Author Archives: canaanboyer

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.

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: 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.

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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.

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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.)

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