Towards a community of practice around cassava: Report from Sierra Leone and Ghana

With contributions from Abdul R Conteh and Isata Kargbo

Members from the NextGen Cassava team visited Sierra Leone from 2-5 July 2018 to integrate the Sierra Leone Agricultural Research Institute (SLARI) into NextGen Cassava under the Community of Practice (CoP).

The team members included Alfred Dixon, Chiedozie Egesi, and Peter Kulakow, all from the International Institute of Tropical Agriculture (IITA) in Ibadan, Nigeria. After arriving in Freetown, the team made courtesy calls to SLARI Headquarters, Ministry of Agriculture, and IITA-country office. At SLARI Headquarter, the Director General introduced the team to SLARI management staff and informed the audience about the purpose of the team’s visit to Sierra Leone.

Alfred Dixon, who was also the former Director General of SLARI, highlighted the importance of SLARI as a partnering institution for the NextGen cassava and the TAAT (Technologies for African Agricultural Transformation) projects. Dixon went on further to unveil the prospects of the TAAT project for Sierra Leone in the first year.

TAAT will work closely with existing projects in upscaling shelf technologies developed by SLARI over the past years through the compact policy document and the introduction of SAH (Semi Autotrophic Hydroponics) technology.  In particular, Dixon mentioned the growing interest demonstrated by Irish Aid on the Provitamin-A cassava (yellow cassava) research to enhance nutritional efficiencies in Sierra Leone.

Chiedozie Egesi, NextGen Cassava’s project coordinator, gave SLARI a presentation on the NextGen cassava project. The project is led from Cornell University with implementing countries located in Africa. The first phase has been successfully completed while the 2nd phase, for which Sierra Leone is a member country, was launched few months ago and is on-going.  This phase will provide technical support in the form of capacity building on varietal release, electronic data capturing, quality data management, cassava database, flowering improvement technology and effective germplasm exchange program to national breeding programs for some selected countries in Africa.

The team also visited the Ministry of Agriculture where they were accorded a warm welcome by the Honorable Minister of Agriculture and his Deputy. In Dixon‘s opening remarks, he mentioned the low levels of productivity Sierra Leone has realized over the past years, which has triggered the intervention of the African Development Bank’s “Feed Africa” initiative under the “High Fives” priorities in Africa.  Dixon went on further to inform the minister about the TAAT program under the Feed Africa initiative for African Countries funded by ADB for which Sierra Leone is member country.  He asked the minister to kindly follow up on Irish Aid as they have expressed interest in nutrition research in Sierra Leone and crop processing zones.

Egesi presented to the minister and his team the objectives of the NextGen cassava project. The minister was very pleased, and confessed that his hope has been restored after this brief interactions and that his ministry is open and willing to work and partner with CGIAR centers more than before.  He extended an invitation to Dixon to be a member of Advisory committee that would be advising him and his team to transform Sierra Leone’s agriculture. The honorable minister accepted the invitation extended to him by IITA DG as he concluded by laying emphasis on the successful model used on cassava flour in Nigeria to be replicated in Sierra Leone.

The team then departed for Njala to continue oral presentation session, assessment of field trials and Laboratory facilities at the Njala Agricultural Research Center (NARC), Njala. After meeting with the NARC center director and presentations from the NARC cassava breeders (Festus Massaquoi, Kumba Koroma and Isata Kargbo), NextGen team members were then taken on a tour of infrastructural facilities at the Njala Agricultural Research Centre.

This tour included visits to the Soil and Plant Analysis Laboratory, Food and Nutrition Laboratory, Biotechnology and Tissue Culture Laboratories, and the newly constructed Post-Harvest Laboratory.  Following the laboratory visit, the team viewed the trials for the cassava breeding clonal and seedling nursery located at the Njala Crop site in Moyamba district, representing the transitional rain forest. Possible solutions, interventions and entering points were discussed as to how the NextGen Cassava project can positively contribute to the cassava breeding program in Sierra Leone to help it meet international standards.

Following the visit to Sierra Leone, the NextGen Cassava COPP was launched at Council for Scientific and Industrial Research- Crop Research Institute (CSIR-CRI) in Kumasi, Ghana during 6-7 July 2018.

CRI Director Dr Stella Ama-Ennin highlighted the importance of having her institute join NextGen since it is the center of specialization for Cassava for West Africa. It also plays a key role in enhancing the country’s Presidential Initiative for Cassava called “One district- One factory” Programme which involves a processing center in each of the rural areas. She also highlighted the challenges in cassava breeding in Ghana and expressed her joy that that these could be alleviated with NextGen Cassava’s tools and support.

Collaborative database development: Lessons from the NextGen experience

By Canaan Boyer

What does it take to create and maintain an open-access genomic database? This is the question that faced the Boyce Thompson Institute, which has been a part of the Next Generation Cassava Breeding project since its inception. Over the years, BTI has developed and supported Cassavabase, an open-access online repository for information from cassava breeding trials. More importantly, however, it has also worked to build capacity in database management and development for NextGen Cassava’s African partners.

Team members from BTI make trips to Africa for field work and visits at partner institutions, an important component of the database development. In addition to this, every year, database managers and data analysts from each breeding institute involved in NextGen Cassava come to BTI to exchange information on database management and collaborate on what needs to be developed for Cassavabase. In these month-long stays, the team is able to engage in in-depth, comprehensive collaboration, ensuring that feedback to make sure Cassavabase continues to meet breeders’ needs is incorporated into the code.

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Alex Ogbonna, Guillaume Bauchet, Rachel Mukisa, and Bryan Ellerbrock at a workshop during the 2017 annual meeting. Experience from fieldwork at partner institutions is critical to ensuring Cassavabase serves the needs of cassava breeders.

“Having all the database collaborators come together like this lets us discuss data curation and learn from each other,” said Guillaume Bauchet, who works at BTI managing Cassavabase. “The goal is to give autonomy to the teams to run their own databases at their institutions.”

Prasad Peteti of the International Institute of Tropical Agriculture (IITA), who has been coming to these trainings at BTI since the beginning of the project, reflected on how far the team has come. “Initially, we were coming to BTI just to learn about development and maintenance of databases. It was more of a one-way flow of information to gain the fundamentals. Now we are developing our own modules and more functionalities.”

Bauchet added, “At BTI, we actually learn a lot from the data and experiences that our partners bring back from their institutions. We’ve achieved a lot since Phase 1. A big part of that phase was all of the logistical things — getting a server, how to ship and install, and so on. That’s been sorted, so in the last couple of years, we’ve really been able to focus on developing tools responsive to the breeder’s needs instead.”

“Now we’re looking towards how we can make the database more useful and incorporate data from new tools, such as near-infrared spectroscopy (NIRS) into it. Phase 2 will focus more on creating a digital ecosystem with the partner institutes, an emphasis on quality, collecting data from farmers’ fields, and a full integration of genotyping data from field to lab.”

Those who have come to BTI for training include:

  • Afolabi Agbona and Prasad Peteti of the International Institute of Tropical Agriculture (IITA) in Nigeria
  • Racheal Mukisa of National Crops Resources Research Institute (NaCRRI) in Uganda
  • Uba Ezenwanyi of Tanzania Agricultural Research Institute (TARI)
  • Adeyemi Oloyede of the National Root Crops Research Institute (NRCRI) in Nigeria
  • Luciana Braatz de Andrade of the Brazilian Agricultural Research Corporation (Embrapa) in Brazil

In addition to the annual training/workshop, the database managers have weekly online meetings with Bauchet and frequently keep in touch with one another. Agbona and Peteti maintain the mirror of Cassavabase on servers hosted at IITA, and provide training to other institutions to help them begin to maintain their own databases.

Partner Spotlight: Boyce Thompson Institute

Feature Image: Guillaume Bauchet (2nd from left) guides workshop participants through a field exercise during the 2017 NextGen Cassava annual meeting. Photo by Bryan Ellerbrock.

More than 10 international institutions are affiliated with NextGen Cassava. In our partner spotlights, we feature profiles on individual institutions and the role each institution plays in the project.

The Boyce Thompson Institute (BTI) based in Ithaca, New York, is one of the founding partners of the NextGen Cassava project. Researchers at BTI code and maintain Cassavabase, an open-access database where cassava breeders can upload the genetic and phenotypic data from their field trials and access data from other breeders around the world.

Establishing a centralized database for  information tracking, genotypic and phenotypic data, and Genomic Selection (GS) prediction analyses was one of the main objectives of NextGen Cassava in Phase 1. Moving into Phase 2, Cassavabase will continue to develop in response to the feedback and needs of breeders. We interviewed Guillaume Bauchet and Lukas Mueller of BTI to learn more about the institute, their work, and how they fit into the NextGen Cassava project.

What is BTI’s role in NextGen Cassava? What are the main activities/objectives being accomplished here?

BTI’s main role in NextGen Cassava is developing  the Cassavabase site as a one-stop shop for NextGen’s breeding data. Our main activities include:

  • Managing data: we handle NextGen’s phenotypic and genotypic data management
  • Developing tools: we support breeders in their day to day activities through breeding database development
  • Capacity building: we train and assist NextGen collaborators in analyzing and bioinformatics.
Lukas Mueller at GCP21 Benin

Lukas Mueller of BTI delivered a presentation on Cassavabase at the 2018 Global Cassava Partnership for the 21st Century Conference in Couteau, Benin. Photo by Canaan Boyer

Are there any Masters/PhD students funded by NextGen at BTI? What is their work focused on?
Currently, there are no Masters/PhD students funded by NextGen at BTI, but we have a lot of institutional representatives involved as data managers/data analysts.

Has the partnership/involvement with NextGen benefited BTI? In what ways?NextGen has been an eye-opener on African agriculture and certainly a great asset to BTI. It has allowed us to see current and future plant research challenges and opportunities.

How does NextGen fit into BTI’s overall mission and goals?
BTI’s aim is to make valuable contributions to general scientific knowledge, biology, and medicine. William Boyce Thompson, BTI’s founder, was convinced that “agriculture, food supply, and social justice are linked.” This is also true of the future of the African continent. 

From its creation, BTI’s mission encompasses the “creation through genetic research of hardier, more nutritious, disease-resistant crop plants and more viable seeds; the study of insects that damage food crops; and the production of new pesticides.”

With NextGen, developing a breeding database for Africa’s major staple crop is fully in line with BTI’s vision and institutional missions.

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As of the end of Phase 1, Cassavabase hosts a great amount of data related to cassava trials.

How do you see NextGen and BTI’s partnership moving forward?
Developing the “digital ecosystem” around breeding is a continuous, major goal within NextGen where BTI’s contribution is significant.

This will work in conjunction with new research activities developed in Phase 2, such as farmer’s knowledge, food preferences, and related methods/technologies (surveys, near-infrared spectroscopy) to tackle underlying research questions. 

How African cassava could protect Southeast Asia from emerging cassava diseases

By Ismail Rabbi, IITA

Header Image: Symptom of cassava mosaic disease (CMD) on young plants. Left row is a susceptible variety (score level 5) while the row on the right is a highly resistant clone (score 1). Photo provided by Ismail Rabbi.

Cassava mosaic disease, caused by the cassava mosaic virus, is the most important disease of cassava in Africa and is now threatening cassava production in Asia. Now, diagnostic molecular markers developed under the Next Generation Cassava Breeding Project can be used to rapidly screen for and mobilize the virus resistance trait into the Southeast Asian cassava varieties and other regions of the world where the disease could potentially spread.

Cassava cultivation in Southeast Asia started in early 1900s, and today it has become one of the major crops in many countries in this region. The first outbreak of the disease in Cambodia and Southern Vietnam was reported in 2015 (Wang et al). According to the Global Cassava Partnership for 21st Century (GCP21) the emergence of this devastating disease threatens the 55 million tons of annual cassava production in the region, and it called for an urgent action to curb its spread.

African cassava breeding programs have successfully developed disease-resistant varieties thanks to years of research and breeding to mitigate the challenge of the disease in the continent. Recent breakthroughs in genetic analyses have uncovered the major genes responsible for the strong resistance against the virus disease in Africa cassava genepool. Diagnostic molecular markers that tag these genes have been developed under the Next Generation Cassava Breeding Project in partnership with the High-Throughput Genotyping Project (HTPG).

In a pilot initiative, Chalermpol Phumichai, a researcher from Kasetsart University, Thailand, crossed a CMD resistant African cassava variety called TME3 into Huay Bong 80 from SE Asia. Genotyping of the progenies from these crosses clearly showed six out of 94 carried the markers for the resistance gene.

Using DNA markers in the absence of the pathogen will allow breeders in Asia to carry out pre-emptive breeding and potentially save cassava production in the region from the onslaught of this devastating virus.

While adoption of these markers is still in its early stages, there has been a lot of interest and request from various breeding programs around the world. The Brazilian Agricultural Research Corporation (Embrapa) has already started to use them to carry out pre-emptive breeding for resistance against the virus disease in Brazil. They submitted nearly 1000 accessions developed from crosses that involve sources of CMD resistance. Field testing of seeds from the marker-assisted selection populations will be carried out at IITA-Ibadan. Hopefully more breeding programs will start using them in the near future, especially in Asian countries such as Vietnam where CMD is emerging as a threat to cassava production.

References: Wang, H.-L., X.-Y. Cui, X.-W. Wang, S.-S. Liu, Z.-H. Zhang, and X. Zhou. 2015. First Report of Sri Lankan cassava mosaic virus Infecting Cassava in Cambodia. Plant Dis.: PDIS-10-15-1228-PDN. Available at http://apsjournals.apsnet.org/doi/abs/10.1094/PDIS-10-15-1228-PDN.

NextGen Cassava 2017-2018 Graduates

Ensuring the future of cassava breeding will require training young scientists to excel. We are proud of NextGen’s new graduates and are excited to see to their contributions to research in the years to come.

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(L to R) Olumide Alabi, Lydia Ezenwaka, Chiedozie Egesi, and Ismail Kayondo at the University of Ghana. Photo provided by Chiedozie Egesi.

Olumide Alabi, a member of International Institute of Tropical Agriculture (IITA)‘s cassava breeding program, researched the empirical estimation of genetic gains in cassava breeding using genomic selection in a one-year breeding cycle. His work demonstrated the utility of the technology and its implications for African cassava breeders.

Lydia Ezenwaka, research officer at NRCRI Umudike Nigeria, worked on genomic markers linked with cassava green mite (CGM). CGM is a dry season pest that damages leaves of cassava plants, which reduces photosynthesis. She identified resistance single nucleotide polymorphism (SNP) markers for use in breeding world-wide.

Ismail Kayondo, of the National Crops Resources Research Institute, identified genomic markers linked with resistance to cassava brown streak disease using wild cassava relatives and CBSD resistance QTL mapping. This work will help develop resistant varieties that can be used to improve cassava lines in East Africa, as well as for pre-breeding cassava lines to protect West Africa from this disease.

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(L to R) Roberto Lozano, Alfred Ozimati, Jean-Luc Jannink, Ikeogu Ugochukwu Nathaniel and Uche Godfrey Okeke at Cornell University. Photo provided by Jean-Luc Jannink.

Roberto Lozano, working with Jean-Luc Jannink at the Department of Plant Breeding and Genetics at Cornell University, focused on ways to improve Genomic Selection (GS) accuracies by incorporating information from separate gene annotation and transcriptomics experiments. His research, upstream of our current breeding efforts, will increase their efficiency as we incorporate the results.

Uche Godfrey Okeke, who also worked with Jean-Luc, worked on developing genomic prediction models for for multiple trait and multi-environment trials. These models create a better picture of the correlations between traits, improving selection for the many traits required to make a good variety. They also allow better targeting of new varieties to agroecological zones.

Ikeogu Ugochukwu and Alfred Ozimati are slated to graduate soon. Ugochukwu, working with NRCRI, Umudike, Nigeria researched high throughput assessment of cassava root quality traits using near infrared and visual reflectance measurements. Alfred is from NaCCRI Namulonge, Uganda, and his research for NextGen focuses on genomic selection for Cassava Brown Streak Disease (CBSD) and yield-related parameters. He has developed tools to help pre-emptive breeding for CBSD resistance in West Africa, to prevent what could be a devastating outbreak of the disease if it were to arrive there.

NextGen partners highlight advances in cassava research at GCP21 2018

From June 11 to 15, members of the cassava research community came together in Cotonou, Benin to participate in the Global Cassava Partnership for the 21st Century (GCP21) conference. NextGen Cassava was well represented, with 23 project members in attendance and several NextGen-led presentations and sessions.

Header Image:Hernán Ceballos of CIAT describes how trait introgression can produce cassava with a single recessive trait, without losing other good qualities like high yield. Breeding methods like these allow efficient production of cassava varieties with desired qualities.

View the NextGen Cassava Twitter feed for more photos and session info from the conference.

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Partner Spotlight: National Crops Resources Research Institute

More than 10 institutions are affiliated with NextGen Cassava. In our partner spotlights, we feature profiles on individual institutions and the role each institution plays in the project.
The National Crops Resources Research Institute (NaCRRI) has been a founding partner of the NextGen Cassava project since its inception. We interviewed Robert Kawuki, cassava breeder at the National Agricultural Research Organization of Uganda and NextGen Cassava country lead, to learn more about the institution’s collaborations.

Header Image: NextGen researchers stand at a NextGen Cassava uniform field trial in Serere District, Uganda. Left to right: Alfred Ozimati, Marnin Wolfe, Robert Kawuki, Williams Esuma, and Chiedozie Egesi. Photo provided by Robert Kawuki.

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