One of the keys to success in coffee is choosing the right variety. But according to World Coffee Research (WCR), most farmers are not sure which varieties they grow. Without having accurate information on the seeds or saplings they plant, producers are unlikely to be able to optimize quality, yields, sustainability, and profits of their crops. And inaccurate identification of a coffee variety can degrade results downstream in the supply chain.
To remedy this gap, WCR has developed an open-access online database of Coffea arabica genotyping data for free use by researchers and identification service providers throughout the world. The project utilizes recent technological advances that have made it inexpensive and fast to obtain accurate genetic identification of plants based on analysis of single-nucleotide polymorphism (SNP) markers.
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 a much lower cost than other genetic markers. Because of these advantages, SNPs have become the marker of choice for variety identification in plants. The SNPs are identified using a Kompetitive Allele Specific (KASP), a type of competitive real-time polymerase chain reaction (PCR) assay that is fluorescence-based.
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 commercial crops by both industry and the scientific community to authenticate varieties, understand genetic diversity and design more efficient breeding schemes. But until now the coffee sector has not had easy, affordable access to such tools. The SNP analysis uses coffee leaves as sample material.
World Coffee Research, based in Oregon, United States, worked with plant breeders and genomics experts from around to refine a pre-existing set of genetic markers to precisely determine the genotypic profiles of some of the coffee varieties popular in Latin America, many of which are also farmed in other regions. This reference panel of genetic markers will serve as a crucial tool in providing affordable genotyping services to coffee producers globally. By granting farmers access to the finest authenticated varieties, this resource establishes a strong foundation for creating value in the coffee industry.
The database tracks 45 SNP markers across 23 varieties from Latin America that can be authenticated using the reference panel. A total of 1,424 samples (coffee leaves) were used to build the reference panel, collected from five countries: Guatemala, El Salvador, Costa Rica, Honduras, Peru.
Partners that provided support to the project, such as access to samples, logistics, and/or genotyping data, included the USDA Agricultural Research Service, CATIE, Instituto del Café de Costa Rica (ICAFE), Honduran Institute of Coffee (IHCAFE), and La Asociación Nacional del Café (Anacafé). Funding was provided by WCR member companies, and the MOCCA program. The data set is being made available for public use without restriction, following the Creative Commons Zero (CC0) Framework.
According to WCR, it's not only farmers that lack accurate information on what they are growing. Seed producers, nurseries, and other 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. This is especially important for seed providers, who mass produce seeds or plants for farmers.
By facilitating the creation of low-cost, rapid genotyping tools, the WCR project supports the professionalization of the coffee nursery and seed sector globally. It enables seed providers and nurseries to produce adequate volumes of genetically pure and healthy seedlings to coffee farmers. Ultimately, this will result in expanded access to improved, resilient varieties, leading to increased production and profits. It reduces farmer risk and strengthens needed renovation programs in target countries. The data set will be expanded to include additional varieties over time.
For more information, see: https://worldcoffeeresearch.org/resources/arabica-ldp-snp-marker-panel