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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.

Partner Spotlight: National Crops Resources Research Institute

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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Partner Spotlight: Tanzania Agricultural Research Institute

By Samantha Hautea

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.

Tanzania officially joined the NextGen Cassava project as a partner in 2016. The partnership has been a productive one, and many positive results have come out of the collaboration. We interviewed Heneriko Kulembeka and Kiddo Mtunda, leads for the NextGen project in Tanzania, to learn more about the work being done in the country.

Header Photo: Heneriko Kulembeka (red) and Kiddo Mtunda (yellow) of TARI with Jonas Ambrose of the Mikocheni Agricultural Research Institute at a cassava seedling nursery in Chambezi Station. Photo by Samantha Hautea 

What is your institution’s name and its role in your country? What kinds of activities does it engage in?

Our institution’s name is the Tanzania Agricultural Research Institute (TARI). This is a semi-autonomous body of the government under the Ministry of Agriculture, responsible for conducting, regulating and coordinating all agricultural research activities in Tanzania. TARI’s mission is to generate and disseminate the application of knowledge and agricultural technologies as catalysts for change in achieving agricultural productivity, food and nutrition security, environmental sustainability, and economic growth, while involving stakeholders in the country and the global community.

Specific functions of TARI include but are not limited to: 1) Conduct, promote and coordinate basic, applied and strategic agricultural research; 2) Advise the government on the formulation of national policies, laws and regulatory frameworks for promoting and regulating agricultural research; 3) Set national agricultural research agenda and priorities in collaboration with key stakeholders.

On behalf of TARI, NextGen Cassava activities in Tanzania are conducted and coordinated by TARI Ukiriguru in Mwanza. Other institutions involved are TARI Ilonga, TARI Kibaha, and TARI Naliendele.

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Heneriko Kulembeka at a cassava field trial at TARI Ukiriguru, Mwanza. Photo by Chris Knight.

What is TARI’s role in NextGen Cassava? 

TARI’s role in NextGen includes germplasm acquisition and utilization, testing genomic selection training population in Year 1 and Cycle 1 materials from current crosses to develop genomic prediction models, optimizing flowering and seed set,  integrating phenotyping tools like NIRS into breeding program, implementing on-farm/gender-responsive activities, and capacity building (human and infrastructure).

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Kiddo Mtunda at a cassava seedling nursery in Chambezi station. Photo by Canaan Boyer

Are there any Masters/PhD students funded by NextGen at TARI? On what are they focused?

Yes. We had two TARI MSc students trained by NextGen Project Phase 1 on cassava breeding. In Phase 2, there are potential MSc/PhD students identified who will also focus on cassava breeding.

Has the partnership/involvement with NextGen benefited TARI? In what ways?

In Phase 1, TARI was able to accomplish the following:
a) Develop a training population
b) Estimate breeding values
c) Develop selection indices using economic weights
d) Select parents and planting crossing blocks
e) Identify testing environments
f) Prioritize traits prioritization and standardize processes
g) Conduct training on R, GS, experimental design, process maps and selection

In the future, we expect that researchers from NextGen and TARI will continue to work closely as one team.

How does NextGen fit into TARI’s overall mission and goals?

NextGen aims to increase the rate of crop improvement using new technologies, a goal which is in line with TARI’s mission as explained above.

Looking to the future, how do you see NextGen and TARI’s partnership developing in the next five years?

In the next five years, NextGen and TARI’s relationship will become stronger and stronger.

Cassava rising: International project inaugurates 2nd phase in Tanzania

DAR ES SALAAM, TANZANIA – On February 22, 2018, scientists and officials from Cornell University and the Tanzanian Ministry of Agriculture officially inaugurated the second phase of a project with a lofty ambition: to revolutionize breeding programs and agriculture in Africa through cassava.

“Another five years will help us strengthen the long-term global sustainability of cassava — a crop important for food security and predicted to stand up to climate change and extended periods of drought or rain,” said Ronnie Coffman, international plant breeder and director of Cornell’s International Programs in the College of Agriculture and Life Sciences who administers the Next Generation Cassava Breeding Project (NextGen Cassava).

“We have the next five years to be very courageous in delivering best bet varieties resilient to major diseases for African farmers,” said Chiedozie Egesi, project manager for NextGen Cassava. “Cassava can be the engine that will revolutionize agriculture in Africa.”

In some ways, cassava may seem an unlikely focus for a flagship project: typically considered a “poor man’s crop” and under-researched, it is the fourth most consumed staple in the African continent after maize, rice and wheat. Yet it is exactly in this gap of knowledge that the possibility for innovation exists.

In the first five years of the project, funded by a grant from the Bill & Melinda Gates Foundation and UK aid from the UK government, NextGen Cassava researchers and partners made major strides in understanding cassava’s genome and flowering, shortened the time to develop new cassava varieties from eight years to five, identified user preferences important to men and women to incorporate into breeding targets, and established Cassavabase, an open-access database for cassava genomic information.

In the second phase of the project, greater emphasis will be placed on delivering improved cassava varieties to smallholder farmers and end-users throughout sub-Saharan Africa. The first varieties from NextGen will be available to farmers in Nigeria within the next 18-24 months.

“A key goal in Phase 2 is to identify traits important to a diverse range of users–including women and marginalized groups–and to engage farmers as research partners to breed new varieties that are adopted and equitably impactful. It is to everyone’s benefit to hear women’s voices and tap into their knowledge about product quality to breed better cassava for everyone,” Coffman said.

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Mansour Hussein, director of R&D at the Ministry of Agriculture in Tanzania, addresses the audience at the 2018 NextGen annual meeting. Photo by Catherine Njuguna

“I consider this a very important investment for the people of Tanzania, Nigeria and Uganda, especially the farming community,” said Mansour Hussein, director of R&D at the Ministry of Agriculture in Tanzania. “I believe the approach taken by NextGen will ensure that the concerns of farmers will be addressed.”

Like many African countries, agriculture plays an important role in Tanzania’s economy, employing over 75 percent of the country’s workforce and accounting for 25 percent of the National Gross Domestic Product. Cassava’s contribution to this sector is limited by lack of access to disease-free planting materials, use of poor farming practices, high post-harvest losses, and low-yielding varieties.

Other notable guests at the ceremony included Jim Lorenzen, NextGen Cassava program officer at the Gates Foundation; Joseph Ndunguru, director, Mikocheni Agricultural Research Institute; Betty Maeda, research and production advisor, USAID-Tanzania; Geoffrey Mkamilo, coordinator for root and tuber crops research, Tanzania; Patrick Ngwendiaji, CEO, Tanzania Official Seed Certification Institute; and Victor Manyong, director R4D, IITA East Africa Hub.

Towards innovation in breeding programs

The inauguration took place during the sixth annual NextGen Cassava meeting, held Feb. 19-24 in Dar es Salaam, Tanzania. During the meeting, NextGen project members and collaborators met to share and discuss achievements in Year 5 and identify opportunities and strategies to improve and move forward in Phase 2.

For the next five years, NextGen Cassava will be structured into three major divisions.

The Breeding Division, led by Egesi, serves as the fulcrum of the project. “Four breeding programs in Africa will implement improved breeding pipelines: the National Root Crops Research Institute (NRCRI) in Nigeria; the International Institute of Tropical Agriculture (IITA) Nigeria (with additional support from IITA/Uganda); the National Crops Resources Research Institute (NaCRRI ) in Uganda; and the Tanzanian Agricultural Research Institute (TARI) in Tanzania,” said Egesi.

Additional activities to support the breeding programs will be carried out in South America at the International Center for Tropical Agriculture (CIAT) and the Brazilian Agricultural Research Corporation (Embrapa), and at the United States Department of Agriculture, Agricultural Research Service (USDA-ARS) Pacific West and the University of Hawaii at Hilo in the USA. In addition, Cornell University, the West African Center for Crop Improvement (WACCI) at the University of Ghana, and Makerere University in Uganda will provide training and support for African cassava breeders for capacity development in target countries.

The Survey Division and its activities will be spearheaded by Hale Ann Tufan, NextGen Cassava’s gender initiative lead in Phase 1. “Successful adoption of cassava varieties depends on meeting diverse user preferences” said Tufan. “We will support the Breeding Division in decision-making and trait prioritization, generating product profiles with measurable breeding targets. Engaging large numbers of diverse farmer groups will enable us to evaluate new varieties on farm, at scale. Gender analysis of participatory evaluation, gender training and trait-level impact analysis on members of participating households will underpin our strategy to ensure new varieties are developed that benefit men, women, boys and girls equally.”

NextGen researchers will work closely with another Gates Foundation project, Breeding RTB Products for End User Preferences (RTBfoods), to jointly carry out survey activities.

The Research Division will be led by Jean-Luc Jannink, research plant geneticist with the USDA-ARS and adjunct associate professor in the Department of Plant Breeding and Genetics at Cornell. “Our primary activities will be to identify, develop, and implement technologies that can be used to deliver improved varieties rapidly and efficiently. We will provide support to the breeding programs to improve their processes, and may propose new technologies to benefit their work,” said Jannink. Among the activities overseen by this division are flowering and seed set, breeding scheme optimization, Cassavabase development, genomic prediction and decision analysis support, and bioinformatics for improving prediction accuracies

The Gates Foundation has made a significant investment in cassava, funding several projects that address various aspects of improving this food security crop.

When farmers modernize the tools they use for agriculture, it can trigger a socio-economic shift in their lives. “Economic transformation begins with agricultural transformation,” said Lorenzen. “At the Gates Foundation, we see agriculture as key to rural development and reducing poverty.”

To identify opportunities for collaboration, several NextGen Cassava-linked projects and institutes also participated in the meeting, including the RTBfoods Project, African Cassava Whitefly Project, Excellence in Breeding, PhenoApps, New Sources of CBSD Resistance in Cassava, the West African Virus Epidemiology Project, Disease Diagnostics for Sustainable Cassava Productivity in Africa, Cassava Source Sink, NARO Uganda, and Bioversity International.

NextGen Cassava is funded by the Bill & Melinda Gates Foundation and UK aid from the UK government

2018 NextGen Cassava Annual Meeting Workshops

From February 19-24, NextGen cassava partners and collaborators will be in Dar es Salaam, Tanzania for the 6th Annual Meeting of NextGen Cassava. This will serve both to share results from the fifth year of the project and to set goals and targets for the next five years.

On the last two days of the NextGen Cassava meeting, participants had the opportunity to participate in workshops and go on field visits.

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