Decoding coffee: DNA sequencing opens doors to enhanced brews

29 Jan 2024 --- Scientists in Italy have tapped into genetics to develop the most complete sequencing yet of the genome of Coffea arabica — a variety producing nearly 60% of the coffee consumed in the world. The chromosome-level assembly was developed using long-read DNA sequencing and computational biology and is touted as a tool for coffee producers to breed flavorful varieties that are also better equipped at handling climate changes and plant diseases.

The study found evidence of significant chromosomal rearrangements, especially in a varietal of C. arabica called Bourbon. These included deletions where fragments of chromosomes were missing, while some cases showed the absence of entire chromosomes.

The findings are particularly significant today, when coffee is battling erratic rain patterns and extreme heat and pest attacks increasingly damage the crop.

As per the International Coffee Organization’s 2023 coffee market report, a decrease in coffee production has been noted in Asia & Oceania (4.7%) and Africa (7.2%) to 49.84 million bags and 17.9 million bags, respectively. This can be attributed to adverse weather conditions negatively affecting key producers in the regions, particularly Vietnam, Côte d'Ivoire and Uganda.

A complete genetic map of Coffea arabica can help manufacturers mitigate such challenges, Dr. Michele Morgante, professor of genetics at the University of Udine, Italy, which conducted the study, tells Food Ingredients First.

“On one hand the availability of a more accurate and complete genome sequence should make it easier to identify genes and mutations involved in determining resilience and tolerance to stress factors and resistance to pathogens.”

The team of scientists used long read DNA sequencing technique to generate Coffea arabica's genetic map.“On the other hand they can benefit from the possibility of generating new and additional genetic diversity by inducing new chromosomal rearrangements and exchanges that we know can be induced for example by in vitro culture of plant cells followed by whole plant regeneration.”

Further, it can also help them brew better coffee. “The same consideration made above for climate stress and pathogens can be applied to flavor traits, with the additional consideration that it may be easier to work on the flavor related traits than on the others because their genetic control should be simpler,” he reveals.

The findings feature in Nature Communications.

Next generation sequencing
Dr. Morgante and his team used next-generation sequencing technology that can read DNA strands up to hundreds of thousands of base pairs in length without interruption.

"In terms of sequencing, we produced the reference genome sequence for the cultivar Bourbon using a so-called third generation sequencing technology developed by Oxford Nanopore Technologies that produces very long sequence reads. We also re-sequenced multiple additional varieties and accessions using a so-called 2nd generation sequencing technology developed by Illumina.”

“The method produces much shorter sequence reads than the previous technology that are however sufficient to detect different types of variations existing among these individuals when they are compared to the reference sequence we built,” he explains.

The Coffea arabica species was recently formed, approximately 50,000 years ago.The long-read sequencing technique has “revolutionized” the field of genome assembly, providing “unprecedented opportunities” to obtain contiguous and accurate chromosome sequences for complex genomes, states the study.

Analyzing arabica
Most of the coffee consumed comes from two species- Coffea canephora, which is also known as robusta and Coffea arabica - a allotetraploid hybrid of C. eugenioides and robusta, states the study.

According to Dr. Morgante, arabica is considered to be qualitatively superior to the robusta and the team wanted to find the reason behind genetic diversity in the species.

“Coffea arabica represents an interesting case in plant genetics because it is a recently formed species (approx. 50,000 years ago) with very limited sequence diversity. Despite this, it seems to bear significant phenotypic diversity and so we were interested in trying to identify how such phenotypic diversity could be generated in the face of very limited sequence diversity.”

“We found that the answer may lie in a variety of chromosomal rearrangements and exchanges that we have identified as present as variants between arabica varieties and accessions," he reveals.

Looking ahead
Following the study, Dr. Morgante expects more investments in genomics, genetics and breeding research focused on Coffea arabica.

“Ethiopia, which is the country of origin of Coffea arabica should be especially interested in better characterizing its germplasm basis with advanced genomic tools such as those we used to identify useful variation in its germplasm as well as to detect possible sources of contamination of its precious germplasm.”

Second only to tea, coffee's popularity is evident in bustling cafes and innovations alike.“We hope to be able to extend our studies of chromosomal rearrangements and exchanges to a broader set of Coffea arabica germplasm and to do it at an even higher resolution with the hope of linking these events to specific characteristics of C. arabica,” he concludes.

The work will also drive coffee breeding programs to select for favorable characteristics, such as resistance to a fungus called coffee rust or low caffeine levels, according to Kassahun Tesfaye, a plant geneticist at the Institute of Biotechnology at Addis Ababa University, Ethiopia.

Booming brews
Second only to tea in popularity, coffee launches are gaining ground worldwide, witnessing the highest growth (+13%) from 2016 to 2020 in the hot beverage space, Innova Market Insights’ data indicates.

Besides product launches, innovations are driving the coffee sector as well, with scientists even turning to bioreactors to create cell-based coffee without soil. Cells from a coffee plant are propagated and grown under sterile conditions, followed by harvesting, drying and roasting.

Meanwhile, Thailand-based Tao Bin is navigating artificial intelligence and the internet of things to create coffee and other flavored drinks.

By Insha Naureen

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