Researchers look at coffee genome to find key to climate-resilient coffee

Climate change could have a massive impact on the cultivation of coffee. While Arabica is the dominant coffee used globally, it is vulnerable to climate change, and requires higher altitudes and lower temperatures.

In addition, it has low genetic diversity, meaning it is susceptible to many pests and diseases and can only be cultivated in a few places around the world where pathogen threats are lower and climate conditions are favorable. Global rising temperatures are making these locations harder to find.

In fact, a recent study suggested large parts of land in the world’s largest producer of Arabica, Brazil, could be rendered economically unfeasible​ for production throughout the course of the century. And coffee leaf rust already causes $1-2 billion in losses annually: posing another threat.

Exploring new varieties

Nestlé plant scientists are focusing on new, higher-yielding Arabica varieties with greater resistance to disease and drought. And the new 'very high quality' Arabica reference genome can help scientists understand how arabica has developed and the key to future coffee species.

The reference genome makes it easier to analyze different traits of coffee varieties to identify specific traits such as resilience to disease or drought. It can also help find qualities such as better yield, coffee cherry size and flavor or aroma characteristics.

"In simple terms, our new reference is like a high-quality map of a big city," said Jeroen Dijkman, head of Nestlé's Institute of Agricultural Sciences. 

"It will help us identify key genetic markers in the Arabica genome that are responsible for specific traits in adult plants. This will help our plant scientists, and other experts to better identify, select and breed new and improved Arabica coffee varieties."

Patrick Descombes, senior expert in genomics at Nestlé Research and one of the paper's co-authors, said: "While other public references for Arabica do exist, the quality of our team's work is extremely high. We used state-of-the-art genomics approaches - including long and short reads high throughput sequencing - to create an advanced, complete and continuous Arabica reference."

Learning from the past

The potential of the genome could come from looking back thousands of years into its history: with the work - published this month in Nature Genetics​ - allowing researchers to trace Coffea Arabica​ back 600,000 years. 

This has unearthed secrets about its lineage, and also show how the population of the species has waxed and waned throughout the Earth’s heating and cooling periods over thousands of years.

“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 the study’s co-corresponding author, Victor Albert, Empire Innovation Professor in the Department of Biological Sciences, College of Arts and Sciences at University at Buffalo.

“A detailed understanding of the origins and breeding history of contemporary varieties are crucial to developing new Arabica cultivars better adapted to climate change.”

One line of Arabica varieties has strong resistance to the disease: and the reference genome can shed light on how this was achieved. The Timor variety formed in Southeast Asia as a spontaneous hybrid between Arabica and one of its parents, Coffea canephora ​(Robusta). The variety therefore gained Robusta’s rust resistance.

That means Albert – who also co-led sequencing of the Robusta genome in 2014​ – and the team can present a highly improved version of the Robusta genome, as well as new sequence of Arabica’s other progenitor species, Coffea eugenioides​.

While breeders have tried replicating this crossbreeding to boost pathogen defense, the new Arabica reference genome has allowed the present researchers to pinpoint a novel region harboring members of the RPP8 resistance gene family, as well as a general regulator of resistance genes, CPR1. 

Tracing coffee's origins

The study has also shed light on some of the important events in Arabica's history.

Arabica was formed as a natural hybridization between Coffea canephora​ and Coffea eugenioides​, whereupon it received two sets of chromosomes from each parent. Estimates for when this occurred range anywhere from 10,000 to 1 million years ago.

The new model suggests Arabica formed sometime from 610,000 to 1 million years ago, researchers say. That means this predated modern humans and their cultivation of coffee.

Coffee plants have long been thought to have developed in Ethiopia, but varieties that the team collected around the Great Rift Valley, which stretches from Southeast Africa to Asia, displayed a clear geographic split. The wild varieties studied all originated from the western side, while the cultivated varieties all originated from the eastern side closest to the Bab al-Mandab strait that separates Africa and Yemen.

That would align with evidence that coffee cultivation may have started principally in Yemen, around the 15th century.

Genetics could hold the key to everything from taste to caffeine

Italian scientists have also been looking at how the genetic makeup of Arabica could help improve coffee production.

Researchers – which included those from Lavazza Group and illycafe – looked at changes at a chromosomal level that can explain different characteristics. That includes characteristics such as taste, caffeine level, and disease resistance.

This could also aid coffee breeders looking to select for low caffeine levels or resistance to coffee rust. ​