The Hidden Pandemics on the Farm

For humans, a pandemic from a novel virus with a 4% mortality rate would be a global catastrophe. Today’s farmers face crop pandemics with mortality rates approaching 100%. That’s not hyperbole: banana plantations around the world are trying to contain a virulent fungus that threatens 100% of the leading variety, Cavendish bananas, and 95% of bananas sold commercially. While staple crops like corn, rice and wheat don’t face the same levels of risk, they face omnipresent threats from resistant pathogens that could decimate crops responsible for nearly half of our daily caloric intake, potentially putting hundreds of millions of people at risk for starvation.

Fortunately, there is a new technology that may come to the rescue of the Cavendish banana (the dominant commercial banana), and provide a template for protecting the staple crops.

Vulnerability to blights is built into the very structure of modern agriculture. To optimize their income, farmers gravitate towards the best yielding crops. The result has been that the staple crops have become more homogenous. The lower genetic diversity leaves the most-prized seeds vulnerable to catastrophic die-offs should a resistant blight, fungus or other pathogen take hold. Nowhere is this better illustrated than in the case of the modern banana.

People prefer seedless bananas, and the Cavendish became the commercial favorite because it is sterile. This means that new plants are created from clones, not seeds, and every new crop planted is genetically identical. While using a standardized plant has eased collecting, fungi also like this attribute because it can easily spread across all identical crops.

It is ironic that the Cavendish banana is in jeopardy from a fungus, as it was chosen to be the commercial banana in the 1950s because of its resistance to the so-called Panama fungus that threatened to wipe out its predecessor. Given the speed with which fungi adapt, it was only a matter of time before fungus would find a way around the Cavendish’s defenses. We saw this in Taiwan in the 1990’s when a new version of the Panama fungus (officially Fusarium TR4) ravaged the island’s Cavendish banana crop. Since it can last for decades in the soil, it was easy for the fungus to hitch on a bit of mud on clothing and escape the island. The fungus moved first through Southeast Asian countries, then to the Middle East and Africa, and it now threatens the massive banana crops of the Americas and the Caribbean. Worse, there is no fungicide that is effective against the disease.

The first alternative seemed to be to breed a new resistant banana, but achieving the desired qualities would be slower than the spread of the disease. Another approach is to use transgenic technology to incorporate resistant genes from wild bananas and other species. That has produced a resistant banana, but the resulting crop is classified as GMO and thus encounters regulatory hurdles and consumer resistance.

By far the most efficient and elegant approach would be to find a way to harness the plant’s own gene repair system to accelerate it to develop natural resistance. This is now possible. The first step is to probe the genetics of resistance and develop an exact description of which parts of the genome protect against the fungus. With a picture of these genetic targets, it’s possible to precisely edit the genome, and do so the same way nature would (with the difference being that instead of playing a numbers game with random mutations, precision gene editing makes the specific changes needed to develop resistance — and only those changes).

Thus, precision gene editing mimics natural selection. Instead of using foreign genetic material to make the change, the chemical construct and genetic scissors used in precision gene editing both disappear once they have done their work. The process is non-GMO, and the result is indistinguishable for what might be produced in nature.

The approach has already produced Canola plants resistant to Sclerotinia, a fungus that can reduce yields by 20 percent. Similarly, potato research has identified the targets that will produce a tuber resistant to Phytophthora, which caused the Potato Famine in 19th century Ireland.

The true advantage of precision gene editing lies in its speed: it’s the only available technology that can produce resistance as fast as new plant pathogens can spread. Natural selection might produce resistance to the fungus given enough time, but it would take far too long to protect the banana. Transgenic technologies introducing new material can take extended time as well and then resulting GMO crops may not be widely accepted. Only with precision gene editing can all edits can be made simultaneously — with crops in the greenhouse in under a year — for nature-identical fruit.

This tool could not come at a more critical time. Beyond the Cavendish banana, blights circle all the major crops as pathogens continually adapt around fungicides and other chemical protections. We have avoided these fortunately to date, but we need to find reliable alternatives. The world dodged a bullet in 2017 when a wheat stem rust called UG99 was successfully contained before it spread from the Middle East to Europe.

In this arms race between crops and pathogens, precision gene editing can breed resistance into plants naturally, reduce a farmer’s reliance of fungicides and greatly slow the development of resistant pathogens as they are challenged less frequently. This fosters greater diversity in the soil, which has the effect of enlisting other fungi to keep things in balance. It’s essential that we stay ahead in this arms race, as falling behind could put hundreds of millions of people at risk of starvation.




Dr. Beetham has over 30 years of experience in the bio-agriculture community, with a passion for moving technology to commercial application.

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Peter Beetham

Peter Beetham

Dr. Beetham has over 30 years of experience in the bio-agriculture community, with a passion for moving technology to commercial application.

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