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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

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.


(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.


(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: NRCRI

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

The National Root Crops Research Institute (NRCRI) in Nigeria has been a NextGen Cassava partner since the inception of the project. We interviewed Dr. Joseph Onyeka, NextGen Cassava breeding lead and head of  the Pathology and Micro Biotechnology Unit at NRCRI, to learn more about the institution and its work.


Dr. Joseph Onyeka in his office at NRCRI.

Dr. Onyeka explained the benefits of the collaboration: “Moving forward, the partnership between NextGen and NRCRI will not only lead to enhancing the efficiency of NRCRI to develop new cassava varieties, but will actually extend to delivering new superior cassava varieties to Nigerian farmers. NRCRI is a leading institution for cassava breeding in Africa and had provided technical backstopping for other African NARs in the past through the cassava breeding Community of Practice (CoP). NRCRI hopes to take the advantage of this network in the region to create a spillover of the benefits from NextGen project to other countries in the region.”

Read the full interview below:

What is NRCRI’s role in NextGen Cassava? What are the main activities/objectives being accomplished here?
NRCRI as the Nigerian national partner of the NextGen project is involved in the implementation of activities under various objectives: Implementing and empirically testing Genomic Selection in African breeding programs, whereby genomic selection is used to speed-up the process of developing and selecting feature varieties for release to farmers. NRCRI is involved in the identification of methods to improve cassava flowering and seed set, which provides opportunity for breeders to tap desirable traits from genetic backgrounds with poor flowering ability. NRCRI is also involved in the development of centralized cassava database through the contribution of information to the database and the application of modern tools for precise data collection. The institute is also a key player in the current drive aimed at understanding gender-related as well as end-user preferred traits in cassava to aid breeders in designing their breeding objectives. The institute is gradually moving to a standardized and rapid throughput phenotyping for key traits using near infra-red spectrometer in cassava breeding.

Are there any Masters/PhD students funded by NextGen at NRCRI? What is their work focused on?
NRCRI has two PhD students funded by the NextGen project. They are Miss Lydia Ezenwaka who is registered with the West African Center for Crop Improvement (WACCI), University of Ghana with a research focus on Genome-wide association study of cassava green mite resistance and other associated traits in Manihot esculenta; and Mr Ugochukwu Ikeogu who is registered with Cornell University, Ithaca, USA with a research focus on high throughput phenotyping and genomic selection for quality traits in cassava.


Okoro Maria Justin, a member of the NRCRI gender team and cassava research program, examines a NextGen Cassava field trial.

In what ways has the partnership/involvement with NextGen benefited NRCRI?
NRCRI involvement with NextGen has greatly benefited the institution in many ways which include improved capacity and efficiency in breeding for farmer-preferred cassava varieties, development of human research capacity through short trainings and workshops, upgrade of laboratory and field research facilities including field vehicles for easy movement.

How does NextGen fit into NRCRI’s overall mission and goals?
The NextGen project aptly fits into the main research focus of NRCRI which has the national mandate for genetic improvement of root and tuber crops including cassava in Nigeria.

How do you see NextGen and NRCRI’s partnership moving forward?
Moving forward, the partnership between NextGen and NRCRI will not only lead to enhancing the efficiency of NRCRI to develop new cassava varieties, but will actually extend to delivering new superior cassava varieties to Nigerian farmers. NRCRI is a leading institution for cassava breeding in Africa and had provided technical backstopping for other African NARs in the past through the cassava breeding Community of Practice (CoP). NRCRI hopes to take the advantage of this network in the region to create a spillover of the benefits from NextGen project to other countries in the region.

Any final thoughts?
Being the only research institute in Africa solely devoted to root and tuber crops, particularly cassava, the goal of NextGen Project is the goal of NRCRI.


First NextGen Cassava PhD student graduates!

May 4, 2017: Dr. Mercy Elohor Diebiru-Ojo earns degree in Plant Breeding and Genetics at the West African Centre for Crop Improvement (WACCI), University of Ghana.

Mercy headshot

ACCRA, GHANA: An exciting milestone for the Next Generation Cassava Breeding project (NextGen) was reached on 4 May 2017, when Mercy Elohor Diebiru-Ojo, of Lagos, Nigeria, successfully defended her thesis titled “Genetic and Physiological Analysis of Flowering in Cassava (Manihot esculenta Crantz)” at the West African Centre for Crop Improvement (WACCI), University of Ghana. Diebiru-Ojo’s WACCI graduate program was funded by AGRA and her research was supported by NextGen.

“I am thrilled to have taken this important step toward realizing my dreams of being among the generation of plant breeders who will work towards upholding and ensuring food security in Africa,” said Diebiru-Ojo. Her work focused on “generating novel genetic information underlying the control of flowering trait in cassava, as well as inducing floral production in cassava in which successful use of plant hormones as plant growth regulators produced the most promising and significant results.”

“Mercy’s work contributes directly to the NextGen project’s goal of improving the flowering and seed set of cassava, the second most important staple-food crop in Africa, after maize,” said Tim Setter, professor and chair of Cornell University’s section of soil and crop sciences, who was one of Diebiru-Ojo’s mentors. “No other continent depends on cassava to feed as many people as does Africa, where 500 million people consume it daily. It is an important crop for food security.”

Despite its importance for food security on the African continent, cassava has received relatively little research and development attention compared to other staples such as wheat, rice and maize. The key to unlocking the full potential of cassava lies largely in bringing cassava breeding into the 21st century.

“Understanding of flowering mechanisms is an essential area of study in cassava breeding, because many elite cassava genotypes flower poorly, if at all,” said Chiedozie Egesi, adjunct professor of plant breeding and genetics at Cornell, who manages NextGen. “If cassava does not flower, it cannot be used in crossing. Some very promising cassava lines cannot then be used in breeding programs. Improved flowering and seed set would allow breeders to fully mobilize the genetic resources in their cassava breeding programs and Mercy’s work contributes directly to this objective.”

Peter Kulakow, cassava breeder at the International Institute of Tropical Agriculture (IITA) who was Dieburu-Ojo’s in-country supervisor, commended her teamwork: “Mercy was able to organize a strong team of technicians to phenotype a cassava flowering of over 700 genotypes in two locations for three years. This has greatly advanced our understanding of variation in cassava flowering.”

WACCI Training
Diebiru-Ojo was enrolled in the WACCI program one year prior to three other NextGen PhD students: Olumide Alabi, Ismail Kayondo, and Lydia Ezenwaka. WACCI, which was founded in 2007 as a partnership between the University of Ghana and Cornell University, aligns perfectly with NextGen’s mission to train the next generation of plant breeders in Africa. The WACCI four-year doctorate program consists of one year of academic study at the University of Ghana and three years of thesis research at the students’ research station/university in their home countries. Students return to Ghana in the last six months of the final year to complete and submit their theses.

Diebiru-Ojo is a good example of how all of these institutes worked seamlessly together, since her supervisory team at WACCI was comprised of professors Isaac Asante, Essie Blay and Eric Danquah at the University of Ghana; she was awarded a fellowship from the Borlaug Leadership Enhancement in Agriculture Program (LEAP) to spend six months conducting preliminary research in the laboratory of Tim Setter at Cornell University; her thesis research at IITA was under the supervision of Peter Kulakow; and mentorship and advice was provided by Setter.

After completing the required year of coursework at the University of Ghana, Diebiru-Ojo returned to her home country of Nigeria, and engaged in fieldwork at the International Institute of Tropical Agriculture (IITA) in Ibadan. As a new PhD, she will continue to work after graduation as International Trials Manager of the BASICS project (Building an Economical Sustainable Integrated Cassava Seed System in Nigeria), developing improved cassava stem multiplication systems and managing production of cassava breeder seed.

Diebiru-Ojo’s plan for the near future is to publish some relevant papers from her thesis as soon as possible, because she is interested in “contributing to the body of science which will lead to advances in cassava breeding.”

Diebiru-Ojo is the first of 10 PhD students supported by NextGen to graduate. In addition to Diebiru-Ojo and the three other students at WACCI, NextGen funds six PhD students based at Cornell, and eight MSc students at Makerere University, Uganda. When trained, these plant breeders will build capacity for cassava breeding in partner countries and beyond.

The NextGen project is led by Cornell University, and works with 10 institutional partners across six countries on three continents: Boyce Thompson Institute (BTI/USA), Embrapa (Brazil), International Center for Tropical Agriculture (CIAT/Colombia), International Institute of Tropical Agriculture (IITA/Nigeria), National Crops Resources Research Institute (NaCRRI/Uganda), National Root Crops Research Institute (NRCRI/Nigeria), University of Hawaii (USA), U.S. Department of Agriculture-Agricultural Research Service, and U.S. Department of Energy Joint Genome Institute. Most recently, NextGen Cassava has expanded to include Tanzania, partnering with the Lake Zone Agricultural Research and Development Institute (LZARDI).

 (Quotes have been slightly edited for clarity.)


NextGen Cassava featured in The Economist

Dr. Chiedozie Egesi, NextGen Cassava project manager

Dr. Chiedozie Egesi, NextGen Cassava project manager

During the recent annual AAAS (American Association for the Advancement of Science) meeting in Washington, D.C., The Economist interviewed Dr. Chiedozie Egesi, NextGen Cassava project manager. Chiedozie spoke about the potential of the NextGen Cassava project to improve the cassava crop and address challenges such as disease, low yield, and vitamin deficiency.

See the full story, “Cassava-nova,” in the online edition of The Economist.

NextGen Cassava Students Test Landmark Phenotyping Tool for Cassava Breeding: Near-Infrared Spectroscopy (NIRS)

17 February 2016: Thanks to Nkechi Ogwo, Ugochukwu N. Ikeogu, and Lilian A. Onyegbulam of the NextGen Cassava Project for the following write-up of a recent visit by NextGen students to test NIRS tools in cassava breeding:

The NextGen Cassava Project has taken significant strides to address the challenges of long breeding cycles in cassava improvement by adopting advanced breeding tools; notably, genomic selection (GS). Efficient implementation of GS in various breeding programs requires informative genotype data as well accurate and fast phenotyping tools. In addressing the phenotyping bottleneck at National Root Crops Research Institute (NRCRI), Umudike breeding program, Dr. Chiedozie Egesi, an Assistant Director, Plant Breeder, and Coordinator of the Programme acquired a hand-held version of the NIRS (Near-Infrared Spectroscopy) device for cassava breeding at the institute. This was supported by the Next Generation Cassava Breeding Project being funded by the Bill & Melinda Gates Foundation.

NIRS is a long-established technology commonly used to estimate organic constituents such as protein, starch, oil, and carotenoid in numerous agricultural products. The NIRS technology is built on the interaction of physical matter with the near-infrared spectral region of light. The sampling process involves the irradiation of a sample with light of specific known frequency or wavelength in the near-infrared region. The estimation of frequency at which specific bonds vibrate enables NIRS instruments to predict from a spectrum the composition of the molecular bonds present in a given sample. The technology has been designed in various forms and shapes.

Hands-on experience using the hand-held NIRS device

Using the hand-held NIRS device to phenotype a cassava root in the field

When compared to the traditional methods of organic components assay, such as the I-check carotene and high performance liquid chromatography (HPLC), NIRS has huge advantages. It is unusually faster than other analytical techniques. For example, for some it takes more than one day to complete the extraction of some organic components and, depending on the system, it might only accommodate fewer than 30 samples for a complete cycle. Conversely, NIRS devices can be used to sample between 500 and 900 samples in a day. The technique is non-destructive and only simple preparation, or no preparation at all, is required of samples. In the case of the hand-held version acquired by NRCRI, Umudike, the instrument can be used directly in the field, which eliminates almost completely the difficulty of sample preparation and transportation. The device is very versatile and can be used for the analysis of several traits simultaneously. More so, NIRS avoids high hazards and problems of organic and other chemical waste disposal that are likely associated with other techniques.

The adoption of this device in phenotyping became necessary because the recent adoption of GS hinged on recent advances in molecular marker technologies with the unprecedented assay of many genetic materials associated with the technologies.

Ugochukwu Ikeogu demonstrates how to use the hand-held NIRS device

Ugochukwu Ikeogu (left) and Wilfred Magangi (right) gain hands-on experience using the NIRS device

The preliminary field application and chemometric process for quantifying important cassava root parameters—namely, starch, dry matter, carotenoid, and cyanide—took off in summer 2015 in NRCRI’s breeding program. The team is led by one of the PhD students, Ugochukwu Ikeogu from Cornell University, Ithaca, USA. For prospective extension of the technology to other breeding programs across Africa, a representative, Mr. Wilfred Abincha Magangi, who is a Master’s student from Makerere University, Uganda, East Africa visited Nigeria to witness the field application of the device.

The adoption of NIRS devices in cassava root component assay promises to increase the accuracy and efficiency of phenotyping and further hasten cassava breeding efforts being undertaken by the biotechnology program of NRCRI, Umudike.

Relating his experiences at the institute, Mr. Magangi during his two-week study visit shared that over and above accommodating huge samples per day, NIRS could be one of the most efficient tools for phenotyping in cassava breeding programmes. It is easy to handle, saves time and costs, and at the same time generates accurate results, as opposed to the other conventional tools used in East Africa. He also added that the NIRS device is less expensive to maintain.

NRCRI staff interviewing Mr. Magangi

NRCRI staff interview Mr. Magangi

The field visits and facility tour presented a knowledge exchange and networking opportunity for both groups. Mr. Magangi, the visiting student from Makerere University, Uganda said, “this experience has been an eye opener; learning a better way to phenotype by trying this unique tool for the first time, communicating with colleagues from West Africa, and learning from their experiences will help East Africa in the future.” It could be anticipated that this huge improvement in cassava breeding will go a long way to reduce the length of cassava breeding cycles and foster early release of improved varieties towards food security. Based on its numerous advantages, one could tell that the adoption of the NIRS tool in Africa is an environmentally friendly and accuracy-enhancing option for cassava breeding programmes when compared with the traditional phenotyping techniques.

This study visit forms part of a wider capacity building initiative of the NextGen Cassava Project.

Less stress, good results and lots of fun in the field using the NIRS device

Good results and fun in the field using the NIRS device



Chiedozie Egesi, of the Next Generation Cassava, project in the news

Great work from our partners at the National Root Crops Research Institute!  As an Assistant Director and head of the cassava breeding team at the National Root Crops Research Institute, Umudike, Chiedozie Egesi has led efforts at developing and releasing to farmers improved varieties of cassava including pro-vitamin A cassava. His research activities involve the use of cross-cutting biotechnology tools in the genetic improvement of cassava including transgenic technologies. Read full article. Continue reading