Australian scientists are on the verge of a world first, engineering a genetically modified banana to thwart the rampant spread of a fungus that poses a global risk to food security. By Richard Cornish.

Saving the banana from a deadly fungus

Two farmers examine unripened bananas hanging from a tree.
Dr Jean-Yves Paul (left) and Professor James Dale with some QCAV-4 bananas.
Credit: Supplied

It lives underground, is finer than spider’s silk and is a growing threat to the global food supply. And now, the fight to contain Fusarium, a genus of fungus that dates back to the earliest days of farming, has led to a technical innovation to save the banana.

Fusarium has been destroying food crops for hundreds of years, affecting everything from grains to tomatoes. The trouble is modern farming methods create the perfect environment for different species of Fusarium to thrive and spread, and climate change is making that spread faster.

Grain grower Jason Cotter, of Tuerong Farm, understands outsmarting this tiny fungus is a constant game of evolution. He grows heirloom varieties of grains on different sites on the Mornington Peninsula, south of Melbourne. One of the problems he faces is crown rot caused by a species Fusarium pseudograminearum.

Crown rot costs Australian grain farmers $400 million a year. It affects the lower stems in wheat and barley, causing the seeds to malform. Cotter says sometimes gaining the upper hand over Fusarium fungi means better fungicides and even new genetically modified varieties.

“The (fungus) problem intensifies when you sow wheat over wheat, year after year,” says Cotter, who is known in the industry for resurrecting and experimenting with hundreds of once-forgotten wheat varieties. Often, he selects those varieties of wheat with the best fungus resistance that thrive in his mild and damp climate. “The grain industry could breed a super multivariant wheat that was completely resistant to Fusarium,” says Cotter. “But it’s an evolutionary race. The fungus would soon evolve to infect it.”

Fusarium is a microscopic fungi that thrives in soil. Under the microscope, it looks like tiny shields or a network of fine filaments. There are more than 300 species of Fusarium fungus, but about 20 are causing havoc with our food systems. Fusarium is destroying date palms in the Middle East and tomato plants in California. In the United States alone, a species named Fusarium graminearum has cost the agricultural industry US$5.6 billion annually. The pathogen causes Fusarium head blight, which sees wheat and other grain seeds wither before they are ready for harvest. Even a mild case renders the grains worthless, as fungal toxins, if ingested, can cause abdominal illness and liver damage.

Fusarium fungi spores are notoriously easy to spread. They are carried in seeds, as well as soil embedded in tractor tyres and trapped in the tread of farm boots. Some species, such as Panama disease, aka Fusarium wilt, can also spread in running water.

The big problem with Fusarium is that once it’s in the soil, it’s almost impossible to eradicate.

Stopping the spread of infected soil is an especially insurmountable task when the food system is so attenuated with various contractors moving between paddocks and farms in intensive production areas. In California, huge swathes of once-productive tomato growing counties have had to switch to other crops due to the spread of Fusarium wilt. One species has evolved to attack lettuces. Fusarium oxysporum forma specialis (f.sp.) lactucae destroys tissues in the taproot, which stops water reaching the leaves and causes them to wilt and rot and the plant to eventually die. It was first reported in Japan in 1955 and has since spread to Brazil, Europe and the US. After first arriving in California in 1980, by 2017, it had spread to lettuces in Florida, halting production of the annual in some areas.

To tackle the fungus some producers have reverted to age-old farming wisdom.

Cotter chooses to avoid costly chemical inputs and relies on old-fashioned crop rotation. He sows rye the season after wheat. The year after, he drills the ground with broad leaf legumes such as broad beans and clover. This diminishes the concentration of the fungal spore load and enriches the soil with nitrogen to give the incoming cereal crop a chance to thrive.

A Danish company is evading the fungus by doing away with soil altogether. Near Odense, west of Copenhagen, the horticultural giant Nordic Greens has built a series of massive greenhouses growing lettuce hydroponically. The company has also done away with the main cause of the fungus’s spread, as humans never touch the plants. Robots plant, tend, harvest and pack the salad greens.

It’s the scientific intervention in the banana industry that could open a new front in the global battle against the Fusarium.

The political and social upheaval caused by a strain of Fusarium fungus called Tropical Race One (TR1) is still being felt today. In the 1950s it spread around the globe and wiped out the then-dominant banana variety called Gros Michel. This big, sweet banana was the bread-and-butter export for many developing tropical nations. The resulting rapid decline in the banana industry and associated loss in rural income in South America caused massive geopolitical upheaval in countries such as Ecuador and Colombia.

Its replacement variety was the Cavendish, a slightly smaller banana resistant to TR1. It was planted from Guatemala to the Philippines and Australia and became the main global species – each plant grown from a cutting, making every plant genetically identical.

In 1967, another strain, TR4, emerged in Taiwan, most likely spread from a wild banana plant in Indonesia where the fungus co-evolved with banana trees. This strain of TR4 Fusarium has since spread to South America and the Philippines, where 85 per cent and 15 per cent of globally exported bananas are grown, respectively. It was detected in the Northern Territory in 1997 and in 2015 it reached Far North Queensland, where careful biosecurity halted the spread. But Australian scientists have hatched a backup plan.

For the past 20 years, a team led by Professor James Dale, an agricultural technologist from Queensland University of Technology, has been trying to breed a new genetically modified banana plant resistant to TR4.

“There is hype that the TR4 Fusarium wilt threat to Cavendish bananas, which make up 95 per cent of global consumption, is caused by lack of genetic diversity. The real cause is demand for cheap, uniform fruit that is artificially ripened in boats as it is shipped from the global south to the north,” he says.

“You can’t do that on a large scale with lots of different-shaped varieties of bananas that need different boxes and that take different times to ripen.”

Dale’s team found a wild TR4-resistant banana plant in Indonesia and mapped its 30,000 genes to identify the one that gave it immunity to TR4’s infection. The scientists then took that gene and inserted it into an agrobacterium – an organism discovered in the early 20th century that can naturally transmit DNA into living plants to cause genetic changes.

The team inserted that agrobacteria into Cavendish bananas and the subsequent transformation created the genetically modified variety, QCAV-4.

In 2012, the team grew the GM banana plants on a test plot near Humpty Doo in the Northern Territory.

“There was already enough TR4 in the soil – we didn’t have to inoculate it,” says Dale. That trial came to a halt when an outbreak of black spot in the territory forced the destruction of all banana plants. It resumed in 2018 on a much bigger scale and, in May this year, QUT sought approval from Food Standards Australia New Zealand and the Office of the Gene Technology Regulator. The public comment window closed with little controversy.

Dale expects the new variety to be approved for human consumption by autumn next year. “It will be the first GM banana in the world,” he says. Asked how it tastes, he replies, “None of us know. Under our licence no one is allowed to eat it until approved. But if TR4 spreads in Australia, consider this banana as our safety net.”

This article was first published in the print edition of The Saturday Paper on December 16, 2023 as "Clone wars".

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