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Comparative Genomics of Gossypium Spp

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Comparative Genomics of Gossypium Spp COMPARATIVE GENOMICS OF GOSSYPIUM SPP. THROUGH GBS AND CANDIDATE GENES – DELVING INTO THE CONTROLLING FACTORS BEHIND PHOTOPERIODIC FLOWERING A Dissertation by CARLA JO LOGAN YOUNG Submitted to the Office of Graduate Studies of Texas A&M University in partial fulfillment of the requirements for the degree of DOCTOR OF PHILOSOPHY Approved by: Chair of Committee, Alan E. Pepper Committee Members, Konstantin V. Krutovsky John Z. Yu Keerti S. Rathore Wayne K. Versaw Head of Department, U. J. McMahan August 2013 Major Subject: Biology Copyright 2013 Carla Jo Logan Young ABSTRACT Cotton has been a world-wide economic staple in textiles and oil production. There has been a concerted effort for cotton improvement to increase yield and quality to compete with non-natural man-made fibers. Unfortunately, cultivated cotton has limited genetic diversity; therefore finding new marketable traits within cultivated cotton has reached a plateau. To alleviate this problem, traditional breeding programs have been attempting to incorporate practical traits from wild relatives into cultivated lines. This incorporation has presented a new problem: uncultivated cotton hampered by photoperiodism. Traditionally, due to differing floral times, wild and cultivated cotton species were unable to be bred together in many commercial production areas world-wide. This worldwide breeding problem has inhibited new trait incorporation. Before favorable traits from undomesticated cotton could be integrated into cultivated elite lines using marker-assisted selection breeding, the markers associated with photoperiod independence needed to be discovered. In order to increase information about this debilitating trait, we set out to identify informative markers associated with photoperiodism. This study was segmented into four areas. First, we reviewed the history of cotton to highlight current problems in production. Next, we explored cotton’s floral development through a study of floral transition candidate genes. The third area was an in-depth analysis of Phytochrome C (previously linked to photoperiod independence in ii other crops). In the final area of study, we used Genotype-By-Sequencing (GBS), in a segregating population, was used to determine photoperiod independence associated with single nucleotide polymorphisms (SNPs). In short, this research reported SNP differences in thirty-eight candidate gene homologs within the flowering time network, including photoreceptors, light dependent transcripts, circadian clock regulators, and floral integrators. Also, our research linked other discrete SNP differences, in addition to those contained within candidate genes, to photoperiodicity within cotton. In conclusion, the SNP markers that our study found may be used in future marker assisted selection (MAS) breeding schemas to incorporate desirable traits into elite lines without the introgression of photoperiod sensitivity. iii DEDICATION To Ryan iv ACKNOWLEDGEMENTS I would like to thank my committee chair, Dr. Alan Pepper, and my committee members, Dr. Wayne Versaw, Dr. Keerti Rathore, Dr. Konstantin Krutovsky, and Dr. John Yu, for their guidance and support throughout the course of my research. I would like to impart my deepest thanks to Richard Percy for providing the cotton material for this research. Thanks go to my friends, colleagues, lab members, USDA-ARS-SPARC employees, and the department faculty and staff for making my time at Texas A&M University a great experience. I also want to extend my gratitude to the Cotton Inc., which provided funding to complete this study. My appreciation goes out to the USDA- ARS for their collaboration in this project. I give my thanks to all the members in the Thesis/Dissertation group at the Texas A&M University Writing Center. I would like to recognize to Dr. Patricia Goodson and Dr. Dominique Chlup for their writing studios. Also, I would like to thank the Texas A&M University Writing Center for their help and motivation in both my DATA sessions with Mary Beth Schaefer and in the Thesis/Dissertation Boot Camp staff. Finally, thanks to my mother and father for their encouragement, my family for their support, and to my husband for his patience and love. I would like to thank the UMID Presidential Fund of the Government of Uzbekistan for providing support for the I.Y.A. to conduct research at Texas A&M University. Also, I thank the USDA-ARS International Research Programs for providing v research grant support for this study under the project P-121. I would like to thank Texas A&M University and Cotton Incorporated for their support by providing a Texas A&M University Regent’s Fellowship and a Cotton Incorporated Fellowship (Project 08-380). I would like to give thanks to A. Millie Burrell for critically reading our manuscript and supporting my through the years. I would also like to thank Natalie Ware for the years of help that she provided in our continued research. Cotton Inc. provided support to conduct our research here at Texas A&M University. Dr. Richard Percy from USDA-ARS-SPARC provided the parental lines PS-6 and K-46 that he has been using in his wild Germplasm conversion since the 1990’s. Dr. Richard Percy from USDA-ARS-SPARC provided the conversion lines of BCF4 (PS-5xwild) and BCF2 (PS-6xwild) populations that he has been working on since the 1990’s. We wish to thank Kostantin V. Krutovsky for helpful advice on strategies to discover homeologs of candidate genes. We would like to thank Texas A&M University undergraduate Chris Lyle for helping collect all the plant populations DNA during 2008 and Hurricane Ike. We would like to thank, Texas A&M University undergraduate and USDA ARS student employee, Kara Allen for all her hard work and dedication in helping analyze and organize the dN/dS and TGBS data. vi NOMENCLATURE amiRNA Artificial micro-RNA B Blue Light BC4F2 Back-Crossed 4 Generations and Filial Generation 2 BC4F5 Back-Crossed 4 Generations and Filial Generation 5 bp Base Pair(s) Btn Biotin dN Non-synonymous Nucleotide Substitution Rate dS Synonymous Nucleotide Substitution Rate FR Far-Red Light GBS Genotype-By-Sequencing InDel Insertion/Deletion Polymorphism IPGB Institute for Plant Genomics and Biotechnology Ka Non-synonymous Nucleotide Substitution Rate kb Kilobase(s) kDa KiloDalton Ks Synonymous Nucleotide Substitution Rate LD Long Day LD Linkage Disequilibrium MAS Marker Assisted Selection miRNA Micro-RNA vii MYA Million Years Ago NJ Neighbor Joining nt Nucleotide nM Nano-Molar PCR Polymerase Chain Reaction PD Photoperiod Dependent PI Photoperiod Independent PR Progeny R Red Light RNAi RNA Interference SD Short Day SID Single Insertion/Deletion Polymorphism SNP Single Nucleotide Polymorphism TGBS Targeted Genotype-By-Sequencing US United States of America USDA-ARS-SPARC United States Department of Agriculture – Agricultural Research Service – Southern Plains Agricultural Research Center viii TABLE OF CONTENTS Page ABSTRACT ...................................................................................................................... ii DEDICATION ................................................................................................................. iv ACKNOWLEDGEMENTS .............................................................................................. v NOMENCLATURE ......................................................................................................... vii TABLE OF CONTENTS ................................................................................................. ix LIST OF FIGURES ......................................................................................................... xii LIST OF TABLES ......................................................................................................... xiv LIST OF EQUATIONS ................................................................................................ xvii CHAPTER I INTRODUCTION AND LITERATURE REVIEW ................................... 1 Introduction .................................................................................................................... 1 What this Study Asked ................................................................................................ 2 Domestication ............................................................................................................. 3 Flowering .................................................................................................................... 6 Long Day versus Short Day Plants ............................................................................. 7 Current Knowledge about the Flowering Process ....................................................... 8 CHAPTER II DUPLICATION, DIVERGENCE, AND PERSISTENCE IN THE PHYTOCHROME PHOTORECEPTOR GENE FAMILY OF COTTONS (GOSSYPIUM SPP.) ........................................................................................................ 22 Synopsis of Phytochrome C ......................................................................................... 22 Duplication, Divergence and Persistence in the Phytochrome Photoreceptor Gene Family of Cottons (Gossypium spp.) .................................................................. 31 Overview ................................................................................................................... 31 Background ............................................................................................................... 32 Results ......................................................................................................................
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