Will Coffee Plants Survive Climate Change? Genomes Reveal Clues from the Past

I gaze at the ever-changing Starbucks menu, flummoxed.

Should I get a skinny caramel macchiato? A java chip frappucino? Or a plain flat white?

The many variations on the coffee theme might suggest a great diversity among the plants behind the drinks, but actually, about 60 percent of coffee is of the Arabica variety. Starbucks uses these beans exclusively, which are grown in only a few places in the world, where pathogens are scarce and climate favorable. Arabica plants are highly vulnerable to many pests and pathogens due to its low genetic diversity, reflecting a long history of inbreeding in small populations.

Now re-sequencing the Arabica genome reveals that nature gave us the much beloved plant – not selective breeding by ancient farmers. A research team from the University at Buffalo relate the refined family history of Coffea arabica in Nature Genetics. “With an estimated production of 10 million metric tons per year, coffee is one of the most traded commodities in the world,” they write. Nestlé Research funded the project.

A Sensor for Climate Change?

Over the millennia, populations of Arabica have surged and plummeted, in sync to periods of global heating and cooling, long before we selectively bred the plant into our preferred brews. Discovering signals in the genome sequences of coffee plants whose ancestors adapted to temperature shifts offers clues to how the plant might fare as the Earth warms.

“A detailed understanding of the origins and breeding history of contemporary varieties are crucial to developing new Arabica cultivars better adapted to climate change. We’ve used genomic information in plants alive today to go back in time and paint the most accurate picture possible of Arabica’s long history, as well as determine how modern cultivated varieties are related to each other,” said author Victor Albert, Empire Innovation Professor in the UB Department of Biological Sciences.

Evidence is abundant for signs of adaptation to past climate fluctuations in coffee genome sequences because the plants evolved in Ethiopia where many human and pre-human remains have been found. Researchers roughly date events that led to today’s crops by considering changes in DNA sequences and mutation rates. Archeological evidence, such as preserved seeds, complements DNA sequence studies.

Crop Species Commonly Double Their Genomes as They Evolve

The genomes of plants, especially those that agriculture has altered, are famous for doubling, tripling, even quadrupling and octupling their chromosome sets as groups hybridize and their merged chromosome sets transmitted.

Durum wheat, used in pasta, has four sets of chromosomes; bread wheat has six. The number of genomes in some sugarcane plants can even exceed eight. When genomes merge, a few redundant genes are jettisoned, and the intermingling chromosome sets settle into a peaceful co-existence of sorts. A new plant variety is born.

But in humans and other animals, just one extra or missing chromosome can be devastating. Having extra sets of chromosomes is termed polyploidy. All of our cells except sperm and egg are diploid, meaning two copies of each chromosome type. Rarely a polyploidy baby is born, but doesn’t live long.

With newer genome sequencing technologies that evaluate bigger chunks of DNA at a time, it’s become easier to catalog the chromosomal doublings that are part of the evolutionary backstory of many plant species. And those multiplications hold clues to adapting to climate change.

A Brief History of Arabica Coffee

The source of coffee, Coffea arabica, has two complete sets of chromosomes (an “allotetraploid”), totaling 44, from a natural merging of the genomes of two forebears. They were the ancestors of present-day Coffea canephora (the source of Robusta coffee, used in the instant variety) and Coffea eugenioides.

The genome doubling that founded coffee likely happened between 350,000 to 610,000 years ago, in the forests around the Great Rift Valley of Ethiopia and northern Uganda. The plants that the researchers collected revealed a geographic split, with wild varieties originating from the western side, while cultivated varieties originated from the eastern side closest to the Bab al-Mandab strait that separates Africa and Yemen.

Mother Nature gave us our modern brews, according to the genetic findings. “The crossbreeding that created Arabica wasn’t something that humans did. It’s pretty clear that this polyploidy event predated modern humans and the cultivation of coffee,” Albert said.

But before coffee became a crop, three population bottlenecks (when many individuals die) narrowed the gene pool, leaving only a few individual plants to found future groups. Genetic diversity plummeted. The initial bottleneck took place about 29,000 generations — or 610,000 years — ago, the investigators estimate, suggesting that Arabica formed before that, from 610,000 to 1 million years ago.

By about 30,000 years ago, two groups of plants remained, one remaining wild, the other seeding the direct predecessors of Arabica. But the plants also crossbred occasionally, slightly mixing the populations.

Cultivation of coffee began in Yemen in the 15th to 16th century. Around 1600, people smuggled Yemeni seeds to India, where growing what would become Arabica coffee began in earnest.

“Yemeni coffee may be the founder of all of the current major varieties. Coffee is not a crop that has been heavily crossbred, such as maize or wheat, to create new varieties. People mainly chose a variety they liked and then grew it. So the varieties we have today have probably been around for a long time,” said Patrick Descombes, of Nestlé Research.

By 1700, the Dutch began growing Arabica in southeast Asia, which became the forebears of the modern coffee plant. One subgroup of Arabica is Typica, from tall and less productive trees compared to other varieties, but with a smooth, sweet brew that is in high demand. A single plant shipped to Amsterdam in 1706 led to cultivation of Arabica in the Caribbean by 1723.

Meanwhile, the French cultivated Arabica on the island of Bourbon (now called Réunion). A lone surviving plant, by 1720, led to founding the modern Bourbon group of Arabica brew. And then the Typica and Bourbon lineages seeded today’s global Arabica cultivars, with a few other wild coffees persisting in Ethiopian forests.

Genetic Diversity Plummets

Over the years, Coffea arabica underwent several population bottlenecks, as natural stress reduced populations to one or a few individuals.

The strangling bottlenecks, along with merging diploid genomes, fueled a plummeting of the genetic diversity of modern coffee plants. That inbreeding has made the crop susceptible to many plant pests and diseases. Infection with the fungus that causes coffee leaf rust, for example, restricts the sites where Arabica coffees grow to only a few locations.

But nature also provides resistance to disease. Natural breeding with other strains – called introgression – in 1927 on the island of Timor led to a hybrid between Arabica and the modern descendants of C. canephora, the source of Robusta, which is immune to coffee leaf rust. But the tradeoff for this natural protection is that the brew doesn’t taste as good to human palates.

Today, knowledge of Arabica’s natural origins and breeding backstory, coupled with the ability to sequence genomes, is enabling researchers to guide future evolution to fashion coffee plants that can better withstand rising temperatures.

DNA Data

The University at Buffalo researchers compared the DNA sequences of each chromosome of 41 wild Coffea arabica plants as well as descendants of its ancestral species, C. canephora (Robusta) and C. eugenioides. The plants were wild or cultivated accessions (plants of the same species collected at one time from a specific location). They included an 18th century specimen that Swedish naturalist Carl Linnaeus used to name the species.

The investigators could then reconstruct the coffee plants’ spread around the world. The strategy also revealed parts of the genome that harbor genes that provide resistance to certain pathogens.

“We used state-of-the-art genomics approaches – including long- and short-read high throughput DNA sequencing – to create the most advanced, complete and continuous Arabica reference genome to date,” said Descombes. A computational modeling program identified DNA sequences that indicate “signatures” of the original “event” that led to coffee.

The Role of Climate Change

The modeling fleshed out what we know of the natural history of coffee. Populations were small from 20,000 to about 100,000 years ago, with extended drought and cooler temperatures from 40,000 to 70,000 years ago.

The plants flourished from 6,000 to 15,000 years ago, when Africa was humid and growth lusher. The wild varieties diverged in their shared evolution from the plants that humans would eventually fashion into Arabica coffee about 30,000 years ago. Interbreeding may have stopped entirely by 8,000 to 9,000 years ago, as sea levels rose.

Will climate change usher in population bottlenecks that may send coffee on the same path as the endangered Cavendish banana, which reproduces asexually and therefore has extremely low genetic diversity, making it highly vulnerable to infection?

The researchers see hope in the Timor variety of coffee from Southeast Asia, which is a Robusta brew and a spontaneous hybrid between Arabica and parent Coffea canephora. It is very disease-resistant.

“When Robusta hybridized itself back into Arabica on Timor, it brought some of its pathogen defense genes along with it,” said Albert. The improved genome sequencing revealed regions that harbor other resistance genes.

I hope that researchers will be able to breed relevant resistance genes into Arabica, so that we can all go one drinking our favorite variations on the coffee theme.