Cornell University
NextGen Cassava

Why is cassava important?

Cassava (Manihot esculenta), a major staple crop, is the main source of calories for 500 million people across the globe. No other continent depends on cassava to feed as many people as does Africa. Cassava is indispensable to food security in Africa. It is a widely preferred and consumed staple, as well as a hardy crop that can be stored in the ground as a fall-back source of food that can save lives in times of famine. Despite the importance of cassava for food security on the African continent, it 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.

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Why genomic selection?

Genomic Selection is a new plant breeding method that uses statistical modeling to predict how a plant will perform, before it is field-tested. Novel statistical models and bioinformatics tools, combined with increasingly abundant genomic information, have enabled the deployment of prediction-based breeding methods such as Genomic Selection in crop breeding programs. Giving breeders the ability to select based on predictions rather than observations will result in much improved genetic gains and efficiency.

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In the News

Thiele and Mueller

New bioinformatics alliance between CGIAR and the Boyce Thompson Institute - BTI (Oct 1, 2014)

Boyce Thompson Institute for Plant Research (BTI) is partnering with CGIAR and its associate centers to create a shared database and bioinformatics platform to help breeders develop improved root, tuber and banana crops. This platform will enable RTB breeders to access and use massive amounts of genotypic and phenotypic data to develop new varieties with precisely targeted traits for disease resistance, higher yields and consumer acceptability

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Ronnie Coffman serves as International Professor of Plant Breeding and Director of International Programs of the College of Agriculture and Life Sciences at Cornell University. Previous positions include Associate Dean for Research and Director, Cornell University Agricultural Experiment Station; Chair of the Department of Plant Breeding and Genetics, and Plant Breeder at the International Rice Research Institute (IRRI). Coffman's work has been important to the development of improved rice varieties grown on several million hectares throughout the world. He has collaborated extensively with institutions in the developing world and served as a board member for several international institutes. He received his Ph.D. from Cornell University and his undergraduate degree from the University of Kentucky, his home state.

Hale Ann Tufan is Project Manager for NEXTGEN Cassava and leads the Gender Responsive Cassava Breeding Initiative. Previously she held a postdoctoral research fellow position at the Natural Resources Institute, UK, where she used RNA-sequencing to decipher cassava defense responses to viral diseases. She has worked as an assistant wheat breeder at the CIMMYT Winter Wheat Improvement Program in Turkey, and at the School of International Development, University of East Anglia UK, studying institutional tensions around implementing molecular breeding in developing countries. She completed her PhD at the John Innes Centre UK, on wheat molecular defense responses to fungal pathogens.

Lukas Mueller is a biochemist and bioinformatician who has been involved with large plant genome databases for many years. Initially working at Arabidopsis database TAIR, he has been directing the SGN database for more than a decade. His group is mainly interested in describing plant genomes and phenomes, and how the two can be linked to help scientists and breeders. He has also been involved in the International Tomato Genome sequencing project and the larger initiative to characterize the Solanaceae, called the SOL project. He is delighted to be part of the Next Generation Cassava Breeding project because it has the potential to improve the lives of so many people.

Charlotte Acharya earned a B.S in Biochemistry/Chemistry from the University of California, San Diego in 1998 and a M.S. in Natural Resources from Cornell University in 2009. She is the lab manager at the Institute for Genomic Diversity (IGD) and has been genotyping agricultural crops since 2003. She also trains scientists from around the world to use genotypes in breeding. This has given her an appreciation for differences in agronomic systems impact breeding objectives. She has genotyped tens of thousands of cereal crop lines through Genotyping By Sequencing (GBS) and is excited to be gathering data for Cassava.

Luis Duque is a Colombian-American lecturer/instructor and Post-Doctoral Associate from the Department of Crop and Soil Science of Cornell University He holds a B.S. in Agronomy from the Universidad Nacional de Colombia and an MSc and PhD in Field Crop Science and Crop Physiology from Cornell. He currently co-teaches Field Crops Systems lecture course and lab. His main research interests include understanding abiotic stresses (drought, heat, water submergence, etc.) of important crop species and their relationship with plant breeding and climate change. He is particularly interested in understanding cassava drought tolerance mechanisms and flowering and their relationship to environmental cues.

Jeffrey Endelman is a Research Associate in the Department of Plant Breeding and Genetics at Cornell University. His diverse training includes chemical engineering (BS), bioengineering (PhD), and crop science (PhD). Jeffrey joined the Cornell community in 2011 and has worked with breeders at CIMMYT to implement genomic selection for wheat and maize.

Martha Hamblin is a Senior Research Associate in the Department of Plant Breeding and Genetics, where she works with Jean-Luc Jannink. Her training is in Botany (MS, Oregon State University) and Drosophila Population Genetics (PhD Cornell University), although she has worked in many different areas during her scientific career, including mosquito egg development and human adaptive evolution. Prior to joining the Department of Plant Breeding and Genetics, she was in the Institute for Genomic Diversity, where she focused on sorghum population genetics and genetic diversity. She now works full time for the NEXTGEN Cassava Breeding project.

Jean-Luc Jannink is a Research Plant Geneticist with the United States Department of Agriculture, Agricultural Research Service and an Adjunct Associate Professor in the Department of Plant Breeding and Genetics at Cornell University. He obtained a PhD in Plant Breeding with a minor in Sustainable Agriculture from the University of Minnesota in 1999. His research focuses on statistical approaches to analyze and interpret the increasing quantity of DNA data available to breeding programs in combination with the phenotypic diversity these programs traditionally excel at putting to use. His goal is to enable programs to make better selection decisions more rapidly.

Tim Setter is Professor of Field Crop Science at Cornell University. In his research, he seeks to further understanding of plant response to environmental factors such as drought and to identify potential targets for future crop improvement. His research, which is mainly on cassava and maize, focuses on physiological and molecular aspects of environmental responses of crops such as regulation of kernel set and the roles of hormonal and photosynthate fluxes. He collaborates with researchers at international organizations on projects to phenotype genetic populations for drought tolerance, and teaches courses on physiology and ecology of crop yield, water status assessment techniques, and the physiology of responses to environmental stresses.

Ismail Yusuf Rabbi, International Institute of Tropical Agriculture, trained in population genetics and plant breeding at the University of Hohenheim, Germany. Research interests revolve around studying the genetic basis of important traits in crop species, with special focus on cassava. He uses both field research and modern genomic tools like GBS to identify genes responsible for disease resistance, nutritional quality, yield-components and plant architecture of cassava. For the NEXTGEN Cassava project, he will be implementing the day-to-day operations that range from designing of crosses, seed processing and germination, DNA extraction and phenotypic evaluation.

Richard Edema is a geneticist with a PhD in Molecular Virology, and Senior Lecturer in the Department of Agricultural Production in the College of Agricultural and Environmental Sciences at Makerere University. He has been involved in a regional sorghum improvement program, and research on validation of molecular markers linked to important traits of maize, cassava, and sorghum. He has worked on capacity building in East Africa for biosafety and environmental impact assessments of transgenic plants. He has mentored over 60 graduate students. He is coordinator of Makerere University's award winning regional MSc program in plant breeding and seed systems, supported by AGRA and RUFORUM. This program has since developed into a model for regional capacity building in East Africa.

Paul Gibson is a Visiting Professor at Makerere University, serving as primary instructor, senior mentor, and statistical advisor in the Regional MSc and PhD programs in Plant Breeding. His lifelong call to meet hunger needs has involved a PhD in Plant Breeding at Iowa State University, and 40+ years of research, teaching, and statistical advising, including 20 years outside the US. He is indispensably supported by his wife, Pauline, also an American national with extensive overseas experience, who teaches English and scientific writing, and serves informally as program nurse, midwife, and hostess.

Yona Baguma is a Principal Research Officer at the National Agricultural research Organisation of Uganda. Yona's contributions to cassava research include restoration of cassava production, and development of natural resource use and disease management practices.His current work focuses on developing drought resilient cassava, cassava double haploids, and the application of tissue culture. Yona has also been involved in developing and implementing biosafety regulatory guidelines and systems in Uganda and beyond.He has mentored many young scientists, and has established several international collaborations and partnerships. He is Editor-in-Chief and Chairperson of the Editorial Board for the Uganda Journal of Agricultural Sciences, Associate Editor for the Journal of Research in Biotechnology, Member and Vice Chairperson of the Uganda National Biosafety Committee, and serves on various boards and committees.

Robert Kawuki has been conducting crop research in Uganda since 2000, first as an MSc student (working on soybean rust; 2000 to 2002), secondly as a research assistant with IITA-Uganda working on banana entomology (2003 to 2004). Robert obtained his PhD in Plant Breeding & Genetics from the University of the Free State, South Africa in 2009. Robert is employed as a cassava breeder by National Agricultural Research Organization of Uganda and based at NaCRRI, working in partnership with international scientists. Robert regards promotion of proven technologies and science communication as key for future of African agriculture.

Anthony Pariyo worked in agricultural extension from 1999-2004, and is now a researcher with the National Agricultural Research Organisation of Uganda, based at NaCRRI. Anthony was initially employed at NaCRRI as research assistant/graduate fellow during his MSc studies that focused on aspects of marker assisted selection and analysis of breeding values of major parental lines for cassava mosaic disease resistance in cassava. On completion of his MSc, he was employed as a research officer (Plant Breeder/Geneticist) from 2008 to date. He plans to complete his PhD studies on 'Genetics of resistance to cassava brown streak disease', by June 2013. His research interest is in the use of efficient crop improvement techniques that rapidly deliver research products to end-users.

Barbara Mugwanya Zawedde is a team-leader for the Biotechnology and Biosafety Education objective of the NEXTGEN Cassava project. She is in the final year of her PhD training at Michigan State University. Her area of specialization is environmental safety and risk communication in relation to genetically engineered crops. Prior to joining the PhD training, Barbara worked for more than five years under the Program for Biosafety Systems, Uganda office, where she also gained experience in biotechnology and biosafety education. She also contributed to the development of a web-based resource for the African Biosafety Network of Experts (ABNE).

Chiedozie Egesi is an assistant director and head of the cassava breeding team at the National Root Crops Research Institute, Umudike, Nigeria. He has led efforts at developing and releasing to Nigerian cassava farmers several 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. Chiedozie supports several African NARS cassava breeding programs in developing adaptive breeding schemes. He has worked previously as a university teacher and a yam breeder and have participated in the development and release of 6 yam varieties.

Emmanuel Okogbenin is a Plant Molecular Breeder/Geneticist with several years working experience as a Cassava Scientist in both national and international organizations in Africa and South America. His research activities are targeted at using advances in molecular biology to enhance the genetic improvement of cassava. He is the CGIAR-GCP Cassava Product Delivery Coordinator for cassava and also leads a consortium of 12 African countries under the Cassava Breeding Community of Practice to promote modern breeding in the NARS. He is currently a Senior scientist with NRCRI, Nigeria and a member of the Cassava Transformation Agenda Core Team for Nigeria.

Jessen Bredenson is a Bioinformatics programmer working on all aspects of GBS sequencing data from quality control to SNP-calling pipeline development to generation of genetic maps for cassava crosses in which agriculturally important traits are segregating.

Simon Prochnik is a Computational Scientist working on cassava genomics, with a focus on SNP calling and haplotype generation, but also working to improve genome assembly and annotation and leveraging these data both to improve GS models and to help investigate putative function of genes/pathways containing SNPs of interest via the Phytozome comparative plant genomics platform (www.phytozome.net).