Swollen shoot virus addressed at cacao genome workshop

The International Conference on the Status of Plant and Animal Genome Research has been held annually at the Town and Country Hotel in San Diego since 1993 and has included a cacao genome session since 2009. The Jan. 13 cacao genome session at this year’s Jan. 12-16 PAG conference included a presentation by Judith Brown of the University of Arizona’s School of Plant Sciences called “Genomic Characterization of the Cacao Swollen Shoot Badnavirus Species Complex in West Africa.”

“It’s known very little about the nature of the pathogen,” Brown said.

The taxonomic name for cacao is Theobroma cacao. Theobroma translates to “food of the gods.” Cacao originated in Mesoamerica and is believed to have been domesticated by the Olmec civilization. In some civilizations, cacao beans were used as currency, and the Aztec civilization utilized cacao in a drink called xocolatl, which gives the Aztec language the linguistic origin of the word chocolate.

The black pod pathogen was first identified in Brazil in 1905, and in 2015, worldwide approximately 800,000 metric tons of cacao were lost to black pod. Fortunately for both chocolate consumers and African cacao farmers, the transoceanic travel originated by the Eastern Hemisphere had previously allowed cacao farming to spread to western Africa, Indonesia and the Caribbean. While a pathogen may devastate a particular region, the cacao supply is diversified. Approximately 3.9 million metric tons of cacao are harvested annually with the Ivory Coast accounting for approximately 42 percent of production, Ghana contributing about 17 percent, Cameroon and Nigeria producing about 13 percent, Indonesia supplying about 8 percent, Ecuador growing about 6 percent, Brazil cultivating about 5 percent and the rest of the world totaling about 6 percent. The loss from all pathogens is approximately 1,681,000 metric tons, or 38 percent of the annual crop.

Cacao swollen shoot disease is caused by badnavirus. A cacao tree which is infected will usually die within three to five years, although some strains result in tree death within one year.

“We started out knowing basically little about what is cacao swollen shoot virus,” Brown said.

It is known that badnavirus is so called because it can be described as BAcilliform DNA virus. Mealybug species are believed to be the vectors which transmit badnavirus.

“We see widely variable symptoms in cacao,” Brown said.

Damage to leaves is a symptom and may be the first observed symptom.

“It’s often difficult to know when the tree is infected until they defoliate,” Brown said.

The first badnavirus genome was sequenced in 1997. Currently 10 strains of badnavirus, including seven in west Africa, have been analyzed.

“I think that represents very good progress,” Brown said.

The other three strains have been found in Trinidad and Sri Lanka. Brown studied 82 genomes from the seven west African strains.

“There are a number of conserved protein domains,” she said.

That limit indicates the likelihood of transmission of viruses between trees from an infected host. “You see a very clear definition,” Brown said.

For the entire 10 viruses Brown did not find a node which would identify a coherent pattern.

“They’re more or less random scattered,” she said. “It’s time to re-evaluate the taxonomy of these viruses.”

Although some conserved protein domains did not match predicted patterns, seven conserved protein domains not previously seen in cacao-infecting badnaviral genomes were identified. Subsequent analysis will attempt to determine virulence and differences in biological characteristics.