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Study author Michelle Nay in a test field in Colombia. (Photograph: courtesy of M. Nay)

Next, Nay planted the beans from her collection in Uganda and Colombia, both in greenhouses and in the field. Her aim was to find out if and indeed how the different varieties react to the fungus’s various pathotypes in each country, and then to identify the genetic basis of disease resistance.

Nay also created a high-resolution genetic profile for each of the 316 bean types based on variations in their DNA known as genetic markers, and identified which markers occurred only in the disease-resistant beans. She subsequently used these markers to predict which progeny would be resistant to which pathotypes in a given country, and which ones would be susceptible to disease.

Improvement on conventional plant breeding

“Our method speeds up the breeding process considerably,” Studer says. It’s a big step forward because crossbreeding had previously been a numbers game and involved testing every single plant for its resistance, he explains. Now, on the basis of a genetic test, it is possible to predict a plant’s resistance without testing it in laborious field trials. “This is a huge help in bean breeding and great news for people who rely heavily on beans as a staple of their diet,” Studer says.

The group’s work to provide disease-resistant beans will also help to cut down on global pesticide use. As things stand today, Studer explains, fungicide use is common for bean cultivation in Latin America, but almost non-existent in Africa because many farmers don’t have access to pesticides, or don’t know how to use them safely and efficiently: “Disease-resistant beans are a double win: famers in Latin America can reduce their pesticide use while farmers in Africa can increase their crop yield pesticide-free.”

Simple, inexpensive and open-source technology

CIAT distributes the seeds from this project to various sub-organisations who then supply them to breeders. The analytical method for determining genetic markers is relatively simple and inexpensive to apply, making it viable for use in agricultural laboratories in the countries concerned. It costs less than 0.2 CHF to test a genetic marker, Nay explains, which is an affordable amount for laboratories in less affluent countries. What’s more, all the findings from this study are available through open access. “This way, our work reaches the people who really need these kind of resources,” Nay emphasises.

Nay and Studer worked on this project in close collaboration with CIAT. The global research centre runs the largest breeding programme in the tropics and has several thousand varieties of bean in its seed repository. At its headquarters in Colombia, CIAT breeds new bean varieties, tests the seeds, and, in partnership with the Pan-Africa Bean Research Alliance, makes the seeds available to farmers for cultivation.

In collaboration with CIAT and supported by the World Food System Center at ETH Zurich, Studer and his group will now conduct a follow-up project to refine their breeding method. While the researchers previously focused on markers for one specific disease, the new project will take a more holistic approach as they attempt to use such genome profiles to predict as many plant characteristics as possible.

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