CRISPR-editing rice crops: Mitigating the impacts of rice disease in sub-Saharan Africa

Rice is a key staple crop in sub-Saharan Africa, with more than 60% of rice produced consumed there. However, the Rice Yellow Mottle Virus (RYMV) causes a disease that has the propensity to wipe out African rice crops. This disease, which is often considered the most dominant rice disease affecting irrigated and lowland ecologies, has since its discovery been observed in nearly all of Africa’s rice-producing countries.

In this study, published in the Plant Biotechnology Journal, researchers aimed to develop resistance to the disease.

The cost of the virus ​

Many of Africa’s rice producers have barely a hectare of land to themselves. In this environment, between 10% and 100% of rice yield is regularly lost to disease, putting strain on food security.

“RYMV has an impact on food security and poverty of smallholder farmers. The impact is variable from one year to the other, dependent of various factors, and is very difficult to quantify precisely. However the disease is often described by African smallholder farmers as one of the main disease of rice and, considering the importance of rice in Africa and in the world, some authors included RYMV in the Top Ten of economically important plant viruses,” Laurence Albar, one of the researchers, told FoodNavigator.

Developing resistance ​

There are currently three resistance genes to RYMV, and mutations in just one of these genes enables a rice strain to achieve resistance. 

While one domesticated rice species, Oryza glaberrima, also known as African rice, has developed resistance in some cases, it is low yielding and not widely used. However, resistance in the higher yielding and more widely used Oryza sativa, is extremely low. While O. glaberrima has almost the full spectrum of resistance genes, the higher-yielding O. sativa does not.

“Very few rice varieties highly resistant to RYMV (without symptoms or impact on yield) were available in the most widely cultivated species of rice (Asian rice): two traditional varieties originating from East Africa, namely Gigante and Bekarosake, and 3-4 additional lines derived from those varieties and developed in the 2000's by rice breeders of West African countries,” Albar told us.

“High resistance has also been observed in several varieties of another cultivated rice species (African rice) that is now only rarely cultivated. These resistant varieties are not very high-yielding, and their characteristics (resistance to other diseases, size, cycle length, etc.) are not what many farmers are looking for. Transferring their resistance to better adapted varieties through classical breeding methods is tedious and time-consuming. That is why genome editing is highly promising.”

The challenge was to develop resistance in higher yielding rice varieties. To do this, the researchers used CRISPR/Cas9 gene editing technology to edit one of the resistance genes, OsCPR5.1, in the Asian Japonica rice variety Kitaake, creating mutations within this gene and thus developing resistance in the rice without any sacrifice in yield.

“Based on greenhouses experiment on the lines we developed (and also on African rice varieties that carry similar mutations), we did not observe any negative side effects on plant development. However these results have to be confirmed in field experiments, in relevant agro-ecosystems, before considering the deployment of the engineered varieties on large areas,” Albar told us.

The key challenge now is to test more African rice varieties to see if they can produce resistance in these. Furthermore, to provide African rice farmers themselves with the edited, resistant rice varieties.

“In the next stage, we will carry out the same approach on high-yield varieties adapted to cultivation by smallholder farmers in African countries. If the absence of negative side effects is confirmed, these varieties can be transferred to smallholder farmers to be deployed on a large scale to avoid RYMV disease and associated yield losses, thus contributing to lift out people of poverty and food insecurity.”

Saving rice crops ​

One of the researchers, Wolf B. Frommer, is an investigator at the Healthy Crops project, an international research consortium whose broad aim is to help smallholder African and Asian rice farmers increase yields and avoid diseases.

The most prominent focuses of the project are RYMV and Bacterial Blight (BB), another particularly devastating rice disease.

“We now also have edited blight resistant rice, especially relevant due to a major outbreak caused by the inadvertent introduction of Asian strains to East Africa, with major damage and rapid spread,” Frommer told FoodNavigator.

“We also have lines for Tanzania and East Africa that are resistant, and did not use editing, maybe not as good as the edited lines, but due to regulatory situation the best possible solution.”

Frommer considers the project’s biggest success developing resistance to BB for India and Africa.

Sourced From: Plant Biotechnology Journal
'Rice Yellow Mottle Virus resistance by genome editing of the Oryza sativa L. ssp. japonica nucleoporin gene OsCPR5.1 but not OsCPR5.2’
Published on: 20 December 2023
Doi: https://doi.org/10.1111/pbi.14266
Authors: Y. Arra, F. Auguy, M. Stiebner, S. Chéron, M. M. Wudick, M. Miras, V. Schepler-Luu, S. Köhler, S. Cunnac, W. B. Frommer, L. Albar