Research in the Hanley-Bowdoin lab is currently supported by the following grants and collaborations:

2015-2020, U.S. – East Africa Research and Education Partnership: Cassava mosaic disease – A paradigm for the evolution of insect-transmitted plant virus pathosystems (PI), NSF PIRE

Participating U.S. Institutions and Senior Personnel

North Carolina State University

  • George G. Kennedy (co-PI), William Neal Reynolds Distinguished Professor, Department of Entomology
  • Ignazio Carbone, Associate Professor, Department of Plant Pathology
  • Jose T. Ascencio-Ibanez, Teaching Assistant Professor, Department of Molecular and Structural Biochemistry
  • Timothy Goodal, Assistant Professor, Department of STEM Education

Rutgers University

  • Siobain Duffy (co-PI), Assistant Professor, Department of Ecology, Evolution and Natural Resources

Auburn University

  • Alana Jacobson, Assistant Professor, Department of Entomology and Plant Pathology

North Carolina Agricultural and Technical State University

  • Louis Jackai, Professor and Head, Department of Natural Resources and Environmental Design

International Participants

Biosciences Eastern and Central Africa – International Livestock Research Institute Hub (BecA-ILRI), Nairobi, Kenya

  • Appolinaire Djikeng, Director
  • Jagger Harvey, Crop Research Senior Scientist
  • Wellington Ekaya, Capacity Building Senior Scientist

Mikocheni Agricultural Research Institute, Dar es Salaam, Tanzania

  • Joseph Ndunguru, Head of Biotechnology and Adjunct Professor at Nelson Mandela African Institute of Science and Technology
  • Peter Sseruwagi, Senior Scientist

This project establishes a research and training partnership between scientists and students in the United States and East Africa to study how plant DNA viruses change over time. Plant DNA viruses have emerged as leading pathogens that threaten crops worldwide. These studies will focus on Cassava mosaic disease, which is endemic to Africa and severely limits the production of cassava, a major food crop across the continent.  Because Africa is one of the fastest growing regions in the world, with a population projected to double to 2.4 billion people by 2050, producing sufficient quantities of high quality, nutritious food is a challenge there. Agriculture is increasingly a global enterprise and finding solutions to food security problems will depend on research partnerships such as this one that explores the basic science of how plant DNA viruses evolve and what limits their ability to adapt over time. Such fundamental knowledge can be used to develop rational, durable strategies to control these important plant pathogens. The project, which relies on the combined expertise and resources of U.S. and African participants, provides an excellent framework for training U.S. students to develop their scientific skills and to work in a global community to help ensure the future security of the developing and developed world.

2014-2016, A transient system for cassava genome editing (PI). NSF BREAD EAGER.

Cassava (Manihot esculenta Crantz) is the second most important crop in Africa and plays a key role in food security for the developing world. Many different cassava cultivars that are adapted to local environmental conditions and have unique tuber properties are grown across Africa and Asia. Farmers often prefer local varieties instead of “improved” cultivars that are less susceptible to disease and pests, which greatly limits cassava production in the developing world. Thus, it is important to develop genetic ap­proaches to improve local varieties as well as elite cultivars that are part of national breeding programs. This project will develop a new approach to introduce site-specific modifica­tions into the cassava genome. An innovative, rapid strategy for modifying the cassava genome that leaves no footprint except for the desired mutation has many poten­tial applications and would complement conven­tional breeding and transgenic approaches used today for cassava improve­ment.

2011-2016, Functional analysis of DNA satellites associated with cassava mosaic disease (PI), NSF BREAD.

International partners at Mikocheni Agricultural Research Institute, Dar es Salaam, Tanzania

  • Joseph Ndunguru, Head of Biotechnology and Adjunct Professor at Nelson Mandela African Institute of Science and Technology
  • Peter Sseruwagi, Senior Scientist

Cassava is an important staple crop in Africa and Asia, where it is eaten by over 700 million people every day. It can grow under drought, high temperature and poor soil conditions, but its production is severely limited by viral diseases including Cassava mosaic disease (CMD) and Cassava brown streak disease (CBSD) is caused by a DNA virus complex that includes seven geminivirus species. The goal of this project is to understand two DNA sequences, SEGS-1 and SEGS-2, enhance and break resistance to geminivirus disease in Arabidopsis and cassava. The specific aims are [1] to identify the functional regions of SEGS-1 and SEGS-2, [2] to elucidate the mechanisms of SEGS-1 and SEGS-2 disease enhancement, [3] determine the source of SEGS-1 and SEGS-2 in plants, and [4] to determine if SEGS-1 and SEGS-2 contribute to CBSD.

2011-2016, GEPR: Epigenome dynamics during DNA replication, NSF Plant Genome (PI). NSF PGRP.


  • William F. Thompson (North Carolina State University)
  • George C. Allen (North Carolina State University)
  • Rob Martienssen (Cold Spring Harbor Laboratory)
  • Matthew Vaughn (Texas Advanced Computing Center)

Plant cells undergo two types of cell cycles – the mitotic cycle in which DNA replication is coupled to mitosis and the endocycle in which DNA replication occurs in the absence of cell division. We used pulse labeling with the thymidine analog EdU, flow cytometry and NexGen sequencing to characterize and compare the DNA replication programs, epigenetic profiles and transcriptomes in cycling plant cells. These studies are focused on mitotic Arabidopsis suspension cells and maize root tip cells during the transition from a mitotic cell cycle to an endocycle during development.