In April 2016, Cornell-affiliated members of the NextGen project visited Tanzania to coordinate with the Tanzanian team on NextGen collaboration. (l-r) Kiddo Mtunda, Heneriko Kulembeka, Geoffrey Mkamilo, Kasele Salum and Chiedozie Egesi (Cornell).
UKIRIGURU, TANZANIA: Tanzania recently became a partner of the Next Generation Cassava Breeding project (NextGen), joining Nigeria and Uganda in the global effort to improve cassava breeding in Africa. This partnership is expected to enhance the project’s efforts to improve livelihoods for African cassava farmers.
“Ta has one of the foremost cassava breeding programs in Africa,” said Chiedozie Egesi, project manager for the Cornell-based NextGen project. “Because Tanzania shares African cassava germplasm, they will benefit from the genomic predictions that NextGen has already developed, use of the NextGen Cassavabase database, and capacity for improved phenotyping.”
Cassava is a vital crop in Tanzania, second only to maize in volume produced and source of calories. More than 80 percent of farmers grow cassava all over the country, producing about 4.5m metric tons of cassava roots on an annual basis. About three-quarters are consumed by people, while the rest is used for livestock feed and industrial use. A widely preferred and hardy staple, cassava is often stored in the ground and locally processed as a source of food in times of famine.
Cassava farmers face many challenges in raising their crop. Tanzania loses an estimated 2.5m metric tons of their annual harvest to Cassava Brown Streak Disease (CBSD), Cassava Mosaic Disease (CMD), and Cassava Green Mite (CGM). There is poor access to improved planting materials and processing technologies, limited use of fertilizers and herbicides, and low investment in cassava research and improvement overall.
To address these challenges, researchers at the Department of Research and Development (DRD) of the Ministry of Agriculture Livestock and Fisheries in Tanzania will collaborate with scientists on the NextGen project largely through ongoing efforts at the Lake Zone Agricultural Research and Development Institute (LZARDI), the oldest agricultural research station in Tanzania. LZARDI scientists are well prepared to contribute to the efforts of other NextGen partners through cassava-related research that currently includes breeding and improvement of cassava, molecular marker-assisted breeding for disease resistance, cassava processing and product development, and cassava agronomy studies.
“Partnering with NextGen should help us develop tools to address biotic stresses like CBSD, CMD and CGM, and improve cassava root yields that will serve to increase cassava production country-wide,” said Heneriko Kulembeka, cassava breeder and NextGen coordinator in Tanzania. “The NextGen project will assist in determine good parental lines for different traits of interest.”
The NextGen Tanzania team consists of Kulembeka; Kiddo Mtunda, cassava breeder and coordinator (Coastal Tanzania); Geoffrey Mkamilo, national team leader of the Cassava Research Program in Tanzania; Kasele Salum, assistant cassava breeder (Lake Zone); and Caroline Sichwale, assistant cassava breeder (Eastern Zone).
NextGen is a global partnership among International Programs at Cornell University, the International Institute of Tropical Agriculture and National Root Crops Research Institute breeding centers in Nigeria, the National Crops Resources Research Institute in Uganda, DRD, the Boyce Thompson Institute, the US Department of Energy, the West African Centre for Crop Improvement in Ghana, and Makerere University in Uganda.
Samantha Hautea is a communications specialist with International Programs.
Because many cassava consumers live in developing countries, the plant has not received the intense breeding that has benefited crops more familiar to the Western world such as corn, wheat and rice. In the past decade, however, cassava has started to garner attention. China and Thailand use it to make high-quality starch, and some countries see the crop as a potential biofuel. What’s more, cassava will likely do well in the world’s changing climate; it survives drought when other crops have failed and flourishes in warmer temperatures.
Big boost in yield
Among the latest and most impressive breeding successes comes from Nagib Nassar, a cassava breeder and professor emeritus of genetics at the University of Brasilia. He has developed a new variety that could dramatically boost yields. Each of his plants produces about 14 kilograms of edible roots after one year whereas traditional varieties yield just two to three kilograms.
Apart from their massive roots, the new cassava plants don’t look too strange until examined under a microscope. Nassar has created chimeras - a fusion of two individuals - by carefully grafting a common cultivar with a wild species and treating the results with a synthetic plant growth hormone. The outer, or epidermal, layer of the new plants’ tissues is from cultivated variety and the inner tissues are from the wild parent.
Encouraged by the vigorous growth of the chimeras, Nassar hopes to investigate the possibility of more crosses. With his graduate student, Nayra Bomfim, he published a paper on the second chimera in the online journal Gene Conserve in January (pdf). “He is a tireless scientist,” says Hernan Ceballos, a cassava breeder at the International Center for Tropical Agriculture in Colombia. Ceballos, who was not involved in the work, adds that the chimeras are interesting but that further work to demonstrate the plants’ productivity is needed.
Nassar’s chimeras aren’t the only new cassava variety out there. Ceballos himself has been working on a variety that would tower high above future farmers’ heads. The "Asparagus Cassava" has no branches - its leaves grow directly from a massive stalk. This variety can be planted more densely than traditional cassava and produce higher yields. Other varieties include a cassava high in vitamin A, which turns the root orange, and one with extra protein.
Getting to the next generation
These promising varieties could be just the beginning in a cassava revolution. “There is a growing recognition for the importance of food security in the most food-insecure areas," says Jim Lorenzen, a senior program officer at the Bill and Melinda Gates Foundation, a major supporter of cassava research. The foundation aided researchers in the sequencing of the cassava genome and, along with the U.K.'s Department of International Development, awarded $25 million in late 2012 to a massive international effort called the Next Generation Cassava Breeding (NEXTGEN) project, which aims to jump-start genetic improvement of cassava.* "It’s a very good time for cassava research," Lorenzen says. He notes that this attitude is reflected in more researchers focusing on cassava and intense interest from African leaders, including Nigeria’s Minister of Agriculture and Rural Development, Akinwumi Adesina.
The project unites researchers at breeding programs in Nigeria, Uganda and the U.S. The scientists involved are currently homing in on key traits needed to breed better cassava plants. Robert Kawuki, a cassava breeder at the National Crops Resources Research Institute in Uganda, is working to identify molecular markers associated with resistance to brown streak disease, one of cassava’s greatest threats in Africa.
Kawuki’s first step in finding genes responsible for disease-resistance is looking at many plants as they grow in the field for the target traits. For brown streak disease, that requires a lot of effort: "You have to uproot the plant from the ground and score each root individually," he says. That may require digging up over 1,600 plants for a single trait. The most promising plants are genotyped, and their data is entered into a computer model. That model will identify molecular markers and decide which plants should be crossed to produce the best genetics for the next generation. The whole approach, called genomic selection, is already used to great effect in the dairy breeding industry, Lorenzen explains.
The ability to accurately predict crosses promises to save a lot of time. Typically, breeders had to wait until their cross-breeds grew to see how they would turn out. New varieties were tested in multiple locations over several growing seasons before release. Aided by the computer model, NEXTGEN’s approach can compress that time line into three to five years by how offspring will fare, says Chiedozie Egesi, an assistant director and head of cassava breeding at the National Root Crops Research Institute in Nigeria. The project is also targeting resistance to cassava’s other plagues: green mites that devastate leaves, cassava bacterial blight that browns stems and defoliates the plants and cassava mosaic virus that yellows leaves and stunts plant growth.
This past weekend Egesi joined a group to meet and discuss the NEXTGEN project’s progress. "The first year was very successful," Lorenzen says. "But it will take time to see how it works out in practice."
Millions of small famers and their families stand to benefit from cassava researchers’ efforts. By the end of this year, more than 9,000 farmers are scheduled to grow Nassar’s chimeras in Brazil. Expect to hear more about the starchy root in the future, as new varieties help feed the tropical world.
Cassavabase developer Lukas Mueller (center), of the Boyce Thompson Institute, in Ithaca, NY, works with researchers from the National Root Crops Research Institute in Nigeria, to develop protocols for the barcoding tools used to submit data to the open-access Cassavabase. CREDIT: C. Egesi
Six months after the launch of the $25.2M NEXTGEN Cassava project at Cornell University, scientists on the project have released Cassavabase, a database that promotes open access data sharing.
www.cassavabase.org features all phenotypic and genotypic data generated by cassava breeding programs involved in the NEXTGEN Cassava project, and makes the data immediately and openly accessible to all users prior to publication. It is being developed by Lukas Mueller, at the Boyce Thompson Institute in Ithaca, NY, adjunct professor of plant breeding and genetics at Cornell.
"In the plant breeding community, data-sharing can be delayed until publication, which can limit the opportunity to use the knowledge by the international plant breeding communities," said Mueller.
Chiedozie Egesi, assistant director and head of cassava breeding at the National Root Crops Research Institute (NRCRI), Nigeria, and Katherine Kahn, senior program officer at the Bill and Melinda Gates Foundation, co-presented about Cassavabase and the advantages of open access data sharing during the G8 International Conference on Open Data for Agriculture, in Washington DC, April 29-30, 2013.
"Open access databases such as Cassavabase enable better decisions based on good quality data by the global cassava breeding community," said Egesi. "Cassavabase will lead to increased efficiency in agricultural research and ultimately improve the livelihoods of African cassava farmers."
At the 2012 Summit at Camp David, G8 leaders implemented the New Alliance for Food Security and Nutrition with the aim of boosting agriculture production in six countries and lifting 50M people out of poverty in 10 years. Critical to food security in developed and developing countries was the implementation of policies and projects to make data readily accessible to users in Africa and worldwide.
"It's great to see the cassava research community lead the way in sharing their data rapidly and openly to maximize opportunities for developing improved cassava varieties for small farmers in sub-Saharan Africa and indeed, globally," said Kahn. She noted that the Bill & Melinda Gates Foundation supports increasing open access to data in all its projects.
"Different versions of cassava genes can be found in all breeding programs. What one program learns about its genes can benefit everybody," said Jean-Luc Jannink, lead scientist on the NEXTGEN Cassava project, research geneticist with the US Department of Agriculture and adjunct professor in the Cornell University department of plant breeding and genetics. "All our learning is leveraged by sharing,"
The benefits of open data sharing through Cassavabase is being lauded by cassava breeders across sub-Saharan Africa, who "currently share a significant amount of cassava germplasm," according to Peter Kulakow, plant breeder at the International Institute for Tropical Agriculture (IITA-Nigeria), a major contributor of data to Cassavabase. "Sharing information will create the opportunity for all African farmers to benefit from the best technologies available to improve the yield and quality of cassava that is needed for food and income."
Data is publicly shared on Cassavabase through adherence to the Toronto Agreement on pre-publication data sharing (Nature 461, 168-170, 2009), by informing users on the data quality and standards, as well as plans for publication. Users are expected to respect etiquette and allow data generators to publish analyses from their data sets first.
Cassavabase will be hosted at IITA-Nigeria by the NEXTGEN Cassava project, providing a "one-stop shop" for cassava researchers and breeders worldwide. In addition to phenotypic and genotypic data, Cassavabase offers access to all Genomic Selection analysis tools and phenotyping tools developed by the NEXTGEN Cassava project, as well as links to auxiliary genome browsers, ontology tools and social networking tools for the cassava community.
Project partners and donors envisage Cassavabase as a tool that will serve the whole cassava community, and that it will last beyond the lifetime of the NEXTGEN Cassava project.
No other continent depends on cassava to feed as many people as does Africa, where 500 million people consume it daily. Africa's small farmers produce more than half of the world's cassava, or about 86 million tons from over 10 million hectares. The tough plant requires few inputs and can withstand drought, marginal soils and long-term underground storage. A cash crop as well as a subsistence crop, the storage roots of the perennial woody shrub are processed, consumed freshly boiled or raw, and eaten by people as well as animals as a low-cost source of carbohydrates.
Despite diverse growing conditions and multiple uses of cassava across sub-Saharan Africa, farmers face similar challenges fighting cassava viruses and drought conditions that adversely affect yield.
The NEXTGEN Cassava project aims to use the latest advances in breeding methodology to improve productivity and yield in cassava production, incorporate cassava germplasm diversity from South America into African breeding programs, train the next generation of plant breeders, and improve infrastructure at African institutions. NEXTGEN Cassava is supported by a $25.2M grant from the Bill & Melinda Gates Foundation and the Department for International Development of the United Kingdom.
Elizabeth Agbamuche, a B.Sc. student, carries out controlled pollination on a cassava flower. Credit: Dr. Ismail Rabbi, IITA
To improve the productivity of cassava -- a rough and ready root crop that has long been the foundation of food security in Africa -- and plant breeding in sub-Saharan Africa, the Bill & Melinda Gates Foundation and the Department for International Development of the United Kingdom have awarded Cornell $25.2 million to host a five-year research project.
Cornell will coordinate work with the National Crops Resources Research Institute (NaCRRI) in Uganda, National Root Crops Research Institute (NRCRI) in Nigeria, International Institute of Tropical Agriculture (IITA) in Nigeria, Boyce Thompson Institute for Plant Research (BTI) on the Cornell campus, and the U.S. Department of Energy Joint Genome Institute at the Lawrence Berkeley National Laboratory in California.
"Partners on the Next Generation Cassava Breeding project will use a state-of-the-art plant breeding approach, known as genomic selection, to improve cassava productivity for the 21st century," said Ronnie Coffman, Cornell professor of plant breeding and genetics, director of International Programs and the grant's principal investigator.
Typically, it takes researchers almost a decade to develop a new cassava variety. Genomic selection can shorten breeding cycles, provide more accurate evaluation at the seedling stage and give plant breeders the ability to evaluate a much larger number of clones without the need to plant them in the target environment. Using genomic selection, new releases of cassava could be ready in as little as six years.
"Increased support for strengthening the research capacity in Africa and harnessing novel technologies are critical to improving overall agricultural productivity and food security for poor people," said Yona Baguma, project coordinator for NaCRRI, who aims to unlock the potential of cassava in Africa and mobilize a new generation of cassava growers.
"The Next Generation Cassava Breeding project provides a great opportunity for us to harness the power of modern science for faster delivery of best-bet cassava varieties for smallholder farmers," said Chiedozie Egesi, assistant director at NRCRI and head of cassava breeding, who works to biofortify cassava with micronutrients to make it more nutritious.
"[The project] will give breeders in Africa access to the most advanced plant breeding technologies to deliver improved varieties to farmers more rapidly," said Peter Kulakow, cassava breeder and geneticist with IITA. "This project will ensure that cassava genetic research is on a par with other top food crops such as wheat, rice, maize and potato."
Africa's small farmers produce more than half of the world's cassava, about 86 million tons from over 10 million hectares. The tough woody plant is predicted to be one of the few crops that will benefit from climate change. It requires few inputs and can withstand drought, marginal soils and long-term underground storage. Cassava is a cash crop as well as a subsistence crop, and the storage roots of this perennial shrub are processed, consumed freshly boiled or raw and eaten by people as well as animals as a low-cost source of carbohydrates. No other continent depends on cassava to feed as many people as does Africa, where 500 million people consume it daily.
The cassava team at Cornell also includes scientific leader Jean-Luc Jannink, research geneticist with the U.S. Department of Agriculture and adjunct professor of plant breeding and genetics, and Tim Setter, chair of the Department of Crop and Soil Sciences. The partners will share cassava data, expertise and information on a website http://www.cassavabase.org, which was developed by Lukas Mueller of BTI.
In addition to using the latest genomic information from cassava sequencing to improve productivity and yield, project partners will incorporate cassava germplasm diversity from South America into African breeding programs, train the next generation of plant breeders and improve infrastructure at African institutions. They will also hold awareness-building workshops for farmers, scholars, researchers and policy makers.