Disease-resistant rice for use in East Africa

Researchers at Heinrich Heine University Düsseldorf (HHU) have, in collaboration with French partners, employed the “marker-assisted breeding” (MAB) technique to develop variants of African elite rice lines that are resistant to a detrimental crop disease. They now present their approach in the scientific journal Rice.

The rice disease “bacterial leaf blight” (for short: BB) is causing significant yield losses in Asia and Africa. It is triggered by the bacterium Xanthomonas oryzae pv. oryzae (Xoo), of which a large number of distinct regional strains exist on various continents.

Asian Xoo strains were unintentionally introduced into East Africa in around 2019 and had a massive impact in Madagascar and Tanzania, among other countries. Although the local African rice varieties are adapted to many of the African bacterial strains, they possess no resistance to these newly arrived Asian strains. The infection subsequently spread from Tanzania into neighbouring countries. A team from the French National Research Institute for Sustainable Development (IRD) headed by Dr Boris Szurek was able to trace the genetic origins of the Xoo variants back to Asia and map their spread into Africa in detail.

The team from the “Healthy Crops” international research project headed by Professor Dr Wolf B. Frommer from the Institute for Molecular Physiology at HHU specialises in developing solutions to fight Xoo and BB. The researchers have found a way to cut the bacterium off from its food supply: Xoo activates specific sugar transporters, the so-called SWEET genes, in the rice plant to obtain sugar on which to feed. The researchers used genome editing to adjust the corresponding sites in the genetic material of the rice to prevent the bacterium switching on these genes, thereby making the plant resistant.

This approach is quick and precise. However, approval procedures for genome-edited plants must be in place in the corresponding country. As this is not the case in numerous East African countries, the team deliberately chose a different approach in the study that has now been published. On the basis of endemic African rice varieties, the researchers developed new lines resistant to the Xoo strains spreading across East Africa without employing genome editing.

Professor Frommer: “To enable our lines to still reach farmers quickly, we transferred resistance genes into three elite rice varieties widely used in Africa by means of the so-called marker-assisted breeding (MAB) technique.”

The MAB technique adds the resistance genes while retaining the general properties of the original varieties. This advanced breeding method uses genetic markers to establish desirable traits in plants on a targeted basis more quickly and precisely than in conventional breeding methods, enabling the typical development periods to be significantly reduced.

Using this method, the scientists in the laboratories at HHU succeeded in developing new rice lines resistant to the Xoo strains identified in Tanzania and Madagascar on the basis of the African elite varieties KombokaP, FARO-44 and NERICA-4. The research team from HHU and their colleagues from IRD now present their findings in the scientific journal Rice.

Dr Yugander Arra, lead author of the study and former Alexander von Humboldt Research Fellowship holder at HHU: “We added several resistance genes to the rice varieties at the same time with the aim of ensuring broad-spectrum resistance to a range of Xoo variants. Accordingly, we can protect the rice lines we have developed not only against the two bacterial strains in Tanzania and Madagascar, but also against selected other Asian and West African strains.”

“With our study, we can offer rice breeders in East Africa robust resistance to bacterial blight in three local rice varieties for field trials. In addition, these lines are suitable for crossing with other local varieties. This can also form the basis for registering the lines as new varieties and ultimately their widespread use by farmers,” says Dr Eliza Loo, co-author of the study and head of the “Healthy Crops” team at HHU.

Dr Boris Szurek from the IRD: “IRD’s continuous monitoring in the different target countries has allowed us to build up an important collection of strains, gathered from the beginning of the outbreak to the present day. This has made it possible to establish a panel of pathogen strains that represents well the genetic and geographic diversity of the invading Xoo population, which is very useful for assessing the resistance spectrum, and therefore the validity of new resistant varieties, as is the case in our study.”

Professor Frommer: “The MAB method we are using now is very time-consuming. By contrast, the state-of-the-art genome editing methods available today enable us to respond to regional needs in a very short period of time. It is to be hoped that the African Union will agree common standards in the future to harmonise the use of genome editing in Africa.”

Original publication

Yugander Arra, Eliza P. I. Loo, Camille Blasco, Emilie Thomas, B. N. Devanna, Melissa Stiebner, Mathilde Hutin, Florence Auguy, Boris Szurek & Wolf B. Frommer. Rapid development of durable bacterial blight resistance in African rice through marker-assisted pyramiding of four resistance genes. Rice (2026)

DOI: 10.1186/s12284-026-00960-2