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University of Florida Thesis Or Dissertation Formatting CHARACTERIZING PHENOTYPIC AND GENETIC VARIATIONS IN THE INVASIVE CHILLI THRIPS, SCIRTOTHRIPS DORSALIS HOOD (THYSANOPTERA: THRIPIDAE) By VIVEK KUMAR A DISSERTATION PRESENTED TO THE GRADUATE SCHOOL OF THE UNIVERSITY OF FLORIDA IN PARTIAL FULFILLMENT OF THE REQUIREMENTS FOR THE DEGREE OF DOCTOR OF PHILOSOPHY UNIVERSITY OF FLORIDA 2012 1 © 2012 Vivek Kumar 2 To my family I would have not succeeded if I had not failed 3 ACKNOWLEDGMENTS The list is countless, but I would like to begin by thanking my major advisor Dr. Dakshina R. Seal who gave me the opportunity to work on this project. His constant support, encouragement and kindle faith in me always boosted me and kept me focused towards the goal. My sincere thanks to Vegetable IPM Lab members of TREC, Cathie Sabines, Carlos, Charles Carter, and Jacinto who played important role in my projects while being behind the scene. Special thanks to graduate committee member Dr. Cindy L. McKenzie for her unwavering support and allowing me to use USDA-ARS facility, without which completion of this project would have been difficult. I would like to extend my thanks to other committee members Dr. David Schuster, Dr. Lance Osborne, Dr. James Maruniak and Dr. Shouan Zhang for their valuable suggestions, constructive criticism and guidance during the doctoral program. I am also grateful to Dr. Ale Maruniak, John Prokop, and Michael Cartwright for helping me with insect molecular techniques and Dr. Robert Shatters, Dr. Aaron M. Dickey for scientific advice to understand the output. I owe sincere thanks to Dr. Wayne Hunter, Lyle Buss and Thomas Skarlisnky who trained me in various photographic techniques and helped me identify different thrips species. I thank Dr. Donald Hall, Dr. Heather McAuslane, Debbie Hall and Maria Bernal for making me aware of the rules and departmental requirements and updating me with the deadlines. I also thank to my colleague and friends at University of Florida Deepak Golasangimath, Megha Kalsi, Amit Gupta, Phalgun Nelaturu, Sudhamshu Acharya, Ameya and Mithila Gondhalekar, Tamrat Wuletaw, Nichole Dobbs, Xiaodan Mo, Germo Tatto for making life happy and easier. Great deal of thanks to Dr. Jeet and Seemanti 4 Sengupta for encouragements, advice and friendly nature. I will always cherish those moments. I am indebted to my parents late Ram Lochan Jha and Kali Jha, and brothers- Pramod Jha, Ashish Jha, Santosh Jha and other family members who showed confidence and continuously encouraged me to complete my doctoral program. The achievements and awards earned during this journey are dedicated to them. Special thanks to my father-in-law Kuldeep Singh Kakkar, whose never ending challenges motivated me to go for higher studies in this great nation. Words fail to express thanks to my wife Garima Kakkar Jha, for her endless, unconditional love and support without whom I could not have accomplished this task. Finally, I would like to thank almighty God for giving me eternal life, his blessings and the path shown during my journey. 5 TABLE OF CONTENTS page ACKNOWLEDGMENTS .................................................................................................. 4 LIST OF TABLES ............................................................................................................ 8 LIST OF FIGURES .......................................................................................................... 9 ABSTRACT ................................................................................................................... 11 CHAPTER 1 LITERATURE REVIEW .......................................................................................... 13 Introduction ............................................................................................................. 13 Background Information .......................................................................................... 14 Economic Host Plants ............................................................................................. 16 Geographical Distribution ........................................................................................ 17 Worldwide distribution ...................................................................................... 17 U. S. invasion ................................................................................................... 17 Host Damage .......................................................................................................... 19 Summary of Damage Symptoms ...................................................................... 20 Identification ............................................................................................................ 20 Life Cycle ................................................................................................................ 21 Management of S. dorsalis ..................................................................................... 22 Cultural Practices ............................................................................................. 22 Chemical Control .............................................................................................. 23 Biological Control ............................................................................................. 25 2 SCIRTOTHRIPS DORSALIS (THYSANOPTERA: THRIPIDAE): SCANNING ELECTRON MICROGRAPHS OF KEY TAXONOMIC TRAITS AND A PRELIMINARY MORPHOMETRIC ANALYSIS OF THE GENERAL MORPHOLOGY OF POPULATIONS OF DIFFERENT CONTINENTS .................. 36 Introduction ............................................................................................................. 36 Materials and Methods............................................................................................ 39 Identification of Specimens ............................................................................... 40 Scanning Electron Microscopy ......................................................................... 40 Morphometric Measurements of Major Body Traits .......................................... 41 Statistical Analysis ............................................................................................ 41 Results .................................................................................................................... 42 Identification of Specimens ............................................................................... 42 Morphometric Measurements of Major Morphological Features ....................... 43 Discussion .............................................................................................................. 45 6 3 COUPLING SCANNING ELECTRON MICROSCOPY WITH DNA BAR CODING FOR MORPHOLOGICAL AND MOLECULAR IDENTIFICATION OF THRIPS ................................................................................................................... 68 Introduction ............................................................................................................. 68 Materials and Methods............................................................................................ 71 Morphological Identification .............................................................................. 71 Molecular Identification ..................................................................................... 72 PCR protocol and sequencing ................................................................... 72 Results and Discussion........................................................................................... 73 4 INTRAGENOMIC VARIATION IN mtCO1 AND rDNA ITS2 OF THREE MAJOR THRIPS SPECIES, SCIRTOTHRIPS DORSALIS, THRIPS PALMI AND FRANKILINIELLA OCCIDENTALIS (THYSANOPTERA: THRIPIDAE) .................. 79 Introduction ............................................................................................................. 79 Materials and Methods............................................................................................ 84 Taxon Sampling ............................................................................................... 84 Morphological Identification of Thrips ............................................................... 84 DNA Processing ............................................................................................... 85 Sequence Alignment and Genetic Distance Matrix .......................................... 86 Results .................................................................................................................... 87 Inter- and Intragenomic Variation ..................................................................... 87 Parsimony Analysis of ITS2 .............................................................................. 90 Discussion .............................................................................................................. 90 Mitochondrial Cytochrome Oxidase I ................................................................ 90 Internal Transcribed Spacer 2 Variation ........................................................... 92 5 SUMMARY ........................................................................................................... 110 LIST OF REFERENCES ............................................................................................. 113 BIOGRAPHICAL SKETCH .......................................................................................... 129 7 LIST OF TABLES Table page 1-1 Plants infested with S. dorsalis as reported in global pest and disease database.
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