THE PROCESS IN MOTION

What does reading the arabica genome change, and where does its editing stand?

Start the scene or choose a stage. The animation simplifies the mechanism; what follows gives the details and the available references.

▶ Play the process01Read02Date03Locate04Sort the young plants05Edit06What holds it back

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In April 2024, Salojärvi and his coauthors publish the reference genome of arabica, the ordered reading of all its DNA, and those of its two parents. They resequence 41 accessions, including an 18th-century specimen and the Timor Hybrid with five of its backcrosses.

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1. ReadIn April 2024, Salojärvi and his coauthors publish the reference genome of arabica, the ordered reading of all its DNA, and those of its two parents. They resequence 41 accessions, including an 18th-century specimen and the Timor Hybrid with five of its backcrosses.
2. DateThree independent methods date the founding cross between the ancestors of canephora and eugenioides to between 610,000 and 350,000 years ago. The estimate of 20,000 years put forward in 2020 is probably an underestimate, biased by bottlenecks, collapses in the number of individuals.
3. LocateThe introgression of the Timor Hybrid, the lasting entry of genes from another species, covers 7 to 11% of the genome of resistant lines. Three candidate genes for rust resistance, RPP8, CPR1 and LRK10L, are isolated on chromosome 4.
4. Sort the young plantsWith these positions, the breeder sorts young plants on markers instead of waiting for rust to pass through the field. But reading does not create diversity: in Brazil, 97.55% of cultivars descend from Typica and Bourbon alone.
5. EditThe CRISPR/Cas9 system cuts DNA at the chosen spot. It is effective in canephora: in 2022, on clone 14, 77% of plants carried the expected mutations. The XMT and DXMT genes are targets for a naturally caffeine-free coffee.
6. What holds it backArabica carries four sets of chromosomes, hence several copies of each gene to edit. Regeneration by somatic embryogenesis is slow, and the European Union still treats edited plants as GMOs. No edited coffee is grown commercially.

To remember: Reading the genome changes the breeder's calendar; it does not create the diversity that is missing.

Read the full article and its sources ↓

In April 2024, Salojärvi and coauthors publish the reference genome of arabica in Nature Genetics. A reference genome is the ordered reading of all the DNA of a species, the map that those looking for a gene will then consult.

They also publish that of its two parents. Arabica was born of the cross of two species, and without their genomes we cannot tell what it got from whom.

The work covers 41 resequenced arabica accessions. Among them, an 18th-century specimen supplied by the Linnean Society of London, which gives a very old point of comparison. Also among them, the Timor Hybrid and five of its backcrosses.

Three independent methods date the founding hybridization between the ancestors of canephora and eugenioides to between 610,000 and 350,000 years before the present. Three methods that converge are what makes a date hold.

The authors explicitly point out that the estimate of 20,000 years put forward by Scalabrin and coauthors in 2020 (Scientific Reports) is probably an underestimate, biased by population bottlenecks. A bottleneck is a collapse in the number of individuals: part of the accumulated diversity disappears with them. The lineage then looks younger than it is.

This date concerns the evolutionary event, not humans. Domestication in Yemen came several hundred thousand years after it.

Salojärvi et al. 2024, Nature Genetics 56, pp. 721-731, pp. 722-725; Scalabrin et al. 2020, Scientific Reports 10, 4642; LC ch. 1 and genetic digest

The same article locates what matters for breeding. The introgression of the Timor Hybrid, that is, the lasting entry into one species of genetic material from another, covers 7 to 11% of the genome of resistant lines.

Three candidate genes for rust resistance (RPP8, CPR1, LRK10L) are isolated on chromosome 4. And the Panamanian Geisha is genetically close to wild accessions collected near Mount Gesha, on the western slope of the Ethiopian Rift.

Having these positions changes the breeder's calendar. Young plants are sorted on markers, instead of waiting for rust to pass through the field to see which ones hold.

The 2026 review raises two reservations. The function of these candidate genes remains to be validated in a tetraploid background. The arabica background carries four sets of chromosomes, hence several copies of each gene to check. And the biosynthetic pathways of aroma precursors remain little explored.

In Brazil, 97.55% of cultivars descend from the Typica and Bourbon groups alone. Reading the genome does not create diversity. It measures what is missing.

Salojärvi et al. 2024, pp. 726-727; Yang et al. 2026, p. 6; WCR, Catalog 2025, p. 10

Genome editing is the next step, and it is at the proof-of-concept stage. Breitler and coauthors (CIRAD) showed in 2018, in Plant Cell, Tissue and Organ Culture, that targeted mutagenesis by CRISPR/Cas9 is effective in Coffea canephora and could speed up its domestication; Casarin and coauthors (Scientific Reports, 2022) obtained on canephora clone 14, with several guides targeting the phytoene desaturase gene, 77% of plants carrying the expected mutations, half of them homozygous on at least one target; Leibrock and coauthors (Food Science and Biotechnology, 2022) identified the XMT and DXMT genes as targets for a naturally caffeine-free coffee and discussed the social acceptability of such a product. The obvious targets are caffeine (eliminating an industrial decaffeination step), the rust resistance genes located in 2024, and heat tolerance; the obstacles are the tetraploidy of arabica, which multiplies the copies to edit, the slowness of regeneration by somatic embryogenesis, and divergent regulatory regimes, the European Union still treating edited plants as GMOs while several producing countries do not. No edited coffee is grown commercially as of the date of this plate.

Breitler et al. 2018, Plant Cell Tissue Organ Cult. 134, doi 10.1007/s11240-018-1429-2; Casarin et al. 2022, Scientific Reports 12; Leibrock et al. 2022, Food Science and Biotechnology 31; Yang et al. 2026, p. 6 (validation in tetraploid background)