Save the coffee / Hilary Rosner

Researchers are racing to introduce new beneficial traits to the alarmingly uniform coffee crops, and this must be done before coffee falls victim to disease or other threats

The coffee that the restaurateur placed next to mini pastries stuffed with guavas was lukewarm and bitter and tasted like chlorine. Some of the guests did not touch it despite their strong desire for caffeine. They stood in Turrialba, Costa Rica, on a narrow balcony overlooking the scrub-covered hills and sipped water or pineapple juice instead of coffee. But they were entitled to a little quality coffee: about twenty people, the best experts of mankind's favorite drink, who gathered in March 2014 at the Center for Tropical Agriculture Research (CATIE), for the purpose of discussing the uncertain future of coffee in Central America.

They gathered to discuss a serious threat: the coffee rot, or roya as it is called in Spanish. The rust is a fungal lesion that is the color of rust that attacks the coffee leaves and prevents them from absorbing the sunlight that is essential for their survival. The fungus has made a name for itself in the coffee crops in the region in recent years and affected half of the approximately four million dunams across Central America and eliminated about 20% of the 2012 crop, compared to the 2011 crop.
The disease outbreak, which is still spreading, is only one crisis that threatens coffee in this period of global warming. After the coffee break held by the group of experts gathered in Costa Rica, the geneticist and breeder of coffee varieties Benoît Bertrand, from the French Center for Agriculture and Development (CIRAD), told her that "most of the coffee varieties today have no chance of resisting the disease and insects, in addition to their sensitivity to rising temperatures and other environmental threats arising from climate change." According to him, if the harvest is small, the coffee growers lose their livelihood. They may uproot the coffee trees and plant other crops, or sell their land to contractors, leaving behind a trail of unemployed agricultural workers and environmental destruction.
Bertrand, with a blue sweater draped over his shoulders and looking like a stylish French filmmaker rather than someone who spends his days belly up to petri dishes, is rightly worried. It turns out that coffee cannot adapt to high temperature or fight off disease, because it lacks essential genetic diversity. Although the list of types of coffee found in the neighborhood cafe looks like a guide book for a trip to exotic regions - sour extract mocha from Indonesia, roasted coffee with a velvety taste from Vietnam, a mug with a soft taste from Madagascar - all this variety hides a surprising fact: the homogeneity of cultivated coffee is unbelievable. In fact, 70% of coffee crops originate from one biological species, Arabica coffee (Coffea arabica). The variety, the growing region and the roasting method are responsible for the wide variety of flavors, but they also mask the genetic history. Almost all the coffee that has been cultivated and nurtured over the course of several centuries, originates from a handful of wild plants from Ethiopia. Today, all the coffee in plantations all over the world contains less than one percent of the diversity found in the wild plants in Ethiopia.
Despite the importance of coffee on a global scale for the economy, politics, and environmental stability, and despite its functions as a cornerstone of cultural life and as an essential supply source of caffeine, it is an "orphan crop", which modern research has largely neglected. There is no giant agricultural company for coffee crops, such as "Monsanto" that deals in agricultural biotechnology and makes a fortune from selling patented seeds. This orphan status does allow small farmers in poor countries to make a decent living growing coffee for export. But on the other hand, this means that there is little investment in science, and thus coffee cultivation remains extremely exposed to any natural hazard. Now, when the threats to cultivated coffee are increasing, researchers have started a race to advance science to save our cup of coffee - before it's too late.
Recruiting diversity
Tim Schilling, a geneticist living in the French Alps, is best known for helping to restore the coffee industry in Rwanda in the early 30s. He made it his goal to bring the much-needed science to the coffee industry. Today, he oversees the "World Coffee Research", a non-profit organization funded by the coffee industry that includes XNUMX companies, large and small. Some call Schilling the "Indiana Jones of coffee," but when he conducts the meeting in Turrialba, in jeans and a white long-sleeved shirt, with black-rimmed owl glasses and thick curls, he looks more like Andy Warhol. Schilling asked the group about the scope of studies examining the effects of climate change and coffee rust on crops. One of the coffee growers in the room raised his hand, with the thumb and forefinger a short distance apart, an international sign for "very little".
Experts fear that the impact of these factors could be enormous. Coffee rot thrives in warm weather, and as the temperature rises the fungus may spread to higher areas. An increase, and even a decrease in the amount of rainfall may also encourage the spread of the fungus. Spraying with fungicides can fight rust, but the sprays are expensive and may not be effective against new strains of the disease.
According to Schilling, the only long-term solution is the mobilization of genetics. As a first step, he wants to use the gene banks of Arabica coffee (C. arabica) and other cultivated coffee species such as Canephora (C. canephora), known in the industry as Robusta, which means strong. Camphor is easier to grow and its yield is higher, but it tastes bitter and is mainly used to increase the volume of inferior types of coffee, such as the coffee served at the CATIE meeting. Cultivated coffee is homogeneous: there are only two species, and yet the multiple varieties of each offer regional genetic variation, just as human populations differ from each other, even though they all belong to the species Homo sapiens. Schilling's master plan involves a relatively simple project that is already underway: swapping coffee varieties between regions and countries, sending plants from the Congo to Brazil, for example, or from Colombia to Honduras, and seeing if they can grow better than the varieties used by local farmers. In 3-4 years the growers will be able to say: "Hey, this coffee from India produces a lot more beans," and then they will be able to choose to sow more of the Indian seeds. As part of this project, scientists in ten countries have identified 30 high-yielding coffee varieties.
Using the genetic diversity between cultivated coffee varieties can help in the short term. However, this will probably not be enough to save the crop. Commercially grown varieties contain only a tiny fraction of the genetic diversity of Arabica coffee and Robusta coffee. And yet, the genetic diversity of the wild plants that correspond to them is truly unbelievable. Recent advances in sequencing the coffee genome have revealed something about the untamed cousins ​​of cultivated beans, which Bertrand calls an "extensive catalog of genes," many of which are housed in gene repositories around the world. He hopes to utilize this rich gene soup to make coffee crops more durable, fertile and very tasty.
The evidence collected at CATIE, regarding the genetic diversity of coffee, overflows. On the other side of the campus where the conference was held, at the end of a dirt road, there is a wooden sign on which is written in yellow letters: "The coffee collection of Ethiopia (of the Food and Agriculture Organization of the United Nations)". Almost ten thousand coffee trees of the Arabica variety, grow here, row after row, and cover about 84 dunams. The plantation was established in the 40s. The selection includes coffee trees collected by various expeditions to Ethiopia, first by the British in World War II and then, in the 20s, by the US Food and Drug Administration (FDA), and by a team of researchers from France. The database also includes coffee trees from Madagascar and other places on the African continent, as well as from Yemen. Unlike seeds of other agricultural crops, such as corn for example, coffee seeds cannot survive in jars stored in refrigerated vaults. Instead they should be grown continuously or kept in a deep freeze. And so in CATIE, one of the most important gene reserves of coffee, the DNA is "stored" as a neglected plantation of coffee trees.
Bertrand is now producing new hybrid varieties of coffee using promising coffee plants from a living gene pool, similar to that of CATIE. The variety he created more than a decade ago, by crossing Arabica coffee with some of its wild cousins, increased the yield by more than 40%. Bertrand and Schilling have now selected 800 plants from CATIE, along with 200 additional plants from gene banks around the world, and sent them to a laboratory in Ithaca, New York, to determine their DNA sequences. This information will help Bertrand assess what qualities each plant might offer.

The researchers are now looking for the genes that may make the plant stronger in different ways: rust resistance, reduced thirst, ability to thrive at high temperatures. To find these plants, Bertrand and Schilling scan the plants with the goal of finding plants that are "blasted with genetic diversity in unbelievable amounts," as Schilling says. They want the widest possible range of traits, in the smallest number of plants. "Then we will crossbreed these plants with plants that have qualities that we all love: wonderful taste, high yield and resistance to diseases that we already know."

to the wild plants
Schilling is convinced that these breeding efforts will produce much better varieties that farmers can grow and coffee roasters can sell and consumers can drink. But he and those who cooperate with him also have another ambition: they want to overcome Mother Nature by introducing new, synthetic varieties of the Arabica variety. In essence, they want to develop a plant that has the taste of Arabica and the properties and yield of Camphor. The intention is to re-do the original hybridization that created Arabica coffee (the hybridization between Canfora coffee and another species, Coffea eugenioides), only that the "parent" group of the hybrid will be much more diverse. To cope with this difficult task, they need to look for more than found in the garden reserves. They should return to the wild plants.

There are currently about 125 known species of coffee, each of which contains more genetic diversity than can be represented in any way in the small sample of the gene bank. And of course new species can still be discovered, assuming the researchers can discover them before they become extinct and disappear.

In 1977 when Aaron Davis finished his doctoral thesis and began looking for wild coffee plants, he did not expect to discover anything new. One day Davis was sitting drinking tea in the Royal Botanic Gardens, Kew Gardens in London, when a famous coffee taxonomy expert happened to sit next to him. Davis asked her how many coffee species there are in the world, where they grow and what their natural habitat is. Her answer to all these questions was: "No one knows." In short, she sent him to find out for himself the answer to his questions. Davis spent the next 15 years wandering around Madagascar, a country known for its variety of coffee, where he found a wide range of species, some already recorded but many unknown to anyone except a few local villagers.

He discovered in Madagascar a coffee plant with the largest fruit, or pod, in the world, approximately three times the usual size, and also a plant with the smallest fruit in the world, about half the diameter of a pinhead. He found two species whose seeds are spread by water, rather than by animals, whose fruits have wings like a folded ribbon. He discovered one species, Coffea ambongensis, whose pods look like brains. Davis' research expeditions showed that wild coffee grows throughout many tropical regions, from Africa to Asia and even as far away as Australia. In Ethiopia, which is now the main territory of Arabica, there are several forests that are packed with Arabica trees, up to two thousand trees per hectare. These plants, Davis believes, have tremendous improvement potential.
However, these wild plants, like their cultivated counterparts, are in trouble: 70% of them are in danger of extinction. 10% of them will disappear within a decade. Alternative land use is the biggest threat. By the 90s, more than 80% of the forests in Ethiopia were cleared. In 2007, Davis' team in Madagascar, where people continue to deforest at an alarming rate, discovered a new species growing in a small area of ​​forest, no larger than the standing area of ​​a baseball player. When it comes to wild coffee plants, he says, in many cases "there's no chance that climate change will have an effect." The plants will simply disappear earlier, along with their surroundings.
Davis worries that researchers are putting too much emphasis on what's already in the gene pools, while potentially vital genetic material is dying out in the wild or being bulldozed. He says that "there is a kind of feeling of 'yes, everything is in our hands, it will be fine', but these wild populations are the storehouse of our genetic resources."

In Ethiopia itself there is another problem. The country, which is the origin of coffee, treasures a large collection of coffee plants that are not found anywhere else in the world. But the government keeps them behind bars and does not allow access to foreign researchers. "A lot of black cats passed between Ethiopia and the coffee industry," explains Davis. "No wonder they are reserved about their genetic resources." A few years ago, for example, a sharp dispute broke out between the coffee chain Starbucks and Ethiopia regarding the country's rights regarding the trademark of cultivated coffee plants from Ethiopia.

The accessibility of germ cells, the organic material stored in gene banks, from Ethiopia could have given Schilling's coffee breeding project a tremendous boost. It is possible that these reservoirs contain essential genes for adapting to high temperatures or growing more pods in a smaller area of ​​land. Schilling hopes that the state's position will soften. In the meantime, the researchers are working with what they have at their disposal.
When Davies rummaged through the archives of Kew Gardens, he discovered records showing that local people in Uganda and elsewhere had, over time, made coffee from wild varieties that grew in their surroundings. The taste was sometimes terrible, but when the wild beans were weighed, they produced a taste that was recognizable as a coffee bean. "Rumor has it that some of the coffee beans used 100 years ago were really excellent. "We're going back and re-examining some of the early civilized species that may have potential, either on their own or in breeding programs," says Davis.
Race against the clock
The outbreak of the coffee scandal hit Central America shortly after Schilling founded the World Coffee Research Organization with the help of an industrial group representing quality coffee companies and boutique companies (the American Association of Coffee Specialists), and with basic funding from the "Green Mountain Coffee" company and the "Coffee Bean International" company. Due to the outbreak, Schilling convened a limited meeting in Guatemala to discuss the organization's ability to operate. Almost immediately he started receiving requests from people who heard about the meeting and wanted to attend it. "It turned into a meeting of about 200 people," recalls Rick Reinhart, executive director of the American Association of Coffee Professionals, and one of Schilling's most important collaborators. "We couldn't accommodate everyone."

Among the interested players was the US Agency for International Development, which invited Schilling to apply for a research grant on coffee rust. The collapse of the Central American coffee industry could ignite a wave of immigration to the US and the US government therefore has an interest in eradicating the disease. The World Coffee Research Organization estimates that the outbreak of coffee rust in 2012 cost coffee growers 548 million dollars. Due to the crisis, the wages of the workers were cut by 15% to 20% and about 441 jobs disappeared. If nothing is done about it, the Central American coffee industry will be completely specialized by 2050.
In 2012, short-term "emergency" responses to the blight crisis began to emerge, such as the supply of fungicides to farmers and credit. However, Schilling believes that a coordinated and much longer-term effort is needed, which will help build a cultivation program of high technology, which will provide growers with new coffee varieties that will withstand climate hazards and pests.
In many respects, the blight epidemic is the prediction of what may happen to coffee worldwide, when new diseases strike defenseless plants, weakened by rising temperatures or extreme weather. Carlos Mario Rodríguez, director of global agronomy for Starbucks, said at the CATIE meeting that Chinese farmers are reporting at least five new types of heldoon. "In the highlands, the farmers didn't know the coffee rot until now, and now they do," said Rodriguez.

For the coffee to survive it must be considerably more durable. Brett Smith, president of a coffee production company from North Carolina in the USA, compares the DNA problem to "going public with very few shares." However, he is confident that Schilling and his colleagues will be up to the task of protecting the coffee.
The only question is whether they will do it ahead of time. "If only we had done this research ten years ago, we wouldn't be facing these problems now," Reinhart says. "If we don't start today, every day we delay is precious time and we could face an existential threat."

And more on the subject
Uncommon Grounds: The History of Coffee and How It Transformed Our World. Revised edition. Mark Pendergrass. Basic Books, 2010.
The Impact of Climate Change on Indigenous Arabica Coffee (Coffea arabica): Predicting Future Trends and Identifying Priorities. Aaron P. Davis et al. in PLOS ONE, Vol. 7, no. 11; November 7, 2012.
The end of the orange juice, Anna Kushment, Scientific American Israel, June-July 2013, page 46.

in brief
Climate change, diseases and harmful insects threaten the cultivated coffee trees.
The homogeneity of coffee crops makes them especially vulnerable: almost all coffee in the world comes from a few plants grown in Ethiopia.
Little scientific research has been directed at coffee cultivation, but this situation is about to change. Scientists are now hurrying to insert new beneficial genes into the coffee crops, using methods of hybridization.

Gene reserves and wild plants are thoroughly surveyed to discover as wide a genetic diversity as possible that will strengthen the crops against the impending crisis.
on the notebook
Hilary Rosner is a freelance reporter based in Colorado. She has written, among others, for the New York Times, Wired, Popular Science and Mother Jones magazines.

Findings
Coffee in crisis
Coffee crops all over the world are remarkably similar to each other genetically. This homogeneity leaves the cultured coffee exposed to threats of diseases, pests, temperature changes and fluctuations in the amount of precipitation. As global climate change occurs, these threats become worse: extreme weather events become more common and fungi and insects spread to areas where they had never been before. Populations of mini bar coffee, with larger pools of genetic variation, are better equipped to deal with these threats. However, they have a problem of their own: deforestation. Here are representative examples of the recently affected areas.

Threats
Diseases: Fungi such as the coffee weevil (Hemileia vastarix) and Colletotrichum kahawae have destroyed crops in Central America and Ethiopia, respectively.
Insects: A small beetle known as the cherry weevil has decimated crops in Ethiopia and elsewhere. Climate change is expanding the insect's habitat.
Deforestation: the loss of habitats for wild coffee species, such as in Ethiopia and Madagascar, means the loss of genetic diversity that could have strengthened cultivated coffee plants.

Climate change: Excess rainfall has significantly reduced crops in India and Indonesia. Seasons of drought and high temperatures have taken their toll on Brazil.