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The Genetic Basis of Barley (Hordeum Vulgare L.) Adaptation to Australian Environment

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The Genetic Basis of Barley (Hordeum Vulgare L.) Adaptation to Australian Environment The genetic basis of barley (Hordeum vulgare L.) adaptation to Australian environment By Bulti Tesso Obsa A thesis submitted for the degree of Doctor of Philosophy School of Agriculture, Food and Wine Discipline of Plant Breeding and Genetics Australian Centre for Plant Functional Genomics May 2016 Declaration i Acknowledgments First, I thank my three supervisors Dr. Delphine Fleury, Professor Peter Langridge and Professor Jason Eglinton for designing such a fantastic research project and for their unreserved support and advice throughout the course of my PhD study. Delphine and Peter recruited me for the IPRS/APA scholarship and assisted me all the way through the application process. As my major supervisor, Delphine has always been in close contact with me and has encouraged me to learn and practice the genotyping skills that were new to me. Thank you Jason and Peter for your continuous encouragement and for helping me understand the overall goal of this project in the perspectives of barley breeding for the Australian environment, which helped me to interpret the final findings. I would like to thank Dr. Joanne Tilbrook who was my independent adviser during the first year of my candidature. I would also like to acknowledge Professor Diane Mather and Associate Professor Kenneth Chalmers for their constructive comments during my major review. I could not have conducted the field trials without the help of Stewart Coventry who was very instrumental in the design, implementation and overall management of the multi-location trials, and he has organized and created conducive situations for my various trips to the trial sites. A big thank you to Timothy March for Genotyping by Sequencing (GBS) and KASP genotyping, and for teaching me the GBS library preparation and genetic linkage map construction. Ridma Jayasinghe deserves a warm gratitude for teaching me about genotyping skills using PCR for the first time. I would also like to thank Dr. Takashi Okada and Dr. Gwenda Mayo for their assistance in the microscopic meristem study. I am indebted to Dr. Fahimeh Shahinnia for her constructive comments and for mentoring me when she was at ACPFG. I would like to thank Anthony Smith, Donna Marie and all the Barley Breeding Program team, University of Adelaide, and Davis Leigh from Minnipa Agricultural Research Centre for providing unreserved assistance for the successful completion of the field trials. I would also like to thank Daniel Carrocci and Florian Krimpzer for assisting in the SNP genotyping and Thanh Phuoc Le for his initial work, which laid the basis for this PhD project. I warmly thank the members of the drought research group at the Australian Centre for Plant Functional Genomics (ACPFG) and all people in the different research groups at ACPFG ii who have supported me throughout my study. I also thank the administrative staff of ACPFG for provision of all the facilities that were essential for my study. I would like to extend my appreciation to the former education manager at ACPFG, Dr. Monica Ogierman, for her all round support and encouragement. I am indebted to the University of Adelaide for giving me the IPRS/APA scholarship. This work was partially funded by the South Australia Grain Industry Trust Fund (SAGIT), Australian Research Council (ARC), Grains Research and Development Corporation (GRDC), the South Australian Government, the Department of Further Education, Employment, Science and Technology, and The University of Adelaide, and I acknowledge them all. Finally, I would like to thank my beloved wife Hamere Tamirat and my wonderful daughters Meti and Kume, and my wonderful sons Firaol and Oliyad for their understanding, encouragement and patience when I have been away from them for long time until the completion of this study. iii To my beloved wife ‘Hamere’, my daughters ‘Meti’ & ‘Kume’, and my sons ‘Firaol’ & ‘Oliyad’ iv Table of Contents Declaration. .............................................................................................................................................. i Acknowledgments ................................................................................................................................... ii Table of Contents .................................................................................................................................... v List of Tables ....................................................................................................................................... viii List of Figures ........................................................................................ Error! Bookmark not defined. List of Appendix Tables ......................................................................................................................... xi List of Appendix Figures ...................................................................................................................... xii Abstract…… ........................................................................................................................................ xiv Chapter 1: General introduction .............................................................................................................. 1 Chapter 2: Literature review ................................................................................................................... 4 2.1 Introduction ....................................................................................................................................... 4 2.2 Phenological control of adaptation and yield in cereals ................................................................... 5 2.2.1 Flowering time: an important adaptive trait of cereals .......................................................... 5 2.2.2 The genetic and physiological basis of flowering in barley .................................................. 6 2.2.3 Integration of photoperiod and vernalization pathways to induce flowering in barley ......... 7 2.2.4 Fine tuning the genetic control of heading time in barley ................................................... 11 2.3 Barley mapping populations for genetic studies ............................................................................. 14 2.3.1 Bi-parental mapping populations ......................................................................................... 14 2.3.2 Advanced backcross quantitative trait loci (AB-QTL) analysis .......................................... 17 2.3.3 Association mapping ............................................................................................................ 19 2.3.4 Nested association mapping (NAM) .................................................................................... 20 2.3.5 Multi-parent advanced generation inter-cross (MAGIC) populations ................................. 20 2.4 Conclusions ..................................................................................................................................... 24 2.5 References ....................................................................................................................................... 26 Chapter 3: Construction of genetic linkage maps for Commander x Fleet, Commander x WI4304 and Fleet x WI4304 doubled haploid populations ........................................................... 37 3.1 Abstract ........................................................................................................................................... 40 3.2 Introduction ..................................................................................................................................... 40 3.3 Materials and methods .................................................................................................................... 42 3.3.1 Plant materials ...................................................................................................................... 42 3.3.2 DNA extraction and genotyping .......................................................................................... 42 3.3.3 Data analysis and linkage map construction ........................................................................ 43 3.3.4 Construction of consensus genetic maps ............................................................................. 43 3.4 Results ............................................................................................................................................. 44 v 3.4.1 Individual genetic linkage maps constructed ....................................................................... 44 3.4.2 Segregation distortion .......................................................................................................... 45 3.4.3 Consensus linkage map ........................................................................................................ 46 3.5 Discussion ....................................................................................................................................... 59 Chapter 4: Genetic analysis of developmental and adaptive traits in three doubled haploid populations of barley (Hordeum vulgare L.) [Published Article] ..................................... 65 Chapter 5: Mapping of yield and grain plumpness QTL in three doubled haploid populations of barley (Hordeum vulgare L.) ........................................................................................ 83 5.1 Abstract ..........................................................................................................................................
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