Genotyping and phenotyping tools

Global tools to enable breeding modernization


Determining the genetic makeup of a plant—the specific variety, otherwise known as its “genotype”—is important at many steps along agricultural supply chains. 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.

In addition to genotyping tools, it’s also critical to build maps that allow breeders to associate the genetic makeup of the plant to important observable traits (the plant’s phenotype), such as whether the plant is tall or short, high yielding or low yielding, has good cup quality or poor cup quality, performs stably in hot and cold environments, etc.

In order to associate genotype and phenotype, it’s critical to also develop careful phenotyping protocols and high-volume/low-cost methods for phenotyping traits of interest. For example, there is no standard approach for phenotyping coffee quality for breeding programs—even though cup quality is one of coffee’s most important traits.


When breeders are armed with low-cost, high-powered genotyping and phenotyping tools and are able to map genetic markers to important traits, modern breeding becomes possible. Coffee can rapidly accelerate progress here by looking to crops that have already developed accurate, repeatable, inexpensive, and rapid genotyping and phenotyping tools.

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.

Tools under development


A global mid-density SNP panel. World Coffee Research, in partnership with plant breeders and genomics experts from around the world, are developing SNP-based genotyping tools. A mid-density SNP panel of around 3,000 SNP markers provides a detailed "fingerprint," which can be used to understand the genetic relatedness of different coffee plants. This is a powerful tool that will be used by plant breeders and scientists who are analyzing the genetic diversity of coffee and designing more efficient breeding schemes for the development of new varieties that respond to farmer and buyer demand. This tool is being developed in collaboration with coffee breeders from around the world and will be made publicly available to the scientific community via the Excellence in Breeding platform. Similar mid-density panels have been developed and deployed for critical food crops, including rice, wheat, potato, cowpea, and groundnut—and now coffee breeders worldwide will benefit from access to the platform, too.


Rapid identification of key traits. WCR is working with partners to develop phenotyping protocols for key coffee traits. In addition, we are exploring high-throughput methods to screen for cup quality potential of breeding populations through a collaborative research program with the Coffee Science Foundation and Specialty Coffee Association.


Global Coffea Arabica Genetic Improvement Research Priorities, 2023

Identifying the top needs of the global coffee breeding community

Molecular breeding ≠ genetic modification

WCR has a strong policy against genetic modification. In molecular breeding, the genetics of the plant are not manipulated in any way. Instead, molecular breeders “peek inside” a plant’s genetics to find genes or markers associated with important traits, which can be done with very young plants. They can use genotyping to choose which plants to mate with others when making new crosses, focusing on those that have markers associated with desired performance traits. Then, instead of planting 1000s of plants in a field and to check which perform the best—which may take 3-7 years for a tree crop like coffee—breeders can take baby plants, genotype them, and see which have the desired markers. The ones that do can be transplanted to the field, and the others discarded. This is hugely time and cost saving. In some cases breeders can even analyze the genetic profiles of individual seeds and subsequently select which to sow and which to disregard, saving them a great deal of time and labor.

This article explains how fruit and vegetable breeders are using these approaches to create tastier, healthier products without using genetic modification.

The mid-density SNP panel will be openly available as soon as the development is finalized and the panel is validated, by the end of 2024.