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Development and Characterization of Rice Genotypes for Water Use Efficiency and Oughtdr Resistance University of Arkansas, Fayetteville ScholarWorks@UARK Theses and Dissertations 12-2017 Development and Characterization of Rice Genotypes for Water Use Efficiency and oughtDr Resistance Anuj Kumar University of Arkansas, Fayetteville Follow this and additional works at: https://scholarworks.uark.edu/etd Part of the Food Processing Commons, Plant Breeding and Genetics Commons, and the Water Resource Management Commons Citation Kumar, A. (2017). Development and Characterization of Rice Genotypes for Water Use Efficiency and Drought Resistance. Theses and Dissertations Retrieved from https://scholarworks.uark.edu/etd/3456 This Dissertation is brought to you for free and open access by ScholarWorks@UARK. It has been accepted for inclusion in Theses and Dissertations by an authorized administrator of ScholarWorks@UARK. For more information, please contact [email protected]. Development and Characterization of Rice Genotypes for Water Use Efficiency and Drought Resistance A dissertation submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy in Crop, Soil, and Environmental Sciences by Anuj Kumar CCS University, India Bachelor of Science in Agriculture, 2004 SVP University of Agriculture & Technology, India Master of Science in Plant Biotechnology, 2007 December 2017 University of Arkansas This dissertation is approved for recommendation to the Graduate Council. ________________________ Andy Pereira, PhD Dissertation Director ________________________ _________________________ Karen A. Moldenhauer, PhD Derrick M. Oosterhuis, PhD Committee Member Committee Member _________________________ _________________________ Edward E. Gbur, Jr., PhD Xueyan Sha, PhD Committee Member Committee Member ________________________ Ainong Shi, PhD Committee Member ABSTRACT Rice, the second largest staple food crop, uses 30% of global fresh water to complete its life cycle worldwide. Water deficits worldwide have become a serious problem affecting rice growth and ultimately grain yield. To solve the water problem globally, improvement of water use efficiency (WUE) and other drought resistance (DR) traits in rice genotypes would be a useful strategy using advanced genomics tools. In this study, our objectives were to 1) analyze phenotypes of the USDA rice mini-core collection (URMC) for WUE and DR related traits, 2) correlate drought response phenes for physiological traits and grain yield in the URMC, 3) utilize molecular genetic dissection of WUE and DR using genome-wide association (GWA) analysis in the URMC, and 4) conduct genome-wide meta analysis of QTLs for DR traits and grain yield components under drought stress. In the results, 35 rice genotypes showing <25% reduction, 14 rice genotypes exhibiting 25-40% reduction, and 8 rice genotypes showing >40% reduction, were drought resistant, moderate drought resistant, and drought sensitive for WUE, photosynthesis, biomass, and other DR traits under drought stress, respectively. The results suggest from the correlation analysis that strong correlation exits between major grain yield components (number of spikelets per panicle, number of filled and unfilled grains per panicle) and major morpho- physiological traits (plant biomass, photosynthesis and WUEi). In the GWA analysis, 24, 16, 26, 10, 19, 23, 7, 17, 11, 14, 17, 15, 29, 12, 18, and 19 significant SNPs were highly associated with WUEi, TR, stomatal conductance, Ci & Ci/Ca , plant biomass, NOTs, RWC, LR, chlorophyll content, and chlorophyll fluorescence (Fv’, Fm’, Fv’/Fm’, PhiPSII, ETR, and qN) and their identified candidate genes for WUEi and DR traits. In the meta-analysis, 13 genome-wide MQTLs were found useful containing higher number of QTLs, lower genetic distance with lower CI. Therefore, this information would be useful for the geneticists to dissect the genetic architecture of WUE and DR traits for developing high yielding drought resistant rice genotypes. ©2017 by Anuj Kumar All Rights Reserved ACKNOWLEDGEMENTS It is my great pleasure to express my thanks to Almighty God, through whose mercy and blessings, I have accomplished this journey through higher education to this PhD. I am honored to be able to complete this stage of my life, which has not always been easy but by the grace of God and help of many around me, has come to completion. I would therefore like to acknowledge my “Mummy and Papa” for their sacrifices, faith, unconditional love, and every support that got me this far. Words are insufficient to give thanks for their untiring help, patience and affection and for being there by my side at all the times of ups & downs through life. With a sense of gratitude and privilege, I would like to express my sincere thanks to my major advisor, Dr. Andy Pereira, Professor, Department of Crop, Soil, & Environmental Sciences, for his valuable guidance, continuous motivation, and unconditional support during my entire research. His patience and insights into the research subject have always made me realize and understand my research at a global level. His infinite capacity for hard work will always be an illuminating light to lead me in all my pursuits in the future too. Distinctive words of thanks are due to Monsanto’s Beachell-Borlaug International Scholars Program (MBBISP) especially Dr. Edward Runge and the entire panel, for awarding me the financial support, necessary facilities, international exposure, timely help whenever required, and for generating all kind of resources supporting the program. I would like to express my fervent thanks to the members of my advisory committee Dr. Karen A. Moldenhauer, Professor, Department of Crop, Soil, & Environmental Sciences, Dr. Derrick M. Oosterhuis, Distinguished Professor, Department of Crop, Soil, & Environmental Sciences, Dr. Edward E. Gbur, Jr., Professor, Agriculture Statistics Laboratory, Dr. Xueyan Sha, Associate Professor, Department of Crop, Soil, & Environmental Sciences, and Dr. Ainong Shi, Assistant Professor, Department of Horticulture, for their valuable advice, constructive suggestions and timely assistance during my research and courses. With great sense of respect and deepest pleasure, I express my appreciation and immense gratitude to Dr. Arvind Kumar, Senior Scientist, International Rice Research Institute (IRRI), Philippines for his guidance and training during my visit at IRRI. I am extremely grateful to Dr. Amelia Henry, Scientist, CESD, IRRI, for her constructive suggestions, skillful help, meticulous supervision, cooperative & caring attitude that helped me at various stages of my experiments and stay at IRRI. It is my great privilege to express my immense sense of gratitude towards my lovely wife Ms. Sumedha Singh whose unconditional love, relentless support, patience & untiring day and night care helped me to accomplish this research in time. My words utterly fail to be able to express my tribute to my brother Mr. Manuj Kumar, sister in law Ms. Priyanka, and my lovely sister Ms. Monika Singh for their continuous encouragement, unconditional love, silent prayers, understanding and patience during my entire life. Special affection for my little, cute nephew “Yug Choudhary” whose innocent smiling face gave me constant inspiration to complete my work and relax during burdened moments. It gives me immense pleasure to express my deep and sincere gratitude towards present and past colleagues and members of my lab Dr. Julie Thomas, Dr. Supratim Basu and Dr. Ramegowda Venkategowda from whom I learnt aspects of plant molecular genetics and physiology, fellow graduate students Ms. Ritu Mihani, Mr. Chirag Gupta, Ms. Miranti Rahmaningsih, Ms. Yheni Dwiningsih, Ms. Jawaher Alkhatani and Ms. Ipeleng Randome with whom I shared lab and field work, and most importantly the untiring assistance in experimental measurements in the greenhouse and field of Ms. Sara Yingling, as well as previous research support in the greenhouse by Ms. Alison Welch, and Ms. Jessica Perkins. To all my lab and field colleagues, I appreciate your intellectual enlightenment and thoughtful suggestions throughout the period of this study and for making this period of life an exciting and pleasant interaction for me in the lab and greenhouses at the University of Arkansas, Fayetteville, Arkansas. I would like to present my bouquet of thanks to all field and office staff members of the department of Crop, Soil, & Environmental Sciences at the University of Arkansas, especially Ms. Joda Fiore who helped me in the early days as a graduate student. I owe deep, profound and fervent thanks to all my friends, batch mates, seniors and juniors for their timely help and best wishes. Finally, I would like to thank all those people who knowingly or unknowingly helped me in my endeavor and I would like to wish everyone whose names are not written here or forgotten unintentionally, the best of luck for their future. As I submit my dissertation, it gives me a sense of immense contentment to express my gratitude to all those who have contributed in their special way to make the completion of my thesis possible, and help me take the step forward towards other goals in life. DEDICATION This dissertation is dedicated to my parents Mr. JASBEER SINGH and Mrs. KANTI DEVI, To Whom I Owe My Identity TABLE OF CONTENTS CHAPTER-I INTRODUCTION AND REVIEW OF LITERATURE INTRODUCTION...........................................................................................................................2 REVIEW OF LITERATURE...........................................................................................................6
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