The key to growing coffee plants that are more resilient to climate change in the coming decades may lie in the ancient past. Researchers at the University at Buffalo have co-created the highest-quality reference genome for Arabica, the world's most popular coffee variety to date, unraveling the secrets of its lineage spanning millennia and continents.
Their findings, published April 15 in the journal Nature Genetics, show that Arabica coffee was developed more than 600,000 years ago in the forests of Ethiopia through natural hybridization between two other coffee species. The study found that Arabica coffee populations ebbed and waned over thousands of years of hot and cold on the planet, eventually growing in Ethiopia and Yemen and then spreading across the globe.
The study's co-corresponding author, Dr. Victor Albert, a professor of imperial innovation in the Department of Biological Sciences at Columbia University's College of Arts and Sciences, said, "We use genomic information from today's surviving plants to go back in time, paint as accurately as possible the long history of Arabica, and determine the relationship between modern cultivars. "
Coffee giants such as Starbucks and Tim Hortons exclusively use Arabica beans to brew the millions of cups of coffee they serve every day as a selling point, and the higher asking price of this bean is partly due to the low genetic diversity due to a history of inbreeding and small population sizes, Arabica beans are susceptible to many pests and diseases, and can only be grown in a few places in the world where the threat of pathogens is low and the climatic conditions are more favorable. Therefore, a detailed understanding of the origins and breeding history of contemporary varieties is essential for the development of new Arabica varieties that are more resilient to climate change.
Using cutting-edge DNA sequencing technology and advanced data science, the team sequenced a new reference genome from which 39 Arabica varieties were sequenced, and even an 18th-century specimen that Swedish naturalist Carl Linnaeus used to name the species.
The reference genome is now available in a publicly available digital database.
Patrick Descombes, one of the study's co-leaders and a senior expert in genomics at Nestlé Research, said: "While it is true that other publicly available Arabica references exist, the quality of our team's work is extremely high. We have employed state-of-the-art genomics methods – including long- and short-threaded high-throughput DNA sequencing – to create the most advanced, complete, and continuous Arabica reference genome to date. "
Humans' favorite coffee actually evolved without human help
Arabica coffee accounts for about 60% of the world's total coffee production, and its seeds help millions of people start the day or stay up late. However, the hybridization that originally created Arabica coffee was done without human intervention.
Coffea arabica was formed by natural crosses between Coffea canephora and Coffea eugenioides, which obtained two sets of chromosomes from each parent. Scientists have struggled to determine the exact time and location of this heteropolyploidization event, with estimates ranging from 10,000 to 1 million years ago.
To find evidence of the initial event, researchers at Columbia University and their partners ran various Arabica genomes through computational modeling programs to find species-based features.
Models show that there have been three population bottlenecks in Arabica's history, with the earliest one occurring about 29,000 generations (or 610,000 years ago). This suggests that Arabica was formed sometime before that, 610,000 to 1 million years ago, the researchers said.
"In other words, the hybridization that produced Arabica was not human," Albert said. It is clear that this polyploidy event occurred before modern humans and coffee cultivation. "
It has long been thought that the coffee plant was developed in Ethiopia, but the coffee varieties collected by the team around the Great Rift Valley, which stretches from southeastern Africa to Asia, show a clear geographical division. The wild species studied are all from the west, while the cultivated varieties are all from the eastern part of the Bab el-Mandeb Strait, which is closest to the separation between Africa and Yemen.
This coincides with evidence that coffee cultivation began primarily in Yemen around the 15th century. The Indian monk Baba Budan is said to have smuggled the legendary "Seven Seeds" from Yemen around 1600 to breed the Indian Arabica cultivar that laid the foundation for today's global spread of coffee.
"It looks like the diversity of Yemeni coffee is probably the originator of all the major varieties at the moment," Descombes said. Coffee is not a crop that has undergone extensive crossbreeding to create new varieties like corn or wheat. People mainly choose their favorite varieties and then plant them. As a result, the varieties we have today may have been around for a long time. "
How the climate affects the number of Arabica
Thanks to the study of human origins, the geo-climatic history of East Africa is well documented, so researchers can contrast climatic events with how wild and cultivated Arabica populations fluctuate over time.
Models show that the region's population was chronically low for a period of 2-100,000 years ago, roughly consistent with the prolonged drought and colder climate that the region is believed to have suffered 4-70,000 years ago. Then, during the humid period of Africa about 6-15000 years ago, the population increased, and the growing conditions at that time may have been more favorable.
During the same period, about 30,000 years ago, wild varieties and those eventually cultivated by humans separated from each other.
Jarkko Salojärvi, an assistant professor at Nanyang Technological University in Singapore and another co-corresponding author of the study, said: "They also occasionally crossbreed with each other, but most likely stopped breeding at the end of the African wet period and about 8,000 to 9,000 years ago when rising sea levels widened the straits. "
Genetic diversity is low threat to Coffea arabic
It is estimated that the effective population for cultivated Arabica coffee is only 10,000 to 50,000 individuals. Low genetic diversity means that it is likely to be completely wiped out by pathogens such as coffee leaf rust, which can cost between $1 billion and $2 billion annually, just like monocultured Cavendish bananas.
The reference genome could further reveal how an Arabica varietal strain acquired strong resistance to the disease. Timor coffee is a spontaneous cross between Coffea arabica and one of its parents, Coffea canephoa, in Southeast Asia. This variety is more resistant than Arabica and is also known as Robusta and is mainly used for instant coffee. So when Robusta crossed with Arabica on the island of Timor, it also brought with it some pathogen defense genes.
Albert also co-led the sequencing of the Robusta genome in 2014, and his current work with collaborators also showcases a highly improved version of the Robusta genome, as well as a new sequence of Coffea eugenioides, another Arabica ancestor.
Breeders have tried to improve pathogen defenses through hybridization, and the new Arabica reference genome allows our researchers to identify a new region that contains members of the RPP8 resistance gene family as well as CPR1, a general regulator of resistance genes.
"These results provide a new target locus for improving Arabica's ability to resist pathogens," Salojärvi said. "
Genomic studies have also provided other new discoveries, such as which wild varieties are closest to the modern-day Arabica coffee. They also found that the early Dutch cultivar "Typica", which originated in India or Sri Lanka, was likely the mother of the bourbon cultivar that the French mainly cultivated. This is no different from rebuilding the genealogy of a very important family.
编译来源：ScitechDaily