Arabica coffee is the most economically important coffee in the world and represents 60% of coffee products worldwide. But the plants it comes from are vulnerable to a disease that, in the 19th century, devastated Sri Lanka’s coffee empire.
Now, an international team of researchers co-led by Nanyang Technological University, Singapore (NTU Singapore) has made a breakthrough that helps protect Arabica plants (Coffea arabica) against the fungal disease called coffee rust.
The other co-leaders of the study, published in Nature genetics They are based at the world’s largest food and beverage company, Nestlé, the University of Montpellier in France and the University of Buffalo in the United States.
The scientists mapped, in great detail, all the genetic material (or genomes) of Arabica and two related coffee plants. This allowed the team to identify a new combination of genes shared by plants that are resistant to coffee rust. With genome data, other useful traits in coffee plants can also be identified.
The discovery of resistance genes paves the way to better protect coffee lovers’ daily dose and maintain the high-quality taste of their drink, thus supporting an industry that employs millions of workers. According to the International Coffee Organization, the livelihoods of 125 million people around the world depend on the coffee business.
Coffee rust has wreaked havoc on coffee-producing nations and continues to wipe out coffee plantations today. The United States Agency for International Development estimated that between 2012 and 2014, a coffee rust outbreak caused about $1 billion in economic damage in Latin America.
Assistant Professor Jarkko Salojarvi from NTU’s Faculty of Biological Sciences, who co-led the research team, said: “The high-quality genomic sequences of the three plant species, along with candidate gene sequences for rust resistance coffee, form the cornerstone for cultivating new varieties of Arabica plants that are more adaptable to change and more resistant to diseases caused by pathogens such as fungi.”
A large consortium of coffee researchers and breeders from Australia, Belgium, Brazil, Canada, China, Colombia, Finland, France, Germany, Indonesia, Italy, Netherlands, South Africa, Spain, Switzerland, Uganda and the United States participated in the project.
Dr Patrick Descombes, senior genomics expert at Nestlé Research and one of the co-leaders of the study, said: “While there are other public references for Arabica, the quality of our team’s work is extremely high. We use state-of-the-art technologies “. next-generation genomic approaches, including high-throughput sequencing of long and short reads, to create the most advanced, comprehensive and continuous Arabica reference to date.”
Poor genetic variability.
Arabica plants have low genetic diversity, making them susceptible to pests and diseases. Cultivated plants generally do not have the genetic trait that confers resistance to coffee rust, caused by the fungus Hemileia vastatrix.
The fungi form yellow-orange spots on the leaves of coffee plants, which eventually wilt and fall. The loss of leaves reduces the quality and quantity of berries on plants harvested for coffee preparation.
To prevent a potentially disastrous destruction of Arabica plants worldwide due to coffee rust, scientists studied the plant’s genomic origins and reproductive history.
They did this by mapping the highly detailed genomic sequences of Arabica and two related coffee-producing plants, Robusta (C. canephora) and C. eugenioides, which are the current ancestors of Arabica.
This was done using advanced techniques, namely PacBio high-fidelity technology to sequence DNA with high precision and high-throughput chromosome conformation capture to create detailed 3D maps of how different DNA segments interact. Genome data is publicly available.
The scientists’ analysis suggested that resistance to coffee leaf rust in Arabica may have been lost when Arabica plants were widely cultivated, since all cultivated Arabica coffee plants are derived from the same strain with very little genetic variability.
However, in 1927 a hybrid of Arabica and Robusta resistant to the disease was found on the island of Timor. Unfortunately, resistance comes with a downside, as the hybrid does not produce coffee that tastes as good as other Arabica plants.
Without alternatives, the descendants of the Timor hybrid plant remain the basis of all coffee rust-resistant variants.
Previous research discovered some genes that potentially conferred resistance against leaf rust in different coffee plants. But without a genome map of the different coffee plants, it was difficult to precisely identify these genes and determine whether they were also found in other coffee plants, which would increase the chances that they encoded resistance. The gene identification process was also slow.
However, with new research mapping the genomes of different coffee plants in great detail, the identification of resistance genes will be faster and more accurate.
Using plant genome information, the researchers analyzed the most common cultivated coffee varieties, which account for around 95% of global coffee production, and compared them to the descendants of the Timor hybrid.
This allowed them to find a region of DNA sequences common between different coffee plants resistant to leaf rust, with a new combination of Robusta-based genes that can transmit resistance in Arabica plants in general. Knowing the existence of these shared genes greatly increases the likelihood that these genetic sequences can effectively defend against leaf rust and could allow breeders to select for them when breeding new coffee varieties.
Through their analysis, the researchers also postulated that Arabica emerged from a chance event 350,000 to 610,000 years ago when Robusta and C. eugenioides plants were naturally cross-pollinated to create the first Arabica plants in nature.
This dating falls between previous estimates: one earlier places the chance event as recently as 20,000 years ago, while others place it as far back as a million years ago. The researchers said the discrepancy from the above figures could be due to historical changes in the population size of wild and cultivated plants, as well as different sources and the limited amount of data used.
By comparing the high-quality genomic sequences of Arabica with those of Robusta and C. eugenioides, the research team found that the three species remain very similar genetically. This suggests that in future breeding programs to ensure that Arabica plants have disease resistance, breeders may consider using other related coffee species, such as Robusta and C. eugenioides.
Using Arabica plants alone to improve the resistance trait is problematic because the study found that even wild Arabica varieties, not just cultivated ones, have very low genetic diversity, making it more difficult to improve disease resistance.
“The low genetic diversity of modern Arabica plants, both cultivated and wild, is an obstacle to their reproduction using wild varieties of the plants. But the close similarities found between Arabica, Robusta and C. eugenioides plants probably facilitate the introduction of interesting traits from the latter two to Arabica,” said Assistant Professor Salojarvi.
The highly detailed genomic sequences mapped for the three coffee plants also mean that other useful traits could be identified in the future, such as drought resistance, better crop yields and more aromatic coffee beans.
These traits can be identified with genetic markers, which can be used to predict the future performance of coffee seedlings, rather than waiting years for the plants to mature and produce berries to find out.
Since the rust-resistant Timor hybrid does not produce coffee as good as regular Arabica plants, the compiled genome data now provides a fast track for researchers to generate new disease-resistant plants that still retain their flavor. Sublime, smooth and sweet Arabica flavor enjoyed by coffee lovers around the world.