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Managing Phomopsis Stem Canker of Sunflower Using Improved Diagnosis and Quantification of the Causal Pathogens Taylor Rae Olson South Dakota State University

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Managing Phomopsis Stem Canker of Sunflower Using Improved Diagnosis and Quantification of the Causal Pathogens Taylor Rae Olson South Dakota State University South Dakota State University Open PRAIRIE: Open Public Research Access Institutional Repository and Information Exchange Theses and Dissertations 2017 Managing Phomopsis Stem Canker of Sunflower Using Improved Diagnosis and Quantification of the Causal Pathogens Taylor Rae Olson South Dakota State University Follow this and additional works at: http://openprairie.sdstate.edu/etd Part of the Plant Pathology Commons Recommended Citation Olson, Taylor Rae, "Managing Phomopsis Stem Canker of Sunflower Using Improved Diagnosis and Quantification of the Causal Pathogens" (2017). Theses and Dissertations. 1184. http://openprairie.sdstate.edu/etd/1184 This Thesis - Open Access is brought to you for free and open access by Open PRAIRIE: Open Public Research Access Institutional Repository and Information Exchange. It has been accepted for inclusion in Theses and Dissertations by an authorized administrator of Open PRAIRIE: Open Public Research Access Institutional Repository and Information Exchange. For more information, please contact [email protected]. MANAGING PHOMOPSIS STEM CANKER OF SUNFLOWER USING IMPROVED DIAGNOSIS AND QUANTIFICATION OF THE CAUSAL PATHOGENS BY TAYLOR RAE OLSON A thesis submitted in partial fulfillment of the requirements for the Master of Science Major in Plant Science South Dakota State University 2017 iii ACKNOWLEDGEMENTS First and foremost, I would like to give a thank you to my dear family. My parents have given me the opportunity to further my education beyond high school, and I am forever in debt to them for everything they have sacrificed for me. I would like to thank my brothers, for encouraging and supporting my interest in agriculture. And most importantly, I would like to thank my fiancé John. He inspires me to be a better person every single day, and always believes in me, even when I don’t believe in myself. He has truly been my rock, and I am forever grateful for him. I would like to sincerely thank my advisor Dr. Febina Mathew for not only giving me the opportunity to pursue my master’s degree, for her patience, guidance, inspiration and support during this research. I genuinely appreciate everything she has done for me not only throughout my master’s degree, but in all areas outside graduate school. She has truly been an invaluable mentor to me and I can’t thank her enough. I would also like to thank all the members of my thesis advisory committee and my graduate faculty representative; Dr. Adam Varenhorst, Dr. Chris Graham, Dr. Larry Osborne, and Dr. Richie Meyers. They have been so generous with their time and have given me continuous support guidance throughout this research. I want to also give a special thanks to everyone in Dr. Mathew’s lab who have generously assisted and directed me throughout my research, especially Brian Kontz and Anjana Adhikari. This research would not have been possible without either of them. Brian’s patience and guidance throughout the molecular diagnostics aspect of this research was more than I could ask for, and Anjana has been instrumental throughout my entire research project, always willing to lend me a hand whether it’s making media, iv plating sunflower samples, or helping with my greenhouse and field experiments. I also want to thank Nathan Braun and Lee Gilbertson, for their continued help with my field trials. Special thanks also to Ms. Kathy Grady for help and guidance with my field trials, and Dalitso Yabwalo for help with spraying fungicides. I would also like to thank all of the temporary and hourly employees working in Dr. Mathew’s lab, without their help this research would not have been possible. I also want to give a special thanks to Dr. Mathew’s other graduate students; Paul Okello, John Posch, Rawnaq Chowdhury, and Krishna Ghimire for their sincere encouragement and moral support throughout all aspects of my master’s degree. They truly made work in the lab more enjoyable, and I wish all the best for them. I would also like to thank Dr. Laura Marek for sending me sunflower seeds from the USDA-ARS North Central Regional Plant Introduction Station (NCRPIS) for the germplasm screening portion of my research. I would also like to extend a sincere thank you to Dr. Sam Markell and Michelle Gilley for their support and for providing me infected sunflower samples from Minnesota and North Dakota for my study. I also would like to sincerely thank South Dakota State University and the Department of Agronomy, Horticulture and Plant Science for the opportunity and financial support, and also the South Dakota Oilseeds council for their financial support for this research. Finally, a special thanks to the National Sunflower Association for their financial support not only in this research but also for awarding me the Curtis Stern Memorial Scholarship to aid with other financial costs that come with graduate school. I am truly grateful. v TABLE OF CONTENTS ABBREVIATIONS……………………………………………………………………....ix LIST OF TABLES………………………………………………………………………...x LIST OF FIGURES……………………………………………………………………..xii ABSTRACT…………………………………………………………………………….xiii CHAPTER 1……………………………………………………………………………...1 1. Literature Review…………………………………………………………..………...1 1.1. Introduction……………………………………………………………………...1 1.1.1. History of Sunflower (Helianthus annuus L.)……………………………...1 1.1.2. Description……………………………………………………………..….2 1.1.3. Production……………………………………………………………..…..3 1.1.4. Growth Stages……………………………………………………..………4 1.1.5. Hybrid Selection……………………………………………………..…….4 1.1.6. Soil Types…………………………………………………………..……...6 1.1.7. Field Selection……………………………………………………..………6 1.1.8. Tillage……………………………………………………....…..…………7 1.1.9. Nutrition and Fertilizer………………………………………..…………...8 1.1.10. Planting Date………………………………………………………………9 1.1.11. Planting Depth……………………………………………………………..9 1.1.12. Row Spacing…………………………………………...………………….9 1.1.13. Plant Population……………………………………………………….......9 1.1.14. Harvest…………………………………………………………………...10 1.1.15. Common Pests in Sunflower……………………...……………………...10 vi 1.1.16. Pest Management………………………………………………………...12 1.2. Phomopsis stem canker……………………………………………..………….14 1.2.1. Introduction……………………………………………………..………..14 1.2.2. Taxonomy of Diaporthe…………………………………...…..…………16 1.2.3. Symptoms………………………………………………….…………….16 1.2.4. Disease Cycle………………………………………………..…………...18 1.3. Management of Phomopsis stem canker…………………………..………….20 1.3.1. Cultural Control………………………………………………….………20 1.3.2. Biological Control……………………………………………..…………21 1.3.3. Chemical Control………………………………………………..……….21 1.3.4. Genetic Resistance…………………………………………………..…...21 Literature cited………………………………………………………………….23 CHAPTER 2…………………………………………………………………………….30 1. Quantitative Polymerase Chain Reaction assays for species of Diaporthe causing Phomopsis stem canker of sunflower………………………………………………30 2.1. Abstract…………………………………………………………………………30 2.2. Introduction…………………………………………………………………….30 2.3. Materials and methods…………………………………………………………34 2.3.1. Diaporthe isolation and identification……………………………………34 2.3.2. Primer and probe development for the qPCR assays……………………..37 2.3.3. Specificity and sensitivity tests for the qPCR assays…………………….38 2.3.4. Reaction conditions for the qPCR assays…………………………………39 vii 2.3.5. Comparison of traditional plating to D. gulyae and D. helianthi qPCR assays…………………………………………………………………….39 2.3.6. Screening genotypes for resistance to D. gulyae and D. helianthi using qPCR…………………………………………………………………….40 2.4. Results………………………………………………………………………..…44 2.4.1. Diaporthe isolation and identification……………………………………44 2.4.2. Primer and probe development for the qPCR assays……………………..44 2.4.3. Specificity and sensitivity tests for the qPCR assays……………………..45 2.4.4. Comparison of traditional plating to D. gulyae and D. helianthi qPCR assays…………………………………………………………….………46 2.4.5. Screening genotypes for resistance to D. gulyae and D. helianthi using qPCR……………………………………………………………………..47 2.5.Discussion……………………………………………………………………….48 Literature cited………………………………………………………………….54 CHAPTER 3…………………………………………………………………………….81 3. Managing Phomopsis stem canker of sunflower (Helianthus annuus L.) using an integrated approach combining fungicide and host genetics……………………..81 3.1.Abstract………………………………………………………………………….81 3.2. Introduction…………………………………………………………………….81 3.3. Materials and methods…………………………………………………………84 3.3.1. Trial locations…………………………………………………………….84 3.3.2. Experimental design and treatments……………………………………..84 3.3.3. Disease assessment……………………………………………………….85 viii 3.3.4. Data analysis……………………………………………………………..86 3.4. Results…………………………………………………………………………..87 3.4.1. Trial locations…………………………………………………………….87 3.4.2. Experimental design and treatments……………………………………...87 Discussion……………………………………………………………………….89 Literature cited………………………………………………………………….95 CHAPTER 4…………………………………………………………………………...106 Conclusions………………………………………………………………………...106 Appendices…………………………………………………………………………108 ix ABBREVIATIONS oC = degree Celsius ANOVA= analysis of variance df = degrees of freedom χ2 = Chi-squared probability LSD = least significant difference ʄ = F-statistic/F-value P = probability DSI = disease severity index percentage DNA = deoxyribonucleic acid qPCR = quantitative polymerase chain reaction ITS = internal transcribed spacer EF1-α = translation elongation factor-1α ACT= actin MAT = mating-type PI = plant introduction Ct = Cycle threshold QoI = quinone outside inhibitor SDH = succinate dehydrogenase Kg = kilogram Ha = hectare spp = species x LIST OF TABLES Table 1.1. Sunflower growth stages and descriptions (Schneiter & Miller 1981)………...5 Table 2.1. Examination panel
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