Chiquita completes banana pan-genome to accelerate disease-resistant breeding

Chiquita Brands International has reached a major milestone with the completion of a banana pan-genome through its innovation joint venture with KeyGene, Yelloway B.V. The development is designed to accelerate the breeding of disease-resistant and climate-resilient banana varieties.

The pan-genome captures genetic variation within Musa acuminata, the species behind commercial varieties including Cavendish and Gros Michel. By mapping the range of naturally occurring variation, the resource enables targeted breeding decisions, supports biodiversity, and strengthens long-term varietal development.

“This pan-genome provides detailed insight into banana genetics, allowing researchers to explore the full genomic landscape,” said Professor Gert Kema, board member of Yelloway and emeritus professor of phytopathology at Wageningen University.

The initiative comes as Fusarium wilt Tropical Race 4 (TR4) spreads to key producing regions including Ecuador, threatening Cavendish, which accounts for more than 95% of global exports. Black Sigatoka, a leaf-spotting fungus, costs the industry over $100 million annually in protective measures that largely slow disease progression without increasing yields.

Peter Stedman, Chiquita’s sustainability director, emphasized the urgency. “TR4 can remain dormant in soil for up to two years, and growers currently have no mechanism to report outbreaks or receive compensation. Combined with Black Sigatoka, these diseases create an unsustainable cost and risk profile.”

The pan-genome was developed using Oxford Nanopore sequencing technology, with match funding from Innocent Drinks’ Farmer Innovation Fund and contributions from partners across the banana value chain. Fernando Garcia-Bastidas, head of Yelloway’s breeding program, said it allows breeders to analyze, select, and deploy the most relevant genetic material, accelerating the development of improved varieties.

“Diversity is critical,” said Anker Sorensen, vice president of new business at KeyGene. “The first varieties we expect to bring to commercial scale in roughly five years will be resistant to TR4 and Black Sigatoka. Beyond that, the pan-genome will support the continuous creation of varieties with improved yield, climate resilience, and other traits.”

Yelloway will provide academic researchers access to the pan-genome through a dedicated web portal, promoting collaboration and further innovation in banana breeding worldwide.

Bananas remain the most purchased fruit in Europe and North America, valued for affordability and nutrition. For Chiquita, safeguarding the crop also supports the livelihoods of millions globally who depend on banana production.

“With this pan-genome, we are future-proofing an industry and helping secure long-term supply, affordability, and sustainability for both consumers and the communities that grow these bananas,” Stedman said.