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Role of Genetic Diversity in the Adaptive Success of Silverleaf Nightshade (Solanum Elaeagnifolium) Under Variable Environmental Pressures

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Role of Genetic Diversity in the Adaptive Success of Silverleaf Nightshade (Solanum Elaeagnifolium) Under Variable Environmental Pressures Role of genetic diversity in the adaptive success of silverleaf nightshade (Solanum elaeagnifolium) under variable environmental pressures by Joshua Singleton, B.S. A Thesis In Plant and Soil Science Submitted to the Graduate Faculty of Texas Tech University in Partial Fulfillment of the Requirements for the Degree of MASTER OF SCIENCES Approved Dr. Rosalyn Angeles-Shim Chair of Committee Dr. Cade Coldren Dr. Venugopal Mendu Dr. Junping Chen Mark Sheridan Dean of the Graduate School August, 2019 Copyright 2019, Joshua Singleton Texas Tech University, Joshua James Singleton, August 2019 ACKNOWLEDGMENTS I would like to thank everyone who has contributed to my personal development and success. Without every single person that has helped me along the way, this all would not have been possible. I would first like to thank my mother and father, who have pushed me to always pursue my dreams and aspirations. I would like to thank my two sisters, my family members, and close friends for their love and support. I would like to thank my lab mates Ritchel B. Gannaban and Puneet Kaur Mangat for their patience and support. I would like to thank Dr. Junping Chen and Dr. Venugopal Mendu for their time and contribution in my graduate committee. I would like to thank Dr. Cade Coldren for his time and patience in setting up the EDYS model for my use in this research, as wells as, helping me learn how to use the EDYS user interface properly. Finally, I would like to thank Dr. Rosalyn B. Angeles-Shim for her overwhelming support and guidance throughout my entire graduate study. ii Texas Tech University, Joshua James Singleton, August 2019 TABLE OF CONTENTS ACKNOWLEDGMENTS .................................................................................... ii ABSTRACT ............................................................................................................v LIST OF TABLES ............................................................................................... vi LIST OF FIGURES ............................................................................................ vii I. REVIEW OF LITERATURE ...........................................................................1 Biology of silverleaf nightshade ........................................................................1 Economic importance of silverleaf nightshade as a noxious weed and a non-host vector of important plant pests and diseases .................................2 Methods of controlling silverleaf nightshade ....................................................4 Chemical control ..........................................................................................4 Mechanical and cultural control ...................................................................5 Biological control.........................................................................................6 Molecular mechanisms underlying the adaptive success of the silverleaf nightshade ..........................................................................................................7 Phenotypic plasticity………………………………………………………7 Genetic diversity…………………………………………………………..8 II. GENETIC DIVERSITY AND POPULATION STRUCTURE OF SILVERLEAF NIGHTSHADE (SOLANUM ELAEAGNIFOLIUM) FROM TEXAS, USA ...........................................................................................18 Introduction ......................................................................................................18 Materials and Methods .....................................................................................21 Cross-species transferability of DNA markers for genotyping..................21 Assessment of genetic diversity across different populations of silverleaf nightshade using morphological and DNA markers ..................22 Results and Discussion ....................................................................................23 Transferability of S. lycopersicum- and S. lycopersicoides-specific DNA markers to silverleaf nightshade ................................................................23 Descriptive statistics of DNA markers used in genetic diversity assessment studies ......................................................................................25 Genetic diversity and population structure of silverleaf nightshade ..........26 Conclusion .......................................................................................................28 III. SIMULATION OF ABOVEGROUND BIOMASS ACCUMULATION OF SILVERLEAF NIGHTSHADE IN CROPLANDS IN RESPONSE TO HERBICIDE PRESSURE ...................................................................................44 iii Texas Tech University, Joshua James Singleton, August 2019 Introduction ......................................................................................................44 Materials and Methods .....................................................................................45 Description of the study site ......................................................................45 Mapping of the study site for silverleaf nightshade density and presence of other vegetation .....................................................................................46 Required parameters to run EDYS simulation ...........................................47 EDYS simulation of silverleaf nightshade aboverground biomass production in the next 25 years under variable herbicide pressure ............48 Results and Discussion ....................................................................................49 Species composition of the study site ........................................................49 Simulation of aboveground biomass production of silverleaf nightshade in the next 25 years ....................................................................................49 Conclusion .......................................................................................................51 BIBLIOGRAPHY ................................................................................................59 iv Texas Tech University, Joshua James Singleton, August 2019 ABSTRACT The genetic diversity present within a plant population is a critical indicator of its capacity for adaptation to environmental variation and change. Solanum elaeagnifolium Cav (silverleaf nightshade; SLN) is an aggressive, highly persistent weed infesting agricultural croplands and rangelands in the US and abroad. The widespread geographical distribution of silverleaf nightshade indicates the presence of genetic mechanisms underlying fitness flexibility that allows the species to adapt to variable ecological niches. Based on DNA marker profiling and structure analysis, we were able to establish a significant degree of variation within all four of the tested SLN populations from different localities in Texas. We suggest from our study that the intracluster genetic variation found between the examined plant populations is entirely the product of obligate outcrossing that has resulted in an innate degree of variability. A simulation of a hypothetical development of herbicide resistance in silverleaf nightshade would be a significant resource to utilize, assess, and reference to design early onset preventive measures as opposed to in-response mitigation measures. The EDYS Simulation Model was used to conduct five independent scenarios to observe the simulated outcomes of differential herbicide control rates. The simulated herbicide resistance control rate of 75% reached a point of no recovery in biomass production in response to persistent annual herbicide control, while the herbicide resistance control rate of 50% and 25% showed both recovery and further growth. The results indicate that there is a threshold at which the value of resistance leads to either the species population dying off or recovering. v Texas Tech University, Joshua James Singleton, August 2019 LIST OF TABLES 1.1 Geographical distribution of silverleaf nightshade ....................................13 1.2 Known host plants of silverleaf nightshade ...............................................17 2.1 DNA markers tested for cross-transferability in silverleaf nightshade ..................................................................................................31 2.2 Sequences of cross-species markers that were used to genotype silverleaf nightshade populations ...............................................................38 2.3 PIC values of SSR markers that amplified polymorphic targets in silverleaf nightshade ..................................................................................40 2.4 Summary statistics of markers used for the assessment of genetic diversity in silverleaf nightshade populations from Texas ........................41 2.5 AMOVA analysis comparing genetic variation within and among individuals and among populations ...........................................................42 3.1 Number of individual plants per species for all plots in the study site ..............................................................................................................56 vi Texas Tech University, Joshua James Singleton, August 2019 LIST OF FIGURES 1.1 Silverleaf nightshade in field. Morphological variation in leaf size and shape; trichome density; flower color, shape, size, and petal number; anther number; berry shape and size of silverleaf nightshade individuals from the same population .....................................10 1.2 Typical growth cycle of silverleaf
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