Assistant Professor Jarkko Salojarvi from NTU Singapore’s School of Biological Sciences co-led an international research team that mapped the genomes of an Arabica plant (pictured) and two related coffee plants. (Source: NTU Singapore)
Arabica coffee is the world’s most critical economic coffee, accounting for 60 percent of global coffee production. But the plants from which it comes are susceptible to a disease that devastated Sri Lanka’s coffee empire in the 19th century.
Now an international team of researchers under joint leadership Nanyang Technological University, Singapore (NTU Singapore) made a breakthrough that helps protect Arabica plants (Arabic coffee) against a fungal disease called coffee leaf rust.
The other co-investigators of the study, the results of which were published in Genetics of natureare based in the world’s largest food and beverage company Cuddlethis University of Montpellier in France and University at Buffalo in United States.
Scientists mapped in detail the entire genetic material—or genomes—of Arabica and two related coffee plants. This allowed the team to identify a up-to-date combination of genes shared by the plants that are resistant to coffee leaf rust. The genome data can also identify other useful traits of coffee plants.
The discovery of resistance genes paves the way for better protection of coffee lovers’ daily doses and maintaining the high quality of their drink’s taste, supporting an industry that employs millions of workers. According to the International Coffee Organization, 125 million people worldwide depend on the coffee business for their livelihoods.
Coffee leaf rust disease has wreaked havoc in coffee-producing countries and continues to devastate coffee plantations. The United States Agency for International Development estimated that between 2012 and 2014, coffee leaf rust outbreaks caused economic losses of about US$1 billion (S$1.36 billion) in Latin America.
Assistant Professor Jarkko Salojárvi With NTU Faculty of Biological Scienceswho co-led the research team, said: “High-quality genome sequences from three plant species, together with candidate genetic sequences for coffee leaf rust resistance, provide the basis for breeding up-to-date Arabica plant varieties that are more resistant to lesions and diseases caused by pathogens such as fungi.”
The project involved a enormous consortium of coffee researchers and growers from Australia, Belgium, Brazil, Canada, China, Colombia, Finland, France, Germany, Indonesia, Italy, the Netherlands, South Africa, Spain, Switzerland, Uganda and the United States.
Dr. Patrick Descombes, Senior Genomics Expert at Nestlé Researchand one of the co-principals of the study, said: “Although there are other public references for Arabica, the quality of our team’s work is extremely high. We have used state-of-the-art genomic approaches – including high-throughput long- and short-read sequencing – to create the most advanced, complete and continuous Arabica reference to date.”
Needy genetic variability
Arabica coffee plant. (Source: NTU Singapore)
Arabica plants have low genetic diversity, making them susceptible to pests and diseases. Cultivated plants typically lack the genetic trait that provides resistance to coffee leaf rust, which is caused by Hemileia vastatrix mushrooms.
The fungi produce orange-yellow spots on the leaves of coffee plants, which eventually wither and fall off. The loss of leaves reduces the quality and quantity of the plant’s berries harvested for brewing coffee.
To prevent a potentially catastrophic devastation of Arabica crops worldwide by coffee leaf rust, scientists investigated the genomic origins and breeding history of the plant.
They did this by mapping the highly detailed genomic sequences of Arabica and two related coffee-producing plants, Robusta (C. canephora) and C. eugenioideswhich are the current ancestors of Arabica.
This was accomplished using advanced techniques, namely PacBio high fidelity technology for high-accuracy DNA sequencing and high-throughput chromosome conformation capture to create detailed 3D maps of the interactions of different DNA segments. The genome data are publicly available (see notes below).
The researchers’ analysis suggests that Arabica leaf rust resistance may have been lost when Arabica plants became widely cultivated, because all cultivated Arabica coffee plants are derived from the same strain and have 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, this resistance has consequences, as this hybrid does not produce coffee with as good a flavor as coffee from other Arabica plants.
In the absence of an alternative, descendants of the Timor hybrid plant still form the basis of all leaf rust resistant coffee varieties.
Previous studies have found some genes that potentially confer leaf rust resistance in various coffee plants. However, without a genome map of the different coffee plants, it has been complex to accurately identify these genes and to determine whether they are also present in other coffee plants, which would escalate the likelihood that they code for resistance. The process of identifying the genes has also been sluggish.
However, thanks to up-to-date studies that map the genomes of different coffee plants in detail, the identification of resistance genes will become faster and more true.
Using plant genome information, scientists analyzed the most popular varieties of cultivated coffee, which account for about 95 percent of global coffee production, and compared them with Timorese hybrid varieties.
This allowed them to find a region of DNA sequence shared by a variety of leaf rust-resistant coffee plants, with a up-to-date combination of Robusta-based genes that could transfer resistance to Arabica plants in general. Knowing that these shared genes exist greatly increases the likelihood that these genetic sequences could indeed defend against leaf rust and could allow breeders to select for them when breeding up-to-date coffee varieties.
In their analysis, the researchers also assumed that Arabica was created as a result of a chance event that occurred 350,000–610,000 years ago when Robusta was bred and C. eugenioides the plants were naturally cross-pollinated, allowing the first wild Arabica plants to be created.
The date falls between previous estimates, with earlier estimates indicating a chance event that occurred 20,000 years ago, while others have put it back as much as a million years. The researchers said the discrepancy in earlier estimates could be due to historical changes in wild and cultivated plant populations, as well as different sources and confined data used.
By comparing high-quality Arabica genome sequences with those of Robusta and C. eugenioidesThe research team found that the three species are still very similar genetically. This suggests that in future breeding programs, to ensure disease resistance in Arabica plants, growers may consider using other related coffee species, such as Robusta and C. eugenioides.
Using only Arabica plants to breed for resistance is problematic because the study found that even wild Arabica varieties, not just cultivated ones, have very little genetic diversity, making breeding for disease resistance complex.
“The low genetic diversity of both cultivated and wild plants of current Arabica has been an obstacle to its breeding using wild plant strains. However, close similarities have been found between Arabica, Robusta and C. eugenioides “These plants will probably facilitate the introduction of intriguing traits from the latter two into Arabica,” Assistant Professor Salojarvi said.
The highly detailed genomic sequences mapped for all three coffee plants also mean that it may be possible to identify other useful traits in the future, such as drought resistance, higher yields and more aromatic coffee beans.
Because the leaf rust-resistant Timorese hybrid doesn’t produce coffee as good as that from typical Arabica plants, the genomic data collected is allowing scientists to quickly breed up-to-date, disease-resistant plants that still retain the refined, soft and sweet Arabica flavor enjoyed by coffee lovers around the world.
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The paper entitled “Genome and population genomics of allopolyploids Arabic coffee reveal the history of diversification of current coffee varieties”, published in Genetics of natureApril 15, 2024 DOI: 10.1038/s41588-024-01695-w
High-quality Arabica, Robusta and C. eugenioides May be Found here.
