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An Untapped Genetic Resource for Abiotic Stress Tolerant Traits for Rice Improvement

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An Untapped Genetic Resource for Abiotic Stress Tolerant Traits for Rice Improvement Mississippi State University Scholars Junction Theses and Dissertations Theses and Dissertations 8-6-2021 Weedy rice (Oryza sativa ssp.): an untapped genetic resource for abiotic stress tolerant traits for rice improvement Shandrea D. Stallworth [email protected] Follow this and additional works at: https://scholarsjunction.msstate.edu/td Recommended Citation Stallworth, Shandrea D., "Weedy rice (Oryza sativa ssp.): an untapped genetic resource for abiotic stress tolerant traits for rice improvement" (2021). Theses and Dissertations. 5272. https://scholarsjunction.msstate.edu/td/5272 This Dissertation - Open Access is brought to you for free and open access by the Theses and Dissertations at Scholars Junction. It has been accepted for inclusion in Theses and Dissertations by an authorized administrator of Scholars Junction. For more information, please contact [email protected]. Template APA v4.3 (beta): Created by T. Robinson 01/2021 Weedy rice (Oryza sativa ssp.): an untapped genetic resource for abiotic stress tolerant traits for rice improvement By TITLE PAGE Shandrea D. Stallworth Approved by: Te-Ming (Paul) Tseng Daniel B. Reynolds Edilberto Redona Shien Lu Daniel G. Peterson Michael S. Cox (Graduate Coordinator) Scott T. Willard (Dean, College of Agriculture and Life Sciences) A Dissertation Submitted to the Faculty of Mississippi State University in Partial Fulfillment of the Requirements for the Degree of Doctor of Philosophy in Weed Science in the Department of Plant and Soil Sciences Mississippi State, Mississippi August 2021 Copyright by COPYRIGHT PAGE Shandrea D. Stallworth 2021 Name: Shandrea D. Stallworth ABSTRACT Date of Degree: August 6, 2021 Institution: Mississippi State University Major Field: Weed Science Major Professor: Te-Ming (Paul) Tseng Title of Study: Weedy rice (Oryza sativa ssp.): an untapped genetic resource for abiotic stress tolerant traits for rice improvement Pages in Study 106 Candidate for Degree of Doctor of Philosophy Rice (Oryza sativa) is the staple food for more than 3.5 billion people worldwide. As the population continues to grow, rice yield will need to increase by 1% every year for the next 30 years to keep up with the growth. In the US, Arkansas accounts for more than 50% of rice production. Over the last 68 years, rice production has continued to grow in Mississippi, placing it in fourth place after Arkansas, Louisiana, and California. Due to increasing rice acreage, regionally and worldwide, the need to develop abiotic stress-tolerant rice has increased. Unfortunately, current rice breeding programs lack genetic diversity, and many traits have been lost through the domestication of cultivated rice. Currently, stressors stemming from the continued effects of climate change continue to impact rice. To counteract the impacts of climate change, research has shifted to evaluating wild and weedy relatives of rice to improve breeding techniques. Weedy rice (Oryza sativa ssp.) is a genetically similar, noxious weed in rice with increased competitive ability. Studies have demonstrated that weedy rice has increased genetic variability and inherent tolerance to abiotic stressors. The aims of this study were to 1) screen a weedy rice mini-germplasm for tolerance to cold, heat, and complete submergence-stress, 2) utilize simple sequence repeat (SSR) markers and single nucleotide polymorphisms to evaluate the genetic diversity of the weedy rice population, and 3) use genome-wide association (GWAS) to identify SNPs associated with candidate genes within the population. DEDICATION This body of work is dedicated to my family, closest friends, and MANRRS. Thank you all for your continued support and encouragement. If it were not for you all, I would not have been able to complete my degree. To my parents, Edwin O. Little and Tifni Jennings, thank you for constantly pushing me to strive for the best. To my grandparents, thank you for opening doors and never giving up. To my best friends, thank you for understanding my absences and missed milestones. Finally, to my brothers, Edwin II and Kenneth, for believing that your sister would always do great things. ii ACKNOWLEDGEMENTS I would like to thank Dr. Te-Ming Tseng for his continued encouragement, guidance, and leadership during my time at Mississippi State University. Thank you for never giving up on me and providing me with a creative space to answer many research questions. Your patience and wisdom have always pushed me to flourish as a weed scientist. To my dissertation committee: Drs. Daniel Reynolds, Ed Redona, Shien Lu, and Daniel Peterson, thank you for always being available during this journey. Your feedback will always be invaluable. To Dr. Brian Baldwin, thank you for seeing the things that most could not and for always being a resource, no matter the subject matter. To Dr. Scott Willard, thank you for always having my back. You have written numerous recommendation letters that have projected me into a promising career. Thank you to the administrative staff in the Department of Plant and Soil Sciences for being my extended family and celebrating my wins as if they were your own. I would also like to thank the Weed Physiology research group: Swati Shrestha, Gourav Sharma, Ziming Yue, Brooklyn Schumaker, Grace Fuller, and many undergraduate student works, visiting scholars, and research technicians who never hesitated to assist me with my research. To my support system: Christien, Johannah, Nicole, Shameca, Nikole, Tai, Lateshia, Brandon, and Jont’e, I cannot thank you all enough. From the unexpected packages and flowers to random phone calls just because thank you for loving me and believing I could do this. iii TABLE OF CONTENTS DEDICATION ................................................................................................................................ ii ACKNOWLEDGEMENTS ........................................................................................................... iii LIST OF TABLES ......................................................................................................................... vi LIST OF FIGURES ...................................................................................................................... vii CHAPTER I. LITERATURE REVIEW ..................................................................................................1 1.1 Introduction ...........................................................................................................1 1.2 Evolutionary Background ......................................................................................2 1.3 Competitive Ability ...............................................................................................4 1.4 References .............................................................................................................6 II. SCREENING DIVERSE WEEDY RICE (ORYZA SATIVA SSP.) MINI GERMPLASM FOR TOLERANCE TO COLD, HEAT, AND COMPLETE SUBMERGENCE STRESS DURING SEEDLING STAGE ........................................................................10 2.1 Abstract ................................................................................................................10 2.2 Introduction .........................................................................................................11 2.3 Materials and Methods ........................................................................................16 2.3.1 Plant Materials ...............................................................................................16 2.3.2 Cold Tolerance Screening .............................................................................17 2.3.3 Heat Tolerance Screening ..............................................................................18 2.3.4 Submergence Tolerance Screening ...............................................................18 2.3.5 Statistical Analysis ........................................................................................19 2.4 Results and Discussion ........................................................................................20 2.4.1 Cold Tolerance Screening .............................................................................20 2.4.2 Heat Tolerance Screening ..............................................................................22 2.4.3 Submergence Tolerance Screening ...............................................................26 2.5 Conclusion ...........................................................................................................30 2.6 References ...........................................................................................................43 III. ASSESSING THE GENETIC DIVERSITY OF WEEDY RICE MINI-GERMPLASM USING SSR MARKERS AND SNPs .............................................................................50 iv 3.1 Abstract ................................................................................................................50 3.2 Introduction .........................................................................................................51 3.3 Materials and Methods ........................................................................................53 3.3.1 Plant Materials ...............................................................................................53 3.3.2 DNA Extraction .............................................................................................54 3.3.3 PCR Amplification using SSR Markers ........................................................54
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