Illustration: Sarah Grillo/Axios

Scientists have sequenced the human genome, thousands of microbes, plants and other animals. But the coffee plant remains a stubborn beast.

Why it matters: Coffee is under increasingly urgent risk from disease and climate change, which have devastated huge batches of crops and today threaten the livelihood of some 125 million people. But biologists, working on mapping and redesigning the plant, think that they are getting closer to saving coffee.

What's going on: Science's understanding of the coffee plant is surprisingly rudimentary, despite the enormous volume of the bean traded globally, its massive popularity among consumers, and its significance for many developing countries.

But in an effort to create new plants, Juan Medrano, a professor at UC Davis, leads a lab that is sequencing the genome of a popular strain of coffee plant.

  • In 2012, a disease called coffee rust began destroying huge amounts of crops in Central and South America. Coffee production in El Salvador, the most affected country, alone dropped by 70% between the 2010-2011 and 2013-2014 seasons.
  • That's when Medrano went looking for information about the coffee genome. But he found nothing. "It was a real surprise to me that so many other species have been sequenced and coffee was kind of like an orphan," he tells Axios.
  • So he and a team at UC Davis set about doing it themselves, focusing on a variety of the popular arabica plant. They published initial findings in 2017 and are continuing to map out the genome, convinced it could be the key to saving coffee.

The goal is a more robust plant: Medrano and other biologists are looking for genes associated with resistance to deadly diseases like coffee rust, or with resilience against increasingly common extreme temperatures and drought. If they can connect genes with the physical characteristics they control, they could create plants that can stand up to steadily worsening threats.

Among the challenges:

  • Mapping the genome is a long and expensive process, made difficult by the complexity of the most popular type of coffee plant, a hybrid of two other species. "It's like doing a puzzle — where you have four puzzles with slight differences mixed together," says Megan Hochstrasser of the Innovative Genomics Institute, a partnership between UC Berkeley and UC San Francisco.
  • And researchers don't always have the raw materials they require. "The lack of research in coffee agronomy and biology in the last 20 years means that there are currently few gene candidates for editing that could result in agronomically relevant traits, like disease and pest resistance, climate adaptation, improved yields or new qualities," says Alvaro Gaitan, director of Cenicafé, Columbia's national coffee research center.

The upside is that the labs have several tools to work with.

  • Medrano's preferred approach is to breed plants, selecting for traits that make them hardy. Humans have been modifying plants this way since they were first domesticated some 10,000 years ago.
  • Another, distinctly 21st century alternative is to deploy CRISPR, a gene editing tool that allows scientists to toggle single genes on and off in a plant or animal's DNA.

The big question: Where to apply those tools in the genome.

  • CRISPR can help find the best targets, says Hochstrasser because it allows researchers to turn off individual genes to see how each affects the plant.
  • But you need an idea of where to start from among the coffee plant's 50,000 genes, says Gaitan, the Cenicafé director. "And for that, we need more research."

What's next: Making tougher coffee plants with CRISPR will soon be within reach, Hochstrasser says. "It's just a matter of time."

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