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Silencing Parasitism Effectors of the Root Lesion Nematode, Pratylenchus Thornei

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Silencing Parasitism Effectors of the Root Lesion Nematode, Pratylenchus Thornei Silencing parasitism effectors of the root lesion nematode, Pratylenchus thornei. This thesis is presented for the degree of Doctor of Philosophy of Murdoch University by Sameer Dilip Khot B.Sc. (Botany) & M.Sc. (Plant Pathology & Mycology), University of Mumbai, India M.S. (Plant Pathology), North Dakota State University, USA Western Australian State Agricultural Biotechnology Centre School of Veterinary and Life Sciences Murdoch University Perth, Western Australia 2018 1 DECLARATION I declare that this thesis is my own account of my research and contains as its main content work which has not previously been submitted for a degree at any tertiary education institution. Signature: Sameer D. Khot Date: 22-01-2018 2 ABSTRACT The root lesion nematode (RLN), Pratylenchus thornei, is a biotrophic migratory pest of plant roots and its infestation causes losses in many economically important crops. RNA interference (RNAi) is a naturally occurring eukaryotic phenomenon and can be used to silence parasitism effector genes of P. thornei using host-mediated RNAi. This may be developed as an environmentally friendly and a cost-effective control strategy. The overall aims of this research were to investigate the effects of in vitro and in planta RNAi silencing of putative P. thornei parasitism effector genes, and their nematicidal effects in two host plants. Five putative target parasitism genes vital for nematode entry into roots (Pt-Eng-1, Pt- PL), feeding (Pt-CLP) and suppressing host defence responses (Pt-UEP, Pt-GST) were identified, validated in silico using comparative bioinformatics, cloned into suitable in vitro transcription and binary vectors, and advanced to RNAi studies. Partial sequences for four of these target effector genes (Pt-Eng-1, Pt-PL, Pt-CLP, Pt-GST) were identified using Rapid Amplification of cDNA (RACE) PCRs and annotated in silico. Protein families, conserved domains, taxonomic and phylogenetic relationships for all four effectors were studied. This sequence information will help inform future investigations involving gene expression and proteomics of the selected putative effectors. In vitro RNAi was used for functional characterisation of the five effector sequences. Effects on nematode phenotype, behaviour, gene expression, and longer-term effects on reproduction were assessed after soaking nematodes in dsRNA through infection of healthy wild type soybean and alfalfa roots. Soaking of mixed stage P. thornei in 1mg/mL dsRNA of target genes for 16 h did not cause phenotypic changes except for Pt-PL, which exhibited straight or slightly curved phenotypes after soaking compared to the normal sigmoid body movement, also evident for green fluorescent protein (gfp) and no dsRNA treated controls. Semi-quantitative PCRs and densitometry analysis revealed a significant reduction of transcript accumulation for all five putative parasitism effector genes. Longer-term effects assessed at 21 dpi reduced nematode reproduction by 40 to 70% for all target genes compared to respective control treatments suggesting that the effectors studied were required for nematode infectivity, survival or reproduction. In planta RNAi involved Agrobacterium-mediated plant transformations to develop axenic transgenic hairy root events of soybean (Glycine max var. Williams 82) and alfalfa 3 (Medicago sativa), and non-axenic hairy roots (composite plants) of soybean. Both hosts were amenable to Agrobacterium-mediated transformation, but hairy root induction was faster in alfalfa than soybean. However, more events were generated for soybean than alfalfa. Transgenic hairy roots confirmed by molecular analyses were challenged with P. thornei and their presence confirmed after 14 dpi. After 21 dpi, nematode numbers and transcript abundance was assessed using semi-quantitative PCRs and densitometry analysis. Host- mediated silencing of the five putative parasitism effector genes using transgenic soybean and alfalfa hairy roots showed a significant reduction in target transcript accumulation and approximately 38 to 75% reduction in P. thornei numbers compared to untransformed wild- type controls. For some events, there was a positive correlation between reduced transcripts and nematode numbers. Based on percent reduction in transcript accumulation of the target genes relative to 18S rRNA as assessed by densitometry, the extent of gene knockdown measured (from most to least) was: Pt-Eng-1, Pt-PL, Pt-CLP, Pt-UEP, and Pt-GST. Similarly, Pt-Eng-1, Pt-PL and Pt-CLP were ranked in the same order, from the lowest to highest reproduction on soybean and alfalfa, indicating a positive correlation between the level of knockdown and reduced reproduction. In soybean, these genes were followed by Pt-GST and Pt-UEP for the percentage of reproduction recorded, whereas, in alfalfa, reduction in reproduction for these two target genes did not differ significantly. Composite soybean with wild-type shoots and transgenic hairy roots expressing Pt-Eng- 1 and Pt-PL genes were developed and provided an opportunity to test the effectiveness of silencing target genes in planta and on nematode numbers in conditions that mimicked natural host infections. For both Pt-Eng-1 and Pt-PL genes, there was a significant reduction in percentage of transcript accumulation relative to 18S rRNA, which correlated with a reduction in nematode numbers by 53.4% and 48.5% for Pt-Eng-1 and Pt-PL, respectively. The amenability of P. thornei to host-mediated RNAi using effector gene sequences, and the overall results of this study, point towards the potential use of this technology to control P. thornei and related RLN species effectively in different host crops. 4 PUBLICATIONS AND PRESENTATIONS Poster Presentations Khot, S., Berryman, D. and Jones, M. G. K. 2015. Bioinformatics, identification and functional characterisation of parasitism effectors of the root lesion nematode, Pratylenchus thornei. VLS Poster Day, Murdoch University, November 11, 2015. Khot, S., Berryman, D. and Jones, M. G. K. 2015. RNAi silencing of parasitism effectors in the root lesion nematode, Pratylenchus thornei. Murdoch Agricultural Research Symposium, Murdoch University, September 01, 2017. Khot, S., Berryman, D. and Jones, M. G. K. 2015. Host-mediated RNAi of Pratylenchus thornei effectors reduces its population. Murdoch University Annual Research Symposium, Murdoch University, November 08, 2017. Oral Presentation Khot, S., Berryman, D. and Jones, M. G. K. 2017. Silencing parasitism effectors of the root lesion nematode, Pratylenchus thornei. VLS Pre-Submission Presentation, Murdoch University, December 08, 2017. Additional presentations Jones, M.G.K., Tan J-H, Khot, S. and Fosu-Nyarko, J. 2016. Effectors of root lesion nematodes. Proceedings of 32nd European Society of Nematologists Symposium, Braga, Portugal, University of Minho, p149. Jones, M.G.K., Iqbal, S., Naz, F., Herath, H., Rana, J., Rahman, S., Khot, S. and Fosu-Nyarko, J. 2017. New technologies for plant breeding. Proceedings of Australasian Biotechnology Association Agbio and Technology meeting, Brisbane. 5 TABLE OF CONTENTS DECLARATION ............................................................................................................................. 2 ABSTRACT ................................................................................................................................... 3 PUBLICATIONS AND PRESENTATIONS ......................................................................................... 5 TABLE OF CONTENTS .................................................................................................................. 6 LIST OF ABBREVIATIONS ............................................................................................................ 10 ACKNOWLEDGEMENTS ............................................................................................................. 11 DEDICATION .............................................................................................................................. 13 CHAPTER 01 GENERAL INTRODUCTION AND LITERATURE REVIEW .......................................... 14 1.1 General Introduction ...................................................................................................... 15 1.2 Pratylenchus thornei: A plant parasitic root lesion nematode (RLN) ........................... 18 1.2.1 Taxonomy and general morphology ................................................................... 19 1.2.2 Life cycle ............................................................................................................... 19 1.2.3 Feeding behaviour ............................................................................................... 20 1.2.4 Economic importance of root lesion nematodes ............................................... 21 1.3 Current nematode control strategies and their limitations ......................................... 23 1.4 Genetic engineering as a potential crop protection strategy against PPNs ................ 24 1.5 RNA interference (RNAi) ................................................................................................ 26 1.5.1 History of RNAi ..................................................................................................... 26 1.5.2 Molecular mechanisms of RNAi .......................................................................... 27 1.5.3 Small RNA pathways ............................................................................................ 39 1.5.4 Natural functions of RNAi
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