Scientists have discovered common genes that protect coffee plants from devastating diseases

Arabica coffee is the most economically important coffee worldwide, accounting for 60% of coffee products worldwide. But the plants it comes from are vulnerable to a disease that devastated Sri Lanka’s coffee empire in the 19th century.

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 leaf rust.

The other co-leaders of the study, published in Nature geneticsare located at the world’s largest food and beverage company Nestlé, the Université de Montpellier in France and the University of Buffalo in the United States.

The scientists mapped out in 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 common to the plants that are resistant to coffee leaf rust. Genome data can also be used to identify other useful properties of coffee plants.

Discovering the resistance genes opens the way to better protect the daily needs of coffee lovers and preserve the high-quality taste of their drink, supporting an industry with millions of employees. According to the International Coffee Organization, the livelihoods of 125 million people around the world depend on the coffee sector.

Coffee leaf rust disease has wreaked havoc in coffee-producing countries and continues to destroy coffee farms. The United States Agency for International Development estimates that an outbreak of coffee leaf rust caused about US$1 billion ($1.36 billion) in economic damage in Latin America between 2012 and 2014.

Assistant Professor Jarkko Salojarvi from NTU’s School of Biological Sciences, who co-led the research team, said: “The high-quality genome sequences of the three plant species, together with the candidate genetic sequences for resistance to coffee leaf rust, provide the cornerstone for breeding of new varieties of Arabica plants that are better able to adapt to changes and more resistant to diseases caused by pathogens such as fungi.”

The project involved a large consortium of researchers and coffee breeders 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 Expert in Genomics at Nestlé Research, and one of the co-leads of the study, said: “Although other public references for Arabica exist, the quality of our team’s work is extremely high. advanced genomics approaches – including high-throughput sequencing of long and short reads – to create the most advanced, complete and continuous Arabica reference to date.

Poor genetic variability

Arabica plants have low genetic diversity, making them susceptible to diseases and pests. The cultivated plants generally do not have the genetic trait that confers resistance to coffee leaf rust caused by the Hemileia vastatrix fungi.

The fungi form orange-yellow spots on the leaves of the coffee plants, which eventually wither and fall. The loss of leaves reduces the quality and quantity of the plant’s berries that are harvested for coffee making.

To prevent a potentially disastrous wipeout of Arabica plants worldwide from coffee leaf rust, the scientists studied the plant’s genomic origins and breeding 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 Arabica’s modern ancestors.

This was done using cutting-edge techniques, namely PacBio high-fidelity technology to sequence DNA with high accuracy, and high-throughput chromosome conformation capture to create detailed 3D maps of how different DNA segments interact. The data for the genomes is publicly available.

The scientists’ analysis suggested that resistance to coffee leaf rust in Arabica may have been lost when Arabica plants became widely cultivated, as all cultivated Arabica coffee plants come from the same stock with very little genetic variability.

However, in 1927, a hybrid of Arabica and Robusta was found on the island of Timor that was resistant to the disease. Unfortunately, the resistance comes with a trade-off, as the hybrid does not produce coffee that tastes as good as that of other Arabica plants.

Since there are no alternatives, the descendants of the Timor hybrid plant still form the basis of all rust-resistant coffee leaf varieties.

Previous research has identified some genes that may confer resistance to leaf rust in various coffee plants. But without a map of the genomes of the different coffee plants, it was difficult to accurately identify these genes and difficult to find out whether they also exist in other coffee plants, which would increase the chance that they coded for resistance. The gene identification process was also slow.

However, now that the new research maps the genomes of different coffee plants in detail, identifying resistance genes will be faster and more accurate.

Using the plant’s genome information, the researchers analyzed the most common cultivated coffee varieties, which represent about 95% of the world’s coffee production, and compared them with descendants of the Timor hybrid.

This allowed them to find a region of DNA sequences common to several leaf rust-resistant coffee plants, with a new combination of Robusta-based genes that could confer resistance in Arabica plants in general. Knowing the existence of these shared genes greatly increases the chance that these genetic sequences can indeed 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 naturally cross-pollinated to create the first Arabica plants in the wild.

This dating falls between previous estimates, with one previous estimate placing the coincidental event at 20,000 years ago, while other estimates went as far back as a million years ago. The researchers said the discrepancy between previous figures could be due to historical changes in the population sizes of wild and cultivated plants, as well as the different sources and 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 are still very similar genetically. This suggests that for 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 only Arabica plants to breed for the resistance trait is problematic because the study found that even the wild Arabica varieties, and not just the cultivated ones, have very low genetic diversity, making it more difficult to breed on disease resistance.

“The low genetic diversity of both cultivated and wild modern Arabica plants poses an obstacle to their breeding using the wild varieties of the plants. But close similarities between Arabica, Robusta and C. eugenioides plants are likely to facilitate the introduction of interesting plant properties. the last two in Arabica,” said Assistant Professor Salojarvi.

The highly detailed genomic sequences mapped for all three coffee plants also mean that other useful traits can be identified in the future, such as resilience to drought, better crop yield 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 bear berries to find out.

Because the leaf rust-resistant hybrid from Timor does not produce coffee as good as that of the usual Arabica plants, the genome data collected now provides a fast route for researchers to breed new disease-resistant plants that still retain the sublime, smooth and sweet taste of Arabica , enjoyed by coffee lovers worldwide.