Coffee’s chromosome mutations: The potential for industry

When you consume arabica coffee from different regions around the world​ and taste the difference between them, you may believe that this difference is down to the genes in the beans.

This, according to a recent study published in the journal Nature Communications, is a misconception. While the different frequency of genes do control taste, it is chromosomal mutations which leads to these differences in frequency.

Steaming cup of chromosomes​

Arabica, unlike robusta, has more than two copies of each chromosome, a phenomenon known as polyploidy. This makes it difficult for arabica to interbreed with other species (which is where most genetic variation come from) meaning that the main source of variation between varieties of such coffee beans is mutation. These mutations occur at a steady rate.

Within the past 50,000 years, arabica was created through the fusion of Coffea canephora (robusta) and a strain called Coffea eugenioides. Variations account for mutations in the chromosomes since this event.

Arabica and robusta

There are two main types of beans used to make coffee: arabica, which is usually considered the more high quality of the two and makes up 60% of coffee sold, and robusta, which makes up the rest.

However, because of climate change, arabica, which must be grown at higher altitudes, is now harder to grow​. Arabica must grow below a certain temperature threshold​, which global rising temperatures are making rarer. Thus, the hardier robusta is taking on more of the market.

Looking at a number of different arabica varieties, researchers found not only variations in taste, but variance in functions such as disease resistance. They also found in some instances, such as in the Bourbon arabica variety, chromosomal rearrangements, additional copies of chromosomes, fragments of chromosomes missing (deletions), and in some cases whole chromosomes absent.

“We have identified chromosomal aberrations of different types as a major source of genetic variation in Coffea arabica. These mutations occur randomly during meiosis, the process that leads to the production of gametes (reproductive cells) probably with a higher frequency in Coffea arabica because of its tetraploid (having four sets of chromosomes) nature,” plant geneticist Michele Morgante, one of the researchers on the study, told FoodNavigator.

Ascertaining how these mutations affect taste between varieties, Morgante admits, is difficult. “Chromosomal differences result in differences in copy number between genes derived from eugenioides and from canephora. If the properties of canephora and eugenioides derived genes in terms of either their expression or their protein product are different, then this could result in qualitative differences that result in differences in taste.

The research could impact industry, but its exact potential is still unknown. Image Source: Getty Images/Travel_Motion

“Since genes from eugenioides and from canephora often have different properties in terms of either their expression or their protein product, having all four genes from one or the other, if these genes are involved in the quality traits of the bean, such as many genes involved in secondary metabolism, they could determine qualitative differences that result in differences in taste.”

Can industry take advantage?​

These discoveries have the potential to be highly consequential to industry. According to Kassahun Tesfaye, one of the researchers, understanding the genome could open up all kinds of advantages for producers, such as allowing coffee breeders to select for low caffeine levels or resistance to fungus such as coffee rust.

“There are treatments that are known to increase the frequency of chromosomal aberrations of different kinds, such as for example in vitro culturing of plant cells followed by whole plant regeneration,” Morgante added.

Is too much caffeine risky?

The research into mutations opens up the potential for producers to pick varieties lower in caffeine. This could be an important development, as excess caffeine consumption, according to new research​ by the US’s Food and Drug Administration (FDA), can be dangerous to one’s health, although this depends a lot on the individual in question.

For healthy adults, 400 milligrams a day is a roughly safe amount, according to the FDA. This is the equivalent of around four or five cups of coffee.

“The industry could screen arabica germplasm searching for varieties/genotypes with chromosomal aberrations that could represent the starting material to obtain improved varieties, but could also, as explained above, embark into programs that induce new chromosomal aberrations to increase genetic variation in the species and improve either quality traits or sustainability traits.” Germplasm is the term used to describe plants, plant parts or seeds used in crop breeding research and cultivation efforts.

However, according to industry itself, it is too early to tell. Nestlé said that it has not yet ascertained whether the study will have a practical impact.

“The correlations between the rearrangement of chromosomes and the differences in the flavour notes are not well known enough yet to have an impact on the way we cultivate arabica beans. Although the discoveries in this paper are highly informative at an academic level, the direct implication on arabica cultivation cannot be estimated yet,” a Nestlé spokesperson told FoodNavigator.

Nevertheless, an improvement in the understanding of how the genome is organised could prove useful, Nestlé said. “Since our capacities to identify genes and molecular markers associated to traits are linked to the quality of the genome assembly that we are using, this study is helpful but will require additional research to breed low-caffeine and/or disease resistant coffee varieties.”

Sourced From: Nature Communications
‘A chromosome-scale assembly reveals chromosomal aberrations and exchanges generating genetic diversity in Coffea arabica germplasm’
Published on: 23 January 2024
Doi: https://doi.org/10.1038/s41467-023-44449-8
Authors: S. Scalabrin, G. Magris, M. Liva, N. Vitulo, M. Vidotto, D. Scaglione, L. Del Terra, M. R. Ruosi, L. Navarini, G. Pellegrino, J. C. Berny Mier y Teran, L. Toniutti, R. S. Liverani, M. Cerutti, R. Di Gaspero & M. Morgante

Sourced From: Nature Food
‘Vapour pressure deficit determines critical thresholds for global coffee production under climate change’
Published on: 12 October 2022
Doi: https://doi.org/10.1038/s43016-022-00614-8
Authors: J. Kath, A. Craparo, Y. Fong, V. Byrareddy, A. P. Davis, R. King, T. Nguyen-Huy, P. J. A. van Asten, T. Marcussen, S. Mushtaq, R. Stone & S. Power

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