Feb 23, 2019

The scientists saving coffee

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."

Go deeper

Coronavirus dashboard

Illustration: Sarah Grillo/Axios

  1. Global: Total confirmed cases as of 3:30 p.m. ET: 710,918 — Total deaths: 33,551 — Total recoveries: 148,900.
  2. U.S.: Leads the world in cases. Total confirmed cases as of 3:30 p.m. ET: 135,499 — Total deaths: 2,381 — Total recoveries: 2,612.
  3. Federal government latest: The first federal prisoner to die from coronavirus was reported from a correctional facility in Louisiana on Sunday.
  4. Public health updates: Fauci says 100,000 to 200,000 Americans could die from virus.
  5. State updates: Louisiana governor says state is on track to exceed ventilator capacity by end of this week — Cuomo says Trump's mandatory quarantine comments "panicked" some people into fleeing New York
  6. World updates: Italy on Sunday reports 756 new deaths, bringing its total 10,779. Spain reports almost 840 dead, another new daily record that bring its total to over 6,500.
  7. What should I do? Answers about the virus from Axios expertsWhat to know about social distancingQ&A: Minimizing your coronavirus risk
  8. Other resources: CDC on how to avoid the virus, what to do if you get it.

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Trump touts press briefing "ratings" as U.S. coronavirus case surge

Photo: Drew Angerer/Getty Images

President Trump sent about a half-dozen tweets on Sunday touting the high television ratings that his coronavirus press briefings have received, selectively citing a New York Times article that compared them to "The Bachelor" and "Monday Night Football."

Why it matters: The president has been holding daily press briefings in the weeks since the coronavirus pandemic was declared, but news outlets have struggled with how to cover them live — as Trump has repeatedly been found to spread misinformation and contradict public health officials.

World coronavirus updates: Total cases surge to over 700,000

Data: The Center for Systems Science and Engineering at Johns Hopkins, the CDC, and China's Health Ministry. Note: China numbers are for the mainland only and U.S. numbers include repatriated citizens and confirmed plus presumptive cases from the CDC

There are now than more than 700,000 confirmed cases of the coronavirus around the world, according to data from Johns Hopkins. The virus has now killed more than 32,000 people — with Italy alone reporting over 10,000 deaths.

The big picture: Governments around the world have stepped up public health and economic measures to stop the spread of the virus and soften the financial impact. In the U.S., now the site of the largest outbreak in the world, President Trump said Saturday he would issue a "strong" travel advisory for New York, New Jersey and parts of Connecticut.

Go deeperArrowUpdated 2 hours ago - Health