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Identification and Characterisation of Resistance to the Take-All Fungus in Wheat

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Identification and Characterisation of Resistance to the Take-All Fungus in Wheat Identification and characterisation of resistance to the take-all fungus in wheat Submitted by Vanessa Elizabeth McMillan To the University of Exeter as a thesis for the degree of Doctor of Philosophy in Biological Sciences, September 2012 This thesis is available for Library use on the understanding that it is copyright material and that no quotation from the thesis may be published without proper acknowledgement. I certify that all material in this thesis which is not my own work has been identified and that no material has previously been submitted and approved for the award of a degree by this or any other University. Signature: ………………………………………………………….. 1 Acknowledgements I would like to thank my supervisors at Rothamsted, Richard Gutteridge and Kim Hammond- Kosack, for all of their help and advice throughout my PhD. Also thanks to my university supervisor Nick Talbot. There are also a large number of people who have helped during this project, including the many summer students, fieldwork and research assistants: James Bruce, Gail Canning, Adrian Czaban, Marcin Czaban, David Franklin, Leanne Freeman, Steve Freeman, Martha Jones, Nicola Phillips, Sarah Usher and Joseph Whittaker. I would also like to thank Garry Talbot, Tim Parfitt, Stephen Goward and all of the Rothamsted farm staff for their help and excellent management of the many take-all field experiments. Other colleagues at Rothamsted have provided advice with lab work including Carlos Bayon, Hai-Chun Jing, Kostya Kanyuka, Martin Urban and Elaine Ward. Thanks also to Rodger White for assistance with the statistical analysis of field trials and field trial design. This project was funded by a CASE PhD studentship from the Biotechnology and Biological Sciences Research Council (BBSRC), with industrial support from HGCA. Finally, thank you to all of my family and friends for their support over the last four years. 2 Abstract Take-all disease, caused by the soil-borne fungus Gaeumannomyces graminis var. tritici, is the most devastating root disease of wheat around the world. Typical take-all symptoms show as black necrotic lesions on the roots and when severe can cause premature ripening and stunting of the wheat crop, resulting in poor grain quality and yield loss. Both cultural and chemical control methods are moderately successful at controlling take-all but plant material that would be useful for take-all control via a genetic approach has not been identified in the UK or elsewhere. The main aim of this project was to identify resistance to take-all within wheat (Triticum spp.). This study explored a new phenomenon in hexaploid wheat (Triticum aestivum) which restricts take-all inoculum build-up (TAB) in the soil during a first wheat crop and also explored tissue based resistance to take-all in hexaploid wheat and a related diploid wheat species, Triticum monococcum. Forty-nine elite wheat varieties were evaluated for their ability to build-up take-all inoculum in first wheat field trials using a soil core bioassay method, and pedigree and molecular marker analyses were carried out to investigate the genetic sources of the TAB trait. The effect of a low or high TAB first wheat variety on take- all disease and yield in a following second wheat crop was evaluated in crop rotation field trials. This work demonstrated that there are significant differences between current elite wheat varieties screened for the TAB trait and that there are probably multiple genetic sources of the trait. Take-all disease was lower and yields generally higher in a second wheat crop after a low TAB first wheat. The susceptibility of fifty elite hexaploid wheat varieties and thirty-four T. monococcum accessions to take-all was evaluated in third wheat field trials. Both T. aestivum (variety Hereford) and T. monococcum (MDR031 and MDR046) genotypes with some partial resistance to take-all were identified. A seedling pot test method as a screen for resistance was also explored but the results were found not to be closely related to the susceptibility of adult plants in field trials. The implications of these new findings for the control of take-all and further research are discussed. 3 Table of Contents Acknowledgements ......................................................................................................... 2 Abstract ........................................................................................................................... 3 List of Figures ................................................................................................................. 8 List of Tables ................................................................................................................. 12 CHAPTER 1: INTRODUCTION ............................................................................... 17 1.1. Soil-borne plant pathogens .................................................................................. 19 1.2. Take-all disease of wheat .................................................................................... 19 1.3. UK wheat varieties .............................................................................................. 22 1.4. The Gaeumannomyces genus .............................................................................. 23 1.5. Take-all infection process and epidemiology ...................................................... 24 1.6. Take-all control methods ..................................................................................... 27 1.6.1. Cultural control ............................................................................................ 27 1.6.2. Biological control ......................................................................................... 29 Take-all decline (TAD) ............................................................................................ 29 Phialophora spp. ..................................................................................................... 30 Introduced biological control agents ...................................................................... 32 1.6.3. Chemical control .......................................................................................... 33 1.7. Genetic control .................................................................................................... 34 1.7.1. Resistance of oats to take-all ........................................................................ 35 1.7.2. Resistance of rye to take-all ......................................................................... 36 1.7.3. Resistance of other grass species ................................................................. 37 1.7.4. Resistance of wheat (Triticum aestivum) to take-all .................................... 38 1.7.5. Difficulties assessing wheat germplasm for resistance to take-all .............. 42 1.8. Aims and Objectives ............................................................................................ 44 CHAPTER 2: GENERAL MATERIALS AND METHODS ................................... 45 2.1. Maintenance of Ggt isolates and long term storage ................................................ 45 2.2. Field trials ................................................................................................................ 45 2.2.1. Soil core bioassay ............................................................................................. 46 2.2.2. Plant sampling and take-all disease assessment .............................................. 47 Spring ...................................................................................................................... 47 Summer .................................................................................................................... 47 2.3. Pot test method ........................................................................................................ 48 2.3.1. Preparing Ggt inoculum ................................................................................... 48 2.3.2. The pot test method ........................................................................................... 49 4 2.3.3. Soil calibration ................................................................................................. 49 2.4. Statistics ................................................................................................................... 49 CHAPTER 3: FIELD EVALUATION OF THE TAKE-ALL INOCULUM BUILD-UP (TAB) TRAIT ........................................................................................... 51 3.1. Introduction ............................................................................................................. 51 3.2. Materials and Methods ............................................................................................ 54 3.2.1. Elite winter wheat varieties and inoculum build-up 2009-2011 ....................... 56 3.2.2. Rotation experiments ........................................................................................ 64 3.2.3. Microscopic analysis ........................................................................................ 68 3.3. Results ..................................................................................................................... 68 3.3.1. Elite winter wheat varieties and inoculum build-up 2009-2011 ....................... 68 3.3.2. Epidemiology studies 2009-2011 ...................................................................... 79 3.3.3. Take-all inoculum build-up 2004-2011
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