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Can the sequencing of coffee genome lead us to the perfect cup?

The double helix structure of DNA in coffee genome

MILAN – The following article, appeared in the issue 19/20 of the magazine Espresso Ideas published by Simonelli Group, provides an important insight into the studies on coffee genome. We reproduce the article below by kind permission of Simonelli Group.

For centuries, caffeine has been a valued psychotropic. It makes us alert, helps us concentrate, improves memory—and is mildly addictive. Today caffeine is the most widely used drug on the planet (though partly due to its presence in aspirin products).

In recent decades, the coffee plant and its treasured, caffeinated seeds have been studied at the molecular level to determine what makes a coffee good—or bad. Scientists’ quickly found their work was cut out for them, after discovering that coffee contains more than 1,000 chemical compounds.

Not to mention the effects that climate, farming, processing and roasting have on those compounds.

With coffee’s incredible complexity, making sure the “good tasting” flavor compounds outnumber “bad” flavors is no easy task. Where on Earth to begin?

Physiology and agronomic studies, along with a better understanding of the physical and biochemical consequences of harvesting and processing, has already yielded significant improvement of quality. The coffee genome could take coffee quality even further.

The Robusta genome was sequenced in 2014, and in 2017, Arabica joined the club

Both genomes give coffee researchers hope of discovering a better-tasting, and possibly even healthier cup. Finding out which genes create desirable flavors and aromas may make it possible to selectively breed or genetically engineer better coffees. (Though weather and farming technique play a huge role as well.)

“The genome sequence contains information crucial for developing high-quality, disease-resistant coffee varieties that can adapt to the climate changes that are expected to threaten global coffee production in the next 30 years,” said Juan Medrano, a geneticist in the UC Davis College of Agricultural and Environmental Sciences and co-researcher on the sequencing effort, which took several years.

“We hope that it will eventually benefit everyone involved with coffee—from coffee farmers, whose livelihoods are threatened by devastating diseases like coffee leaf rust, to coffee processors and consumers around the world,” he said.

To sequence the Arabica genome, Medrano teamed with molecular breeder Van Deynze, as well as Cantu, a plant geneticist. Coincidentally, as they were starting their research, the team met farmer Jay Ruskey, who was growing the first commercial coffee plants in the continental United States at his farm near Santa Barbara. Ruskey had also planted coffee trees on roughly 20 other farms, from San Luis Obispo to San Diego, launching what he believes will become a new specialty-coffee industry for California.

Working with Ruskey, the UC Davis researchers collected genetic material—DNA and RNA samples—from various tissues and developmental stages of 23 Geisha coffee trees growing at Ruskey’s farm.

Coffea arabica’s complex genome

Coffea arabica is a hybrid cross derived from two other plant species: C. canephora (robusta coffee), and the closely related C. eugenioides. As a result,C. arabica‘s genome has four sets of chromosomes, unlike many other plants—and humans—which have only two chromosome sets.

The researchers sequenced samples from the 23 Geisha coffee trees to get a glimpse of the genetic variation within the Geisha family and among 13 other C. arabica varieties, which will also be important for developing plants that can resist disease and cope with other environmental stresses.

One interesting find: The Geisha genome is made up of 1.19 billion base pairs—about one-third the size of the human genome

Going forward, the researchers will try to identify genes associated with coffee quality, in hopes that these will provide a better understanding of the flavor profiles of Geisha coffee.

Genomic tools including genetic maps offer the opportunity to accurately decipher the genomic aspect of coffee’s quality components. These should allow coffee researchers to identify the genomics involved in the variability of quality, a first step toward the identification of the genes involved in the natural variability of coffee quality.

Tastes and smells: also addictive?

The newly mapped genome is also unlocking the origins of the tastes and smells that keep us hooked on coffee. “We’ve identified many different genetic aspects of aroma and flavor,” says Albert.

The Science study highlighted genes that make alkaloid compounds, which are known bitter flavors, as well as enzymes that make flavonoid compounds.

Finding out exactly which genes are responsible for the most desired flavors or aromas may make it possible to produce coffee that delivers more of what we love through selective breeding or genetic engineering

Coffee’s caffeine-producing enzymes could also help decaffeinate your brew. “So to make decaf coffee, you wouldn’t have to go through the process of extracting the caffeine. You could just grow coffee beans that don’t make it at all,” says Albert.

Coffee’s complicated chemistry will continue to be revealed by genome analysis, which could provide the basis for breeding or genetic manipulation strategies to maximize coffee’s good elements (rich flavor, disease resistance) and minimize its weaknesses (bitterness, undesirable levels of acidity, climate incompatibility). “Anything that’s known about coffee and of interest could be targeted genetically,” Albert says.

Why do Plants Produce Caffeine?

While the answer to how coffee trees developed caffeine has yet to be answered, the genome could help find it.

Caffeine may stop animals from eating the leaves due to their high caffeine content. (Brewed coffee leaves don’t taste anything like tea, though. If they did they’d already be on the market.) It’s also possible that caffeine leaches into the soil around coffee trees, keeping seeds from other plants from growing there. Or caffeine may attract pollinators in the same way it does humans—by giving them a jolt, so they come back for more.

“It wouldn’t surprise me if all three of these theories are correct to some degree,” evolutionary biologist Victor Albert told Smithsonian magazine. Albert co-authored a comparative analysis in the journal Science about the sequencing of C. Arabica and caffeine biosynthesis.

It might seem logical that coffee would be related to tea or cacao, since they all contain caffeine. But the genome study shows that the genes that brew caffeine in coffee are different from the ones that make the compound in tea and cacao. Albert told Smithsonian, “Coffee and tea last shared a common ancestor maybe 100 million years ago. Coffee and chocolate perhaps 120 million years ago. So we’re talking about plants that have been separated for a very long time that have independently evolved the capacity to make caffeine.”

Can The Coffee Genome Help Crops Survive Climate Change?

Worldwide coffee production is currently dependent on just a few varieties, which makes them vulnerable to disease, pests and climate change. Until now, few scientific papers dealt with the identification of genes that determine coffee quality.

Daniel Zamir of the Hebrew University of Jerusalem hopes the genome can be used to boost coffee breeding and keep production reliable.

“The key for ensuring that coffee can survive as an affordable crop lies in the genetic variation,”

Zamir wrote in a perspective article accompanying the Science study. He called for use of genomic-assisted breeding projects in coffee exporting countries to ensure coffee’s future.

Jose Kawashima, president and CEO of Mi Cafeto Co. Ltd., a specialty coffee company in Japan, stresses the importance of the coffee genome’s discovery for all levels of coffee production.

“Having worked in the coffee industry for over 40 years and visited coffee farms around the world, I have never witnessed as many quality C. arabica coffee farms under duress due to deteriorating social issues and the impacts of climate change,” he said. “It is urgent that this scientific discovery be used to implement practical improvements at the farm level to sustain the future of the coffee industry.”