Cornell University
NextGen Cassava

Martha Hamblin

The NEXTGEN Cassava family lost Martha Hamblin on March 15, 2015 to ocular melanoma.

Martha once said that for all her years working in science, it hadn't amounted to "a hill of beans" when it came to the betterment of human welfare. But she was wrong: her last scientific project is "amounting"--to a hill of cassava. Martha essentially wrote and shepherded to approval the NEXTGEN Cassava Breeding Project. Even after receiving her diagnosis, she kept involved in the project's scientific work and kept tabs on essentially all of its components, ensuring that nothing fell between the cracks. In addition, her consistently perceptive insights and seemingly magical clearing of the tangled undergrowth of scientific writing were an invaluable help to the other researchers. Her impact on this project will be felt for years to come.



NEXTGEN Cassava Project Meeting (February 2015 in Kampala, Uganda)

People

Boyce Thompson Institute

Guillaume Bauchet, gjb99@cornell.edu

Guillaume is a postdoctoral associate at BTI, where he works with Lukas Mueller. Previously, he completed his PhD at INRA-Montpellier SupAgro, focusing on the quantitative genetic aspects and molecular diversity in tomato. He has training in plant genetic resources (M.Sc, Wageningen University) and experience in practical plant breeding in various environments (USA, Morocco, Thailand). Guillaume works now toward the development and implementation of genomic tools for the NEXTGEN Cassava Breeding project.


Naama Menda, naama.menda@cornell.edu


Lukas Mueller, lam87@cornell.edu

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 NEXTGEN Cassava Breeding project because it has the potential to improve the lives of so many people.


Alex Ogbonna, ogbalex@yahoo.com

Alex Ogbonna is an Associate Database Curator and the contact person for Cassavabase at the National Root Crops Research Institute, Umudike, Nigeria.


Isaak Yosief Tecle, iyt2@cornell.edu

Isaak Yosief Tecle is trained in plant breeding and genetics (PhD, Cornell '06). His research focus is developing bioinformatics tools that help plant breeders make efficient decisions in their crop improvement programs. This includes developing intuitive web-tools for statistical analysis, visualization and sharing 'omics' data. He is currently working on a genomic selection web-tool for the project.


Cornell University


Chiedozie Egesi, cne22@cornell.edu

Chiedozie Egesi is Project Manager for the NEXTGEN Cassava project. He 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 has participated in the development and release of six yam varieties.

Oluwabusayo Sarah Adeyemo, osa7@cornell.edu

Dr. Adeyemo joins Cornell University bringing her experience and expertise in molecular biology and genetic transformation of model plant species. After completing her BSc and MSc studies in Biochemistry and Crop Improvement (respectively) from the University of Ibadan, Nigeria, she obtained a PhD in Genetics from University of Cologne, Germany, having conducted research in Circadian Biology and Flowering in Arabidopsis and Cassava at both the Max Planck Institute for Plant Breeding Research (MPIPZ) and the International Center for Tropical Agriculture (CIAT) in 2009. She joined Prof. R. Dickstein’s laboratory at the University of North Texas where she contributed significantly in the study of Medicago truncatula mutants defective in biological nitrogen fixation and nitrogen responsiveness using a genetics approach. Her current research with the NEXTGEN Cassava project focuses more on the underlying physiological and molecular approaches to hasten flowering, seed set and life cycling of cassava.


Ariel Chan, ac2278@cornell.edu

Ariel Chan is a graduate student in the Department of Plant Breeding and Genetics at Cornell University, where she works with Martha Hamblin and Jean-Luc Jannink. She is interested in probabilistic systems analysis and modeling and is working on genotype imputation for genomic selection.


Ronnie Coffman, wrc2@cornell.edu

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.


Dunia Pino Del Carpio, dpd64@cornell.edu

Dunia is a Research Associate in the Department of Plant Breeding and Genetics at Cornell University where she works with Jean-Luc Jannink and Martha Hamblin. Dunia earned her MS and PhD in Plant Breeding and Genetics at Wageningen University in the Netherlands where she studied the genetics of nutritional composition in Brassica rapa. During her postdoctoral research at the University of Düsseldorf in Germany, she became interested in the developmental processes that determine phenotypic traits in plants. Within the NEXTGEN Cassava breeding project she will address the incorporation of genetics and developmental biology into statistical models.


Roberto Jesus Lozano Gonzalez del Valle, rjl278@cornell.edu

Roberto Lozano is a PhD student in the Department of Plant Breeding and Genetics at Cornell, where he works with Jean-Luc Jannink and Martha Hamblin. Prior to joining the graduate program, he was working in the Genomics Research Unit (Peru), where he focused on potato genomics and bioinformatics. For the NEXTGEN Cassava project, he will be working in Genomic Selection, attempting to increase GS prediction accuracies by incorporating biological information into the model.


Peter T. Hyde, pth7@cornell.edu

Peter Hyde earned his MS in Plant Breeding at Cornell University 2010. He then worked for Antika Co. Ltd., a seed company that was being supported by the Alliance for a Green Revolution in Africa located in Wa, Upper West Region, Ghana. After returning to Cornell he began working for the NEXTGEN Cassava project as the lab and greenhouse technician for Tim Setter. His primary goals focus on investigating the physiology of flowering and seed set in cassava, and how it could be manipulated in order to facilitate breeding efforts.


Jean-Luc Jannink, jj332@cornell.edu

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, tls1@cornell.edu

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.


Tammy Thomas, tjt2@cornell.edu

Tammy Thomas has worked with finance and human resources at Cornell University for over 20 years and been involved with International Programs of the College of Agriculture and Life Sciences for the past six years. Tammy is responsible for the financial management of the NEXTGEN Cassava project.


Hale Ann Tufan, hat36@cornell.edu

Hale Ann Tufan 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.


Marnin Wolfe, mw489@cornell.edu

Marnin is a Postdoctoral Associate in the Department of Plant Breeding and Genetics at Cornell University where he works with Jean-Luc Jannink and Martha Hamblin. Marnin completed a PhD in Ecology and Evolutionary Biology at the University of Pittsburgh where he studied adaptation to climate in wild populations of the plant genetic model organism Arabidopsis thaliana. Marnin's research addresses the connections between genotype, phenotype and environment in both wild and domesticated plants experiencing either natural or artificial selection. Marnin joined the NEXTGEN Cassava Breeding project in September of 2013.



International Institute of Tropical Agriculture

Olumide Alabi, olumerit2003@gmail.com

Olumide Alabi holds a bachelor’s degree in Crop Science from Federal University of Technology Akure, and a master’s degree in Applied Genetics from the University of Ibadan in Nigeria. He joined the African Rice Centre in Ibadan as a research fellow for the completion of his master’s thesis on the topic “Genetic analysis of rice interspecifics for yield components.” Olumide Alabi worked briefly with Africa rice and later joined the cassava breeding program of International Institute of Tropical Agriculture. His PhD research is on the empirical estimation of genetic gains in cassava breeding using genomic selection in a one-year breeding cycle. Olumide Alabi is registered at the West African Centre for Crop Improvement, at the University of Ghana in Legon.


Peter Kulakow, P.Kulakow@cgiar.org


Uche Godfrey Okeke, ugo3@cornell.edu

Uche Godfrey Okeke's interest in agriculture led him to pursue a bachelor’s degree in animal breeding and genetics from the Federal University of Technology, Owerri, Nigeria. He continued to a master’s in Bioinformatics and Systems Biology from the University of Helsinki, Finland. During this time he also worked as a bio-informatician at the DNA Sequencing and Genomics Lab, Institute of Biotechnology, University of Helsinki where he was responsible for microbial genome assembly, differential gene expression analysis, metagenome assembly, downstream sequence analysis (motif finding, chIP-seq analysis) and other biostatistics analysis. Uche is currently a PhD student at the Department of Plant Breeding and Genetics, Cornell University under the NEXTGEN Cassava breeding project.


Prasad Peteti, pvnsprasad@gmail.com


Ismail Yusuf Rabbi, I.Rabbi@cgiar.org

Ismail Yusuf Rabbi trained in population genetics and plant breeding at the University of Hohenheim, Germany. His research interests revolve around 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.


Ikpan Andrew Smith, a.ikpan@cgiar.org


Makerere University


Mikidadi Abubakar, MSc student, mikisb2340@yahoo.com


Esther Sarah Amuge, MSc student, amugeesther@yahoo.com

Amuge Esther Sarah is a Ugandan with a Bachelor of Science degree in Agriculture from Makerere University. She is currently doing a master's degree in Plant Breeding and Seed Systems at Makerere University. She is under the scholarship of the NEXTGEN Cassava Project, working on grafting to enhance flowering in cassava. She has finished the first year of coursework and is now going to continue with her research work. She is very grateful to the NEXTGEN project for this opportunity.


Stella Ayesiga, MSc student, sabigirwa@yahoo.com


Richard Edema, redema12@yahoo.com

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, pgibson@siu.edu

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.


Pauline Gibson


Yasmin Ibrahim, MSc student, hussinyasmin@yahoo.com


Aquilino Legge, MSc student, aquilinowani@yahoo.com


Wilfred Magangi, MSc student, wilabin@yahoo.com

Wilfred earned his BSc in Biology at Masinde Muliro University-Kenya. Now he is sponsored by the NEXTGEN Cassava project to study his MSc in Plant Breeding and Seed System at Makerere University-Uganda. He is doing research on Calibrating Near-Infrared Spectroscopy to use in phenotyping cassava root traits in Uganda. He is attached to the National Crop Resource Research Institute-Uganda.

Emmanuel Frank Mrema, MSc student, emmanuel.oroya@yahoo.com


Ann Ritah Nanyonjo, MSc student, nanyonjoritah@yahoo.com


Severin Ntivugurzwa, MSc student, ntiseverin@yahoo.fr


Valentor Okui, MSc student, valvineraks@yahoo.com


National Crops Resources Research Institute


Afolabi Agbona, a.afolabi@cgiar.org


Yona Baguma, baguma1234@yahoo.com

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 other boards and committees.


Gilbert Gumisiriza, gumisiriza@gmail.com


Paula Iragaba, pi48@cornell.edu

Paula Iragaba is a PhD student in the Department of Plant Breeding and Genetics at Cornell University, where she works with Professor Michael A. Gore. She is attached to the National Crops Resources Research Institute (NaCRRI), Uganda, on the NEXTGEN Cassava Breeding project. Prior to coming to Cornell, she completed a BSc Agric, an MSc in Plant Breeding and Seed Systems, and a PGD in Gender and Local Economic Development from Makerere University, Uganda. Under NEXTGEN, Paula’s PhD will focus on breeding cassava varieties that suit the needs and trait preferences of cassava smallholder farmers, especially women. She will be working closely with smallholder cassava farmers in Uganda to examine their cassava trait preferences. Thereafter she will optimize protocols for measurement of some of the identified priority traits and do marker-trait association study for those key traits in the existing training population at NaCRRI.


Robert Kawuki, kawukisezi@yahoo.com

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.Robert regards promotion of proven technologies and science communication as key for the future of African agriculture.


Ismail Siraj Kayondo, kayondocontact@gmail.com

Ismail Siraj Kayondo is a PhD student at the West Africa Centre for Crop Improvement (WACCI), College of Agriculture and consumer Science, University of Ghana. He is attached to the National Crops Resources Research Institute (NaCRRI) on the NEXTGEN Cassava Breeding project. His PhD research focuses on introgression of cassava brown streak virus resistance (CBSD) using wild cassava relatives and CBSD resistance QTL mapping. Previously, he held a teaching assistant position with the regional MSc plant breeding program housed by Makerere University and Regional University’s forum (RUFORM). He completed his MSc in Plant Breeding and Seed Systems at Makerere University on groundnut rosette virus disease resistance breeding.


Nassib Mugwanya, nmugwanya@gmail.com

Nassib Mugwanya is the Outreach Officer of the Uganda Biosciences Information Center (UBIC), at the National Crops Resources Research Institute. Previously, Nassib worked as a research assistant on the Biosciences for Farming in Africa Project (B4FA), as well as assisting to teach agricultural communication in the Department of Extension and Innovation Studies-Makerere University. Nassib’s interest is to communicate agricultural science in a way that empowers farmers.


Grace Nakabonge, gnakabonge@gmail.com

Grace Nakabonge holds a PhD in molecular plant pathology from the Forestry and Agricultural Biotechnology Institute, University of Pretoria. She has conducted research on molecular taxonomy, characterization and identification of plant pathogens as well as understanding their genetics, phylogeny and management. She has also been involved in research on conservation of plant genetic resources and has 8 years working experience as a lecturer with Makerere University. For the NEXTGEN Cassava project she is involved in the conservation aspects of cassava and is spearheading the establishment of Cassava in-vitro conservation unit at NaCRRI.


Adeyemi Olojede, yemiolojede@yahoo.com


Alfred Adebo Ozimati, aao62@cornell.edu

Alfred Adebo Ozimati is from the National Crop Research Resource Institute (NaCRRI), Namulonge, Uganda. He holds a BSc in Horticulture (Makerere University), as well as an MSc in Plant Breeding and Seed systems (Makerere University), and is currently a PhD student at Cornell University, working in Prof. Jean-Luc Jannink's laboratory. His research in this project focuses on genomic selection for Cassava Brown Streak Disease and yield-related parameters.


Anthony Pariyo, tkakau@yahoo.co.uk

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. 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.


Simon Peter, abahsp@gmail.com


Ezenwanyi Uba, ubaezenwanyi@yahoo.com


Amarachukwu Uzoechi, amalinks83@yahoo.com


Barbara Mugwanya Zawedde, bmugwanya@gmail.com

Barbara Mugwanya Zawedde is a team-leader for the Biotechnology and Biosafety Education objective of the NEXTGEN Cassava project. She completed 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 her 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).


National Root Crops Research Institute

Chiedozie Egesi, cegesi@yahoo.com

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 has participated in the development and release of six yam varieties.


Lydia Ezenwaka, lydiaezenwaka@yahoo.com

Lydia Ezenwaka is a Research Officer in the Biotechnology Programme at National Root Crops Research Institute, Umudike, Abia state, Nigeria. Her research activities are targeted at using biotechnology tools for the genetic improvement of cassava. She had her first degree in Plant Science and Biotechnology. She successfully accomplished research work as an undergraduate which was published in international journal. She later pursued a Master of Science degree in Plant Breeding and Genetics. She is presently undergoing PhD studies in Plant Breeding and Genetics at WACCI, University of Ghana which is been funded by NEXTGEN Cassava breeding project. Her PhD research will focus on allele mining and breeding for cassava green mite. She is also involved in the Gender Responsive Cassava Breeding Initiative with Hale Tufan of Cornell University.


Ugochukwu Nathaniel Ikeogu, , uni3@cornell.edu

Ugochukwu Nathaniel Ikeogu has a Bachelor of Agriculture and Masters in Plant Breeding and Genetics from Michael Okpara University of Agriculture, Umudike (MOUAU), Nigeria. Research activities include hybridization and generation of botanical seeds for increased variability and selection in cassava, including germplasm improvement and the introgression of traits from wild and exotic lines into elite varieties. His current research is addressing yield gain in cassava through improved dry matter, starch and mosaic disease resistant using genomic selection tools.


Joseph Onyeka, jonyeka@yahoo.com


Tessy Madu, tessmadu@gmail.com

Tessy is a social scientist with the National Root Crops Research Institute, Umudike, Nigeria, with the Gender Responsive Cassava Breeding Initiative. She has her MSc in Agricultural Geography and a PhD in Rural Development. Her current role is researching the Farming System of the South East Agro-ecological zone of Nigeria, conducting training of women farmers in processing, and the utilization and marketing of root and tuber crops with a strong emphasis on value addition. Her remits also include the development and management of collaborative projects in research networks for effective technology and knowledge sharing among relevant Institutes. Tessy is currently working with Hale Tufan as the gender focal point for NEXTGEN Gender Responsive Cassava Breeding Initiative in Nigeria.


Stephen Ahamefule Nwaogu, sanhereonly@yahoo.com

Stephen Ahamefule Nwaogu is a research assistant working under Dr. Chiedozie Egesi in the Biotechnology Programme, National Root Crops Research Institute (NRCRI) Umudike, Nigeria. He is presently a Masters student in Plant Breeding and Genetics in Michael Okpara University of Agriculture, Umudike (MOUAU), Nigeria. Activities in the NEXTGEN Cassava project include field trial management, data collection (biotic and abiotic stress), pre- and post-harvest data and hybridization to generate botanical seeds for increased variability and selection in cassava, including germplasm improvement. His current research is on drought tolerance in the training population, and on genomic selection.


University of California, Berkeley

Jessen Bredeson, jessenbredeson@berkeley.edu

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.


US Department of Energy-Joint Genome Institute

Simon Prochnik, seprochnik@lbl.gov

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).


External Project Advisory Committee

Ed Buckler, Cornell University, esb33@cornell.edu


Ben Hayes, Department of Primary Industries, Australia, ben.hayes@depi.vic.gov.au


Steve Rounsley, Dow Agrosciences, steve.rounsley@gmail.com


David Meyer, Dow Agrosciences, dhmeyer@dow.com


Oliver Wonekha, Ugandan Ambassador to the United States