Partner Spotlight: Boyce Thompson Institute

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, has been one of the founding partners of the NextGen Cassava project since its inception. 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.

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.

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.

32090062_1715399445170024_1253913863821197312_o.jpg

(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.

33846041_1734752976568004_7355084906889740288_o

(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.

Continue reading

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.

Continue reading

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.

IMG_3799

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).

IMG_2552

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.