As an enigmatic plant disease threatens one of the most important legume crops in Africa, a Pan Africa network of plant breeders collected germplasm and leveraged state-of-the-art genotyping to find the genetic markers for resistance to the disease. The discovery — made possible by the collaboration of scientists across the continent compiling their local varieties and breeding lines — is the most promising tool to date in the battle against groundnut rosette disease (GRD).

Groundnuts are an important part of diets throughout Africa, supplying protein, healthy fats, vitamins and micronutrients to people who often rely on starchy grains, roots and tubers, while serving a valuable role in crop rotations with cereals, nitrogen-fixation and restoration of soils. 

But as with any other crop, plant disease is a constant threat to productivity, especially in the tropics, and GRD has been especially challenging for groundnut farmers in Africa, reducing pod yields by up to 100 percent. Because GRD is a viral disease, fungicides don’t work, and while insecticide sprays can control aphids that transmit the disease, chemicals are not always practical for smallholder farmers. The most effective solution is growing varieties resistant to GRD, but breeding for resistance has proven difficult and time-consuming due to the complexity of the disease.

The recent discovery of the genetic markers for that resistance started with a local problem and local resources. Farmers in each country needed a GRD-resistant variety, and breeders in each were working hard to develop those varieties. 

With an assist from the Feed the Future Innovation Lab for Peanut, groundnut breeders from across Africa submitted thousands of lines from their breeding programs, which were honed into a core collection of 300 lines representing genetic diversity.

“The groundnut breeders in 10 countries freely came together, contributing lines and varieties to constitute one of the largest collections of breeding lines ever assembled in Africa,” said David Okello, a senior researcher with Uganda’s National Semi-Arid Resources Research Institute and leader in the work in Eastern and Southern Africa. “This unique set of genetic material is not fully sequenced and phenotyped and is being used by many breeders as the source of relevant traits to improve local materials, and often, as advanced lines in variety trials enroute to release.” 

Ugandan plant breeder Esther Achola, a PhD student at Makerere University, tapped into that core collection, working over three growing seasons in two hotspots for GRD to find the lines that appeared most resistant to the disease, then analyzed those lines to establish marker-trait associations. Analysis uncovered several markers in two major genomic regions, which can be developed into routine assays and validated for future genomics-assisted selection for GRD resistance in groundnut.

The journal Theoretical and Applied Genetics recently published the work, which entailed a team of African, American and European scientists. 

“This opens an exciting chapter for GRD resistance studies and breeding for groundnut in Africa. For the very first time, we have insights into GRD resistance on the groundnut genome,” said Achola. “This work has paved the way for marker-assisted breeding for GRD which will enable breeders to develop GRD-resistant varieties for farmers in a shorter time.”

Collaborating with the network of African breeders and using the latest genomic tools, Achola and the team have made breeding for GRD more efficient and effective than thought possible even a few years ago. Breeders are now able to be more predictive and design more effective breeding programs before even setting foot in the field. The work also enables breeders to identify groundnut lines with specific alleles for GRD resistance, making it possible to pyramid resistance or combine alleles for durable resistance.

The researchers noted that more work needs to be done to characterize the pathogen, its vector and other hosts to better understand the disease.

“We also need to leverage up-to-date technologies such as next Generation Sequencing, Rapid Generation Advance, high throughput phenotyping, and genome editing to better understand GRD resistance,” Achola said. 

The GRD-resistance markers are an early result of the Pan Africa collaboration — a group that has formalized into the Groundnut Improvement Network for Africa — but future benefits are limitless. 

Here are a few keys to their success of the network:

• First, all of the predominant groundnut classes important to local farmers and consumers were included in the core collection. 
• Second, the breeding programs in 10 countries — Senegal, Ghana, Uganda, Malawi, Mali, Niger, Burkina Faso, Togo, Zambia and Mozambique — were willing to share this valuable germplasm, and the countries were willing to move it across borders, a sure sign of a vibrant and healthy seed system. 
• Third, the team recognized that genome sequencing had become much quicker and less expensive, and genomic tools to make sense of this genetic sequence data were more accessible than ever.

Full understanding of GRD will require more research, including evaluating farmer-preferred varieties in multiple locations under heavy disease pressure (the network of national programs and breeding programs offer this opportunity). The key to this collaborative spirit is trust and confidence that the value created is much greater, for all partners, than if each organization and individual were working in isolation.

Sharing varieties and leveraging local knowledge promises to improve groundnut productivity and quality. Plant breeding, new breeding technologies and agronomic improvements are among the best strategies for food security and climate change adaptation and mitigation.

Local demand, local knowledge and technology is creating a vibrant seed system and greater productivity for African farmers and consumers.

Check out the article “Genome-wide association studies reveal novel loci for resistance to groundnut rosette disease in the African core groundnut collection" in Theoretical and Applied Genetics.