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RENEE MONTAGNE, HOST:

All week here on MORNING EDITION we've been talking coffee.

(SOUNDBITE OF SONG "COFFEE TIME")

NATALIE COLE: (Singing) Coffee time, let's listen to some jazz and rhyme and have a cup of coffee.

MONTAGNE: If you are hooked on coffee, as some of us are, you may want to listen closely. Coffee plants are facing threats - among others, disease and climate change. To protect them, scientists are looking to coffee's genes. Here's NPR's Dan Charles.

DAN CHARLES, BYLINE: There's an agricultural research institute near Turrialba in Costa Rica where you can see and touch the history of coffee, maybe also part of its future. The coffee trees here, spread across 25 acres, take you back to coffee's origins.

EDUARDO SOMARRIBA: So the story starts in Africa, no? East Africa.

CHARLES: Eduardo Somarriba, a researcher at the Center for Tropical Agricultural Research and Education - CATIE - is walking me through long rows of small coffee trees. There's a wooden sign in front of the trees: Coffee Collection of Ethiopia. Every tree here has a number.

CARLOS CORDERO: (Spanish spoken)

CHARLES: Carlos Cordero, another scientist here, chooses tree number 4535 at random and looks up this entry in a catalog of the collection that he brought along.

CORDERO: (Spanish spoken)

CHARLES: The seed that grew into this tree came from the highlands of Ethiopia, where this particular species of coffee, Coffea arabica, grows wild. Scientists from the U.N.'s Food and Agriculture Organization collected the seed in Ethiopia and brought it here 50 years ago.

CORDERO: (Through translator) Introduced here in 1965 in June.

CHARLES: Not far away from this tree, CATIE also has samples of another coffee species - Coffea canephora - often called robusta.

SOMARRIBA: Which basically what we see here, these trees over here.

CHARLES: The robusta trees are bigger. They're also hardier than arabica plants. They're widely grown in Vietnam and parts of Africa, but robusta coffee has a bitter taste, and some purists look down on it. This whole collection is like a storage vault for a piece of coffee's ancient and wild African past. But the interesting thing about it is that today's commercial coffee production is based on only a tiny slice of it. Arab traders brought coffee plants from Africa to the Middle East and to Europe many centuries ago. In the 1700s, Europeans brought two lines of Coffea arabica - two genetic types - to Latin America.

SOMARRIBA: We got the Bourbon line and also the Typica line. And then combinations between these two, no?

CHARLES: These two types of coffee trees - just those two - are the ancestors of much of the coffee in Latin America and really in the world today. In fact, there's a lot more genetic variety in this one little field at CATIE than there is in all the coffee plantations of Central and South America - and that is part of the problem. Because coffee faces some serious threats - a changing climate, for instance. Prime growing areas in the mountains will get hotter and plants will suffer. Even more urgent right now is a problem called leaf rust.

EMILIA UMANA: See how many plants don't have leaves anymore?

CHARLES: Yeah, yeah.

UMANA: That's leaf rust.

CHARLES: Emilia Umana, who works for the coffee trading company ECOM Trading, has stopped her car right in the middle of a lonely road in the Tarrazu region of Costa Rica. Ahead of us, up on the side of a mountain, there's a swath of coffee bushes that have been stripped bare by disease. Leaf rust swept across much of Central America this past year, also parts of South America. Several countries have declared it a national emergency. Millions of farmers are looking for answers. One potential answer could be new varieties that can fend off the disease. A few such varieties already exist. Emilia Umana stops her car again.

UMANA: Look at these plants. You see those little orange spots on the leaves? That's leaf rust. And see the other ones that don't have any? Those are leaf rust-resistant plants.

CHARLES: If I was a farmer, she says, I'd just plant these.

UMANA: I mean I love them. They're really tough. They're just like the John Deere of the coffee.

CHARLES: Unfortunately, this variety, called Catimor, is not perfect.

UMANA: Many people don't like it. People say it doesn't taste as good.

CHARLES: In fact, some people say Catimor could be the downfall of coffee. One of its grandparents is from the robusta side of the coffee family, and you can taste that robusta bitterness in its beans. Researchers are hoping to create something better - a plant as tough as Catimor with beans sweet enough for any taste test. Maybe what they need to fight leaf rust or adapt to a warming planet are genes that are hidden in the collections of coffee trees at CATIE, or maybe, says CATIE's Eduardo Somarriba, it's out there in the forests of Africa, where coffee still grows wild.

SOMARRIBA: So we have to really go back to the forest, capture what is in the wild, bring them into the analysis of the science, to really in somehow save this genetic variability.

CHARLES: Somarriba says there's been very little money available for this. Very few of the coffee trees in CATIE's Ethiopian collection have been genetically analyzed. That's even more true of other coffee species, relatives of arabica and robusta. Somarriba says these tropical trees are like neglected children.

SOMARRIBA: Coffee and cocoa - some people call them orphan crops. Because really the development of them, despite their importance in trade, like we have an international center for maize and wheat, no? We don't have one for coffee.

CHARLES: Why?

SOMARRIBA: I don't know. Maybe it's because it's in the tropics or something like that? I don't know.

CHARLES: Some people in the coffee industry now are saying this kind of neglect has to end. It's not just to fend off threats from leaf rust, for instance. Peter Giuliano, from the Specialty Coffee Association of America, says the genetic storehouse of CATIE's collections or in the wild may also contain treasures of taste.

PETER GIULIANO: One of the biggest stories of the last five years in coffee is the sort of discovery of this variety called Geisha.

CHARLES: Geisha trees are the offspring of a coffee tree in Ethiopia that collectors brought to CATIE in Costa Rica in the 1950s. Seeds from that tree found their way to a farm in Panama. And then coffee connoisseurs found that this variety, grown in that environment, had a unique and wonderful taste.

GIULIANO: Very quickly this coffee from this farm became sort of a rock star in the coffee world.

CHARLES: It sold for incredible prices at auctions. And now coffee retailers are thinking maybe there are more varieties like this waiting to be uncovered. Earlier this month, Peter Giuliano organized a big meeting of the Specialty Coffee Association just about coffee genetics. Some of the biggest names in the high-end coffee business talked about leaf rust, about conserving what's left of forests in Ethiopia, where Coffea Arabica grows wild, also about breeding new varieties. Giuliano says it was a heavy dose of science for a roomful of business people and coffee lovers.

GIULIANO: But everyone was up for it and really inspired. And now we can make good decisions about how we want to grapple with these problems that we're facing.

CHARLES: They've already made one decision. Many coffee roasters, including some of the big ones, are helping to fund a new research institute called World Coffee Research. And one of its first projects is a genetic analysis of the coffee tree collections in Costa Rica at the research center called CATIE. Dan Charles, NPR News.

(SOUNDBITE OF MUSIC)

MONTAGNE: Later today, join us for a coffee klatsch in NPR's virtual coffeehouse. At noon Eastern time, Dan and Allison Aubrey, along with special guests from the series, will be answering questions in a Google hangout. Get in on the conversation by going to NPR.org/Coffeehouse.

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