Flint, Laura J. (2014) Identification, prevalence and impacts of viral diseases of UK winter wheat. PhD thesis, University of Nottingham.
Access from the University of Nottingham repository: http://eprints.nottingham.ac.uk/14143/1/Thesis-to_print_and_bind.pdf
Copyright and reuse:
The Nottingham ePrints service makes this work by researchers of the University of Nottingham available open access under the following conditions.
· Copyright and all moral rights to the version of the paper presented here belong to the individual author(s) and/or other copyright owners. · To the extent reasonable and practicable the material made available in Nottingham ePrints has been checked for eligibility before being made available. · Copies of full items can be used for personal research or study, educational, or not- for-profit purposes without prior permission or charge provided that the authors, title and full bibliographic details are credited, a hyperlink and/or URL is given for the original metadata page and the content is not changed in any way. · Quotations or similar reproductions must be sufficiently acknowledged.
Please see our full end user licence at: http://eprints.nottingham.ac.uk/end_user_agreement.pdf
A note on versions:
The version presented here may differ from the published version or from the version of record. If you wish to cite this item you are advised to consult the publisher’s version. Please see the repository url above for details on accessing the published version and note that access may require a subscription.
For more information, please contact [email protected] IDENTIFICATION, PREVALENCE AND IMPACTS OF VIRAL DISEASES OF UK WINTER
WHEAT
LAURA JANE FLINT, BSc.
Thesis submitted to the University of Nottingham
for the degree of Doctor of Philosophy
December 2013
Abstract
The potential for viruses to be causing the plateau in the yield of UK wheat (Triticum aestivum) was investigated. Mechanical inoculation of Cynosurus mottle virus to wheat cv. Scout and cv. Gladiator caused 83% and 58% reduction in the number of grains produced, highlighting the potential of viruses to cause disease and yield loss.
Viruses historically detected in cereals in the UK were not found to be prevalent following real time reverse transcriptase polymerase chain reaction testing of 1,356
UK wheat samples from 2009-2012 using eleven assasys developed in the project.
This included an assay for Cynosurus mottle virus, which was based on its complete genome sequence which was obtained for the first time in this project. Viruses detected were Barley yellow dwarf virus-MAV (6 samples) (BYDV-MAV), Barley yellow dwarf virus-PAV (6 samples) (BYDV-PAV) and Soil-borne cereal mosaic virus (12 samples) (SBCMV). There was a higher prevalence of viruses in the south, thought to be due to warmer temperatures which benefitted insect vectors and the molecular processes of infection. Viruses were most commonly detected in the variety JB Diego, perhaps because this variety has no known resistance to viruses.
The low prevalence of known viruses could also have been because they were outcompeted or replaced by previously unknown ones. Next generation sequencing was used to test 120 samples from an organic site, including wheat, weeds and insects, to search for novel viruses. Testing of twelve storage regimes for insect traps using BYDV-PAV infected Sitobion avenae for recovery of PCR amplifiable
RNA using 18S rRNA and BYDV-PAV assays found that 0.5 M EDTA was the most successful regime which was therefore used in the collection of samples for sequencing. Known viruses such as BYDV-PAV were detected along with some additional potentially novel viruses (eight possibly novel viruses or strains of viruses with four in wheat). One such virus was apparently present in 25% of all wheat
I samples tested, making it potentially very significant. This could be important for unlocking the yield potential of wheat because it could be a cryptic virus which is highly prevalent.
In order to control the spread of viruses their methods of transmission must be understood, therefore testing of seeds and resulting plants from Cynosurus mottle virus infected material was done. Tests did not detect the virus, therefore it was concluded that seed transmission does not occur. However, further tests are required.
In conclusion this study indicates that known viruses are not currently a major problem for UK winter wheat. However, novel viruses that are a problem may be detected in the future perhaps by next generation sequencing. Additonal viruses from abroad would add to the threat. The impact of all viruses in wheat may be greater in the future due to climate change.
II
Acknowledgments
I would like to thank my supervisors Prof Matthew Dickinson, Prof Neil Boonham,
Adrian Fox and Dr Judith Turner for their advice and support throughout this project.
I appreciate it a lot, thank you.
In addition thank you to all staff and students at The Food and Environment
Research Agency (Fera) who have always offered guidance and have become friends.
In particular I would like to thank Dr Ian Adams, Ben Barratt, Samantha Bennett, Ian
Brittain, Mark Daly, Tracey Chantry, Rachel Glover, Val Harju, Dr Toby Hodges, Dr
Jennifer Hodgetts, Dr Philip Jennings, Louisa Kitchingman, Lynn Laurenson, Dr Jeff
Peters, Dr Stephane Pietravalle, Anna Skelton, Danny Skelton, Dr Moray Taylor, Gilli
Thorp and Dr Jennifer Tomlinson.
Thank you also to staff of the Imaging department at The University of York, especially Meg Stark, for use of their transmission electron microscope.
Thank you to the funders of this project who were the cereals and oilseed division of the Agriculture and Horticulture Development Board (AHDB-HGCA) and
D S I w some of those from the HGCA at