend beyond peppers. The gene pyramiding technique represents a powerful strategy that could be applied to other plants facing viral pathogens. “This approach we developed for peppers can be applied to other crops, and we are now challenging this goal in other vegetables,” says Dr. Koeda.

Further research efforts on this complex topic will hopefully help us minimize the damage to crops caused by viral plant diseases.

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