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THE PREVALENCE and MOLECULAR MECHANISMS of SINGLE-SITE FUNGICIDE RESISTANCE in the APPLE SCAB PATHOGEN, VENTURIA INAEQUALIS a Di

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THE PREVALENCE and MOLECULAR MECHANISMS of SINGLE-SITE FUNGICIDE RESISTANCE in the APPLE SCAB PATHOGEN, VENTURIA INAEQUALIS a Di THE PREVALENCE AND MOLECULAR MECHANISMS OF SINGLE-SITE FUNGICIDE RESISTANCE IN THE APPLE SCAB PATHOGEN, VENTURIA INAEQUALIS A Dissertation Presented to the Faculty of the Graduate School of Cornell University in Partial Fulfillment of the Requirements for the Degree of Doctor of Philosophy by Sara M. Villani February 2016 THE PREVALENCE AND MOLECULAR MECHANISMS OF SINGLE-SITE FUNGICIDE RESISTANCE IN THE APPLE SCAB PATHOGEN, VENTURIA INAEQUALIS Sara M. Villani, Ph.D. Cornell University 2016 ABSTRACT Apple scab, caused by the fungal pathogen Venturia inaequalis is among the most prevalent and economically important diseases in commercial apple orchards in regions with temperate climates worldwide. The absence of durable apple scab resistance in the majority of commercially desired cultivars often mandates numerous fungicide applications each season to successfully manage the disease. Highly effective single-site fungicides have enhanced the ability to manage a number of phytopathogenic fungi, including V. inaequalis. Unfortunately the highly specific nature and repetitive use of these fungicides has led to their diminished efficacy and widespread resistance in V. inaequalis. The identification of the prevalence of single-site resistance in populations of V. inaequalis and an understanding of molecular mechanisms of resistance to these fungicides can aid in the rapid detection of fungicide resistance, the deployment of fungicide anti-resistance management strategies, and the development of efficient and effective chemical management programs for apple scab control. In this dissertation, a combination of applied and basic research was implemented to gain further understanding of the molecular mechanisms associated with practical resistance to DMI and QoI fungicides in isolates and/or populations of V. inaequalis. Microscopy-aided mycelial growth assays were used to determine sensitivity phenotypes to the DMI fungicides myclobutanil and difenoconazole and to the QoI fungicide trifloxystrobin. The majority of populations of V. inaequalis collected throughout the Northeastern, Mid-Atlantic, and Mid-Western United States were found to have reduced sensitivity or practical resistance to myclobutanil, but not difenoconazole. Illumina sequencing and reverse-transcriptase quantitative PCR were used to identify the contribution of target gene overexpression and the presence of upstream repeated elements in myclobutanil and difenoconazole resistance. Another molecular technique, allele- specific quantitative PCR was used to evaluate the role of target gene heteroplasmy in the quantitative resistance response and practical resistance to trifloxystrobin in isolates and populations of V. inaequalis. Additionally, baseline sensitivity of V. inaequalis to three SDHI fungicides was determined, and the sdhB gene, a target for SDHI fungicides, was identified and characterized. In summary, the results of this dissertation contribute to the identification and understanding of mechanisms associated with single-site fungicide resistance in V. inaequalis. BIOGRAPHICAL SKETCH Sara Michelle Villani was born on April 17, 1983 to Constance Villani and the late Dr. Michael G. Villani. She has a younger sister, Kate Villani and a wonderful Soft Coated Wheaten Terrier, Allie, with whom she’s been able to share her entire graduate experience. Sara’s interest in applied agricultural research began in 1999 in the entomology laboratory of Dr. Greg Loeb at the Cornell University New York State Agricultural Experiment Station in Geneva, NY. As a summer research technician for seven years in Dr. Loeb’s program, Sara had the opportunity to become involved in several projects focusing on insect pests of grapes and small fruit, including the implementation of tydeid mites, Orthotydeus lambi, as biological control agents of grape powdery mildew. After earning a B. Sci. in Chemistry from the State University of New York at Geneseo in 2005, Sara joined the plant pathology program of Dr. Herb Aldwinckle at the New York State Agricultural Experiment Station as a research technician and assisted on research of the fire blight pathogen, Erwinia amylovora. Sara joined the Cornell University Tree Fruit and Berry Pathology program led by Dr. Kerik Cox in 2007, where she has continued to conduct research to this day. After conducting research on fungicide resistance in brown rot and apple scab and presenting results at regional and national research and extension meetings with Dr. Cox, Sara decided pursue her doctorate in plant pathology at Cornell University as part of the Employee Degree Program in 2012. Her research goals included investigating the prevalence of single-site fungicide resistance in the apple scab pathogen Venturia inaequalis, and gaining better understanding to the molecular mechanisms governing this resistance. In December 2015, Sara will become a member of the Plant Pathology faculty at North Carolina State University. iii DEDICATION In memory of my father: Your guidance, encouragement, generosity, and love are always with me. To laugh often and love much; To win the respect of intelligent people and the affection of children; To earn the approval of honest critics and endure the betrayal of false friends; To appreciate beauty; To find the best in others; To give of one’s self; To leave the world a bit better, whether by a healthy child, a garden patch, or a redeemed social condition; To have played and laughed with enthusiasm and sung with exultation; To know even one life has breathed easier because you have lived… This is to have succeeded. -Ralph Waldo Emerson iv ACKNOWLEDGMENTS I would like to extend a general acknowledge to everyone who has made my past 16 years at Cornell University an enriching and truly enjoyable experience. I must first thank Dr. Kerik Cox for his unwavering confidence, for his selfless leadership, and his enthusiasm for research. Kerik, you have not only played a vital role in my career direction, but as a mentor, you have made me a better researcher, teacher, and leader. As a friend, you have been one of my greatest supporters and listeners, and have prepared me for success beyond Geneva. I would also like to thank my graduate committee, Dr. Thomas Burr, Dr. Dave Rosenberger, and Dr. Lailiang Cheng for their guidance in research and professional development. I also greatly appreciate the assistance of the many undergraduate who have come and gone in the Cox program including Jess Raes, Charlotte Lehman, Jenny O’Brien, Kathryn Abbot, Juliana Freier, Mike Ellis, Chi Kong Poon, Gabe Brind-Amour, Katrin Ayer, Erin Miller, Shawn Lyons, Pippa Lehman, Zack Frederick, Kate Villani, Allison Wentworth, Emily Adams, Jake Grimaldi, Devin Henry, Jessica Hoffman, Shirley Kuehne, and Jason Hagel. Outside of academia, I would like to thank my grandparents for their generosity and support through the entirety of my education and for their persistence in bugging me about getting a graduate degree! Lastly, but certainly not least in importance, I’d like to thank my mother and sister Kate. Without your endless love, support, and willingness to puppy-sit my dog, this dissertation would have continued to be a mere “thought”. v TABLE OF CONTENTS BIOGRAPHICAL SKETCH ......................................................................................................... iii DEDICATION ............................................................................................................................... iv ACKNOWLEDGMENTS ...............................................................................................................v LIST OF FIGURES ....................................................................................................................... ix LIST OF TABLES ......................................................................................................................... xi CHAPTER 1 INTRODUCTION ...........................................................................................................................1 WORKS CITED ............................................................................................................................16 CHAPTER 2: PREVALENCE OF MYCLOBUTANIL RESISTANCE AND DIFENOCONAZOLE SENSITIVITY IN POPULATIONS OF VENTURIA INAEQUALIS ABSTRACT ...................................................................................................................................26 INTRODUCTION .........................................................................................................................28 MATERIALS AND METHODS ...................................................................................................31 RESULTS ......................................................................................................................................37 DISCUSSION ................................................................................................................................54 ACKNOWLEDGMENTS .............................................................................................................61 WORKS CITED ............................................................................................................................63 CHAPTER 3: OVEREXPRESSION OF THE CYP51A1 GENE AND REPEATED ELEMENTS MEDIATE DIFFERENTIAL SENSITIVITY TO DMI FUNGICIDES IN VENTURIA INAEQUALIS ABSTRACT ...................................................................................................................................68 INTRODUCTION .........................................................................................................................70
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