Examining the WCR Arabica genetic fingerprint database

World Coffee Research explains how its Arabica genetic fingerprint database will dramatically reduce the cost of coffee variety identification and genetic traceability.

Just like wine varieties Pinot Noir or Cabernet Sauvignon, Bourbon, Pacamara or Geisha are not only used as descriptions of coffee varieties, but also as marketing terms.

To appreciate specific varieties within Arabica coffee species, World Coffee Research (WCR) has launched an Arabica coffee genetic fingerprint database that will make variety authentication cheaper and simpler.

“Verification of coffee varieties is important to ensure quality control of plant material available to farmers around the world. WCR is making the database openly accessible to the scientific community so it can be used by public and private laboratories for variety verification,” said WCR Director of Strategy and Communications Hanna Neuschwander.

“This unique achievement brings new technologies to coffee to dramatically reduce quality control costs and ensure the future of high-quality coffee.”

WCR research scientist in plant breeding and genomics Dr. Santos Barrera says previous WCR studies have confirmed the need for such tools to better support quality control in seed lots and nurseries.

“We saw the need to develop a fingerprint database and created a reference point for the coffee industry. If, for example, a supposedly disease-resistant variety turns out to be susceptible to debilitating infections, this could have devastating economic consequences for the farmer,” says Barrera.

Determining the genetic makeup of a plant – the specific variety, also known as the genotype – is important at many steps along agricultural supply chains. This Arabica genetic fingerprint database uses 45 molecular Single Nucleotide Polymorphism (SNP) markers, small genetic variations scattered throughout a plant’s DNA sequence, to create a unique genetic fingerprint for 23 of the most commonly used coffee varieties. recognized in commercial coffee production in Latin America. .

“A SNP is basically a molecular tool for measuring genetic differences between individuals. Small variations in patterns tell us who is who,” says Neuschwander.

Neuschwander says SNP markers can be analyzed more quickly than other genetic markers.

“To build a variety verification database like this, you need to test many trees – not just one or two trees per type, but hundreds or thousands – to define which SNP patterns are associated, for example, Bourbon versus Geixa versus Pacamara , and so on. You need to figure out which pattern identifies that specific variety and distinguishes it from another. That’s what the database does,” she says.

“If a research laboratory has the technology to take a DNA sample from a coffee plant and ‘read’ the SNPs in that sample, they could use the database to match the SNP to the specific coffee variety, determining its genotype. .”

Neuschwander says one of the most important applications of the database is the development of low-cost variety authentication to support the evolving coffee seed sector.

“Similar tools are widely used in other crops by seed producers, seed traders and food manufacturers, but until now, these tools have been too expensive or impractical for large-scale use in coffee,” says Neuschwander.

Barrera states that, in coffee, the predominant way of identifying varieties currently is through morphological identification.

“Morphological authentication involves identifying the structure and shape of the plant” – in other words, visual inspection. “This approach, however, is much less accurate than genetic identification,” he says.

“There are other types of molecular markers, such as simple sequence repeat (SSR) markers or microsatellites, that can be used for genetic identification. These are very effective for diversity analysis, but very expensive, costing around $130 per sample. SNP markers are more accurate for authentication and much more affordable, priced at about $10 per sample.”

Processing a sample of a coffee variety, says Neuschwander, involves using an awl to obtain a small amount of leaf tissue, which is sent to the laboratory for analysis. From there, the tissue is crushed and placed in a machine that isolates the DNA.

“Say the owner of a batch of coffee seeds wants to check the genetic purity of their trees to ensure they are the correct variety. They collect small pieces of leaves from the trees they want to authenticate and send them to a genotyping laboratory. DNA is extracted from the leaf samples and the SNP profile is read. The sample’s SNP fingerprint is then compared to the known SNP fingerprint for the strain in question. When the fingerprints match, the variety can be confirmed,” he says.

“It is very common to use SNPs in other groups of plants, as it is a “faster, cheaper and better” method. Now that this database is available to the coffee sector, it is a game-changer that allows for more accurate and cost-effective genetic traceability.”

The WCR breeding team developed the database, led by WCR plant breeding and genomics research scientists Drs. Jorge Berny and Barrera. The database is based on a panel of SNP markers developed by research geneticist Dr. Dapeng Zhang of the United States Department of Agriculture (USDA) Agricultural Research Service.

“The reference database was validated and refined by WCR using more than 30,000 tree leaf samples in six countries, including Guatemala, Honduras, El Salvador, Nicaragua, Costa Rica and Peru between 2021 and 2023,” says Barrera.

Several institutions facilitated access to the leaf samples used to create and validate the database, including the Tropical Center for Agricultural Research and Higher Education, the Costa Rican Coffee Institute, the Honduran Coffee Institute, and the National Coffee Association of Costa Rica. Guatemala. The USDA Foreign Agricultural Service’s Maximizing Opportunities in Coffee and Cocoa in the Americas (MOCCA) program funded the work.

“The idea is that any laboratory can use the database to identify varieties without the need for a geneticist or breeder to analyze the data. If you don’t have the capacity to build your own genotyping lab and finance the lab equipment, they can simply send samples to commercial labs in the US or Europe,” says Barrera.

WCR plans to add fingerprints for additional varieties in the coming months and years.

To ensure the coffee community has immediate access to this service, WCR worked with Sweden-based Intertek AgriTech to validate and refine the database and technical protocols. Intertech Agritech has since launched a high-volume laboratory testing service primarily targeting seed lots, nurseries and coffee research programs. They typically require a minimum of 376 samples. Intertek AgriTech is an ISO-certified quality assurance laboratory providing laboratory services to the global agricultural sector.

“Now that WCR is making the database publicly available, it can also be used by other providers to develop their own DNA testing services,” says Neuschwander.

“If you’re a nursery and you want to check that you’re selling the variety you think you are, you need to be able to send your samples somewhere and check them. This database makes these services possible and more accessible, not only for a large private seed company, but also for a national coffee research institute that wants to test seed lots of its own national variety.”

Neuschwander says this public reference panel of SNP-based genetic markers serves as a crucial tool and a leap forward for the coffee industry to authenticate varieties, reducing risk and increasing value for farmers. She says an example of the impact such a tool can have on large-scale coffee production can be found in El Salvador.

“The government of El Salvador is undertaking a national renewal plan, with the aim of producing and distributing more than 150 million plants over the next decade, as part of its commitment to revitalizing the country’s coffee sector. These plants are expected to generate 1.8 to 2 million bags of exportable green coffee, stimulating the country’s economy and supporting the livelihoods of producers across the country,” says Neuschwander.

“This SNP panel is being used to validate the authenticity of the trees it intends to distribute to farmers, in order to ensure that they are the high-performing varieties selected to meet the country’s ambitious production targets. WCR is excited to be a partner in this work to sustain El Salvador’s high-quality grain supply.”