Blog Accelerating bean breeding to respond to market demands in East Africa: ACIAR’s Rapid Cooking Bean Project for health, nutrition and fuel efficiency
In East Africa, where beans are a dietary staple, a transformative initiative by the Australian Centre for International Agricultural Research (ACIAR) is reshaping the future of nutrition and cooking efficiency through the 'Rapid Cooking Bean Project' (RCBP) with reduced cooking time and enhanced nutritional quality in common beans (CROP/2018/132).
The project usesadvanced breeding technologies, including pedigree selection, genomic selection and optimal contribution selection (OCS) to accelerate the development of common bean varieties that cook at least 30% faster and contain 15% more iron and 10% more zinc than traditional varieties. RCBP is a collaborative effort between The University of Western Australia (UWA) and members of the Pan-Africa Bean Research Alliance (PABRA) through the Alliance of Bioversity International and CIAT, and six National Agricultural Research and Extension Organisations (NARES) in Burundi, Ethiopia, Kenya, Rwanda, Tanzania and Uganda. The project not only focuses on scientific innovation but also on empowering a new generation of African plant breeders with new skills including gender-inclusive training.
The project is implementing a novel breeding approach (BRIO) to accelerate breeding for rapid cooking and biofortified beans. BRIO stands for accurate breeding values (B), rapid cycles (R), index selection (I) and optimal contributions selection (OCS) (O). The BRIO approach was implemented by the Alliance in Uganda in 2019 by intercrossing a diverse set of 160 founder parents. This was followed by rapid two-year cycles of overlapping early generation recurrent selection. Faster-cooking beans released by partners in this project will lower household fuel use and labor, especially for women, while addressing regional micronutrient deficiencies. Through strategic breeding cycles and inclusive capacity-building, RCBP is creating a ripple effect across agriculture, nutrition and gender equity, making it a powerful model for sustainable development in the region.
Now in its fifth year, RCBP has made significant progress in accelerating the development of improved common bean varieties. Project staff at the Alliance's Uganda office have successfully completed five years of crossing and selection for cooking time and nutrition, while partner countries have evaluated grain yield and selected pure lines for potential release as new varieties. The project has achieved key milestones in both population improvement and product development.
Grouping candidate parents into different market classes to inform the selection of parents.
A training program for partner countries in RCBP was held at the Alliance's Uganda office from March 24-28, 2025, where researchers identified a major bias in seed colors of beans in RCBP, with the majority belonging to the black bean market class. Black-seeded beans are a small market segment in East Africa. This bias towards black beans may be the result of genetic associations between rapid cooking, high grain yield and black seed color. Dr. Clare Mukankusi Mugisha - the Lead Common Bean Breeder at the Alliance - will implement commercial crossing of rapid-cooking black beans in RCBP with large-seeded beans types in the red mottled and sugar category, which are a valuable segment of the East African bean market.
The BRIO method has the capacity to change selection goals through the use of OCS. Professor Wallace Cowling, the project leader at UWA, showed that crossing designs could be optimized to favor market segments with the most valuable seed colors and size. During the training program, the project team redesigned the crossing strategy to focus more on favored market classes. The researchers assembled and physically inspected the seed stocks of the current RCBP progeny and classified them according to market preferences. They learned how to implement OCS in software ‘MateSel’ to favor important market classes in East Africa, and generated a new optimized crossing list which was used to begin the sixth crossing round in RCBP in 2025.
The training program ensured that crossing in RCBP aligned with the targeted product profiles of beans in East Africa. In most countries in East Africa, large and medium-sized bush beans represent up to 74% of the market, and climbing beans representing 16% of the market.
In Ethiopia, small bush beans represent a significant proportion of the market. The team followed the market segments as identified by common bean researchers in East Africa in the Eastern and Central Africa Bean Research Network (ECABREN), which is part of PABRA.
The training program was led by Dr. Renu Saradadevi (Research Associate based at UWA) and Ms. Winnyfred Amongi (Research Associated at the Alliance), and trainees included Mr. Roy Odama (Alliance), Ms. Dagmawit Tsegaye (Ethiopian Institute of Agricultural Research, EAIR) and Dr. Immaculate Mugisa (National Crops Resources Research Institute Uganda (NaCCRI). Training occurred at the Alliance's Uganda office at the National Agricultural Research Laboratories located in Kawanda, outside Kampala.
Dr. Clare Mukankusi noted that ECABREN focuses on medium to large-seeded bean types, particularly red and red mottled, sugar, and yellow beans, which are highly preferred across the region. Small-seeded red and white beans also hold a significant share of the market and are crucial to regional food systems, especially in Ethiopia, she added. The week was filled with excitement as the bean breeders grouped lines into various market classes to strategically design market-led crosses. By integrating detailed market insights into the breeding process, the team is strengthening the link between scientific innovation and practical value, ensuring that the improved beans developed under the RCBP project meet the diverse needs in the region.
Left to Right: Ms Dagmawit Tsegaye (EIAR), Mr. Roy Odama (Alliance-Uganda), Dr. Clare Mukankusi (Alliance-Uganda), Dr. Immaculate Mugisa (NaCRRI), Ms. Winnyfred Amongi (Alliance-Uganda), Dr. Renu Saradadevi (UWA).
Technical challenges and rewards
Under the guidance of Dr Saradadevi and Ms Amongi, the team assigned the existing lines into four major groups and generated an optimized mating list in MateSel, a software tool that supports optimal contribution selection to enhance genetic gain while managing diversity.
Diversity of common bean genotypes in cycle 2B
Dr. Saradadevi emphasized that MateSel has played a strategic role in guiding and implementing the RCBP project's optimised crossing designs since 2019. MateSel can restrict matings within or across specific market classes, depending on desired traits and breeding goals.
Dr Saradadevi showed the results of her most recent data analysis RCBP, which show significant genetic gains from cycle 1 to cycle 2. The mean cooking time was reduced by 14% per year based on estimates from genomic analysis. At the same time, mean grain yield in partner country field trials also increased by 7%. Rapid-cooking bean varieties selected in partner countries are on track for release in the next few years. However, the first biofortified varieties (beans enriched with high levels of Fe and Zn) will likely be small-seeded bush types, largely due to unfavourble genetic linkages between micronutrient content and other traits of interests.. The development and release of large-seeded biofortified beans will require additional breeding cycles, but the foundation has been firmly laid for achieving this goal.
