Traceability and Training Tools

Strengthening seed suppliers to build a stronger coffee seed sector

The problem

Worldwide, most farmers do not have access to high-quality coffee plants, which exposes them to tremendous unnecessary risks. In most parts of the world, when it’s time for a coffee farmer to plant a new tree on their farm, he has two choices: Save his own seed, or obtain it from a neighbor or local nurseries. Many nurseries are in remote areas and primitive, producing questionable varieties of questionable plant health. In most cases, these nurseries take or buy seeds from local farmers or institutions but do not take into consideration genetic traceability and purity of the seed—in other words, they often don’t know for certain what variety they are selling. Training is limited or nonexistent for most nursery owners; most learn on-the-fly and have scarce access to technical assistance. Additionally, a majority of 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. For the specialty market, where specific coffee varieties like Geisha, Maragogype or Pacamara create value and can generate higher prices for farmers, it’s even more important to have access to accurate variety information.


Best practice manuals and supporting videos. To fill an urgent gap in knowledge about best practices, from 2019–2021, WCR developed a series of three manuals of best practices with supporting videos for producing genetically pure and healthy seedlings, as well as on good business practices, tailors for nurseries both small and large. These manuals are accessible in Spanish, English, and French. Supporting videos are available in Spanish, English, French, Luganda, and Lugisu. In 2023, WCR developed a series of five complementary videos to support Robusta Clonal Coffee Nursery Management. All of these resources are freely available to all (see below).

Genetic traceability tools—low-density SNP panel. Genotyping tools are regularly used in other commercial crops by both industry and the scientific community to authenticate varieties, understand genetic diversity and design more efficient breeding schemes. These tools are not widely available in coffee, or have so far been too expensive or impractical to use. Now, WCR is leading the charge to develop rapid, reliable, accurate and affordable genotyping tools for both arabica and robusta.

Recent technological advances have created accurate, repeatable, inexpensive, and rapid options for the genetic identification of plants. A method of testing that analyzes the presence of single-nucleotide polymorphism (SNP) markers has become the method of choice for genotyping in many plant species. The pattern of these tiny variations dispersed through a plant’s DNA sequence can be used to create a genetic “fingerprint” for a variety. SNP markers are accurate and can be analyzed quickly and at much lower cost than other genetic markers. Because of these advantages, SNPs have become the marker of choice for variety identification in plants.

A panel of 40-50 SNP markers provides a quick and definitive genetic fingerprint to authenticate specific coffee varieties. This is especially important for seed providers, who mass produce seed or plants for farmers. Accurate identification of specific coffee varieties ensures that when breeders develop improved varieties, their higher potential is able to be captured by farmers. This tool is also of value to others including individual farmers seeking to identify the varieties on their farm or coffee companies looking to validate a source of supply.

WCR has developed a low-density panel for arabica (a robusta panel is fortchoming in 2024) and has made the database available in the public domain; commercial genotyping services for variety authentication are available through Agritech. This is an ISO-certified service that can be utilized by the coffee community for high-quality analysis and timely delivery. The approach puts genotyping quality and cost on par with many elite private sector companies.

For pricing and/or to use this service, contact Intertek Agritech directly by emailing Petra Vanroggen (


Coffea arabica KASP genetic markers for low-density genotyping

An open-access resource for building rapid coffee variety identification services using SNP markers

Assessment. To build a strong and professional coffee seed sector, WCR assists key countries to evaluate their seed systems, and identify gaps and roadmaps for future investment. In addition, we support individual seed suppliers to assess their genetic purity and variety traceability systems using new, low-cost genotyping tools (see above).

The impact

Supporting the professionalization of the coffee nursery sector globally and putting better tools in the hands of seed producers and nurseries worldwide allows expanded access to improved, resilient varieties for smallholders, leading to increased production and profits. Such steps leading to increased production and profits, creating value for farmers.



Resources for coffee nursery management

A set of resources for successful nursery operation

Good Practice Guides: Supporting Videos

Series supporting guides on practices for successful coffee seed production and nursery management

Robusta Clonal Coffee Nursery Management: Supporting Videos

Series supporting the UCDA's “Clonal Robusta Coffee Nursery Manual”