2018 NextGen Cassava Annual Meeting, Day 1 Recap

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.

After a brief introduction and scene-setting, Chiedozie Egesi, NextGen project director, delivered a presentation highlighting some of the key achievements of the first 5 years of the project.

Continue reading

Cornell receives $35M to support cassava development for smallholder farmers in sub-Saharan Africa

Cassava is vital to the food security of millions of Africans who eat some form of the root crop daily. Although cassava breeders are making progress, they still face significant challenges in developing disease-resistant varieties that also increase overall yield and respond to the needs of smallholder farmers and processors. Cornell University will expand international efforts to deliver improved varieties of cassava to smallholder farmers in sub-Saharan Africa with $35 million in new funding from the Bill & Melinda Gates Foundation and UK aid from the United Kingdom.

“This grant funds a second five-year phase that will allow us to build on previous work and focus on getting improved varieties into farmers’ fields,” said Ronnie Coffman, international plant breeder and director of Cornell’s International Programs in the College of Agriculture and Life Sciences, who leads the project.

During Phase 1 of the Next Generation Cassava Breeding project — also funded by the Gates Foundation and UK aid from 2012 to 2017 — researchers shortened the breeding cycle for new cassava varieties by improving flowering and using genomic selection. Through analyzing plant genotypes and identifying cassava lines with desirable traits, such as resistance to cassava brown streak disease or high dry matter content, breeders also improved their ability to make selections based on genetics and probability without having to wait for seedlings to reach adulthood. These methods save breeding time for a crop where flowering and sexual propagation are issues.

Another goal of Phase 1 was to make cassava genomic information publicly accessible on an open database. Cassava researchers all over the world are now comparing results and improving breeding programs without duplicating efforts by using Cassavabase. To reduce cost per progeny and improve the quality of data uploaded to Cassavabase in Phase 2, NextGen researchers will use additional methods of whole genome sequencing.

“Our focus for the next five years will be to translate this research into breeding practices to increase impact,” said Chiedozie Egesi, NextGen project director and adjunct professor of plant breeding and genetics at Cornell, who is based at the International Institute of Tropical Agriculture (IITA) in Nigeria. “We have a strong gender component to Phase 2. A key goal will be to identify traits preferred by women farmers and end-users and incorporate them into new cassava lines.

chiedozie-edited-lorez

Field technician Tessy Uwangue, and Chiedozie Egesi, project leader for the Next Generation Cassava Breeding project, check field plots of cassava at the International Institute of Tropical Agriculture in Nigeria for signs of disease. PHOTO PROVIDED

Egesi said, “We believe we will accelerate genetic gain as well as adopted genetic gain, increase the yields and resilience of cassava production by smallholder farmers, and move African cassava breeding toward greater capacity.”

“Among the 30 new clones developed at IITA using our methods, 10 had higher dry matter yield than any clone currently available for smallholder farmers in Nigeria,” said Jean-Luc Jannink, a research plant geneticist with the United States Department of Agriculture, Agricultural Research Service (USDA-ARS) and Cornell adjunct associate professor in the Department of Plant Breeding and Genetics at Cornell. “Dry matter yield is a close proxy to food yield. Conservatively, we believe that we will increase the rate of genetic gain in cassava by 30 to 50 percent.”

Said Peter Kulakow, IITA cassava breeder and geneticist: “Genetic gain is a measure of the improvement of plant performance between generations and a goal of most modern breeding programs. Swifter improvements mean more new varieties can be tested and released.”

At the sixth annual Next Gen Cassava meeting, Feb. 19-24 in Dar es Salaam, Tanzania, teams of NextGen breeders, geneticists, data analysts, computer programmers, food technologists, social scientists and crop protectionists will be focusing on goals for Phase 2 and discussing how to better coordinate and leverage the exchange of germplasm and genotypic and phenotypic data from each other.

Developing capacity for sustainable breeding programs

Compared with other major staples like maize, rice and wheat, cassava has undergone few advances in productivity and yield over the last 50 years, making it an ideal candidate for breeding improvement. Because cassava is clonally propagated and has a low multiplication rate, it can take almost six to eight years before a new cassava variety makes it from breeders’ nurseries through field trials to farmers’ fields. Most breeding efforts focus on product development — goals set by scientists and researchers without accounting for the preferences of farmers. In practice, this can result in poor adoption of new varieties and unrealized potential.

“It is critical for breeders to be able to incorporate the diverse needs and preferences of end users into new varieties,” said Hale Ann Tufan, Survey Division Lead for NextGen Cassava. “Our trials in Nigeria and Uganda have revealed that there are significant differences in preferred traits between men and women, as well as various regional cassava processing methods. By understanding how descriptors for ‘good’ varieties, such as softness and texture, can be translated into phenotypes, we can develop methods to efficiently evaluate them along with traits such as disease resistance and climate resilience.”

Strengthening the capacity of national breeding programs will be critical in achieving self-sustaining breeding systems in sub-Saharan Africa. Over the next five years, NextGen researchers will continue to train the next generation of sub-Sahara African cassava breeders in modern plant breeding techniques like genomic selection and improved breeding methods.

International and regional partnerships are another important element of sustainability. NextGen researchers are reaching out to their counterparts in Ghana, Rwanda, Mozambique, Sierra Leone and the Democratic Republic of Congo to create a broader network of researchers who can work together to improve livelihoods and food security.

Chiedozie_Hawaii_lorez.jpeg

Sharon Motomura, Chiedozie Egesi and Joana Norton, of the Next Generation Cassava Breeding project, flash the ’shaka’ sign of ‘aloha’ in front of an international hybridization plot at the University of Hawaii in Hilo. The plot is planted with high-yielding cassava from Africa that is resistant to viruses and elite material from South America with high dry matter and high beta carotenes. The site provides a disease-free environment for testing. PHOTO PROVIDED

In Africa, NextGen collaborators include the International Institute of Tropical Agriculture and the National Root Crops Research Institute in Nigeria; the West Africa Centre for Crop Improvement in Ghana; the National Crops Resources Research Institute and Makerere University in Uganda; and the Tanzania Agricultural Research Institute in Tanzania. In South America, collaborators include Embrapa in Brazil and the International Center for Tropical Agriculture in Colombia. In the US, collaborators are Cornell University (who leads the project), the Boyce Thompson Institute at Cornell, the University of Hawaii, and the USDA-ARS in Ithaca.

For more information, visit www.nextgencassava.org

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.

DSC01777

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.

file-1

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.

 

Ugandan researchers bring gender equality to cassava breeding

By Samantha Hautea 22 September 2017

ZOMBO, UGANDA – This October, researchers with the Next Generation Cassava Breeding project (NextGen Cassava) will launch their first gender-responsive participatory variety selection (PVS) trials in Uganda. These trials engage both men and women farmers in identifying the top cassava varieties for Ugandan consumers and producers.

Robert Kawuki

Robert Kawuki is a a cassava breeder based at the National Crops Resources Research Institute (NaCRRI) overseen by Uganda’s National Agricultural Research Organisation (NARO).

“By releasing a cassava variety for the highland areas, we aim to reduce the acreage of the local low-yielding varieties and potentially increase productivity,” said Robert Kawuki, a cassava breeder based at the National Crops Resources Research Institute (NaCRRI) overseen by Uganda’s National Agricultural Research Organisation (NARO).  “We will also have the opportunity to gain experiential learning from the process, as the PVS trials will include an assessment of a fermented cassava product locally referred to as ‘kwon,’ in that part of Uganda.”

Selecting cassava varieties for cultivation is a long and daunting process. For example, in 2013, researchers began with 3000 cassava seedlings that were established in the Zombo district of northern Uganda. From these, they systematically narrowed the selection size to the most promising clones, which were then advanced to the subsequent season. In 2016, they identified the top 30 clones for the highlands. From these, the six most promising clones were selected, which are the varieties that will be planted in farmers’ fields this October and harvested in November 2018 as part of the trials.

For the first time, these trials will use a gender-responsive research protocol developed by researchers trained in gender-responsive methods and tools. Stephen Angudubo, an agricultural economist, and Winifred Candiru, a research assistant doing socio-economic research, will be working with the NextGen project to implement the protocol, monitor the trials, and evaluate the reported data.

Farmers participate in a group discussion held during the GREAT Gender Responsive Root, Tuber and Banana Breeding course in 2016-17

Farmers participate in a group discussion held during the GREAT Gender Responsive Root, Tuber and Banana Breeding course in 2016-17.

The trials will be conducted with the support of NextGen Cassava researchers who participated in the GREAT Gender-responsive Root, Tuber and Banana Breeding course held at Makerere University in 2016-17: Ritah Nanyonjo and Williams Esuma  from Uganda, and Andrew Smith Ikpan, Okoro Maria Justin, and Tessy Ugo Madu from Nigeria.

“The implementation will involve researchers, farmers and pre-identified agricultural extension workers as well as pre-trained village assistants to guide farmers in collecting data and monitoring farmer-managed fields,” Candiru explained. “Farmers will have the chance to be involved in various stages of the process, including preference analysis and sensory evaluation before and after harvest.”

Farmers selected for participation in the trials will include men and women as well as youth (18-35 years old) and adults (36-70 years old). Working with the researchers, evaluation criteria for the clones will be developed through group discussion. After evaluating how the clones perform in the field, researchers will then conduct a preference analysis and sensory evaluation of the varieties after they have undergone typical processing into the favored local consumable product known as “kwon.” Finally, the outcomes from the researchers’ evaluation and selection will be compared with farmer varietal preferences to determine similarities and/or differences. Ideally, this process will allow the identification of the clones that combine excellent suitability for processing and good agronomic characteristics in the field.

The aim of the participatory trial is to identify the best performing cassava clones suitable for adoption by the farming communities in the highlands of Uganda. Based on the outcomes of these trials, the top two clones will be distributed and officially released to farmers as the first highland cassava in Uganda. The others will be used for further breeding and development of better cassava clones.

“We see high potential that these new cassava varieties bred for the highlands will not only increase productivity, but do so equitably,” said Hale Tufan, project manager for GREAT. “Designing a PVS trial in a gender-responsive manner increases the likelihood that women, as well as men, will benefit equally from these new varieties.”

Tufan added that she hopes the outcome of these trials will set a precedent for gender responsiveness as a standard in research conducted at NaCCRI.

NextGen Cassava is a project funded by a $25 million, five-year grant from the Bill & Melinda Gates Foundation and the Department for International Development of the United Kingdom.. Both projects are managed through International Programs in the College of Agriculture and Life Sciences at Cornell University with partners in the U.S. and Africa.

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.)

Sources:
www.wacci.edu.gh
www.nextgencassava.org

NextGen PhD Student Visits Cornell for training on Prediction Modeling

May 13, 2016, Ithaca NY: Olumide Alabi, NextGen Cassava PhD student with the International Institute for Tropical Agriculture (IITA) in Ibadan, Nigeria, recently visited Jean-Luc Jannink’s laboratory group at Cornell University for training on prediction modeling. Olumide reports on his visit here:

Date: 8th March to 6th April, 2016

Location: Dr. Jean-Luc Jannink’s Research group, Plant breeding and genetics department, Bradfield Hall, Cornell University, Ithaca, NY

Practical skill acquisition in genomic prediction modeling forms the basis of my brief visit to Cornell. I got handy explanation on prediction modeling processes as they apply to past and present genomic selection cycles as being implemented in IITA-NextGen Cassava Breeding Project.

Three major objective activities included:

  1. The prediction modeling for the IITA-Genomic Selection

Marnin Wolfe, postdoctoral associate at Cornell, was able to guide me from the known in Genomic predictions in general to the unknown with practical step-by-step activities using the IITA-NextGen cassava dataset. I received concrete training on the use of single step model and information on the limitation to it, as it could be computationally intensive with large datasets. Also, I was trained on two-step model, formation of the kinship matrix using the “A.mat” function, model.matrix, kin.blup phenotype dataset curation for prediction modeling, G-BLUP model, RR-BLUP model, the inclusion of multiple random effects in prediction modeling using the EMMREML model and general theories and coding syntaxes associated with these above-mentioned models. One of the newest concepts to me in all was when I was guided through the IITA-Cycle 3 prediction, de-regressed BLUPs, especially with the theory and concept of reliability estimation, PEV,  and how these influence the accuracy of our predictions. Marnin did well in guiding me through these concepts both theoretically and practically, coupled with exercises, reading assignments, brainstorming sessions. To wrap it up, I was guided through the entire IITA-GS Cycle 3 prediction model; the code was provided to me by Marnin with detailed explanations.

  1. Fitting the appropriate model for the genetic gain estimation

Estimating the “Expected Gain” in GS application in cassava is not a straight-forward thing, as the selection of the parents is based on selection index built from the GEBVs of traits and individuals. In the gain estimation using the conventional breeder’s equation, there is a little adjustment in GS concept, which is basically the selection accuracy factor in the model. To obtain this, we had to correlate the S.I_GEBVs (Predicted) of lines and the S.I_BLUPs (Observed). In my brainstorming with Marnin, we came up with the concept highlighted below:

rA = corr(S.I_GEBVs, S.I_BLUPs)

Where S.I_GEBVs = wtGEBVT1 + wtGEBVT2 + wtGEBVT2…+ wtGEBVTN

wt = the economic weight used for trait T in the selection index model

S.I_BLUPs = wtBLUPT1 + wtBLUPT2 + wtBLUPT2…+ wtBLUPTN

Hence, the rA could be appropriately fitted in the breeder’s equation for the expected gain estimation.

  1. GWAS exploration on the plant type dataset

Dunia (Research Associate) guided me through GWA-studies with the use of datasets on plant type and the associated SNP data. For better handling of the categorical nature of the Plant Type trait (compact_1, open_2, umbrella_3 and cylinderica_4), Marnin suggested the classification of the trait as binomial scores (E.g. Compact: 0_absent, 1_present), hence coding the scores as a trait per time. It was to enable us to fit a GLIMMIX model with the flexibility of a link function for variance components.

  1. I participated in the research group and graduate student seminars and symposiums.

Skills acquired

I can practically implement Genomic prediction with more confidence on availability of appropriate dataset. I got a detailed understanding of the past IITA GS Cycle selection and a first-hand understanding of the present Cycle 3 predictions (Thanks to Marnin). I got a better clue on several aspects in statistical modeling to be included in my thesis report, especially the expected gain estimation concept and some genomic prediction steps.

Acknowledgement

My appreciation goes to Dr. Jean-Luc Jannink for the time and audience given to me while I was in Ithaca; the meeting for updates in his office and facilitation of my visit; amidst other.

Many thanks to Marnin for devoting much time in coaching me. In fact, he was my tutor all through the period I was in Ithaca. Dunia did a great job as well as my NextGen graduate student colleagues, Ugo, Uche, and Alfred. Alex of BTI is appreciated for his kind gestures all through my time in Ithaca. I would not but mention the logistics from Dan’s end, Karen and the team in IP-CALS office.

I want to thank my supervisors in IITA, Drs. Peter Kulakow and Ismail Rabbi, for granting the home-support needed to visit Cornell this period. Thanks to Dr. Chiedozie Egesi and Dr. Hale Tufan. My final appreciation goes to the Cornell-NextGen Cassava project for the full support. My regards to all.

Olumide during his training at Cornell and with Marnin Wolfe, bottom left

Olumide during his training at Cornell and with Marnin Wolfe, bottom left

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.