Genotyping and phenotyping tools

Global tools to enable breeding modernization


Coffee lacks some of the basic tools that other crops have used to modernize variety development. For example, in order to utilize modern breeding approaches, it’s necessary to have accurate, repeatable, inexpensive, and rapid options for genotyping plants in a breeding program. (Genotyping is a way of “peering inside” the plant to observe its genetic makeup.)

But genotyping tools are not enough—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.

Tools under development


A global mid-density SNP panel. World Coffee Research is part of a collaboration with the USDA, DaRT, Intertek, and 32 coffee institutions in 21 countries to develop a low-cost global arabica and robusta genotyping tool for breeders to use. The platform uses the DaRTag technology to track single-nucleotide polymorphism (SNP) variation. These variations can be thought of as creating unique genetic “fingerprints” that can then be associated with key performance traits. Similar mid-density panels have been developed and deployed for critical food crops covered by the CGIAR Excellence in Breeding program, 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.

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, in 2022.

We hope to make these publicly available in late 2022!