What genetics research can do for coffee

Nearly 4000 kilometres north of the equator sits 17-hectare farm Good Land Organics. While agriculture has long been a thriving industry in Califo undefined

rnia, this particular farm is host to a variety of non-native and exotic crops – one of which is coffee.

California-grown coffee is important for two reasons, the first being that it’s never been done before in the 48 contiguous states of the US.

Coffee is a crop traditionally grown in the tropical regions that hug the equator. The “coffee belt” extends about 25 degrees north and south of the equator and is home to prime coffee-growing countries including Costa Rica, Colombia, Brazil, Kenya and Ethiopia.

Good Land Organics, on the other hand, is even further north, at a latitude nine degrees from the top of the coffee belt, according to reports from the University of California, Davis.

The second reason is that it has recently provided scientists at UC Davis with accessible, high-quality, disease-free coffee plants for research and testing. In January, the university announced that a team of researchers, led by geneticist Juan Medrano, had successfully sequenced the Coffea arabica genome and made it publically available. This information is crucial for scientists, breeders and industry experts in improving coffee quality, yield, resistance to disease and pests, adaptation to climate and more.

Made in the USA
Good Land Organics owner Jay Ruskey has been growing coffee for nearly 15 years, after being introduced to the idea by farm adviser Mark Gaskell.

Ruskey was already growing exotic fruits such as finger limes, cherimoya, passionfruit and dragon fruit, but he was sceptical when Gaskell brought over some coffee trees to grow.
“Honestly I didn’t think it’d work,” Ruskey says. “There was a degree of naïveness, but being naïve to the coffee industry ended up being a good thing.”

Although the coffee did very well, the success wasn’t without trial and tribulation.

“I spent many years refining our cultivation practices and improving post-harvest processes,” Ruskey explains. “My biggest surprise was all that is involved in post-harvest.”

Along the way he often looked to the coffee industry for help and came back empty-handed, due to the crop’s primitive nature. With irrigation, fertiliser, and placement in relation to sun, “we were testing things farmers never did before, so there weren’t many parameters”, he says.

Farmers in traditional coffee-growing regions don’t have access to the resources or research that many first-world farmers like Ruskey do. “Because of the technologies and resources we have,” he adds, “latitude is now part of the coffee equation, whereas it wasn’t thought possible before.”

Arbica flower

The scientific method
Similar to Ruskey’s introduction to the idea of growing coffee, Medrano was encouraged by peers in Central America to apply his genetics background to Coffea arabica.

Despite the species supporting more than 70 per cent of global coffee production and a multi-billion-dollar industry, he believes coffee has generally been neglected in the research world.

“Coffee has been an orphan in regards to studied crops, with very little done in genomics,” says Medrano, whose experience is focused on animal genomics. “If you look at any other crop or domestic animal, technology has advanced and provided opportunity for studying and learning from its DNA.”

Medrano attributes this to a disconnect between production and commercialisation, a “separation that prevents anyone from truly investing in the crop”. While big brands prosper in the booming specialty coffee market, smallholder farmers in Central America, including Medrano’s home country Guatemala, have seen their livelihoods decimated by disease because they don’t have access to resources supported by research. In 2012 and 2013, an epidemic of coffee leaf rust (Roya amarilla) swept through the region, afflicting more than 50 per cent of crops, according to the Colombian Coffee Growers Federation (FNC).

Needless to say, Medrano was interested in seeing what genomics could do for coffee but he needed collaborators, so he recruited UC Davis colleagues Allen Van Deynze, a plant breeder, and Dario Cantu, a plant pathologist.

Once Medrano had his team, he sought out funding and plant material – the former being much more difficult to procure than the latter. Because of the aforementioned disconnect in the coffee industry, Medrano had a hard time securing financial support for his project: “Everyone thought it was interesting and very important, but no one was willing to put in funding.”
Fortunately a beverage maker out of Japan came through to fund the project. The Suntory Group’s Global Innovation Center Limited saw an opportunity to contribute to the scientific advancement of coffee, which makes up a portion of Suntory Group’s beverage portfolio.

And thanks to Ruskey’s well-established crop just down the coast, obtaining plant material to study was much easier. “We thought we would have to go to Central America for samples,” Medrano admits, “but then we met Jay and realised we could collect our samples here [in the US]. It was a perfect match.” In addition to proximity, Ruskey had a well-established coffee crop that was healthy and free of any disease traditional to the coffee world.

Dario Cantu

Among his varietals was one in particular: UCG-17 Geisha. This is the varietal that Medrano and his colleagues used for developing the Coffea arabica genome sequence. Though not widely used on coffee plantations around the world (most common are Typica and Bourbon), Geisha is a highly appreciated varietal because of its unique flavour and high cupping quality.

Global research efforts
While the team’s efforts have been historic, this isn’t the first time the coffee genome has been sequenced. In 2003, Cenicafé, the research and development arm of FNC, commenced significant genomics studies of the Coffea arabica and Coffea eugenioides species. Meanwhile, Brazil was conducting similar research, and France was focused on sequencing Coffea canephora, the species more commonly known as Robusta.

Due to the coffee belt region’s susceptibility to disease and Colombia’s placement perfectly along the belt, Cenicafé was largely motivated to leverage genomics for disease mitigation and prevention. According to FNC, the research deepened knowledge of both coffee leaf rust and the coffee berry borer, which both thrive on the wet, tropical climate. Coffee leaf rust attacks the plant’s leaves, causing them to prematurely shed and restrict coffee berry growth. The coffee berry borer attacks and destroys the berry, drilling into the centre to live and reproduce.

With this new information, scientists can develop resistant varietals. But their development can take decades, says Álvaro Gaitán, Director of Cenicafé, “so genomics studies can help coffee breeders reduce the costs and time required to release improved seeds [to growers]”.

Time is of the essence when the original breeding cycle to develop new varieties can take 12 years or more. Additionally, it can take nearly four years to completely switch out a farm’s varietal. Because “95 per cent of farmers are small producers with coffee plantations of less than two hectares,” says Gaitán, “better coffee varieties are needed to improve their economic stability and to ensure a continuous coffee supply to the market.”

The industry’s driving forces
While disease was Cenicafé’s main driving force behind the genomic studies, California’s needs are different. The arid climate is less susceptible to moisture-based diseases. Instead, drought-stricken California has been more concerned with having enough moisture for its agriculture industry. As such, climate change is a big focus for Medrano and his team.

Environmental experts say global temperatures are on track to increase 4 degrees Celsius or more by 2100 in regions around the world, including parts of North America.

“These increases will affect coffee significantly,” Medrano says.

“We will have to produce coffee at higher altitudes and latitudes. Jay has proved [the latter] can be done, which provides necessary alternatives with the effects of climate change.” Further, the genome project provides necessary DNA information to develop coffee varieties that can adapt with the climate.

The other focus of the research is on coffee quality, both of the plant and the consumed product.

“Many farmers rely on coffee growing for subsistence, so we need to get them higher-yielding coffee,” says Ruskey. “If we can provide breeders with genetics information to create higher yield, then it’s one more tool for breeders to get farmers what they need.”

According to UC Davis, the researchers will also focus on identifying genes and molecular pathways associated with coffee quality to gain a better understanding of the flavour profiles of Geisha coffee.

Juan Medrano

Cenicafé is also dedicating genetics studies to climate change and quality, says Gaitán. “Understanding the effects of the environment on the expression of genes […] opens the door to a wider and perhaps more complex offer in terms of cup quality. Gene characterisation can reveal which parts of the DNA are related to bean size, caffeine content and many other traits that the market is looking for today.”

Ruskey sells his green coffee at local farmers markets, where he earns US$60 to $80 per pound. It’s also won several cupping quality awards. “We see hints that are favourable for having an industry for coffee in coastal California,” says Ruskey, referring to the expanding market for specialty coffee and California’s affinity for premium goods.

“It fits the Southern Californian environment,” adds Medrano. “There’s the interest and the wealth. The coffee industry has been growing 5 per cent per year, so there’s definitely the demand for it.”

On a global scale, Medrano’s research, as well as that from Cenicafé and others, means greater access to valuable information and data that can potentially help players in every link of the global supply chain.

While California has long been investing in technology and knowledge for its agriculture industry, Medrano says advancements will ultimately require a shift on the part of the global coffee industry and more support in the area of science. The new genome sequence is publicly available on, the public database for comparative plant genomics coordinated by the US Department of Energy’s Joint Genome Institute. GCR

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