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Coffee leaf rust returns

From the November 2018 issue.

The pathogen responsible for crop devastation in 2012 is still a major threat. World Coffee Research reveals its plans to fight coffee leaf rust once more, and why genetics is not the only cure.

In the past few years, farmers in Honduras and Nicaragua have had growing concerns for their Lempira crops. Leaves that were thought to be resistant to rust started developing clusters of yellow-orange lesions, a foretelling sign that the once resistant cultivar is no longer.

Researchers have since confirmed the unwanted spread of one of the industry’s most debilitating diseases.

They believe it is only a matter of time before rust resistance in most of the existing resistant varieties breaks down, perhaps in as soon as five to 10 years in many countries.

At the Association for Science and Information on Coffee conference in Portland in September 2018, World Coffee Research (WCR) announced that fighting coffee leaf rust through genetic resistance will no longer be enough to protect farmers from significant crop losses.

“It’s a sad reality but this is a wake-up call that all genetic resistance so far will be broken in the next few years. We should not doubt it. It’s going to happen,” WCR Scientific Director Dr Christophe Montagnon tells Global Coffee Report. “At the same time it’s an opportunity to invest in quite a lot of domains that we’ve been forgetting because we – the coffee science community – have been resting on our laurels and not investing enough in what we subscribed to.”

Coffee leaf rust, a fungus that cripples the productivity of coffee trees, has wreaked havoc on coffee production, particularly in Latin America, since an epidemic hit in 2012. Some farms lost 50 to 80 per cent of their production, and more than 1.7 million people were forced out of work.

For the past 30 years, Montagnon says breeders around the world have relied on Mother Nature’s genetic resistant gift: the resistant Timor hybrid (Hibrido de Timor), a natural cross between Arabica and Robusta found in the 1950s, and related interspecific hybrids Sarchimor and Catimor. Now, the resistance genes brought by the Timor hybrid are being overcome by new rust strains. Moreover, the quality of the Timor hybrid descending varieties is often questioned. “You have to remember that the creation of Catimors and Sarchimors happened before the rise of specialty coffee. At this stage people weren’t bothered too much about quality. It was a single source of resistance, and it worked,” Montagnon says.

“The Timor hybrid has provided a good service for 30 years but now it’s over. In a provocative way we can say the Timor hybrid was a poison gift. It was a gift at the time but in many ways we had it too easy – in that we didn’t put much effort into our next steps or consideration of what could happen if the resistance wore down. But now it has.”

However, as coffee leaf rust proceeded to devastate crops, the global coffee industry united to develop new coffee cultivars, such as F1 hybrids, a genetic crossing between two genetically distant Arabica parents. According to Montagnon, the F1 hybrids, such as the Centroamericano variety, solve the first issue of rust resistance. Tick. Then they solve the issue of productivity. Tick. And eventually they solve the problem of quality because of their Ethiopian parent. Tick again.

“The F1 hybrids are outstanding. They are so important as a genetic solution not just because of their rust resistant genes but because of their hybrid vigour, which makes them much healthier than other cultivars,” Montagnon says.

However, we should learn from the past. It is very likely that the resistance of F1 hybrids will also be overcome, maybe sooner than later, hence why WCR is preparing with a global comprehensive strategy, combining genetic and non-genetic solutions.

“We won’t win the war with a genetic solution alone. It is necessary but not sufficient. It’s not sustainable,” Montagnon says.

WCR will search for new genetic resources within Ethiopia’s large reservoir of stored germplasm, unexplored until now.

“Quite simply, the library of genetic cultivars was never considered because the Timor hybrid was so effective. The mentality was, in short: ‘why bother?’”

Montagnon says, however, that such genetic resources are at risk because they are located in institutes that are struggling to maintain them. To ensure their longevity, WCR has partnered with Croptrust and established an international mandate to conserve genetic resources of coffee crops around the world. WCR and Croptrust aims to raise US$25 million in an endowment fund with US$1 million a year set to help conserve genetic resources forever.

“If we want to be efficient and benefit from natural genes of resistance, we need to preserve coffee genetic resources for generations to come,” Montagnon says.

A medium to long-term solution is revisiting interspecific hybrid crosses and trying to recreate them rather than relying on Mother Nature to present the answer. Already WCR has conducted the first new creations of “Arabusta”, a cross between Arabica and Robusta varieties.

Aside from genetic strategies, Montagnon says education on plant health is one of the simplest and most effective approaches to defend against rust.

One of the key lessons learned from the 2012 leaf rust epidemic in Central America was a notable correlation between low coffee prices and the presence of leaf rust due to farmers’ reduced maintenance of trees. With the current market situation unfavourable for many farmers, fears are growing for a repeat performance.

“If we as humans become tired or exhausted, we are more likely to get a flu or disease, and it’s the same for coffee,” Montagnon says. “A healthy plant is more likely to defend against leaf rust and be tolerant to disease, but if coffee prices remain low, with low farm maintenance as a result, we might see another rust epidemic in the next one or two years.”

WCR is working on ways to increase better plant management, including the use of shade and nutrition, or in human terms, “how to build muscles and give the plants the strength to fight rust and disease”.  Until now, spraying chemicals on crops has been considered a common and effective practice to control leaf rust, but recent studies from WCR and the French Agricultural Research Centre for International Development (Cirad) showed that good fertilisation can be as effective as spraying fungicide in protecting a genetically susceptible coffee to rust.

For the past few decades Montagnon says the industry has been so “gifted” with the effective Timor hybrid that little research has been done on coffee leaf rust itself: where it lives, how it populates, its lifecycle, why it mutates, its genetic structure, etc. In a case of keeping your friends close and enemies closer, Montagnon says it’s time to understand the complexities of coffee leaf rust.

To do this, WCR has signed a research agreement with top rust experts from Purdue University Northwest in the United States. At present, they are finalising the genome sequence of coffee leaf rust, which will reveal its genetic diversity and help understand mutations and host pathogen interactions. 

“For me, one of the greatest achievements in fighting against leaf rust is bringing Purdue University on board. They have years of studying rust, not specific to coffee but in general. That’s what we need to do – bring more and more super brains from different friends of science and apply it to our coffee industry,” Montagnon says.

A new complementary strategy is biocontrol. Already with Vicosa University, WCR has screened more than 1500 antagonist fungi, surveyed in native forests, and from the sample, has selected 12 candidates ready for field study – four endophytes and eight myco-parasites.

“We have amazing results coming in, which means we are validating antagonists to rust so that we can ultimately spray natural organisms that will limit rust expansion,” Montagnon says.

Not all solutions are for tomorrow. Some solutions will be ready in the next five years. However, WCR is working for short to long- term protection of the coffee industry.

Last but not least, it is the responsibility of all those travelling between origin countries to develop a heightened sensitivity and awareness for appropriate phytosanitary practices to prevent spreading fungi and other diseases from farm to farm or region to region. Delaying the introduction of new strains in a country is of tremendous importance for the coffee growers of that country.

“The last leaf rust crisis in Central America saw a loss on average of 40 to 50 per cent of production. People were badly affected from the crisis and some even left the coffee sector,” Montagnon says. “We can’t afford that to happen, it would stretch the industry, but if it does, we want to be prepared.”

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