Examining WCR’s Arabica genetic fingerprinting database

genetic fingerprinting

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

Like the Pinot Noir or Cabernet Sauvignon varieties of wine, Bourbon, Pacamara, or Geisha are not merely used as coffee varietal descriptions, they’re also employed as marketing terms.

To appreciate specific varieties within the Arabica species of coffee, World Coffee Research (WCR) has released 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 worldwide. WCR is making the database openly accessible to the scientific community so that it can be used by public and private labs for variety verification,” says WCR Director of Strategy and Communications Hanna Neuschwander.

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

WCR Research Scientist in Plant Breeding and Genomics Dr. Santos Barrera says prior 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 can have devastating economic consequences for a farmer,” Barrera says.

Determining the genetic makeup of a plant — the specific variety, otherwise known as its genotype — is important at many steps along agricultural supply chains. This database of genetic fingerprints for Arabica uses 45 Single Nucleotide Polymorphism (SNP) molecular markers — tiny genetic variations dispersed through a plant’s DNA sequence — to create a unique genetic fingerprint for 23 of the most commonly recognised coffee varieties in commercial coffee production in Latin America.

“A SNP is basically a molecular tool to measure the genetic differences between individuals. Small variations in the patterns tell us who’s who,” says Neuschwander.

Neuschwander says SNP markers can be analysed quicker than other genetic markers.

“In order to build a variety verification database like this one, you need to test a lot of trees – not just one or two trees per type, but hundreds or thousands – in order to define which SNP patterns are associated with, for example, Bourbon versus Geisha versus Pacamara, and so on. You need to find which pattern identifies that particular variety and distinguishes it from another. That is what the database does,” she says.

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

Neuschwander says one of the database’s most important applications is the development of low-cost variety authentication to support coffee’s evolving 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 to use for coffee on a wide scale,” Neuschwander says.

Barrera says that in coffee, the predominant way that varieties are identified currently is through morphological identification.

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

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

To process the sample of a coffee variety, Neuschwander says, involves using a hole puncher to obtain a small amount of leaf tissue, which is sent to a lab for analysis. From there, the tissue is ground, and placed in a machine that isolates the DNA.

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

“It’s pretty common to use SNPs in other plant groups as it’s a “faster, cheaper, and better” method. Now that this database is available to the coffee sector, it’s a gamechanger that allows for more precise and cost-effective genetic traceability.”

WCR’s breeding team developed the database, led by WCR Research Scientists in Plant Breeding and Genomics Drs. Jorge Berny and Barrera. The database builds on a SNP marker panel developed by Research Geneticist Dr. Dapeng Zhang from the United States Department of Agriculture (USDA) Agricultural Research Service.

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

Multiple institutions facilitated access to leaf samples used to create and validate the database, including The Tropical Agricultural Research and Higher Education Center, Instituto del Cafe de Costa Rica, Honduran Institute of Coffee, and Guatemalan National Coffee Association. The USDA Foreign Agricultural Service Maximising Opportunities in Coffee and Cacao in the Americas (MOCCA) program funded the work.

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

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 high-volume lab testing service, targeted mostly to seed lots, nurseries, and coffee research programs. They typically require a minimum of 376 samples. Intertek AgriTech is an ISO-certified quality assurance laboratory that provides lab services to the global agricultural sector.

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

“If you’re a nursery and you want to verify that you are selling the variety you think you are, you need to be able to send your samples somewhere and verify them. This database makes those services possible and more affordable, not only for a big private seed company but for a national coffee research institute that might want to test the seed lots of their own national variety.”

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

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

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

This article was first published in the November/December 2023 edition of Global Coffee Report. Read more HERE.

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