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Plasmopara Halstedii in Sunflower TECHNISCHE UNIVERSITÄT MÜNCHEN Lehrstuhl für Pflanzenzüchtung Characterization of the PlARG locus mediating resistance against Plasmopara halstedii in sunflower Silke Wieckhorst Vollständiger Abdruck der von der Fakultät Wissenschaftszentrum Weihenstephan für Ernährung, Landnutzung und Umwelt der Technischen Universität München zur Erlangung des akademischen Grades eines Doktors der Agrarwissenschaften genehmigten Dissertation. Vorsitzender: Univ.-Prof. Dr. C. Schwechheimer Prüfer der Dissertation: 1. Univ.-Prof. Dr. C.-C. Schön 2. Univ.-Prof. Dr. R. Hückelhoven Die Dissertation wurde am 06.10.2011 bei der Technischen Universität München eingereicht und durch die Fakultät Wissenschaftszentrum Weihenstephan für Ernährung, Landnutzung und Umwelt am 14.11.2011 angenommen. Table of Contents 1 Introduction ............................................................................................................ 1 1.1 Origin and distribution of cultivated sunflower .................................................. 1 1.2 Disease resistance in plants ............................................................................. 2 1.3 Molecular resources in sunflower ..................................................................... 8 1.4 Forward genetic approaches .......................................................................... 10 1.5 Objectives ....................................................................................................... 13 2 Material and methods .......................................................................................... 14 2.1 Plant material ................................................................................................. 14 2.1.1 Sunflower lines ........................................................................................ 14 2.1.2 Mapping populations ............................................................................... 15 2.2 Resistance tests ............................................................................................. 15 2.3 Molecular analyses ......................................................................................... 17 2.3.1 Nucleic acid isolation ............................................................................... 17 2.3.2 cDNA synthesis for RT-PCR and 454 sequencing .................................. 19 2.3.3 Analyses of molecular markers ............................................................... 20 2.3.4 BAC clone and cDNA sequencing .......................................................... 22 2.3.5 Copy number analysis ............................................................................. 22 2.4 Genetic mapping of the PlARG locus ................................................................ 22 2.4.1 Linkage mapping analysis ....................................................................... 22 2.4.2 Selection of recombinant lines ................................................................ 23 2.4.3 BAC library screening and mapping of BAC end sequences .................. 26 2.5 Sequence analysis of BAC clones ................................................................. 26 2.5.1 Assembly of BAC 454 sequences ........................................................... 26 2.5.2 Gene annotation of BAC 454 sequences ................................................ 27 2.6 Transcriptome analysis .................................................................................. 28 2.6.1 cDNA-AFLP ............................................................................................. 28 2.6.2 Assembly of bulked segregant transcriptome analysis 454 sequences .. 29 2.6.3 Identification of resistance gene candidates in the cDNA assemblies .... 30 3 Results .................................................................................................................. 31 3.1 Localization of PlARG ....................................................................................... 31 3.1.1 PlARG on linkage group 1 ......................................................................... 31 3.1.2 Fine mapping of the PlARG target region .................................................. 31 3.1.3 Linkage group 1 originates from H. argophyllus ...................................... 34 3.2 Characterization of the target region .............................................................. 38 3.2.1 Identification of BAC clones .................................................................... 38 3.2.2 Anchoring of BAC contigs ....................................................................... 39 3.2.3 BAC clone sequencing and assembly ..................................................... 41 I Table of Contents 3.2.4 BAC clone characterization ..................................................................... 44 3.2.5 Candidate genes belong to the TIR-NBS-LRR type ................................ 45 3.2.6 Copy number variation of RGC151 ......................................................... 52 3.3 Transcriptome based studies ......................................................................... 55 3.3.1 Resistance gene candidates are differentially expressed ....................... 55 3.3.2 cDNA-AFLP identified differentially transcribed fragments of the general defense response .................................................................................... 58 3.3.3 Bulked segregant transcriptome analysis - sequencing, preassembly processing, and assembly ....................................................................... 63 3.3.4 Bulked segregant transcriptome analysis identifies candidate genes for PlARG ....................................................................................................... 64 3.3.5 Two bulked segregant transcriptome analysis derived candidate genes map on linkage group 1 ........................................................................... 69 4 Discussion ........................................................................................................... 71 4.1 Relevance of wild species for sunflower breeding ......................................... 71 4.2 Challenges using wild species for plant breeding .......................................... 72 4.3 Structural characterization of the PlARG locus ................................................. 75 4.4 Alternative approaches to identify candidate genes for PlARG ........................ 81 4.5 Evaluation of different approaches to identify candidate genes for PlARG ....... 85 4.6 Conclusions and outlook ................................................................................ 87 5 Summary .............................................................................................................. 91 6 Zusammenfassung .............................................................................................. 93 7 References ........................................................................................................... 95 8 Supplementary Material .................................................................................... 111 8.1 Supplementary Tables ................................................................................. 111 8.1.1 Laboratory ............................................................................................. 111 8.1.2 Primers .................................................................................................. 116 8.1.3 BAC clones and BAC end sequences ................................................... 120 8.1.4 Reference genes ................................................................................... 138 8.1.5 Bulked segregant transcriptome analysis ............................................. 141 8.2 Sequence Resources ................................................................................... 147 8.2.1 BAC derived resistance gene candidate sequences ............................. 147 8.2.2 Predicted amino acid sequences of BAC derived candidate genes ...... 159 8.2.3 cDNA-AFLP sequences from isolated transcript-derived fragments ..... 160 8.2.4 Bulked segregant transcriptome analysis derived resistance gene candidate sequences ............................................................................ 161 8.3 Sequence Alignments .................................................................................. 164 II Table of Contents 9 Acknowledgements ........................................................................................... 184 10 Curriculum vitae ................................................................................................ 186 III Abbreviations Abbreviations AFLP amplified fragment length polymorphism Avr avirulence BAC bacterial artificial chromosome BIBAC binary bacterial artificial chromosome BES BAC end sequence bph bases per hash BR resistant bulk BS susceptible bulk BSA bulked segregant analysis BSTA bulked segregant transcriptome analysis CAPS cleaved amplified polymorphic sequence CC coiled-coil domain CLI cotyledon limited infection cM centi Morgan CMS cytoplasmic male sterility CUGI Clemson University Genomics Institute DNA deoxyribonucleic acid E expect value EST expressed sequence tag FLI Fritz Lipmann Institute HICF high information content fingerprinting HR hypersensitive cell death response hss hash saving steps Indel insertion / deletion events LRR leucine-rich repeat MAMPs microbial-associated molecular patterns MAS marker assisted selection NBS nucleotide binding site NCBI National Centre
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