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Coffee varieties of mesoamerica and the caribbean

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Rapid Coffee Variety Identification

Creating value from seed to sale
Coffee Arabica Genetic Diversity

The problem

One of the essential, and largely invisible, problems facing the coffee industry is the lack of a coffee seed sector. The vast majority of smallholder farmers do not know the variety they grow in their fields, do not know that more appropriate varieties exist that could increase their profitability, and do not have access to better plants. This matters because different varieties do different things. And if farmers don’t know or can’t trust what they have, they are exposed to huge risk. As it stands, seed producers, nurseries, farmers, and supply chain actors do not have the needed tools to identify and trace varieties as they move from seed gardens to nurseries, from nurseries to farmer fields, from the field to the port, and from there into roasting drums around the world.

Additionally, some varieties are valued more highly in the growing specialty coffee market. Accurate identification of specific coffee varieties supports value-creation and ensures that when breeders develop improved varieties that their higher potential is able to be captured by farmers. Variety authentication is critical for:

  1. Countries: To be assured of the authenticity of their plant varieties and to protect them

  2. Seed producers and nurseries: To create and maintain variety traceability from seed to sale

  3. Farmers: To be sure of what variety they are growing, to manage the varieties effectively, and to be able to capture the higher value associated with improved varieties

  4. Roasters: To have traceability assurance on the coffees arriving for roasting

To build a strong and professional coffee seed system that creates value for all, there is therefore a need to develop efficient (i.e., inexpensive and rapid) variety authentication methods.

The solution

The traditional approach to species or variety identification involves observation and recording of physical (also called morphological) characteristics of the plant, such as height, leaf shape and color, etc. This approach is not especially good at distinguishing between coffee varieties and is time-consuming. Furthermore, morphological characteristics are often multigenic (caused by multiple genes), not available at all growth stages, and influenced by environment, thus making it difficult to assess them quickly and objectively. 

Recent technological advances have created accurate, repeatable, inexpensive, and rapid options for the genetic identification of plant types down to the level of varieties. In particular, a method of testing that analyzes the presence of single-nucleotide polymorphism (SNP) markers has become the testing approach of choice for variety identification in plants. SNPs are the most abundant class of genetic variation (polymorphism) in plant genomes. These variations can be thought of as creating a genetic “fingerprint” for a given variety. In particular, SNPs are accurate, and can be analyzed quickly and at a much lower cost that other forms of genetic variation. Because of these advantages, SNPs have become the marker of choice for variety identification in plants, and SNP-based genetic fingerprinting has become the standard for plant variety identification across a range of crops.

It is in this context that World Coffee Research, in partnership with the USDA and IRD, are developing a global Arabica and Robusta SNP panel (a reference dataset containing enough SNPs required to estimate genetic diversity and distinguish variety) to be used in support of two urgent goals:

  1. Authentication of variety in foundation seed programs (e.g., in mother seed gardens that provide the foundation for all of the new plants generated in an area or country), and

  2. The introduction of SNPs into WCR’s global breeding program and collaborative regional breeding hubs to increase the capacity of such programs to breed more efficiently and effectively.

Additionally, such a program could allow transformative opportunities for the entire coffee sector around:

  • Variety traceability

  • Supply management

  • Variety protection

  • Quality control

The impact

Being able to authenticate varieties faster and much, much more cheaply will be a foundational step in creating value for farmers. Supporting the professionalization of the coffee nursery sector globally and putting better tools in the hands of coffee breeders worldwide will allow our nurseries to produce adequate volumes of genetically pure and healthy seedlings to small-scale coffee farmers. This will also result in expanded access to improved, resilient varieties for smallholders, leading eventually to increased production and profits. It reduces farmer risk and strengthens needed renovation programs in target countries.


A visual representation of SNPs

  • Location: United States of America
  • Leaders: George Kotch (WCR)
  • Partners: USDA, IRD
  • Timeline: 2020