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Radiation Hybrid Fine Mapping of Two Fertility-Related Genes: Marking the Path to Wheat Hybrids

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Radiation Hybrid Fine Mapping of Two Fertility-Related Genes: Marking the Path to Wheat Hybrids RADIATION HYBRID FINE MAPPING OF TWO FERTILITY-RELATED GENES: MARKING THE PATH TO WHEAT HYBRIDS A Dissertation Submitted to the Graduate Faculty of the North Dakota State University of Agriculture and Applied Science By Filippo Maria Bassi In Partial Fulfillment for the Degree of DOCTOR OF PHILOSOPHY Major Department: Plant Sciences December 2012 Fargo, North Dakota North Dakota State University Graduate School Title RADIATION HYBRID FINE MAPPING OF TWO FERTILITY-RELATED GENES: MARKING THE PATH TO WHEAT HYBRIDS By Filippo Maria Bassi The Supervisory Committee certifies that this disquisition complies with North Dakota State University’s regulations and meets the accepted standards for the degree of DOCTOR OF PHILOSOPHY SUPERVISORY COMMITTEE: Shahryar F. Kianian, Ph.D. Chairperson Anne Denton, Ph.D. Mohamed Mergoum, Ph.D. Phillip McClean, Ph.D. Justin Faris, Ph.D. Approved: December 12, 2012 Richard D. Horsley, Ph.D. Date Department Chair ABSTRACT Over one billion people, more than 1/9th of the global population, are undernourished. Feeding the ever increasing population has to be the most important goal of plant sciences. Since cultivated areas are not likely to increase, I will need to produce more with what is available. This can be summarized in one word: yield. Unfortunately, wheat’s yield is expected to increase only 1.13% by 2019, a prediction that if converted into reality will likely indicate that I failed to cope with the world demographic increase. A new strategy to revolutionize wheat production is required, and some believe that this change might be represented by wheat hybrids. Achieving adequate commercial production of wheat hybrids has the potential to nearly double the yield of one of the world’s most important staple food. The first fundamental step toward this goal is to develop feasible methodologies to sterilize the male part of the complete wheat flowers. Two fertility-related genes are the primary target of this study, namely the species cytoplasm specific on chromosome 1D, and the desynaptic locus on chromosome 3B. This dissertation summarizes the important achievements obtained toward the cloning of the two loci by means of radiation hybrid functional analysis. Radiation hybrid is a technique that employs radiation to create genetic diversity along the targeted chromosome. Chapter 1 explains in details how this methodology can be applied to plants. The use of radiation hybrid mapping permitted creating a comprehensive map of wheat chromosome 3B, as discussed in Chapter 2, and then expanded the mapping information to identify the 2 Mb location of the desynaptic locus desw2, as discussed in Chapter 3. A similar approach on chromosome 1D allowed first to pinpoint the location of the species cytoplasm specific gene to a region of 2 Mb, as discussed in Chapter 4, and then ultimately to find a strong candidate for this locus, as discussed in Chapter 5. Now that the molecular locations of these genes have been unraveled by this study, their sequence can be streamlined into transformation to ultimately produce female wheat plants, and consequently hybrids. iii ACKNOWLEDGEMENTS I wish to thank: Justin Hegstad and Allen Peckrul for capable technical support throughout the research. For fundamental experimental help Dr. Matthew Hayden, Dr. Etienne Paux, Dr. Yong Gu, and Dr. Wojtek Pawlowski. My advisory committee that has supported me every single step of the way, bearing with my poor cooking, while enjoying the long hours of student-grilling during the various exams: Dr. Anne Denton, Dr. Justin Faris, and Dr. Phillip McClean. Dr. Mohammed Mergoum who had to cope with my field inexperience, and surprising enough for the both of us, he succeeded in making a breeder out of me after all. My advisor Dr. Shahryar Kianian, who has never once told me that I did a good job, no matter how hard I tried, but I know that deep inside he was happy to be my advisor (some days better than others) and really helped me throughout these three cold years in Fargo. The other members of the WGE family who had to survive long years with me around: Dr. Ajay Kumar, who stole one first authorship but gave in return a deep and true friendship for which I will always be thankful; Dr. Farhad Gavami with whom I fought a lot as much as laugh together, and did some great research with; Dr. Monika Michalack DJ, Dr. Kristin Simmons, and Rissa who are the true responsibles for the success of the scs project; Mona Mazaheri, who has caused me more than one headache and managed to paint our shower curtain red, but who has also been a great friend; to Farid and Ali, who I am sure will go out there and become the best damn scientists that this world has to offer; to Andrzej who tried to save my soul but instead found himself stuck with a friend from the wrong side of the heaven’s doors. An apologies goes to my family who had to bear with my absence, and probably will not be able to understand what I am writing, but always always always supported me, no matter how deep was the hole I was digging myself into, they were always there with a ladder to take me out. My sister, with whom I enjoy arguing, but that I love with all my hearth. A special thank goes to the funding sources that made my research possible: Program M&B Sardegna, and Monsanto Beachell-Borlaug International Scholarship that made me one of the few decently paid PhD student in the country, but also introduced me to great students from all places in the world, and especially made me meet my beautiful Dorothy, who is sitting across the table from me as I write these words. iv DEDICATION This goes to the man that inspired and fomented my dedication to plant science and to the challenge of feeding the world: Dr. Norman Borlaug. My deepest regret is that I never had a chance to meet you; I can only picture how amazing it would have been to have a chance in Des Moines of shaking the hand of the man who fed a billion people. As a scientist I know that you have just become part of the natural circle of life and that you cannot hear me now, but if you could I would like to tell you that your example is inspiring thousands of young students, that what you did for us will never be forgotten, and hell you put together some catchy phrases. “There is no peace on an empty belly” Norman Borlaug v TABLE OF CONTENTS ABSTRACT ........................................................................................................................................... iii ACKNOWLEDGEMENTS ..................................................................................................................... iii DEDICATION ......................................................................................................................................... v LIST OF TABLES .................................................................................................................................. xi LIST OF FIGURES ............................................................................................................................... xii LIST OF ABBREVIATIONS................................................................................................................. xiv LIST OF APPENDIX TABLES............................................................................................................. xvi LIST OF APPENDIX FIGURES ......................................................................................................... xvii 1. MUTAGENOMICS: THE ADVANCE OF RADIATION HYBRIDS FOR STUDYING GENES AND GENOMES IN PLANTS .......................................................................................................... 1 1.1. Effect of radiation on plant genomes .............................................................................. ……...1 1.1.1. Considerations on the effect of radiation for the development of mutant populations ..... 3 1.2. Radiation hybrid for mapping genomes .................................................................................... 6 1.2.1. The four key aspects of radiation hybrid mapping ............................................................ 7 1.2.2. Radiation hybrid mapping in animal systems ................................................................. 10 1.2.3. Radiation hybrid mapping in plant systems .................................................................... 10 1.2.4. Comparison of animal and plant radiation hybrid projects ............................................. 13 1.3. Applications and prospects for radiation hybrids in plants ...................................................... 15 1.3.1. Radiation hybrids for mapping and cloning genes .......................................................... 15 1.3.2. Radiation hybrid mapping and comparative genomics ................................................... 18 1.3.3. Radiation hybrids and the new sequencing technologies .............................................. 20 1.4. References .............................................................................................................................. 21 2. RADIATION HYBRIDS OF CHROMOSOME 3B REVEAL A DEPENDENT RESPONSE OF THE DNA-REPAIR MECHANISM TO THE STATE OF CHROMATIN .......................................... 30 2.1. Introduction ............................................................................................................................. 31 2.2. Methods .................................................................................................................................
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