Genetic testing finds mismatched specialty coffee varieties on Ecuador farm

Researchers at Universidad Técnica Particular de Loja reported on October 9 that genetic testing of specialty coffee plants on one farm in southern Ecuador found discrepancies with the varieties under which their seeds were sold. Two of four identified plant types did not match their declared commercial identities. The finding matters to growers because a mismatch may emerge only after years of planting and crop management.

The report concerns plants grown from seeds marketed as Sidra and Gesha at a farm in Loja province. The seeds had been bought without genetic or phytosanitary certification, according to the study. About three years after planting, visible differences among the plants prompted researchers to investigate their identity. The research was published in Frontiers in Plant Science in July; Universidad Técnica Particular de Loja provided the October 9 account of its findings.

What genetic tests found in Sidra and Gesha plants

Researchers grouped the plants into four morphotypes, or types distinguished by their visible features, and used DNA markers to compare their genetic profiles. Two sampled Sidra morphotypes matched Sidra. A third morphotype from the Sidra lot had a profile compatible with Batian, a coffee variety of Kenyan origin. Batian is genetically distinct from the Ethiopian landraces to which Sidra is related.

The Gesha case was more qualified. Plants bought under that name matched an Ethiopian landrace and were genetically similar to a Geisha reference accession held by CATIE in Costa Rica. They were not identical to that reference. The comparison does not establish a more specific variety name for those plants, so the result should not be read as proof that they were Batian or that every plant in the Gesha lot had the same identity.

How far the Ecuador findings can be applied

The study examined one farm and a limited number of plants. Researchers genotyped one representative plant for each of the four morphotypes. That method identified differences among the sampled types, but it did not measure genetic diversity within each type or establish the composition of the complete seed lots. The authors say the case cannot show how common mismatches are across Ecuador.

The team also assessed whether visible plant features could help distinguish the four types. Its analysis classified the sampled morphotypes with 82.4% overall accuracy under a leave-one-out validation method. Internode length, the distance between growth points along a branch, was especially useful in separating them. Those results concern the plants studied; they do not establish a field test that growers can apply reliably across other farms or seed lots.

What a separate seed-quality assessment shows

A separate World Coffee Research assessment provides wider context for the risk of incorrectly identified planting material. It examined Arabica seed sources in El Salvador, Guatemala, Honduras, Nicaragua and Peru under the MOCCA program. More than 36% of participating seed lots had very high genetic noncompliance: no more than half of the tested trees in those lots conformed to the expected identity. Only 26% of lots had conformity of at least 90%.

The five-country assessment did not include Ecuador, and its figures cannot be used as an estimate for the Loja farm or for Ecuadorian seed supplies. World Coffee Research identified limited certification tools, weaknesses in traceability and limited technical assistance among challenges facing seed producers. It also noted that even genetically conforming seed plantations did not always follow practices intended to reduce contamination risks, including isolation, traceability and adequate storage.

What researchers plan to examine next

The Ecuador researchers say they want to examine more plants and farms, building stronger genetic and physical references for coffee varieties. Such work could help develop ways to verify planting material before it reaches growers' fields. For now, the documented result is a discrepancy among sampled plant types at one farm, alongside a separate regional assessment showing seed-quality problems in five other countries.