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Illycaffe on building better coffee

From the November 2018 issue.

The release of the first fully open-access genome sequence for Coffea arabica has provided researchers around the world with a vital tool in developing more resilient coffee plants.

After almost a decade of development, an illycaffè and Lavazza-led partnership has successfully mapped and released an open-access genome sequence of Arabica coffee.

“Illycaffè started this research because we were convinced that understanding the genetic structure of coffee would lead to developing better quality coffee,” says Furio Suggi Liverani, Corporate Director of Research and Development at illycaffè.

“Illycaffè started working on [this project] in 2010. Due to its cost, we met with Lavazza in 2012 [and together] decided to pay for sequencing to complete the job.”

The joint-funded Coffea arabica Genome Sequencing Project was carried out by numerous laboratories, including Istituto di Genomica Applicata (IGA), IGA Technology Services, DNA Analytica, and the Universities of Trieste, Udine, Padova, and Verona in Italy.

Liverani says the public release of the genome will accelerate the research done by scientists around the world to improve coffee, in terms of both quality and resilience.

“Usually, agronomists crossbreed different varieties in order to find new ones. It takes a very long time,” Liverani tells Global Coffee Report. “Developing a coffee plant hybrid through traditional methods can take 30 to 40 years.

“If you know how the genome works, you can better understand which characteristics you want to pass onto the new plant. It’s a tremendous compression of time.”

Liverani says that knowing the genetic structure of the coffee enables producers to breed hybrid plants that highlight certain features of its progenitors.

“You can improve the coffee quality through gene research if you know the genes you are interested in,” he says.

“For instance, the gene of caffeine expression. If you want a coffee with low caffeine, you analyse and look at the genes of several plants. Then, you choose the plants that have lower caffeine expression and crossbreed them.”

Professor Michele Morgante, Scientific Director of the Istituto di Genomica Applicata, says Coffea arabica is a complex plant, with twice the number of chromosomes of Coffea canephora – commonly called Robusta.

“One of the main difficulties was to distinguish between the sequences derived from the two progenitor genomes of Arabica, Coffea canephora and Coffea eugenioides, which are extremely similar,” Morgante says in a public statement.

Coffea arabica is a tetraploid species, meaning it carries four copies of the 11 chromosomes typical of the genus Coffea. Arabica is the only tetraploid species in the Coffea family. Technically, it has as an allotetraploid genome because it is the result of a hybridisation between two diploids, which  have two copies of 11 chromosomes.

This genome sequence was derived from a Coffea arabica plant of the Red Bourbon variety. Ripe coffee cherries were sourced from a coffee plantation in the Ahuachapan region of El Salvador and used as starting material for DNA extraction.

The genome was sequenced with Illumina technology at the Istituto di Genomica Applicata in Udine. Due to its complex nature, Morgante says the common whole genome shotgun approach was not ideal.

“To tackle this problem, we used a hierarchical sequencing approach, in which the genome is divided into relatively small portions before being reconstructed,” he says.

The Universities of Padova and Verona predicted and functionally annotated 78,311 genes in Coffea arabica, using ribonucleic acid sequencing from 12 different samples derived from eight different organs of the plant.

Though this is not the first coffee genome sequencing project to take place, Liverani says it is the only one to release its findings to the public.

“There are other studies – one in France, one in the United States, and another in Colombia. The difference is they did not [provide open access to] their results,” he says.

The genome can be downloaded from the World Coffee Research (WCR) website, who has partnered with illycaffè to carry out further study on the genome.

“At the moment, we have just completed the genome and have not applied it,” Liverani says. “The surprises will come now.”

Liverani says illycaffè’s research with WCR aims to understand the relationship between coffee quality and the territory it is grown in.

“We are thrilled to be able to convey this Arabica genome to the global coffee and research community freely and openly,” says Tim Schilling, CEO and Founder of WCR, in a public statement. “Advanced genetics research is essential to coffee’s future as a sustainable crop, and to exploring the thrilling diversity of flavours found in coffee.

“Having access to a whole sequenced genome is an essential precursor to unlocking the potential of genetics research to transform coffee production.

“Our scientists are looking forward to working with other organisations, countries, and governments to make use of the treasures within this genome to make coffee more profitable to farmers and better tasting for consumers.”

This is not the only research project using the genome illycaffè is currently involved in. A second study, heavily involving the European coffee community, has the goal of creating more disease-resistant plants.

As well as disease, illycaffè’s Liverani says increasingly harsh environments are threatening the future of coffee production.

“The only way to [combat the effects] of climate change is to develop more resilient plants,” he says. “The formula for building the plant is contained in the genome.

“Using this instrument, [researchers] can improve and [accelerate] this research.”

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