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Genetic and Molecular Characterisation of Resistance Factors and Candidate Genes for Scab Resistance in Apple (Malus X Domestica Borkh.)

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Genetic and Molecular Characterisation of Resistance Factors and Candidate Genes for Scab Resistance in Apple (Malus X Domestica Borkh.) Aus dem Institut für Agrar- und Ernährungswissenschaften (Geschäftsführender Direktor: Prof. Dr. R. Jahn) der Naturwissenschaftlichen Fakultät III (Dekan: Prof. Dr. P. Wycisk) der Martin-Luther-Universität Halle-Wittenberg Fachgebiet: Pflanzenzüchtung Genetic and molecular characterisation of resistance factors and candidate genes for scab resistance in apple (Malus x domestica Borkh.) Dissertation zur Erlangung des akademischen Grades doctor agriculturarum (Dr. agr.) von Diplomagrarwissenschaftler Anastassia Boudichevskaia Verteidigung am: 02.02.2009 Halle/Saale 2009 Aus dem Institut für Agrar- und Ernährungswissenschaften (Geschäftsführender Direktor: Prof. Dr. R. Jahn) der Naturwissenschaftlichen Fakultät III (Dekan: Prof. Dr. P. Wycisk) der Martin-Luther-Universität Halle-Wittenberg Genetic and molecular characterisation of resistance factors and candidate genes for scab resistance in apple (Malus x domestica Borkh.) Dissertation zur Erlangung des akademischen Grades doctor agriculturarum (Dr. agr.) vorgelegt von Diplomagrarwissenschaftler Anastassia Boudichevskaia geb. am 28.11.1974 in Ashkhabad, USSR Gutachter: Prof. em. Dr. habil. W. Eberhard Weber Prof. Dr. Klaus Pillen Fr. Prof. Dr. habil. Viola Hanke Verteidigung am: 02.02.2009 Halle/Saale 2009 Table of Contents Table of Contents Page Abbreviations I Tables III Figures VI 1. Introduction 1 1.1 Breeding in apple 1 1.2 Major apple diseases 4 1.3 Apple scab 7 1.3.1 Biology 8 1.3.2 Plant symptoms 9 1.3.3 Apple scab races 10 1.3.4 Resistance breeding strategies 12 1.4 Molecular techniques in plant breeding 16 1.5 Plant resistance genes 24 1.6 Outline of the thesis 31 2. Material and methods 34 2.1 Plant material 34 2.1.1 Identification and mapping of a major scab resistance 34 gene from R12740-7A 2.1.2 Identification of HcrVf-type candidate genes 35 2.1.3 Scab assessments 36 2.2 Molecular methods 37 2.2.1 Extraction, purification and quantification of DNA 37 2.2.1.1 Extraction of genomic DNA from plants 37 2.2.1.2 Extraction of double-stranded PCR products 38 from amplification reactions 2.2.1.3 Extration of DNA fragments from agarose gels 39 2.2.1.4 Agarose gel electrophoresis 39 Table of Contents 2.2.1.5 DNA quantification 39 2.2.1.6 Restriction of genomic DNA 40 2.2.2 Total RNA isolation 40 2.2.2.1 Quantification of RNA 41 2.2.2.2 cDNA synthesis 41 2.2.3 Host and vectors systems 42 2.2.3.1 Isolation of plasmid DNA 42 2.2.3.2 Ligation of PCR products 42 2.2.3.3 DNA transformation 42 2.2.4 Molecular marker techniques 44 2.2.4.1 RAPD (Random Amlified Polymorphic DNA) 44 markers 2.2.4.2 SCAR (Sequence Characterized Amplified 45 Region) markers 2.2.4.3 SSR (Simple Sequence Repeats) markers 46 2.2.5 Identification of HcrVf-type candidate genes 47 2.2.5.1 PCR amplification of HcrVf-type candidate 47 genes 2.2.5.2 Development of gene-specific primers 48 2.2.6 RT-PCR 49 2.2.7 Vf2ARD transcription profiling and Real-Time PCR 49 2.2.8 Southern hybridisation 51 2.2.9 Sequence analysis 53 2.2.10 Molecular maps construction 53 2.2.10.1 Vr1 linkage mapping 54 2.2.10.2 Mapping of the Vf candidate genes 54 2.2.11 Computerized data analysis 54 3. Results 56 3.1 Development of molecular markers for the scab resistance 56 gene Vr1 from R12740-7A Table of Contents 3.1.1 Seedling scab assessments 56 3.1.2 RAPD marker identification 57 3.1.3 SCAR marker development and analysis 61 3.1.4 Vr1 linkage mapping 62 3.1.5 Analysis of Vr1-Vf gene combinations 65 3.2 Molecular analysis of HcrVf-type candidate genes 67 3.2.1 Identification of HcrVf-type candidate genes 67 3.2.2 Sequence analysis of the HcrVf – type candidate genes 68 3.2.3 Analysis of the HcrVf-type candidate gene Vf1RSA 72 3.2.3.1 Transcriptional analysis of the Vf1RSA 76 candidate gene 3.2.3.2 Genetic mapping of the Vf1RSA gene 78 3.2.4 Analysis of the HcrVf-type candidate gene Vf2ARD 80 3.2.4.1 Transcriptional analysis of the Vf2ARD 82 candidate gene 3.2.4.2 Evaluation of Vf2ARD transcript levels with and 83 without scab infection 3.2.4.3 Presence of the Vf2ARD homologues 85 in Malus genome 3.2.4.4 Genetic mapping of Vf2ARD gene 86 4. Discussion 89 4.1 Scab resistance phenotyping 89 4.2 DNA markers linked to the scab resistance gene Vr1 91 from R12740-7A 4.3 Vr1 linkage mapping 93 4.4 Utility of Vr1 marker AD13 for marker assisted selection 94 4.5 Molecular analysis of candidate genes homologous to HcrVf 95 genes for scab resistance in apple 4.6 Expression and mapping of two HcrVf-like candidate genes: 97 the Vf1RSA and Vf2ARD Table of Contents 4.7 Existence of a further Vf - like locus located closely to Vf 99 on apple linkage group LG 1 5. Summary/Zusammenfassung 102 5.1 Summary 102 5.2 Zusammenfassung 104 6. Literature cited 107 7. Annex 126 Abbreviations List of Abbreviations APS ammonium persulfate bp base pair °C Celsius degree cM CentiMorgan CTAB Cetyltrimethylammonium bromide ddH2O double destilled water ddNTP 2',3'-dideoxynucleotide triphospates DNA deoxyribonucleic acid dNTP Desoxy-Nucleotide Triphosfate EDTA Ethylene Diamin-N,N,N'N'-tetra acetic acid Fig. figure g gramm GMAL Geneva Malus number h hour IPTG Isopropyl-β-D-thiogalactoside l litre LB Luria-Bertani medium LG Linkage Group LOD Logarithm of the odds LRR Leucin Reach Repeat µg microgram M Molar MAS Marker Assisted Selection min minute µl microlitre µM micromolar mM millimolar NBS Nucleotide Binding Site ng nanogram nm nanometre no. number PCR Polymerase Chain Reaction pH potential of hydrogen pmol picomol PVP polyvinylpyrrolidone QTL Quantitative Trait Loci RAPD Random Amplified Polymorphic DNA RNA ribonucleic acid RNase ribonuclease RT room temperature rpm rotations per minute SCAR Sequence Characterized Amplified Region I Abbreviations sec second SSR Simple Sequence Repeat Tab. table TAE Tris-Acetate-EDTA (buffer) TE Tris HCl-EDTA (buffer) TEMED N,N,N'N'-Tetramethylethylendiamin Tris Tris-hydroxymethyl-aminomethane U unit (enzyme activity) UV ultraviolet v. version x-GAL 5-Brom, 4-chlor, 3-indoxyl β-D-galactosid BAZ Bundesanstalt für Züchtungsforschung an Kulturpflanzen (Federal Centre for Breeding Research on Cultivated Plants) IOZ Institut für Obstzüchtung (Institut of Fruit Breeding) Dresden, JKI part of BAZ, Julius Kühn Institute II Tables Tables Table1: List of powdery mildew resistant sources 6 Table 2: Outstanding or promising disease resistance 15 varieties in Europe according to Sansavini et al. (2004) Table 3: Comparison of the most common used marker 18 systems after Korzun (2003) Table 4: Strategies utilized by plant pathogens (after Hammond- 26 Kosack and Jones, 2000) Table 5: Apple populations investigated in study for scab resistance 35 Table 6: Scab assessment scale 36 Table 7: Apple families investigated in study for Vr1 scab 57 resistance and segregation data obtained by seedling inoculations Table 8: Correspondence between scab resistance field data 65 and Vr1-SCAR marker AD13 in the populations 03/205 (Regia x Pinova) and 03/206 (Regia x Piflora) Table 9: Relationship between presence of two SCAR markers 67 AL07 (Vf) and AD13 (Vr1) and scab resistance in apple population 00/216 (Regia x Rebella) Table 10: Amino acid sequence comparisons of cloned HcrVf 69 homologues with HcrVf1 and HcrVf2, respectively (BlastX, NCBI GenBank) Table 11: Sequence distances between the cloned HcrVf 70 homologues and the HcrVf1/HcrVf2 proteins Table 12: Correspondence between scab resistance data 75 and presence of the Vf1RSA fragment in the populations 05/230 (‘Pinova’ x M. sieversii A96/53-13) and 06/004 (‘Golden Delicious’ x M. sieversii A96/57-4) Table 13: Results of the BLAST searches in nucleotide sequences 76 databases (NCBI GenBank) for the Vf1RSA specific sequences cloned from R12740-7A and two M. sieversii genotypes Table 14: Segregation of the Vf1RSA specific PCR product (313 bp) 78 in two apple progenies 05/230 (Pinova x M. sieversii A96/53-13) and 06/004 (Golden Delicious x M. sieversii A96/57-4) III Tables Annex A1: World apple production according to FAO data (2006) 125 A2: List of scab resistant sources after Gessler et al. (2006) 126 A3: Amplification of HcrVf gene homologues in a set of 127 apple cultivars and scab resistance sources with PCR primers Vf1 and Vf2 A4: Buffers and solutions for DNA extraction (adapted 128 from Doyle and Doyle, 1987) A5: Composition of buffers and solutions for DNA 128 transformation A6: Molecular primers used for the amplification of the 130 Vf candidate genes and their mapping; their sources, sequences and annealing temperatures A7: PCR profiles for molecular primers used for 131 identification, characterization and mapping of the Vf candidate genes A8: Decamer primers of arbitrary sequence from Operon 133 Technologies (Alameda, CA, USA) used in this study A9: Molecular markers used for Vr1 linkage mapping and 136 molecular resistance tests; their sources, sequences and annealing temperatures A10: Sequence of the cloned OPAD13950 RAPD fragment 137 A11: PCR profiles for molecular markers used for the Vr1 138 linkage mapping and molecular resistance tests A12: Polyacrylamide gel electrophoresis 140 A13: Composition of solutions for Southern blot analysis 141 A14: Representation of marker data for 90 individuals of the 142 population 03/206 (Regia x Piflora) used for construction of genetic map for the Vr1-carrying linkage group LG 2 A15: Seedling scab assessments in family 05/230 after 144 greenhouse inoculation and its genetic analysis with the Vf1RSA and CHVf1 primers A16: Seedling scab assessments in family 06/004 after 145 greenhouse inoculation and its genetic analysis with the Vf1RSA and SSR primers IV Tables A17: Seedling scab assessments in family 04/214 after 148 greenhouse inoculation during two years and its genetic analysis with the CH-Vf1 SSR marker A 18: Multiple nucleotide sequence alignments of HcrVf1 150 (GenBank acc.
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