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Enhancing African orphan crops with genomics

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Results of surveys of African plant breeders, taken from the article.
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FTA communications

Originally appeared on the World Agroforestry’s website

Malnutrition in many African nations is widespread but can be addressed by diversifying food systems with a wider range of nutritious crops. To support this, the African Orphan Crops Consortium is applying genome-enabled methods to improve the production of under-researched (‘orphan’) crops on the continent.

“Orphan crops”, explains Ramni Jamnadass, lead author of a Comment piece about the Consortium just published in Nature Genetics, “are crops that have received only minor investments in the past, but often are well adapted to local environments and cultures and are nutritious, being rich in vitamins, essential minerals and other micronutrients important for healthy diets. The reasons for their past neglect include a focus over the last century on increasing the yields of major crops as the primary providers of calories but with less attention being given to providing crucial micronutrients.”

In some cases, too, orphan crops have been difficult to research and improve because of their particular biologies. With the advent of new crop improvement methods that include genomic approaches, however, such barriers are easier to overcome.

The Consortium works on 101 orphan crops chosen as priorities for consumers and farmers in Africa. These encompass plants that are part of Africa’s historically neglected bounty of biodiversity. Many of the species are at threat, meaning that if they are not improved and brought into wider cultivation now, the opportunity to do so will be lost forever. The plant species included feature a wide range of nutritious foods, such as edible roots, leaves, seeds, and fruit.

The Consortium develops genomic resources of these crops and makes these available freely to all. At the same time, the UC Davis-led African Plant Breeding Academy empowers the continent’s plant breeders to use these resources through an intensive training and mentoring program. The Academy is a model for the importance of continuing education and professional development of Africa’s scientists. By the end of 2019, 114 alumni from 27 African nations, collectively working on more than 100 crops, had graduated. In the Academy’s teaching, participants share their experiences to support translational learning so that new breeding approaches can be fully exploited. This involves considering ‘orthologous’ genes that contribute to the same function across crops and for which knowledge of their role in one crop may be applied to another.

As Africa’s national economies transform there will be new opportunities for orphan crops to support forward-looking healthful food systems. These are needed to counter the current trend toward more homogenised diets, something which applies worldwide, with its negative consequences for human health and the environment.

Jamnadass concludes: “Though the challenges involved are complex, the rewards for society in diversifying food production are large. We encourage more colleagues to engage in orphan crop research and to support such work in Africa and globally.”

Read the article

Jamnadass R, Mumm RH, Hale I, Hendre P, Muchugi A, Dawson IK, Powell W, Graudal L, Yana-Shapiro H, Simons AJ, van Deynze A. 2020. Enhancing African orphan crops with genomicsNature Genetics.

The team of authors above was drawn from ICRAF; University of Illinois, Urbana; University of New Hampshire, Durham; Scotland’s Rural College, Edinburgh; University of Copenhagen, Frederiksberg; and University of California, Davis. The African Orphan Crops Consortium is supported by the African Union’s Development Agency. A list of other core Consortium partners is given in the article and on the Consortium’s web site.

About World Agroforestry (ICRAF)
World Agroforestry (ICRAF) is a centre of scientific and development excellence that harnesses the benefits of trees, including food trees, for people and the environment. Knowledge produced by ICRAF enables governments, development agencies and farmers to utilize the power of trees to make farming and livelihoods more environmentally, socially and economically sustainable at multiple scales. ICRAF is a partner of FTA and one of the 15 members of the CGIAR, a global research partnership for a food-secure future. We thank all donors who support research in development through their contributions to the CGIAR Fund.

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  • Achieving sustainable cultivation of cocoa

Achieving sustainable cultivation of cocoa

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There is a growing demand for cocoa. However, cultivation is dependent on ageing trees with low yields and increasing vulnerability to disease. There is growing concern about the environmental impact of cultivation in areas soil health and biodiversity. There is therefore an urgent need to make cocoa cultivation more efficient and sustainable to ensure a successful future. These challenges are addressed in Achieving sustainable cultivation of cocoa.

Part 1 reviews genetic resources and developments in breeding. Part 2 discusses optimising cultivation techniques to make the most of new varieties. Part 3 summaries the latest research on understanding and combatting the major fungal and viral diseases affecting cocoa. Part 4 covers safety and quality issues whilst the final part of the book looks at ways of improving sustainability, including the role of agroforestry, organic cultivation and ways of supporting smallholders. With its distinguished editor and international range of expert authors – including a number from CGIAR Research Program on Forests, Trees and Agroforestry (FTA) scientists – this collection will be a standard reference for cocoa scientists, growers and processors.

Part 1 Genetic resources and breeding

1. Taxonomy and classification of cacao: Ranjana Bhattacharjee, International Institute of Tropical Agriculture (IITA), Nigeria; and Malachy Akoroda, Cocoa Research Institute of Nigeria, Nigeria;
2. Conserving and exploiting cocoa genetic resources: the key challenges: Brigitte Laliberté, Bioversity International, Italy; Michelle End, INGENIC (The International Group for Genetic Improvement of Cocoa), UK; Nicholas Cryer, Mondelez International, UK; Andrew Daymond, University of Reading, UK; Jan Engels, Bioversity International, Italy; Albertus Bernardus Eskes, formerly CIRAD and Bioversity International, France; Martin Gilmour, Barry Callebaut, USA; Philippe Lachenaud, Centre de coopération internationale en recherche agronomique pour le développement, France; Wilbert Phillips-Mora, Center for Tropical Agriculture Research and Education, Costa Rica; Chris Turnbull, Cocoa Research Association Ltd., UK; Pathmanathan Umaharan, Cocoa Research Centre, The University of the West Indies, Trinidad and Tobago; Dapeng Zhang, USDA-ARS, USA; and Stephan Weise, Bioversity International, Italy;
3. The role of gene banks in preserving the genetic diversity of cacao: Lambert A. Motilal, The University of the West Indies, Trinidad and Tobago;
4. Safe handling and movement of cocoa germplasm for breeding: Andrew Daymond, University of Reading, UK;
5. Developments in cacao breeding programmes in Africa and the Americas: Dário Ahnert, Universidade Estadual de Santa Cruz, Brazil; and Albertus Bernardus Eskes, formerly CIRAD and Bioversity International, France;

Part 2 Cultivation techniques

6. Cocoa plant propagation techniques to supply farmers with improved planting materials: Michelle End, INGENIC (The International Group for Genetic Improvement of Cocoa), UK; Brigitte Laliberté, Bioversity International, Italy; Rob Lockwood, Consultant, UK; Augusto Roberto Sena Gomes, Consultant, Brazil; George Andrade Sodré, CEPLAC/CEPEC, Brazil; and Mark Guiltinan and Siela Maximova, The Pennsylvania State University, USA;
7. The potential of somatic embryogenesis for commercial-scale propagation of elite cacao varieties: Siela N. Maximova and Mark J. Guiltinan, The Pennsylvania State University, USA;
8. Good agronomic practices in cocoa cultivation: rehabilitating cocoa farms: Richard Asare, International Institute of Tropical Agriculture (IITA), Ghana; Victor Afari-Sefa, World Vegetable Center, Benin; Sander Muilerman, Wageningen University, The Netherlands; and Gilbert J. Anim-Kwapong, Cocoa Research Institute of Ghana, Ghana;
9. Improving soil and nutrient management for cacao cultivation: Didier Snoeck and Bernard Dubos, CIRAD, UR Systèmes de pérennes, France;

Part 3 Diseases and pests

10. Cocoa diseases: witches’ broom: Jorge Teodoro De Souza, Federal University of Lavras, Brazil; Fernando Pereira Monteiro, Federal University of Lavras and UNIVAG Centro Universitário, Brazil; Maria Alves Ferreira, Federal University of Lavras, Brazil; and Karina Peres Gramacho and Edna Dora Martins Newman Luz, Comissão Executiva do Plano da Lavoura Cacaueira (CEPLAC), Brazil;
11. Frosty pod rot, caused by Moniliophthora roreri: Ulrike Krauss, Palm Integrated Services and Solutions (PISS) Ltd., Saint Lucia;
12. Cocoa diseases: vascular-streak dieback: David I. Guest, University of Sydney, Australia; and Philip J. Keane, LaTrobe University, Australia;
13. Insect pests affecting cacao: Leïla Bagny Beilhe, Régis Babin and Martijn ten Hoopen, CIRAD, France;
14. Nematode pests of cocoa: Samuel Orisajo, Cocoa Research Institute of Nigeria, Nigeria;
15. Advances in pest- and disease-resistant cocoa varieties: Christian Cilas and Olivier Sounigo, CIRAD, France; Bruno Efombagn and Salomon Nyassé, Institute of Agricultural Research for Development (IRAD), Cameroon; Mathias Tahi, CNRA, Côte d’Ivoire; and Sarah M. Bharath, Meridian Cacao, USA;

Part 4 Safety and sensory quality

16. Improving best practice with regard to pesticide use in cocoa: M. A. Rutherford, J. Crozier and J. Flood, CABI, UK; and S. Sastroutomo, CABI-SEA, Malaysia
17. Mycotoxins in cocoa: causes, detection and control: Mary A. Egbuta, Southern Cross University, Australia;
18. Analysing sensory and processing quality of cocoa: Darin A. Sukha and Naailah A. Ali, The University of the West Indies, Trinidad and Tobago;

Part 5 Sustainability

19. Climate change and cocoa cultivation: Christian Bunn, Fabio Castro and Mark Lundy, International Center for Tropical Agriculture (CIAT), Colombia; and Peter Läderach, International Center for Tropical Agriculture (CIAT), Vietnam;
20. Analysis and design of the shade canopy of cocoa-based agroforestry systems:Eduardo Somarriba, CATIE, Costa Rica; Luis Orozco-Aguilar, University of Melbourne, Australia; Rolando Cerda, CATIE, Costa Rica; and Arlene López-Sampson, James Cook University, Australia;
21. Organic cocoa cultivation: Amanda Berlan, De Montfort University, UK;
22. Cocoa sustainability initiatives: the impacts of cocoa sustainability initiatives in West Africa: Verina Ingram, Yuca Waarts and Fedes van Rijn, Wageningen University, The Netherlands;
23. Supporting smallholders in achieving more sustainable cocoa cultivation: the case of West Africa: Paul Macek, World Cocoa Foundation, USA; Upoma Husain and Krystal Werner, Georgetown University, USA.

This book is available for order from the publisher, Burleigh Dodds Science Publishing.

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  • A global strategy for the conservation and use of coconut genetic resources 2018-2028

A global strategy for the conservation and use of coconut genetic resources 2018-2028

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This strategy came from extensive worldwide consultations, with support from Bioversity International, Agricultural Research Center for International Development (CIRAD), the CGIAR Research Program on Forests, Trees and Agroforestry (FTA) and ACIAR/DFAT, and outlines the means to conserve/use as much representative diversity as possible. More than 100 million people living in fragile coastal areas depend on coconut for their livelihoods. Globally, the demand for coconut products is expanding and offers new opportunities for increasing incomes for millions of small-scale coconut producers. At a time when the demand for coconut and coconut products is growing worldwide, it is important to conserve and utilize the rich biological diversity of the crop. This evolving Strategy will provide the benchmark for effectively implementing the comprehensive conservation and research agenda proposed by the international coconut research community, as a route to the enhanced wellbeing of millions of coconut smallholders across the globe.

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  • The Global Strategy for the Conservation and Use of Coconut Genetic Resources 2018 -2028: summary brochure

The Global Strategy for the Conservation and Use of Coconut Genetic Resources 2018 -2028: summary brochure

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This summarises the Global Strategy for the Conservation and Use of Coconut Genetic Resources, introducing context & status of coconut germplasm conservation and use. Its 7 objectives are: i) strengthen commitment to conserve & use coconut genetic resources (CGR); ii) ensure sustainable ex situ CGR conservation; iii) assess coconut genetic diversity, identify critical gaps in ex situ collections, & implement collecting missions; iv) strengthen in situ conservation & ensure high quality planting material available/used; v) develop resources for safe international germplasm movement; vi) enhance CGR use by better germplasm characterization and evaluation; vii) re-enforce COGENT as a global platform serving Strategy implementation.

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  • Money grows on clove trees in Sulawesi

Money grows on clove trees in Sulawesi

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A trainer talks to participants about improving management of citrus trees. Photo by Endri Martini/ICRAF
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Cengkeh (cloves) accounted for 27% of seedlings produced in project-sponsored nurseries.
Photo by Endri Martini/ICRAF

A recently completed project in Sulawesi, Indonesia, illustrates how tree genetic resources can positively affect livelihoods.

The Agroforestry and Forestry in Sulawesi: Linking Knowledge with Action (AgFor Sulawesi) research in development project, which began in 2011, aimed to improve equitable and sustainable agroforestry and forestry-based livelihood systems through a focus on livelihoods, governance and sustainable environmental management.

One way it did so was by providing rural communities with better quality plant genetic material, improved on-farm management practices, marketing knowledge and capacity building in governance and environmental management.

As the project came to a close in March 2017, James Roshetko, FTA researcher from the World Agroforestry Centre (ICRAF), talked about using genetic resources to improve smallholders’ approaches.

“We started off by identifying the main species on farmers’ land, but also the species that the farmers were most interested in, the marketing opportunities and where farmers actually made the most money,” said Roshetko, who managed the project.

“The most important species were cacao, durian, cloves, rubber, nutmeg, coconut, black pepper, coffee, rambutan and teak,” he explained. They later included oranges, jackfruit and another timber called surian.

“A lot of those are commodity crops,” he added. “Even if the farmers have what we might call subsistence farming systems, they still need to sell something for cash in this day and age.”

The tradability of the products, whether globally or nationally, was key as a main income source for the participants.

Watch: Agroforestry and forestry in Sulawesi

A trainer talks to participants about improving management of citrus trees.
Photo by Endri Martini/ICRAF

FTA researchers provided quality germplasm (seeds and seedlings) as the genetic resource, set up nurseries, and promoted species that could benefit people’s incomes.

After beginning in four districts, the project expanded to six more, thus covering 10 districts across South Sulawesi, Southeast Sulawesi and Gorontalo provinces.

“One of the first things that we would do was see if people were interested in developing tree nurseries. Before we were working in these areas, there were almost no nurseries at the farm level. In each district there might be one nursery,” said Roshetko.

“We introduced the concept that each farmer group could have its own nursery.”

As of September 2016, there were 308 nurseries in the 10 districts, he explained, which had produced 1.66 million high-quality seedlings.

Durian was among the commodity crops promoted by AgFor Sulawesi.
Photo by Endri Martini/ICRAF

Of the seedlings, cloves accounted for 27%, while rubber was 24%, durian was 14%, pepper was 9%, cacao was 7% and nutmeg was 5%. This represented 86% of the total seedling production. Overall, seedlings of 60 different species were raised in the nurseries.

The farmers had the choice to become part of the AgFor Sulawesi project, Roshetko said. Project staff toured the districts, undertook community consultation and disseminated information about AgFor Sulawesi to arouse people’s interest.

Rather than financial incentives, Roshetko said the farmers were offered “knowledge, science and material to improve their own livelihoods.” They were told: “when we’re done, you’re going to be a better farmer and you’re going to be better off.”

Groups were not pushed to participate and a few indeed dropped out as the process continued. However, the majority stayed on. Over 630,000 people felt they had benefitted from the knowledge and technology introduced by the project, according to an impact assessment.

Following the project’s completion and with the support of government, though the nurseries may shrink in size, Roshetko expects that most will continue operating and raising quality seedlings for their own needs. One-third may function as commercial enterprises.

While much of the project was focused on development activities, there were still ample opportunities for research. The team looked at gender roles and economics, farmer agroforestry systems, cacao pests and diseases, as well as extension and nursery approaches, among others. As of March 2017, 19 peer-reviewed manuscripts had been published, with others under review.

Read also:

During AgFor Sulawesi’s lifespan, project staff published 18 booklets and fact sheets that provided farmers with guidelines and new knowledge on agroforestry systems. These were developed during farmer field schools and other project activities.

Participants in project trainings increased not only production but also their incomes through a greater understanding of the market.

FTA researchers identified pala trees, producing nutmeg and mace, as one of the species that held potential for farmers in Sulawesi.
Photo by Endri Martini/ICRAF

The effects were tangible, with Roshetko citing the example of a low-income woman who said that by increasing her agricultural production she was able to put her children through university.

With training a key aspect, the scientists introduced, for example, top grafting in cacao gardens as an alternative way to replace old trees that had become less productive. A top-grafted tree can return to full production sooner than a new seedling would reach full production.

Many of the farmers’ challenges came down to “simple management”, said Roshetko. “They may have been cacao farmers for years but these people never went to a training where their questions and priorities were the main focus.”

In line with FTA Flagship 1, AgFor Sulawesi used tree genetic resources to bridge gaps in production and promote resilience. The associated research is expected to improve genetic resources knowledge.

Some projects may lack opportunities for discussion or offer advice that farmers cannot afford to implement. AgFor Sulawesi, however, had an impact because staff encouraged participants to explain their specific situations, before addressing relevant problems. Roshetko said the approach was: “How can we help improve the situation from where the farmers started?”

Read also:

By Hannah Maddison-Harris, Communication and Editorial Coordinator, CGIAR Research Program on Forests, Trees and Agroforestry (FTA)

The Agroforestry and Forestry in Sulawesi: Linking Knowledge with Action (AgFor Sulawesi) project is mapped to FTA and funded by Global Affairs Canada and the CGIAR Fund Donors. It involved local communities, civil society groups, conservation organizations and universities to improve farmers’ incomes through agroforestry and natural resource management systems. AgFor Sulawesi was a collaboration between the Center for International Forestry Research (CIFOR), the World Agroforestry Centre (ICRAF), universities and non-governmental organizations (NGOs).

This research was supported by the Government of Canada, represented by the Minister of International Development, acting through Global Affairs Canada/GAC.

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