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Map-Based Cloning of Susceptibility Factors for Bymovirus in Barley (H

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Map-Based Cloning of Susceptibility Factors for Bymovirus in Barley (H Map-based cloning of susceptibility factors for Bymovirus in barley (H. vulgare L.) Dissertation zur Erlangung des Doktorgrades der Agrarwissenschaften (Dr. agr.) der Naturwissenschaftlichen Fakultät III Agrar- und Ernährungswissenschaften, Geowissenschaften und Informatik der Martin-Luther-Universität Halle-Wittenberg vorgelegt von Herrn M.Sc. Ping Yang geb. am: 11.04.1984 in Nanchuan City, China Gutachter: Prof. Dr. Andreas Graner Prof. Dr. Rod Snowdon Verteidigt am 27/01/2014 Halle/Saale Acknowledgements First of all I would like to thank my supervisor Dr. Nils Stein (PI of Genome Diversity, IPK) for giving me the opportunity to work in the Plant - KBBE ViReCrop project (Financed by the German Ministry of Education and Research, BMBF), and integrating me into the international barley research group (Genome Diversity, IPK) as well as giving me great freedom to sharp my scientific career. I will always be very grateful for his constructive criticism, constant encouragement, patient support and inspirational advice, which are necessary for me to perform the scientific project and complete my PhD dissertation during last three years. Then, I wish to gratefully appreciate Prof. Andreas Graner (Director of IPK) for accepting me as PhD student at the Martin-Luther-University (MLU), Halle-Wittenberg. It’s my great pleasure to get his encouragement, fruitful discussions and suggestions in the progress reports. I thankfully acknowledge Dr. Patrick Schweizer (PI of Pathogen Stress Genomics, IPK) for being my scientific mentor for excellent discussion and valuable suggestions. I also appreciate Prof. Rod Snowdon (Head of Department of plant breeding, Justus-Liebig-University) for agreeing as my supervisor to evaluate this thesis. I also want to thank all my colleagues in Genome Diversity group for their scientific supports as well as giving friendly and positive atmosphere. Special thanks to Dr. Benjamin Kilian for providing natural collections of barley germplasms, Dr. Axel Himmelbach and Dr. Ruvini Ariyadasa for constructing the physical contig, Dr. Ruonan Zhou for marker development, Neele Wendler for GBS-analysis. And also thank Matthias Jost, Dr. Rajiv Sharma and Dr. Kerstin Neumann for academic and non-academic discussions. I am also very grateful to all the efforts from my work partners. It’s my thankful opportunity to closely and wonderfully cooperate with Prof. Frank Ordon (Head of institute for Resistance Research and Stress Tolerance, JKI) and his group members Dr. Antje Habekuß for her kindness and helping a lot on phenotypic analysis as well as Dr. Thomas Lüpken and Dr. Dragan Perovic for performing genetic mapping. I would like to appreciate Dr. Jochen Kuhmlehn (PI of Plant Reproductive Biology, IPK) and Dr. Götz Hensel for generating transgenic plants, Dr. Martin Giersberg (Yeast Genetics, IPK) and Dr. Udo Conrad (PI of Phytoantibodies, IPK) for help with protein purification, Dr. Uwe Scholz (PI of Bioinformatics and Information Technology, IPK), Dr. Burkhard Steuernagel and Martin Mascher for help with the bioinformatics analysis. For sharing research materials I gratefully thank Dr. Carole Caranta (Head of the Plant Genetics and Breeding Department of INRA) for providing plasmids of Matchmaker™ GAL4 Two-Hybrid System, Dr. Dimitar Kostadinov Douchkov (Pathogen Stress Genomics, IPK) for providing plasmids for vector construction and IPK GeneBank for providing hundreds of winter barley accessions. For technical assistances I will give special thanks to Jelena Perovic for her kindness and perfect assistance on most of my laboratory works, and Mary Ziems for wonderful greenhouse work, Jacqueline Pohl for screening TILLING mutants, Dörte Grau (JKI) for phenotypic analysis, Isolde Tillack for protein purification, Susanne König and Ines Walde for Sanger sequencing. I also would like to give many thanks to Dr. Britt Leps and Mrs. Jacqueline Heidecke for their efforts that made my daily life convenient in Gatersleben. Finally, I could never find any words that are desirable enough to describe my love and gratitude to my family. Please allow me to express my deep and sincere gratitude to my parents for giving my life, health, strength and opportunity to pursue my dreams, and special thanks to my dear wife for her patience, kindness, understanding and incredible supports. And last but not least to all the peoples who gave me any suggestions, helps and inspirations over last 29 years of my life! Contents 1. Introduction ............................................................................................................. 1 1.1 Genetics of resistance to plant viruses .............................................................. 1 1.2 Soil-borne barley yellow mosaic virus disease .................................................. 5 1.2.1 Barley yellow mosaic virus complex ............................................................ 5 1.2.2 Genetic resistances to the barley yellow mosaic virus disease ................... 9 1.3 Barley genomic resources for map-based cloning ........................................... 11 1.4 The goals of the study ..................................................................................... 15 2. Material and methods ........................................................................................... 16 2.1 Plant material .................................................................................................. 16 2.1.1 Mapping populations for rym7 ................................................................... 16 2.1.2 Mapping population for rym11 ................................................................... 16 2.1.3 Worldwide diversity collection for re-sequencing and allele mining ........... 17 2.2 DNA and RNA extraction, cDNA synthesis...................................................... 18 2.3 Polymerase chain reaction (PCR) ................................................................... 19 2.4 Sanger sequencing and sequence analysis .................................................... 20 2.5 Screening of BAC libraries, BAC sequencing, detecting overlap and identifying candidate genes .................................................................................................... 21 2.6 Marker development and genotyping .............................................................. 22 2.6.1 Primer design ............................................................................................ 22 2.6.2 Marker development ................................................................................. 22 2.7 Screening for chemically induced mutants by TILLING ................................... 24 2.8 Plasmid vector construction and agrobacterium-mediated transformation ...... 24 2.9 Computational data analysis ........................................................................... 25 2.9.1 Linkage and syntenic analysis................................................................... 25 2.9.2 Haplotype analysis and Median Joining (MJ) network .............................. 26 2.9.3 Phylogenetic analysis ................................................................................ 26 2.9.4 Three dimensional (3D) modeling of protein structure .............................. 27 2.10 Artificial and natural infection with Bymovirus and testing for resistance ....... 28 3. Results .................................................................................................................. 29 3.1 Gene-based high-density mapping of rym7 ..................................................... 29 3.1.1 Gene-based marker development ............................................................. 29 3.1.2 High-density mapping of rym7 and comparative analysis of conserved synteny to sequenced grass genomes ............................................................... 30 3.1.3 Screening for segmental RILs ................................................................... 33 3.1.4 Hv-eIF(iso)4E - a potential candidate of rym7? ......................................... 33 3.2 Map-based cloning and characterization of the gene rym11 ........................... 34 3.2.1 Map-based cloning of rym11 ..................................................................... 34 3.2.2 Functional verification of HvPDIL5-1 ......................................................... 39 3.3 Natural variation, geographical distribution and origin of rym11 ...................... 45 3.3.1 Natural variation of HvPDIL5-1 .................................................................. 45 3.3.2 Geographical distribution and origin of rym11 ........................................... 50 3.4 Diagnostic markers for rym11 functional alleles .............................................. 53 3.5 Phylogenetic analysis of PDI gene family ........................................................ 56 4. Discussion ............................................................................................................ 61 4.1 PROTEIN DISULFIDE ISOMERASE 5-1 is a new Bymovirus susceptibility factor in barley and highly conserved between plants and animals ....................... 61 4.2 Naturally occurring diversity of Bymovirus resistance could represent the consequence of adaptation to virus infested environments ................................... 64 4.3 Barley resistance breeding requires access to multiple sources of naturally occurring resistance .............................................................................................. 66 4.4 Barley physical map is
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