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Andrew Sarkodie Appiah Doctor of Philosophy UNIVERSITY OF Studies on Groundnut rosette disease in Ghana and genomic analysis of a novel Phasey bean virus in Australia Andrew Sarkodie Appiah B. Sc. (Hons), M. Phil Submitted in fulfilment of the requirements For the degree of Doctor of Philosophy UNIVERSITY OF TASMANIA February, 2017 DECLARATTION OF ORIGINALITY AND AUTHORITY OF ACCESS This is to certify that: This thesis contains no material which has been accepted for a degree or diploma by the University or any other institution, except by way of background information and duly acknowledged in the thesis. To the best of my knowledge and belief, no material previously published or written by another person, except where due acknowledgement is made in the text of the thesis, nor does the thesis contain any material that infringes copyright. The publishers of the papers (as indicated in next section) hold the copyright for that content, and access to the material should be sought from the respective journals. The remaining non- published content of the thesis is not to be made available for loan or copying for two years following the date this statement was signed. Following that time, the remaining non- published content of the thesis may be made available for loan and limited copying and communication in accordance with the Copyright Act 1968. The research does not contain any studies with human participants or animals performed by any of the authors Andrew Sarkodie Appiah University of Tasmania February, 2017 i ACKNOWLEDGEMENTS I would like to express my sincere gratitude to my primary supervisor, A/Prof. Calum Wilson (University of Tasmania) and Co-supervisors Dr Robert Tegg (University of Tasmania) and Prof. Samuel Kwame Offei (University of Ghana) for their support, patience and insightful comments which led to significant improvements of this thesis. I am so grateful to you for steering me in the right direction to make this thesis a reality. I could not have imagined having better advisors and mentors for my PhD study. My sincere thanks also go to Mrs Annabel Wilson, Dr Tamil Thangavel (Tasmanian Institute of Agriculture) Dr Alison Dann, Mr Shane Hossel and Mr Peter Cross (Department of Primary Industries, Parks, Water and Environment) for their immense contribution towards the execution of the research. I am also grateful to Dr Samuel Amiteye, Mr Jonathan Amponsah and Mr Iddriss Mohammed (BNARI, Ghana Atomic Energy Commission) for their assistance with field work conducted in Ghana. I thank my fellow lab mates at the New Town research Laboratories (Mark Balendres, Kritika Krishnamorthy and Sabine Tanois) for the stimulating discussions, and for sharing our coffee breaks and lunch times together. I am grateful to the Australian Government for the AusAID scholarship. This has been a great opportunity for me to further my education. The generous offer has adequately empowered me to contribute my quota to the development of Agriculture in Ghana. I am also thankful to the Ghana Atomic Energy Commission for granting me study leave with pay and for supporting my field work which was conducted in Ghana. I would like to express my profound gratitude to my wife (Vivian), children (Carlis, Thelma and Caitlyn) for their unfailing support, continuous encouragement and prayers throughout my years of study. My sincere thanks also go to my parents, brothers and sisters for their support and prayers. Finally, I would like to thank the Almighty God for His protection and guidance. Without Him, this accomplishment would not have been possible. ii STATEMENT OF CO-AUTHORSHIP AND CONTRIBUTION TO PUBLICATIONS The following people and institutions contributed to the publication of work undertaken as part of this thesis: 1. Andrew Sarkodie Appiah Tasmanian Institute of Agriculture, UTAS, Australia BNARI, Ghana Atomic Energy Commission, Accra 2. Samuel Kwame Offei College of Basic and Applied Sci., University of Ghana, Accra 3. Robert Stevee Tegg Tasmanian Institute of Agriculture, UTAS, Australia 4. Frederick Leo Sossah Jilin Agricultural University, College of Agronomy, China 5. Murray Sharman Department of Agriculture & Fisheries, Brisbane, QLD, Australia 6. Calum Rae Wilson Tasmanian Institute of Agriculture, UTAS, Australia Paper 1: Appiah, A. S., Offei, S. K., Tegg, R. S., and Wilson, C. R. (2016). Impact of groundnut rosette disease on nutritive value and elemental composition of four varieties of peanut (Arachis hypogaea). Annals of Applied Biology 168: 400 – 408 (Chapter 3). Paper 2: Appiah, A. S., Offei, S. K., Tegg, R. S., and Wilson, C. R. (2016). Varietal response to groundnut rosette disease and the first report of Groundnut ringspot virus in Ghana. Plant Disease 100:946-952 (Chapter 4) Paper 3: Andrew S. Appiah, Frederick L. Sossah, Robert S. Tegg, Samuel K. Offei, Calum R. Wilson (2017). Assessing sequence diversity of Groundnut rosette disease agents and the distribution of Groundnut rosette assistor virus in major groundnut-producing regions of Ghana. Tropical Plant Pathology 42:109–120 (Chapter 5) iii Paper 4: A.S. Appiah, R.S. Tegg, M. Sharman and C.R. Wilson (2017). Host range, complete genome sequencing and molecular phylogeny of a novel Polerovirus from Australian legumes. Manuscript under preparation. (Chapter 6) Conference presentations Appiah, A.S., Tegg, R.S., Wilson, C.R. Studies on Groundnut rosette disease and other legume viruses. Africa Australia Research Forum on Mining, agriculture and development: Bread from Stones? A joint conference of The Crawford Fund and the Africa Australia Research Forum. 25th - 28th August 2013, Perth, Australia. Appiah, A.S., Tegg, R.S., Wilson, C.R. Host range, genome sequencing and molecular phylogeny of a novel Polerovirus from Australian legumes. Australasian Plant Pathology Society (Tasmanian Division) 2016 Symposium, 29th April, 2016, Ross, Tasmania, Australia. Andrew S. Appiah, Robert Tegg, Samuel K. Offei, Calum R. Wilson. Studies on Groundnut rosette disease and implications of the newly reported Groundnut ringspot virus for groundnut production in Ghana. American Phytopathological Society’s Annual Conference ‘Science to practice’, 30th July to 3rd August, 2016, Tampa, Florida, USA Candidate was the primary author of all papers, contributed to the conception and design of the study and executed field and laboratory work. Candidate also contributed to the analysis and interpretation of data and drafted significant portions of the paper, revision and final approval of all articles. Robert Tegg contributed to the design of the experiment, guided statistical analysis and interpretation of data and revision and final approval of the manuscripts. Samuel Offei contributed to the conception of of the research, revision and final approval of the manuscript. iv Calum Wilson contributed to the conception and design of the research project, guided statistical analysis and interpretation of results, provided technical support, revision and final approval of all manuscripts. Frederick Leo Sossah assisted with data collection and analyis and the final approval of the manuscript for Chapter five. Murray Sharman provided the Queensland isolate of the PhBMYV and the Aphis craccivora vector used in the study (Chapter six) and a contributed to the revision and final approval of the manuscript. v Declaration of Agreement We the undersigned agree with the above stated “proportion of work undertaken” for each of the above published (or submitted) peer-reviewed manuscripts contributing to this thesis: ___________________ ______________________ Andrew Sarkodie Appiah Calum Rae Wilson Candidate Supervisor School of Land and Food School of Land and Food University of Tasmania University of Tasmania Date: February 24, 2017 Date: February 24, 2017 __________________ _____________________ Robert Steven Tegg Samuel Kwame Offei Co-Supervisor Co-Supervisor School of Land and Food Biotechnology Centre University of Tasmania College of Basic and Applied Sciences Date: February 24, 2017 University of Ghana, Legon Date: February 24, 2017 vi ABSTRACT Viruses present a major challenge to the production of major food crops worldwide, including legumes. The diseases they cause have profound effects on both plant growth and the quality of produce, resulting in significant losses. The current study investigated the proximate and elemental composition of four groundnut (peanut, Arachis hypogaea L.) cultivars infected with groundnut rosette disease (GRD), screened local cultivars of groundnut for resistance to GRD, detected Groundnut ringspot virus for the first time in Ghana and assessed the genetic diversity within Ghanaian isolates of Groundnut rosette assistor virus (GRAV), Groundnut rosette virus (GRV) and satellite RNA of GRV and compare those with known isolates from other African countires. In a related study, the complete genome of an isolate of novel virus infecting Phasey bean (Macroptilium lathyroides L.) in Australia; Phasey bean mild yellows virus (PhBMYV) was sequenced with evidence of genomic recombination found and its transmission to other legumes demonstrated. Proximate analysis of seeds from GRD-infected groundnuts showed a decrease in moisture and ash content, while fat and energy content increased. Protein and carbohydrate content varied inconsistently between seeds of diseased and healthy plants of the different cultivars. Instrumental neutron activation analysis (INAA) of ten elements within leaves, stems and seeds revealed elevated levels of K, Al and Cl in leaves, stems and seeds in at least three of the four GRD-infected cultivars while Na was
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