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Coffea Arabica Genetic Diversity

Understanding whether coffee's "genetic toolkit" is big enough

The problem

The wider a species’ genetic diversity, the greater its capacity for resilience to meet challenges such as diseases, pests, and changing weather—all problems we expect to increase in the coming decades. We know Coffee arabica has limited genetic diversity, but we don’t know exactly how limited it is.

In order for coffee breeders to create the next generation of coffees with resilience traits, it’s necessary to know what genetic diversity exists in the species and where to locate it. It is possible that huge reserves of genetic diversity exist in arabica germplasm collections that can be tapped to alleviate current and future constraints to arabica supply and quality.


The solution

Nearly 1,000 unique accessions from the CATIE coffee germplasm collection, which contains the overwhelming bulk of genetic diversity available today outside of the Ethiopian forests,  were genotyped using whole-genome DNA re-sequencing to measure genetic diversity/similarity.

We looked at 809 C. arabica, 58 C. canephora (robusta), 17 “Arabustas,” 10 C.eugenioides, 12 C. sessiliflora, and 7 each of C. pseudozanguebariaeC. anthonii, and C. brevipes samples. In all, we sequenced 249 billion base pairs in 947 DNA samples.  


The results of our genetic diversity study indicate that arabica have very little diversity (only 1.2% pairwise genetic diversity)—much less than was expected. This makes the species especially vulnerable to disease, climate change, and other threats. The most commonly grown coffee varieties are even more genetically narrow than the research collection, containing only .5% pairwise genetic diversity.


Understanding the limits of arabica genetic diversity allows us to develop an informed, rigorous strategy for breeding programs to introduce more diversity—and therefore more resilience—into the arabica species. Our study determined that 100 of the arabica we tested capture ~90% of the total genetic diversity available in the species. They are the 100 most diverse plants available in research collections. This group of super-diverse varieties, called the Core Collection, will be the basis for multiple future breeding efforts. We are propagating these 100 varieties and planting them in research fields on three sites: In El Salvador at the World Coffee Research farm and in Costa Rica at CATIE and the Starbucks research farm. They will be a living resource for coffee researchers and breeders for decades to come.

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  • Location: Costa Rica
  • Leaders: Benoit Bertrand
  • Partners: CATIE; Department of Soil and Crops and Department of Horticultural Sciences, Texas A&M University
  • Cost: $200,000
  • Timeline: COMPLETE