Genetic lineages of Colombia's cacao black pod pathogen cut across the Andes

Black pod disease destroys up to a quarter of the world's cacao each year, roughly 700,000 metric tons worth more than $2 billion ^[1]. In Colombia the dominant Phytophthora on cacao is P. palmivora ^[2]. The new study in Phytopathology, chosen as an editor's choice, is described as the first comprehensive portrait of the pathogen's genetic structure in the country ^[3].

The team started from a sensible hypothesis. Colombia's Andes split into western, central and eastern cordilleras, and that terrain has historically limited how people, crops and organisms move ^[4]. The team, led by Silvia Restrepo, president of the Boyce Thompson Institute, expected the ranges to keep P. palmivora in separate populations that evolved on their own, as the Andes have done for other cacao pathogens ^[5]. They compared the isolates at hundreds of positions across the genome ^[6]. A mountain barrier would have shown up as clusters sorted by region.

A population reproducing without sex does not generate that much variety by itself ^[8]. By the study's reasoning, the lineages came in from outside, more than once and from different sources, and were then carried over the mountains ^[8]. The report names infected plant material as the most likely carrier ^[8]. "Cacao germplasm moves extensively across Colombia through breeding and distribution programs, and that movement creates a human-mediated dispersal network," Restrepo said, one that "can distribute unrelated pathogen lineages across regions that would otherwise be disconnected" ^[9]. The route is inferred from the genetic pattern. The report does not describe tracing any particular shipment.

The sampling covered a lot of ground but went thin at each site. Seventy-three isolates from 48 locations works out to about 1.5 per site ^[1]. That is enough to show that lineages are shared across regions. It is too few to estimate how common any one cluster is in a given valley. The mating-type result has the same limit. Every one of the 73 isolates was A2 ^[7], so A1 turned up nowhere in the sample, and the authors' call to keep A1 out of Colombia assumes it is not already there ^[16].

Restrepo explained the stakes in terms of breeding and quarantine. "Understanding how a pathogen is structured across a landscape is not an academic exercise," she said. "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." ^[10]

Virulence was scored on cacao leaves ^[11], and the study does not say how those results carry over to pods. Isolates first collected from leaves were significantly more aggressive on leaves than isolates collected from pods ^[14]. The authors call that an early hint of tissue-specific adaptation that needs follow-up ^[14]. If it holds, a leaf assay could understate how dangerous a pod-derived isolate is on the pod itself.