Plant breeders are leading a global effort to unlock the genetic secrets of Capsicum, building disease-resistant varieties from a treasure trove of untapped chili diversity.
In the sweltering fields of South India, where farmers stoop to harvest brilliant scarlet chilies destined for drying racks and distant markets, an invisible war is raging. The enemy isn’t drought or soil — it’s microscopic. Lethal viruses, wilting bacteria, and voracious thrips devastate pepper crops across Asia and Africa, where smallholder farmers rely on these fruits not just for income, but for survival.
But in a lab half a world away, Derek Barchenger is fighting back — with seeds.
Barchenger, a plant breeder based at the World Vegetable Center in Taiwan, doesn’t grow chilies for taste or spice—at least not primarily. His work digs deep into the genome of Capsicum, the genus that includes everything from sweet bell peppers to fiery ghost chilies. His mission: to unlock disease resistance buried in their DNA and return it to the farmers who need it most.
“When you ask seed companies what they want, the answer isn’t yield — it’s disease resistance,” Barchenger explains. “Viruses, fungi, pests. These are what wipe out harvests.”
A Crop with Global Roots — and Global Gaps
Despite being a staple in diets and markets from Mexico to Myanmar, peppers are a paradox. They’re grown everywhere — especially in Asia, which produces over 60% of the world’s peppers — but yields in many regions lag far behind global averages. While European growers produce over 40 tons per hectare in glasshouse operations, many African and Southeast Asian farmers harvest barely half that.
“The genetic potential is there,” Barchenger says. “The problem is, we haven’t been using it.”
Why? Unlike tomato, which has benefited from decades of intensive genetic research and breeding, Capsicum remains surprisingly underexplored. Many of the world’s seed banks hold vast collections of wild and cultivated pepper varieties, but most come with no passport data, no disease ratings, no phenotypic profiles — just seeds in cold storage, waiting to be understood.
Cracking the Chili Genome
To change that, Barchenger joined forces with researchers across Europe, Israel, and Asia in a sweeping initiative called G2P-SOL — Genotype to Phenotype for Solanaceous Crops— funded by the EU’s Horizon 2020 program. Together, they sifted through more than 15,000 pepper accessions from gene banks across the globe. From these, they created a streamlined core collection of 423 genetically diverse lines.
Then came the hard part: growing them in six environments — from tropical Taiwan to arid India — measuring traits like fruit shape and size, and testing them against some of the world’s worst plant diseases.
For farmers in India’s “dry red chili belt,” the stakes couldn’t be higher. The area is ground zero for chili leaf curl virus, a devastating pathogen spread by whiteflies. In trials across Asia, Barchenger and his team exposed their core collection to the virus in real-world farm settings. The result? A trove of valuable data — and something even rarer: durable resistance.
“We found multiple SNPs — tiny genetic variants — associated with resistance across locations,” Barchenger says. “That’s a big deal. It means we’re finding traits that actually hold up outside the lab.”
Derek Barchenger is a pepper breeder at the World Vegetable Center. Photo: WorldVeg
From Wild Roots to Resilient Crops
The team’s approach wasn’t just shotgun sequencing. By linking specific genes to physical traits — a process known as genome-wide association studies, or GWAS — they began building a map of resistance. For example, they found strong bacterial wilt resistance on chromosomes 6 and 12, and clear viral resistance on chromosome 3.
They also confirmed what many breeders already suspected: resistance is often race-specific. What works against one strain of virus in Indonesia may fail entirely in Nigeria. That’s why multilocation screening—across climates, pathogen strains, and production systems—is essential.
But while this genetic treasure hunt is yielding results, there’s a long way to go. Capsicum has over 40 wild relatives, many of them still uncharacterized. Their potential to contribute resistance traits remains largely untapped.
“It’s like we’ve been fighting a war with a few old rifles in the closet,” Barchenger says. “Meanwhile, there’s a whole armory of wild genetics we haven’t even opened.”
Breeding for the Frontlines
Perhaps the most urgent aspect of Barchenger’s work is where his seeds end up. Each year, the World Vegetable Center distributes pre-breeding lines to partners around the world — public institutions, universities, and increasingly, private seed companies in South Asia and Sub-Saharan Africa. In India alone, about 85% of chili seed comes from the private sector.
In a world rocked by climate change, emerging pathogens, and market instability, building those seeds isn’t just about plant science. It’s about resilience — for the farmer, the family, the food system.
“We’re not releasing finished varieties,” Barchenger clarifies. “We’re supplying the raw materials — the resistance traits — that companies and governments can use to build better seeds.”
So the next time you taste the searing heat of a chili or the sweet crunch of a bell pepper, remember: it’s not just flavour that matters. It’s survival.