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Eradicating hunger through the African Orphan Crops Consortium


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Baobab fruit, Kilifi, Kenya - Photo by World Agroforestry
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Training scientists in advanced plant genomics is set to transform nutrition in Africa. The Food and Agriculture Organization of the United Nations works with the African Orphan Crops Consortium to assist its member countries.

The African Orphan Crops Consortium is an African-led, international consortium founded in 2011 with the goal of sequencing, assembling and annotating 101 African orphan crops. The Consortium was approved by African heads of state at the African Union Assembly and is led by the New Partnership for Africa’s Development (NEPAD).

ICRAF’s Working Paper n. 296 – Breeders’ views on the production of new and orphan crops in Africa: a survey of constraints and opportunities [PDF]
The Consortium and its African Plant Breeding Academy, which is run by the University of California, Davis, comprise the most comprehensive and integrated crop-improvement venture on the continent. The Academy is funded by Mars Inc and the Alliance for the Green Revolution for Africa, among many other donors, and is hosted by World Agroforestry (ICRAF) in Nairobi, Kenya. The Academy trains African plant scientists and breeders to develop better crop varieties faster from genetic ‘maps’ of orphan crops. It has trained 85 of its target 150 African scientists to use DNA-sequence information to breed more nutritious, productive and resilient varieties that can withstand threats from environmental change.

‘The Consortium and the African Plant Breeding Academy have created synergy across the continent to promote African orphan crops and assist improvement of these crops through knowledge, skill, and technology transfer to African scientists,’ said Ermias Abate Desta, a graduate of the Academy. ‘This initiative is creating a network of “new breed” African plant breeders with a shared vision of a continent with no hunger, malnutrition and poverty. I am part of this great movement.”

‘Orphan crops’ refers to a diverse range of plant species that are economically and socio-culturally important but which are neglected by science and research because they are not widely traded commodities. The Consortium is raising the importance of these species and accelerating research activities for plant growth and development. By 2030, the use of nutritious, climate-resilient African crops stimulated by the Consortium’s work is expected to be a part of dietary improvements in 20% of rural populations and 10% of urban populations.

Read more –> For year round micronutrients, ten species of fruit trees are better than just a few

African orphan crop Adansonia digitata L. Photo: World agroforestry/Ake Mamo

 

 

 

 

 

 

 

 

 

The orphan crops include annual and biennial shrubs, bushes and trees that act as principal food sources for the 600 million people living in rural Africa. The Consortium has been sequencing the genomes of 101 species to allow scientists to efficiently improve the crops’ productivity, climate resilience, disease and pest resistance and nutritional quality and also training African scientists to best use the genetic information. All completed genetic ‘maps’ are published online with open access, with the intellectual property held by the African Union.

In 2017, the Food and Agriculture Organization of the United Nations (FAO) signed a letter of intent with the Consortium to assist member countries of FAO develop policies, regulations and laws that facilitate the genetic improvement of orphan crops; strengthen institutional and human capacities of member countries for research and development of genomic tools, plant breeding and seed-delivery systems; and convene neutral platforms for stakeholder engagement to advocate for greater investments in breeding nutritious and climate-resilient crops.

ICRAF’s Working Paper n. 276 -Supporting human nutrition in Africa through the integration of
new and orphan crops into food systems [PDF]
In 2018, the Consortium’s work was formally recognized at the October meeting of FAO’s Committee on Agriculture (COAG). During the Consortium’s side event at COAG, eight graduates from the African Plant Breeding Academy shared information about their work to help fight malnutrition in their own nations through transferring research methods and results and through training.

FAO Director of Nutrition and Food Systems, Anna Lartey, told the meeting that the Consortium’s approach has the potential to spur a revolution for orphan crops in Africa. Moreover, Lartey highlighted how the program can contribute to the nutrition targets of the United Nations 2030 Sustainable Development Agenda, with a focus on the Decade of Action for Nutrition, which is a UN commitment to eliminate malnutrition from 2016 to 2025.

‘Together we have created a movement to end hunger and malnutrition in Africa. Stunting will be eliminated in your lifetimes, if not earlier,’ said Howard-Yana Shapiro, Chief Agricultural Officer of Mars Inc and co-founder of the Consortium.

Read more –> ‘Fruit-tree portfolios’ for nutrition and health: a new approach

Completed tree genome projects under AOCC

  1. Apple-Ring Acacia (Faidherbia albida) –> published sequenced genome: http://dx.doi.org/10.5524/101054
  2. Horseradish Tree (Moringa oleifera [UGent version]) –> published sequenced genome: http://dx.doi.org/10.5524/101058
  3. Marula (Sclerocarya birrrea)  –> published sequenced genome: http://dx.doi.org/10.5524/101058
  4. Jackfruit (Artocrpus heterophyllus) –> published sequenced genome: http://dx.doi.org/10.5524/101057
  5. Breadfruit (Artocarpus altilis) –> published sequenced genome: https://doi.org/10.3390/genes11010027
  6. Drumstick tree Moringa oleifera [BGI version])

 

Further references

  1. Sahu SK et al. (2020) Draft genomes of two Artocarpus plants, jackfruit (A. heterophyllus) and breadfruit (A. altilis). Genes, 11: 27, https://doi.org/10.3390/genes11010027.
  2. Hendre PS et al. (2019) African Orphan Crops Consortium (AOCC): status of developing genomic resources for African orphan crops. Planta, 250: 989-1003, https://doi.org/10.1007/s00425-019-03156-9.
  3. Dawson IK et al. (2019) The role of genetics in mainstreaming the production of new and orphan crops to diversify food systems and support human nutrition. New Phytologist, 224: 37-54, https://doi.org/10.1111/nph.15895.
  4. Chang Y et al. (2018) The draft genomes of five agriculturally important African orphan crops. GigaScience, 8: giy152, https://doi.org/10.1093/gigascience/giy152.
  5. Dawson IK et al. (2018) Delivering perennial new and orphan crops for resilient and nutritious farming systems. In: Rosenstock T., Nowak A., Girvetz E. (eds) The Climate-Smart Agriculture Papers, Springer, Cham. https://doi.org/10.1007/978-3-319-92798-5_10.
  6. Hickey JM et al. (2017) Genomic prediction unifies animal and plant breeding programs to form platforms for biological discovery. Nature Genetics, 49: 1297-1303, doi: 10.1038/ng.3920.
  7. Muchugi A et al. (2016) Genome sequencing to unlock the potential of African indigenous fruit tree species. Indian Journal of Plant Genetic Resources, 29: 371-372, doi: 10.5958/0976-1926.2016.00074.7.

 

Partners in the African Orphan Crops Consortium

  1. Alliance for a Green Revolution in Africa (Nairobi, Kenya) is supported by the Bill and Melinda Gates and the Rockefeller foundations. The Alliance partners in many ways, including contributing USD 1.1 million to the African Plant Breeding Academy.
  2. Agricultural Research Council (Pretoria, South Africa) supports by by sequencing genes (transcriptomes).
  3. Benson Hill Biosystems is a plant biology, analytics and cloud computing company focusing on global food systems. It is providing all Consortium plant breeders with advanced computational technology to accelerate their breeding programs.
  4. Biosciences Eastern and Central Africa, International Livestock Research Institute Hub (Nairobi, Kenya) is a shared agricultural research and biosciences platform providing laboratory services to African and international scientists conducting research on African agricultural challenges. It provides the Consortium with laboratory and project support, training of breeders, and the curation of germplasm.
  5. BGI (Shenzhen, China) is the world’s leading genomic sequencing organization. It is involved in sequencing, annotating, assembling and curating many of the 101 African orphan crop genomes as well as supporting development of the Consortium.
  6. CyVerse (Tucson, USA) is a collaborative organization that has developed a cyber-infrastructure for data-intensive biology driven by high-throughput sequencing, phenotypic and environmental data sets. It has helped the Consortium with analysis and curation of sequence and genotype data.
  7. Corteva Agriscience is a private agricultural company focusing on development of crops. Corteva is helping train plant breeders and development of genomic resources.
  8. Food and Agriculture Organization of the United Nations (FAO) (Rome, Italy) supports the development of the Consortium through a letter of intent with specific areas of support.
  9. Google Genomics (Mountain View, USA) provides rapid transfer of data worldwide using cloud space.
  10. Illumina Inc (San Diego, USA) develops technology and kits for use in genetic research and has provided the Consortium with reagents to sequence the gene complement of 50 species and has donated their HiSeq 4000 Sequencer to the laboratory to sequence 10,000 accessions of African crops.
  11. Integrated Breeding Platform provides data management systems for plant breeders. The Platform provides training to breeders through the UC Davis Plant Breeding Academy.
  12. The James Hutton Institute (Dundee, Scotland) is a non-profit research institute specializing in plant breeding. It provides gene sequencing tools and analyses to breeders.
  13. Keygene Inc, (Rockville, USA) is an international company supplying genomic tools for plant breeding. It provides tools to breeders.
  14. LGC (Hoddesdon, UK) is an international life-sciences measurement and testing company, providing reference materials, genomics solutions and analytical testing products and services. It has also provided genotyping services for plant breeders.
  15. Mars, Incorporated (McLean, USA) is one of the world’s largest privately-owned food companies; it has provided over USD 2 million for the African Plant Breeding Academy, scholarships for breeding programs and support for laboratory personnel.
  16. New Partnership for Africa’s Development (Midrand, South Africa) is a technical body of the African Union which provides administrative, logistical and political support.
  17. Oxford Nanopore, (Oxford, UK) is a genomics company providing DNA and RNA sequencing technologies. It provides its platform and reagents to breeders.
  18. Thermo Fisher Scientific (Waltham, USA) helps companies and organizations solve their research challenges; it has donated four Proton sequencers and four Chef Stations and reagents. It recently acquired Life Technologies, which had donated four Ion proton machines to the Consortium.
  19. UNICEF (New York City, USA) supports the development of the Consortium.
  20. University of California, Davis (Davis, USA) is one of the world’s leading agricultural universities. It manages the Academy and co-leads the laboratory and scientific program.
  21. VIB-UGhent Center for Plant Systems Biology (Ghent, The Netherlands) is a non-profit research institute in the life-sciences sector that has 1200 scientists conducting basic research on molecular mechanisms. It has helped with bioinformatics and annotation of plant genomes.
  22. Wageningen University (Wageningen, The Netherlands) is a world-leading agricultural university working closely with the Consortium to define the nutritional value of African crops and breeding lines.
  23. World Agroforestry (ICRAF) (Nairobi, Kenya) hosts the laboratory and the Academy and helps manage its data.
  24. World Food Programme is the food-assistance branch of the United Nations and the world’s largest humanitarian organization addressing hunger and promoting food security. It supports the Consortium in a variety of ways.
  25. World Wildlife Fund for Nature (Washington DC, USA) has worked with the Consortium since its inception, helping with initiation and vision

For more information about the African Orphan Crops Consortium visit: www.africanorphancrops.org

This research was conducted by World Agroforestry (ICRAF) as part of the CGIAR Research Program on Forests, Trees and Agroforestry, the world’s largest research-for-development program to enhance the role of forests, trees and agroforestry in sustainable development and food security and to address climate change. The Center for International Forestry Research (CIFOR) leads the Research Program in partnership with the Alliance of Bioversity International and CIAT, Centro Agronómico Tropical de Investigación y Enseñanza (CATIE), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (CIRAD), International Bamboo and Rattan Organisation (INBAR), ICRAF and Tropenbos International (TBI). The work of the Research Program is supported by the CGIAR Trust Fund.

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Plant breeders contribute to achieving food security across Africa


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Participants take part in a practical session during the course. Photo by ICRAF
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The third class of graduates from the UC Davis Africa Plant Breeding Academy pose for a group photo. Photo by ICRAF

Thirty-four plant breeders from 18 countries graduated from the UC Davis African Plant Breeding Academy in May 2018.

The advanced plant breeding course was delivered by the Seed Biotechnology Center of the University of California Davis, in collaboration with the New Partnership for Africa’s Development (NEPAD) and the African Orphan Crops Consortium (AOCC).

The course, hosted by one of the CGIAR Research Program on Forests, Trees and Agroforestry’s (FTA) partner institutions — the World Agroforestry Centre (ICRAF) — in Kenya, equips practicing African plant breeders with advanced theory and technologies in plant breeding, quantitative genetics, statistics and experimental design to support critical decisions. This was the third cohort of the course, with participants drawn from Benin, Burkina Faso, Cameroon, Egypt, Ethiopia, Ghana, Kenya, Malawi, Mali, Niger, Nigeria, Senegal, South Africa, Sudan, Tanzania, Uganda, Zambia and Zimbabwe.

The program was delivered by a team of tutors and complemented by guest speakers, including Leena Tripathi of the International Institute of Tropical Agriculture (IITA) who covered banana improvement through transformation and gene editing, Damaris Achieng Odeny of the International Crops Research Institute for the Semi-arid Tropics (ICRISAT) on finger millet genomics, Dusty Vyas of LGC Genomics on genotyping sequencing and DNA analysis, and Alex Lipka of the University of Illinois on genomic selection. Participants also visited the International Livestock Research Institute’s Trepathi lab and glasshouse.

The plant breeders presented various proposals, explaining how they would put their newly acquired skills into practice. Mayada Beshir of the Agricultural Research Corporation in Sudan and Ermias Abate Desta of the Amhara Agricultural Research Institute of Ethiopia were each awarded US$5,000 from Mars Incorporated and Illumina for their winning proposals.

“Sorghum is the most important crop for us in Sudan and is widely produced by smallholders. We are experiencing the effects of climate change, as everywhere, and are observing new traits or stresses that have not been seen before. Sorghum productivity is declining yet the government is working hard to avail land, water and inputs,” said Bashir.

“As a breeder going through this training, my role is to help the farmer. The farmer will consume part of the harvest and sell the rest for income. I will produce a better variety of sorghum that is resistant to the stresses we are seeing right now and add nutrient value with better yield.”

Read more: Orphan crops for improving diets

“Tef is a staple crop and is grown only in Ethiopia,” said Desta. “It is an orphan crop because it hasn’t captured the attention of the international scientific community. My work is to identify varieties of tef that are tolerant to soil acidity, a common problem in highly productive areas of the country. I will use my prize money to produce soil acidity-tolerant genotypes of tef. Smallholders cannot afford the lime that needs to be applied to acidic soils for amelioration. Acid-tolerant varieties of tef will help as a management strategy and improve their yields.”

“The UC Davis African Plant Breeding Academy is part of the African Orphan Crops Consortium,” explained Allen van Deynze, a primary instructor at the academy. “The goal of the consortium is to make nutritious crops productive for Africa. The plant breeding academy is delivering food security in the continent. The people here today are the ones who are going to make the difference. Those who have passed through the academy are the ones who have taken on the challenge to make sure that everyone has nutritious food on their table.”

Participants take part in a practical session during the course. Photo by ICRAF

“When you go back, remember all that you have learned will be wasted if you fight, compete or do not collaborate,” said Tony Simons, director general of ICRAF. “It is a great honor to partner with all the institutions that support this program, because out of all the initiatives that ICRAF has implemented in the last 40 years, this has been one of the most impactful.”

Recounting the start of the consortium that led to the UC Davis African Plant Breeding Academy, Howard Shapiro, chief scientist at Mars Incorporated, acknowledged the organizations and individuals who contributed to the consortium. Of the 101 crops that were selected for sequencing, 47 are trees and the remainder are annual crops.

“No one had ever considered to do this amount of research on crops,” noted Shapiro. “Major foundations and organizations chose one crop — cassava, maize — and that is all they work on. Our idea was that we could fix the nutritional productivity of 101 food crops that are not only the backbone of rural Africa, but are also important in urban centers. An idea of paradise is that we can end chronic hunger and malnutrition by improving the nutritional quality and productivity of the 101 food crops. All those who have passed through the academy are the ones who will deliver this paradise.”

“We have sequenced 10 species for the AOCC,” noted Xin Liu of BGI. “We are trying to release data as soon as possible. You can combine this data for better application and breeding processes for all the crops. We made a commitment three years ago to sequence 101 crops. We have our own sequencers that can be used to generate more data and we would like to contribute all the science and technology we can to this consortium.”

The Alliance for a Green Revolution in Africa (AGRA) is a primary partner of the academy and has sponsored 31 plant breeders of the second and third cohorts. It also funded master and doctoral courses for over 400 of the 500 plant breeders in Africa. So far, 18 countries have released over 600 varieties of crops.

Read more: Tree seed selection, genome sequencing, improvement of priority species and more

“We realized that the breeding field keeps changing. This course has helped us keep up and modernize our breeding efforts,” said Rufaro Madakadze, program officer of AGRA’s Africa Seed System. “We fund training to develop technologies that people will use.”

Speaking on behalf of the class, Maureen Atemkeng of Nigeria expressed gratitude to the academy, particularly for the opportunity to interact with international experts. She added that the course helped in building principles of efficiency, responsibility and sustainability for the next generation.

“Hunger and malnutrition can be eliminated in our lifetime,” said Rita Mumm, director and primary instructor of the academy. “The vision of the African Plant Breeding Academy is to train 150 plant breeders. Graduates, you will continue to work together, contribute your talent to teams, and join the African Association of Plant Breeders. I exhort you to mentor the next generation of plant breeders. Share your knowledge and experience.”

In closing, Ramni Jamnadass, coleader of ICRAF’s Tree Productivity and Diversity research unit that hosts the AOCC, encouraged the graduates to contribute to breeding programs that will banish food and nutrition insecurity in Africa.

The course is delivered in three two-week sessions spread over 18 months at the ICRAF campus in Nairobi. Since its inception in 2013, 89 plant breeders have successfully completed the course and covered more than 99 species, of which 57 are African orphan crops.

By Susan Onganyo, originally published at ICRAF’s Agroforestry World. 

This research forms part of the CGIAR Research Program on Forests, Trees and Agroforestry, which is supported by CGIAR Fund Donors.

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Orphan crops for improving diets


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A fruit hangs on a baobab tree. Photo by Katja Kehlenbeck/ICRAF
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A fruit hangs from a baobab tree. Photo by Katja Kehlenbeck/ICRAF

Orphan crops, so-called because they are considered neglected and underutilized, are typically overlooked in terms of resources for their promotion. But they are now being brought out of the shadows, along with their potential health and environmental benefits.

At present, orphan crops are not extensively researched, despite their potential for realizing economic and dietary benefits for the people who cultivate and consume them, as well as bringing environmental gains to the landscapes where they are grown.

This is due in part to the “nonstandard and unimproved” landraces being grown in some locations, which are not as productive, robust or of as high quality as they could be. However, through plant genetics and crop improvement, the potential of orphan crops to address issues of malnutrition and hunger in Africa can be enhanced, if the necessary market interventions to support their use are also correctly implemented.

The African Orphan Crops Consortium (AOCC), which aims to obtain complete sequences of DNA of 101 neglected food crops, and the African Plant Breeding Academy (AfPBA), which empowers crop breeders from across Africa through skill development, networking and information sharing, are working to improve these crops and promote their utilization.

The AOCC, based in Nairobi and launched in 2011, is hosted by the World Agroforestry Centre (ICRAF), one of the CGIAR Research Program on Forests, Trees and Agroforestry’s (FTA) partner institutions. Its research is now in the spotlight following recent articles from The Economist and the Financial Times.

According to ICRAF’s Prasad Hendre, the Genomics Laboratory Manager at the AOCC, the consortium is “all about giving a voice to underprivileged African farmers through their crops, making the crops sustainably profitable for individual smallholder farmers, their families and communities.”

Members of the African Plant Breeding Academy’s Class II pose for a photo to mark their graduation. Photo by ICRAF

So far, of the overall target, AOCC researchers have fully sequenced 10 genomes and partially sequenced 19.

“The AOCC is working on 101 orphan crops – 50 trees and 51 annuals – shortlisted through larger consensus between farmers, policy makers, governments, agricultural research organizations, philanthropists and private entities,” Hendre said.

“As a first step, we are trying to bring scientific equality to these crops by making the cutting-edge application-oriented scientific tools available through group leadership of the AOCC. It is all about bringing useful and innovative technology to the doorsteps of the African research community, primarily the plant breeders, who can develop new varieties to suit local, regional and global demands.

“At the core of these technologies is the genome sequence of any crop, which directly or indirectly shapes the outcome of these crops on farms. By predicting the effect of a specific DNA signature on the performance of an individual, it is possible to design a next generation of ‘smart’ crops which are high yielding, efficient, highly nutritious and capable of facing environmental challenges. It is also important to impart the right skillsets to African plant breeders who are largely practicing traditional methods of crop improvement. The new tools and methods in their hands can speed up variety development.”

AfPBA, an initiative of the AOCC, is focusing on this skill enhancement by training African plant breeders to use genomic tools and incorporate them into breeding programs.

Mehmood Hassan of ICRAF, who is also FTA’s capacity development coordinator, explained that AfPBA is a collaboration between the University of California, Davis and ICRAF, while the New Partnership for Africa’s Development and the Alliance for a Green Revolution in Africa are also closely involved.

The academy aims to equip 250 African breeders with advanced breeding skills and approaches by 2023 and to expand their horizons to incorporate African orphan crops, including trees, into their breeding agendas, according to Hassan. So far, more than 50 breeders in two groups have successfully graduated, with a third group of 34 set to graduate in June 2018.

A variety of mango grows on a farm in Machakos County, Kenya. Photo by ICRAF

“Several of the past graduates have already influenced breeding programs by expanding the focus from calorific crops to crops with wider nutritional value,” Hassan said.

AfPBA also mentors the trainee breeders in formulating international grant proposals. A few breeders have already been able to attract additional financial resources to support and expand their programs to include some of these new tools.

“The benefits of breeding these crops will be many,” said Hendre. “For local African orphan fruit tree crops, an additional benefit could be their conservation, encouraging farmers to plant highly productive varieties on farms in a sustainable manner, as compared to extractive non-sustainable harvesting from parklands, semi-wild or forest landscapes.”

“For annuals, it will help in improving their acceptance as mainstream crops due to developing easy to cook, easy to cultivate, tasty and nutritious high-yielding varieties,” he added.

For both trees and annual crops, the primary beneficiaries are expected to be farmers, who will be able to diversify their farms with multiple marketable options made available through newly developed varieties. Certified seed sellers are also likely to be among the primary beneficiaries.

Meanwhile, secondary beneficiaries will include local traders, who will be able to buy and sell the products. Tertiary beneficiaries will be both local and global food processors, who will have the chance to diversify their offerings with nutritious, sustainable and locally sourced foods.

In line with this, once improved crops are bred, both farmers and seed distributors need to be encouraged to make use of them.

“Farmers can be encouraged to adopt new varieties if they are shown benefits. The most important benefit a farmer can see is through increased income. ICRAF and FTA can help farmers see that there is a demand for their products and how they can use that opportunity to market their farm produce and enhance income,” said Hendre. “Other benefits for the environment and human health can be shown using ecological and health indicators for soil, climate and community health, among others.”

Prasad Hendre demonstrates some of the advances in technology in genome sequencing during a laboratory visit. Photo by ICRAF

“Adopting improved varieties requires engaging with certified producers of planting material – be this seed or vegetatively propagated plants in the case of some crops – who can supply improved varieties to the farmers,” he added.

The prospects look good, with some orphan crops holding significant potential for wider consumption and improved nutrition.

“A few of these crops already have global or regional markets, such as African eggplant, African bush pear and African bush mango, Allanblackia, amaranth, baobab, marula, moringa and shea. Releasing improved varieties helps farmers to follow more profitable and sustainable cultivation practices, and allows product standardization, which lead to greater demand and better market prices. In the future, I can see many more of these crops reaching a global market as global consumer preferences change,” Hendre said.

With these efforts and the promising progress to date, new and improved varieties of orphan crops may one day sit alongside current staple foods in stores and on plates, both across Africa and around the world.

By Hannah Maddison-Harris, FTA Communications and Editorial Coordinator 

This work forms part of the CGIAR Research Program on Forests, Trees and Agroforestry (FTA), which is supported by CGIAR Fund Donors. 

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