The starchy root vegetable, cassava, is extremely important to more than a billion people worldwide, mainly across the tropics. When a new plant pathogen emerged in Southeast Asia (an area that includes Laos, Cambodia, Vietnam, Thailand and the Philippines), the disease threatened the food security of some of the planet's most vulnerable people.
Had the epidemic spread, the consequences would have required a large, sustained increase in food aid at a time when aid budgets are shrinking. Instead, scientists were able to alter the course of the disease by cracking the enigma of what causes it.
Alarm bells activated
Named cassava witches' broom disease (CWBD) due to its ability to cause plant deformities, the disease turns a tall, leafy plant into something that resembles a broom - a cluster of poles that culminate in a burst of excessive and stunted branching.
Despite symptoms first being reported in 2005, no one in the world knew anything about the cause of this new disease. Was it caused by a virus, bacterium, worm, fungus or an insect?
The disease seemed to disappear for a while. Then reappeared with a vengeance in the 2010s. As the rate of spread accelerated, alarm bells rang internationally. ACIAR stepped up and launched a research project under the leadership of Dr Jonathan Newby of the International Center for Tropical Agriculture (CIAT).
Within 18 months, CIAT identified the pathogen and achieved much more, including several surprise findings.
Pathologists and DNA sleuths
Initially, CIAT and their in-country partners faced a major challenge. To avoid spreading the disease globally, only laboratories in the affected regions could be used.
Fortunately, capacity-building efforts by CIAT meant that Laos possessed both affected crops and newly built research facilities. These house world-class plant pathologists within CIAT's Cassava Crop Protection team. Among them is Mr Juan Pardo, currently leading the Molecular Pathology Laboratory in Laos.
Together with other experts, they examined infected plant materials, analysed symptoms and extracted DNA, sequencing snippets of genomic material. This established links between symptoms and the DNA fingerprints of the causal agent.
Back in Colombia, at CIAT headquarters, the DNA information was put through high-powered computational analytics called bioinformatics. These modern methods can crack the genetic identity of any organism.
Implications
The discovery then made a string of biosecurity advances possible. The scientists:
- sequenced the pathogen's entire genome
- developed diagnostic DNA markers that can rapidly detect the fungus' presence in cassava material, allowing for rapid biosecurity responses
- enabled both the production of planting material that is certified 'disease-free' and its distribution to affected farmers.
Dr Wilmer Cuellar, who heads CIAT's Cassava Crop Protection team, said the identification of Ceratobasidium theobromae provided the foundations needed to alter the course of the epidemic and enhance the world's biosecurity defences.
It also produced 2 surprise twists.
The fungus is more dangerous than first realised
Once the fungal genome was fully sequenced, scientists realised Ceratobasidium theobromae of cassava is exceptionally like the organism that causes vascular streak dieback in cacao.
That meant 60 years' worth of research on the cacao disease could fast-track efforts to combat CWBD. However, there was also a more ominous implication.
Dr Newby noted that in both cases, the diseases emerged in Southeast Asia - but in a family of crops native to Latin America. That pattern alarmed the CIAT scientists.
'It means there is a reservoir of fungus within the natural Southeast Asian landscape that can either jump hosts or expand its host range and produce novel plant diseases on a family of Latin American crops,' said Dr Cuellar. 'Cacao and cassava are not the only crops affected. We now know that the fungus can infect avocado.'
It turns out that the biosecurity risk posed by the fungus was far greater than anyone had known.
The danger was more imminent than expected
By 2025, CWBD went from a mystery wrapped in a riddle to a fungus whose growth on cassava plants was now literally visible given the quality of new information available.
'It's like the mind's eyes were opened,' said Dr Cuellar. 'With that gain in insight came a shock.'
As the CIAT team published the second of their scientific papers, surprise sightings started coming in. Symptoms that were now obviously CWBD were identified in cassava plantations in Latin America. First in Guyana and then northern Brazil.
The disease had already spread, jumping continents. 'The diagnostic DNA markers we developed confirmed this conclusion,' said Dr Newby.
Suddenly, there was a greater threat looming, especially to food security in Africa. A breeding program was needed - and needed urgently. This could test and identify cassava gene variants that defend against the fungus (called disease resistance genes).
Like all research centres within the CGIAR system, CIAT maintains gene banks for all its mandate crops, including cassava. These gene banks preserve genetic diversity present within the crop's broader gene pool.
When a range of diverse cassava material was grown in CWBD-affected field trials, the scientists saw tantalising early evidence that cassava may well possess resistance genes. Unfortunately, a monumental barrier prevented their deployment.
Moving forward and a key message
CIAT had managed to unmask the cause of CWBD without being able to fully grow the fungus artificially in the laboratory.
As Mr Pardo from CIAT's Cassava Crop Protection team explained, the fungus Ceratobasidium theobromae does not undergo its full life cycle when grown on Petri dishes. 'To make matters worse, the form we can grow is not infectious,' he said. 'That means we can't infect cassava under the controlled conditions we need to breed disease-resistant varieties.'
The team, nonetheless, discovered that the spores (produced by fungal fruiting bodies) are capable of infecting cassava.
In the wild, the fungus only makes spores during the rainy season, between June and September in Laos. Making things even harder for breeders, the spores are light sensitive and perish quickly.
To solve this impasse, new infrastructure was completed in May 2025 at the Laos facilities. A large cassava growth chamber equipped with irrigation and humidifiers now allows for spore production year-round.
Funding for this new phase came from ACIAR in the form of a follow-up grant worth $AU3.5 million through to 2028. The aim of the new project is to develop disease-resistant cassava production systems.
'With the ability to produce spores, we could finally pinpoint the mechanism of infection,' said Mr Pardo. 'That means understanding how spores initiate an infection, which tissue is attacked and why the plant's immune system fails to detect it.'
It also kickstarts a breeding program and other research, which can help farmers cultivate cassava in ways that reduce disease risks so cassava-dependent rural communities (and economies) around the world can breathe a sigh of relief.
ACIAR projects: Addressing the rapid emergence of Cassava Witches' Broom Disease in Laos (CROP/2023/157); Disease-resilient and sustainable cassava production systems in the Mekong region (CROP/2022/110); Establishing sustainable solutions to cassava diseases in mainland Southeast Asia (AGB/2018/172).
