Extraordinary Call
Other agencies:
USD 770.000
Counterpart Amount:
USD 1.000.000
Execution time
36 Months
Total Amount:
USD 1.770.000
Participating countries:
Colombia Colombia Costa Rica Costa Rica Dominican Republic Dominican Republic Guatemala Guatemala Honduras Honduras Panama Panama France France United States United States
Funding source:
Other agencies 44% Counterpart Amount 56%

Executive Summary

Coffee cultivation is of strategic importance for most of the member countries of FONTAGRO. It is one of the main agricultural products for export and foreign exchange generation in the region. Latin America is the main producer in the world of Coffea arabica, a highly appreciated species in the world market for its best quality and which represents 70% of the market. Climate change is expected to negatively affect coffee production worldwide, particularly in Latin America. The genetic improvement of coffee is a slow process, which is why modern tools are required to study the coffee genome and its biology to accelerate the development of new varieties that increase quality, productivity and protect the crop from damage associated with climate change. 

The project objective is to increase the knowledge of the coffee genome and the exploration and use of germplasm, through: 1) the construction of the physical map of coffee based on the two diploid species that originated the tetraploid species (Coffea arabica): C. eugenioides and C canephora; 2) the use of new sequencing technologies to elucidate the genes that are present in the coffee genome and 3) Development of genomic tools to facilitate the selection of coffee varieties adapted to the effects of climate change, dissemination of results and strengthening of the existing scientific network of coffee producing countries. 

The technological solution

The genetic improvement of coffee varieties is a very slow process, since it is a perennial crop. In addition, it requires extensive experimental plots and measurements during various harvests. Genomics allows the identification and location of important genes and their rapid characterization in progenies of interest and is an essential tool to assist in the genetic improvement of coffee and other perennial crops. 

Improved varieties are the cheapest alternative and the easiest technology to manage disease problems, and acquire better adaptation to climate change. 

Work with hybrid populations has shown the expression of genes that react differentially to specific growing conditions, such as shade and full sun exposure. The rapid and successful selection of materials that can behave well in both conditions will favor the formation of varieties with a high potential to respond adequately to changing climate conditions. 

Identifying gene markers for these conditions can results in significant savings in time and costs of variety development, which must be designed to respond to local conditions. 


A total of 25,575 different gene sequences were identified. The various hybrids studied were separated by groups according to their greater or lesser adaptability to sun and shade conditions. The use of new technologies in the genome sequencing of the Coffea eugenioides and C. arabica species was successfully adapted. 
Two genomes were assembled and two public databases with the sequences derived from the project were created on the portal: C. eugenioides and C. arabica. Four CENICAFE doctoral students were trained at top-tier universities such as the University of Arizona, Purdue University, University of California Davis, and Penn State University. 

Two international workshops were held with the participation of scientists and industry representatives from 9 countries, in San José de Costa Rica, in 2012, and in Armenia, Colombia in 2014. 

Five researchers from the project made presentations at the Annual Plant and Animal Genome (PAG) Conferences in California between 2011 and 2014. 


The direct beneficiaries were the dozens of researchers involved in research on the coffee genome, and the four doctoral students who carried out their thesis studies on topics related to the project at top-level universities. As well as the hundreds of researchers and professionals who participated in the events where the results were presented. 

 Thousands of coffee growers in the region could benefit indirectly, when the information generated in the project is used to develop varieties that are more productive and resistant to pests and diseases and resilient to climate variability and change. 

Sustainable Development Goals

Climate action Partnerships for the goals

Main donors

Participating Organizations

  • CENICAFE - Colombia
  • Centro Agronómico Tropical de Investigación y Enseñanza (CATIE) - Costa Rica
  • Consejo Dominicano del Café (CODOCAFE) - República Dominicana
  • Instituto del Café de Costa Rica (ICAFE) - Costa Rica
  • IHCAFE - Honduras
  • MIDA - Panamá
  • PROMECAFE - IICA - Guatemala
  • AGI - Estados Unidos
  • CBCB - Estados Unidos
  • International Center for Tropical Agriculture (CIAT) - Colombia
  • ICGN - Francia
  • Institut de Recherche pour le Développement (IRD) - Francia

Graphics and data

Financing by country (in USD)
FONTAGRO Amount Other agencies Counterpart Amount

Geolocated Map


With the support of
Fondo Coreano de Alianza para el Conocimiento en Tecnología e Innovación (KPK)