Black pod disease destroys up to a quarter of the world's cacao every year , roughly 700,000 metric tons, worth more than $2 billion. The water mold responsible across the Americas is Phytophthora palmivora , and in Colombia it is the dominant Phytophthora on cacao. How it travels among the country's three Andean regions, though, has remained an open question.
A study published in Phytopathology and selected as an editor's choice now provides the first comprehensive portrait of the pathogen's genetic structure in Colombia. An international team of researchers genotyped and virulence-tested 73 isolates gathered from 48 locations across the country's three main cacao-growing regions. What they found confounded expectations.
An elegant hypothesis, decisively overturned
Colombia's Andes divide into three cordilleras—western, central, and eastern—creating a topography that has historically constrained movement of people, crops, and organisms across the country's highland terrain. The research team, led by Silvia Restrepo , president of the Boyce Thompson Institute, hypothesized that this mountain complex would similarly limit the spread of P. palmivora , producing populations that had evolved separately on either side of the ranges, much as the Andes have shaped population genetics in other cacao pathogens.
The data said otherwise. The team scanned the genomes of all 73 isolates, looking for differences scattered across hundreds of positions in the genetic code. The analysis sorted the samples into seven distinct genetic clusters. Not one of them mapped to geography. In other words, the Andes were not a barrier.
“Understanding how a pathogen is structured across a landscape is not an academic exercise,” said Restrepo. “It determines whether a resistant variety bred in one valley will hold up in the next one, whether quarantine lines are drawn in useful places, and how quickly the pathogen can evolve around whatever defenses growers deploy.”
Then came the clue that explained it
Every one of the 73 isolates was the A2 mating type.
P. palmivora needs two compatible mating types, A1 and A2, to reproduce sexually. With only A2 present, sexual recombination isn't happening—the population is reproducing clonally, a conclusion the genetic data independently confirmed.
Clonal organisms don't generate this much diversity on their own. If the variation isn't being created inside Colombia, it must have arrived from outside it—repeatedly, from different source populations, and then been carried across the mountains.
The most likely culprit is infected plant material. “Cacao germplasm moves extensively across Colombia through breeding and distribution programs, and that movement creates a human-mediated dispersal network—one that can distribute unrelated pathogen lineages across regions that would otherwise be disconnected,” said Restrepo.
A warning for breeders
The team also tested how aggressively each isolate attacked cacao leaves. Virulence varied enormously—the most damaging isolate drove disease progression more than tenfold faster than the control strain, while others caused less damage than the control.
Critically, that variation showed no relationship to genetic cluster. An isolate's DNA fingerprint says nothing useful about how dangerous it is.
The disconnect between genetic structure and virulence carries a practical implication. Growers and breeders cannot rely on molecular markers to identify dangerous strains. Virulence screening must use actual inoculation assays, and resistance breeding programs must incorporate isolates spanning the full virulence spectrum, not just genetic diversity.
The researchers also found that isolates originally collected from leaves were significantly more aggressive on leaves than pod-derived isolates were—an early hint of tissue-specific adaptation that warrants follow-up.
What to do about it
The study's management recommendations follow directly from its findings. Because human movement of plant material appears to be the primary dispersal mechanism, phytosanitary protocols around germplasm exchange need to be strengthened. And since the population is uniform for mating type, keeping A1 out of Colombia should be a national priority—the arrival of a compatible partner would unlock sexual recombination and, with it, the potential for rapid evolution of more aggressive strains.
The authors call for coordinated action across Colombia's cacao regions and for growers to diversify the cacao genotypes they plant, reducing selection pressure on any single source of resistance.
Colombia is one of the world’s major cacao producers, and the country's output feeds a global chocolate trade that depends on genetic diversity in its source crop. P. palmivora in Colombia is a nationwide presence—genetically diverse, geographically unconstrained, and phenotypically unpredictable—that arrived through human action and continues to spread the same way. The response, the authors conclude, must match that scale.
Support was provided by the Facultad de Ciencias, Departamento de Ciencias Biológicas and Vicerrectoría de Investigación y Creación of the Universidad de los Andes, FEDECACAO-FNC, and the Fondo Nacional de Ciencia “Francisco José de Caldas.”
About the Boyce Thompson Institute (BTI)
As an independent nonprofit research institute affiliated with Cornell University, our scientists are committed to advancing solutions for global food security, agricultural sustainability, and human health. Through groundbreaking research, transformative education, and rapid translation of discoveries into real-world applications, BTI bridges fundamental plant and molecular science with practical impact. Discovery inspired by plants . Learn more at BTIscience.org .
Phytopathology
Experimental study
Cells
High Genetic Diversity of Phytophthora palmivora in Colombian Cacao: Evidence Against Geographic Barriers
30-Jun-2026
The author(s) declare no conflict of interest.