Skip to content

How a consortium is changing Africa’s food systems.

The African Orphan Crops Consortium (AOCC) is a unique collaboration of public-private institutions whose goal is to eradicate stunting, hunger, and chronic malnutrition in the Africa. It specifically focuses on providing options for sustainable livelihoods and nutrition to African farmers through supply of high quality seeds of single season crops (annuals) and tree crops with specific focus on the health of women and children.

There are about 45 trees and around 50 single season crops with a few vines, shrubs and herbs in the list of species. These crops are highly nutritious with high levels of vitamins, minerals, antioxidants, and are important for African agricultural – ecosystem. These crops play an important role in the diets of smallholder farmers and also they also contribute to local markets and have cultural value. They have limited resources in crop development and few plant breeders focusing on them.

Many of the crops are not well-adapted and grown by farmers under sub-optimal conditions on the farms or backyards, whereas many of the trees are grown with minimal or no care on farm boundaries, backyards, community yards and other nondescript areas. As a result, low yields are achieved, despite their nutritional value. Due to newer risks arising due to climate change scenario, it becomes very important to be future ready to address some of the forecasted challenges such as high temperature, erratic rainfall and new diseases and pests. At present products from these crops or trees often reach local markets but in future they will see expansion into major rural and urban markets in Africa and also into global export markets

Dr Howard Shapiro, Chief Agriculture officer, Mars Inc.; Dr. Ibrahim Mayaki, Chief Executive Officer, New Partnership for Africa’s Development; African inter-governmental organization (NEPAD) and Mr Coulibaly Sangafowa, the Minister of Agriculture, Ivory Coast conceived the idea of AOCC in 2011. Dr Shapiro initiated the consortium the same year as a commitment to the Clinton Global Initiative in Washington, D.C. to tackle the problem of nutritional security in Africa. The initiative’s goal was to establish financial and strategic support; advocacy with international community and capacity building.

The consortium was established to enable African farmers and scientists to incorporate the latest technologies and strategies available to rapidly advance plant breeding and productivity of nutritious crops important to African diets. The consortium conducted an Africa-centric survey with participation from African plant breeders, sociologists, anthropologists, nutritionists, policy makers, scientists, farmers, government representatives, universities and various other stakeholders to identify 101 African orphan or neglected crops important to African diets.

This heralded the establishment of the African Plant Breeding Academy (AfPBA), by the University of California, Davis (UC Davis) – a very important capacity building initiative in December 2013. The academy will train 250 African plant breeders over the next five years in modern breeding tools such as genomic assisted selection (MAS), selection theory, efficient statistical designs and objective measurements of traits. World Agroforestry Centre (ICRAF) hosts the AfPBA and has built a state of the art genomics lab for the consortium. The Centre has played a key role in providing tree germplasm resources and has a track record of tree domestication and improvement. Once the AOCC agenda was finalized BGI, genome sequencing powerhouse, extended its full support to undertake the whole genome sequencing of all the crops.

Life Technologies joined in 2013 and pledged next generation sequencing technologies to explore and discover the genomic diversity otherwise known as single nucleotide polymorphism (SNP) within these species. They have also donated four Ion Proton sequencers, two Ion Chefs, four Ion One Touch 2s, one Pippin Prep system and agreed to provide consumable and technical support to re-sequence 100 accessions from each of the 101 species to the AOCC genomics lab.

The germplasm for annual crops was offered by various Consultative Group for International Agricultural Research (CGIAR) institutions like IITA, ICRISAT, Bioversity, BecA/ILRI, CIAT, and ARC and national partners such as Kenya Agriculture and Livestock Research Organization (KALRO) and Kenya Forestry Research Institute (KEFRI).

Other partners who have offered scientific and technical support, data analytics, data storage and data logistics are iPlant Collaborative, LGC, University of Ghent and Google. The consortium was also granted Illumina Inc.’s Greater Good Initiative grant for the year 2015 to sequence the transcriptome of 50 AOCC species using Illumina’s NGS technology with instrument and technical support from Agricultural Research Council (ARC), South Africa. To help in design of the SNP assays, LGC Genomics has offered low-cost marker-assays to African breeders working on the selected crops.

Already, with first AfPBA class graduating, the AOCC has increased capacity in this area with several additional grants for breeding these crops obtained from foundations such as Bionnovate, and NWO-WOTRO Science for Global Development of the Netherlands. Many more collaborative grants have been applied for the long term goal is to convince African governments to better support development of these important crops for their countries.


African Plant Breeding Academy (AfPBA) trains first cohort of 21 plant breeders

The AfPBA has trained the first cohort of 21 plant breeders who graduated in December 2014. The second training course will start end of this year. The selection of plant breeders is done on competitive basis and the plant breeders with sufficient field experience and zeal to stretch their horizons beyond traditional breeding practices are selected at the pan-African level.

 The BGI starts whole genome sequencing of 14 AOCC species

BGI has started working on sequencing of 14 crops namely Adansonia kilima, Adansonia digitata, Vigna subterranea, Lablab purpureus, Casimiroa edulis, Annona senegalensis, Moringa oleifera, Solanum aethicopicum, Eleusine coracana, Faidherbia albida and Sclerocarya birrea. Many of the annuals have simple genomes with less heterozygosity, whereas most of the trees have complex genomes with high heterozygosity. BGI is trying different technical and analytical approaches depending on the complexity of genomes. Other AOCC partners have already sequenced the genomes of an additional 12 crops.

The ICRAF nursery team and genebank unit supports the germinate seeds and grow until leaves are ready to have their DNA isolated. In the last five months since the genomics lab started, it has completed 100 re-sequencing runs for common bean (Phaseolus vulgaris), spider plant (Cleome gynandra) and finger millet (Eleusine coracana).

The lab has improved its efficiency by having successful runs of over 85 percent of total executed runs within the brief period of its operation.

The African Orphan Crops Consortium is a partnership between BecA/ILRI (Nairobi, Kenya), BGI (Shenzhen, China), Ghent University (Ghent, Belgium), Google (MountainView, USA), LGC (Hoddedson, UK), Life Technologies (Thermo Fisher, Carlsbad, USA) Mars, Incorporated (Maclean, USA), New Partnership for Africa’s Development (NEPAD, (Nairobi, Kenya), iPlant Collaborative (Tucson, USA), UC Davis (Davis, USA), World AgroForestry Centre (Nairobi, Kenya) and World Wildlife Federation, (Washington, DC).

By: Prasad Hendre and Allen van Deynze