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Genetic Dissection of Disease Resistance to Phoma Medicaginis in Medicago Truncatula

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Genetic Dissection of Disease Resistance to Phoma Medicaginis in Medicago Truncatula Genetic dissection of disease resistance to Phoma medicaginis in Medicago truncatula This thesis is submitted to Murdoch University for the degree of Doctor of Philosophy by Lars Gian Kamphuis MSc The Australian Centre for Necrotrophic Fungal Pathogens, Division of Health Sciences, SABC, Murdoch University July, 2007 Supervised by: Dr Simon R. Ellwood and Professor Richard P. Oliver i Declaration and list of published papers I declare that this thesis is my own account of my research and contains as its main content work which has not been previously submitted for a degree at any tertiary education institute. Papers that have been published from the research described in this thesis are: Ellwood S.R., Kamphuis L.G. and Oliver R. P. (2006). Identification of sources of resistance to Phoma medicaginis isolates in Medicago truncatula SARDI core collection accessions, and multigene differentiation of isolates. Phytopathology 96 1330-1336. Kamphuis L. G., Williams A.G., D’Souza N.K., Pfaff T, Ellwood S.R., Groves E.J., Singh K.B., Oliver R.P. and Lichtenzveig J. (2007). The Medicago truncatula reference accession A17 has an aberrant chromosomal configuration. New Phytologist 174: 299-303. Kamphuis L. G., Lichtenzveig J., Oliver R. P. and Ellwood S. R. (2008). Two alternative trait loci correlate with resistance to spring black stem and leaf spot in Medicago truncatula. BMC Plant Biology submitted. ………………………. Lars Gian Kamphuis ii ABSTRACT Phoma medicaginis is a necrotrophic fungal pathogen, commonly found infecting Medicago truncatula and M. sativa in temperate regions of Australia. To identify, characterize and differentiate eight P. medicaginis isolates from Western Australia, morphological phenotypes and five gene regions (actin, β- tubulin, calmodulin, internal transcribed spacer, translation elongation factor 1-α) were examined. Sequence comparisons showed that specimens isolated from M. truncatula in Western Australia formed a group that was consistently different from, but closely allied to, a P. medicaginis var. medicaginis type specimen. Characterization of three P. medicaginis genotypes showed that all exhibited a narrow host range, causing disease only in M. sativa and M. truncatula among eight commonly cultivated legume species sampled. Infection of 85 M. truncatula accessions showed a continuous distribution in disease phenotypes, with the majority of accessions susceptible. Differences in disease phenotypes suggest that M. truncatula harbours specific and diverse sources of resistance to individual P. medicaginis genotypes. To characterize the genetic basis of resistance to P. medicaginis two F2 populations derived from crosses between the resistant accession SA27063 and the susceptible accessions SA3054 and A17 were phenotyped for disease symptoms. Highly significant recessive QTLs for resistance to P. medicaginis OMT5 were identified in each mapping population. In SA27063 x A17 a QTL named resistance to the necrotroph Phoma medicaginis one (rnpm1) was identified on the short arm of LG4. In SA27063 x SA3054 a QTL (rnpm2) was identified on the long arm of LG8. Further fine mapping of the areas surrounding the QTLs is underway to identify the genes underlying rnpm1 and rnpm2. iii Examination of the recombination frequencies between genetic markers on the long arms of chromosomes 4 and 8 in the SA27063 x A17 cross revealed an apparent genetic linkage between these chromosomes. Subsequent analysis of other crosses showed this unexpected linkage relationship is characteristic for genetic maps derived from A17. Furthermore F1 individuals derived from crosses involving A17 showed 50% pollen viability or less. This semisterility and the unexpected linkage relationships provide good evidence for a reciprocal translocation in A17 between chromosomes four and eight. The implications of the distinctive chromosomal rearrangement in A17 on genetic mapping, genome sequencing and comparative mapping are discussed. The Mt16kOLI1plus microarray was used to identify transcriptional changes in M. truncatula expressed in defence against P. medicaginis. Three- hundred-and-thirty-four differentially expressed transcripts showed a change of two-fold or more in either the resistant or susceptible interaction, and most of the Phoma-regulated genes could be assigned to functional categories which have been reported to be involved in plant defence responses. RT-qPCR and HPLC- UV confirmed involvement of the octadecanoid and phenylpropanoid pathways in response to P. medicaginis infection. Faster induction of lipoxygenase genes and constitutively higher levels of certain phenolic metabolites were observed in resistant plants. iv ABBREVIATIONS 4CL 4-coumarate CoA ligase ACC 1-aminocyclopropanecarboxylic acid synthase BAC bacterial artificial chromosome BGL β-1,3-glucanase bp base pairs CA4H cinnamic acid 4-hydroxylase CCOMT Caffeoyl CoA O-methyltransferase cDNA complementary DNA Chit chitinase CHI chalcone isomerase CHR chalcone reductase CHS chalcone synthase cm centimetre(s) COMT caffeic acid O-methyltransferase CT theshold cycle DMSO dimethyl sulfoxide DNA deoxyribonucleic acid dNTP deoxyribonucleotides (ie.dATP, dCTP, dGTP, dTTP) EDTA ethylenediaminetetraacetic acid ERF Ethylene Responsive Element Binding Factor EST expressed sequence tag ET ethylene F5H ferulate-5-hydroxylase g gram(s) GOI gene of interest HPLC high performance liquid chromatography hpi hours post infection hr(s) hour(s) HSD honestly significant difference IFMT Isoflavone O-methyl transferase IF2H Isoflavone 2'-hydroxylase IF3H Isoflavone 3'-hydroxylase IFR Isoflavone reductase IFS Isoflavone synthase ITS internal transcribed spacer JA jasmonic acid L litre(s) LOX lipoxygenase MeJA methyl jasmonate γ⎧ microgram(s) mg milligram(s) min minute(s) v μL microlitre(s) m metre(s) mL milliliter(s) mM millimolar mm millimetre(s) mol mole mRNA messenger RNA MS mass spectrometre ng nanogram(s) nm nanometre(s) OPR 12-oxophytodienoic acid 10, 10-reductase ORF Open Reading Frame o/n over night PAL phenylalanine ammonia lyase PCR polymerase chain reaction PDA potato dextrose agar PDF plant defensin pH potential of hydrogen PIGs Phoma induced genes PR protein pathogenesis related protein PRG Phoma repressed genes RNA ribonucleic acid RNAi RNA interference RNase ribonuclease ROI reactive oxygen intermediates ROS reactive oxygen species RT room temperature RT retention time reverse transcriptase quantitative polymerase chain RT-qPCR reaction SA salicylic acid SAR systemic acquired resistance SDS sodium dodecyl sulfate TC Tentative consensus TE Tris EDTA TF transcription factor UV ultra violet VR vestitone reductase WMA wheat meal agar vi ACKNOWLEDGEMENTS I would like to start by thanking Professor Richard Oliver for giving me the opportunity to come over to Perth and commence my PhD with the Australian Centre for Necrotrophic Fungal Pathogens (ACNFP). I greatly appreciated the constant support, mentoring and guidance throughout my PhD of my two supervisors Prof Richard Oliver and Dr Simon Ellwood. Over the last four years Simon was my partner in crime on the Phoma project and I am positive that our work together will ultimately lead to the cloning of resistance genes to Phoma medicaginis in M. truncatula. Special thanks to my good friends and colleagues Dr Theo Pfaff and Dr Judith Lichtenzveig for your support during my PhD. Your opinions and suggestions on my research have proven invaluable and have had a good influence on me as scientist. Wherever your research careers might take you, I am sure we will stay in touch! I am also grateful to my fellow medic PhD students Nola and Angela and Dr Huyen Phan for their input, encouragement and ideas on my work and the many laughs we have had in the “medic office”. I would also like to thank Emma and Megan for taking good care of the laboratory and glasshouse, without you two the “medic lab” would not be the same. Without the input of all “medics” the translocation paper (see chapter 6) would not have come together. I would also like to thank the remaining members of the ACNFP, for their help in one way or another. The friendly working environment and Friday afternoon drinks with the group will be missed. I would also like to thank the GRDC for funding this research project. vii To my sister Esmé, who has always provided me constant love and support, I am forever grateful. To my parents, Anja and Jan, you sacrificed much to provide me with the quality of life and helped me become the scientist and person I am today. This thesis is dedicated to you both with love and thanks for all you have done throughout my life. Your visit to Perth put a smile on my face and I promise that we will regularly visit you in Holland now that I am no longer “a poor student”. To my best friend Jeroen Werij, thanks heaps. The many phone conversations and your visit to Perth were greatly appreciated and were welcome distractions from my PhD. We will stay in touch no matter where our science careers will take us! Finally, I wish to thank my beautiful girlfriend Fiona for taking this journey with me. Your love, humour and patience throughout my PhD helped me through the tough times. I am looking forward to a long and happy future together! viii TABLE OF CONTENTS Declaration and list of published papers............................................................ii ABSTRACT........................................................................................................ iii ABBREVIATIONS ..............................................................................................v
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