Iowa State University Capstones, Theses and Graduate Theses and Dissertations Dissertations 2014 Phenology of infection on apple fruit by sooty blotch and flyspeck species in Iowa apple orchards and phylogenetic analysis to assess the evolutionary origins of sooty blotch and flyspeck on apple Siti Izera Ismail Iowa State University Follow this and additional works at: https://lib.dr.iastate.edu/etd Part of the Agricultural Science Commons, Agriculture Commons, and the Plant Pathology Commons Recommended Citation Ismail, Siti Izera, "Phenology of infection on apple fruit by sooty blotch and flyspeck species in Iowa apple orchards and phylogenetic analysis to assess the evolutionary origins of sooty blotch and flyspeck on apple" (2014). Graduate Theses and Dissertations. 13866. https://lib.dr.iastate.edu/etd/13866 This Dissertation is brought to you for free and open access by the Iowa State University Capstones, Theses and Dissertations at Iowa State University Digital Repository. It has been accepted for inclusion in Graduate Theses and Dissertations by an authorized administrator of Iowa State University Digital Repository. For more information, please contact [email protected]. Phenology of infection on apple fruit by sooty blotch and flyspeck species in Iowa apple orchards and phylogenetic analysis to assess the evolutionary origins of sooty blotch and flyspeck on apple by Siti Izera Ismail A dissertation submitted to the graduate faculty in partial fulfillment of the requirements for the degree of DOCTOR OF PHILOSOPHY Major: Plant Pathology Program of Study Committee: Mark L. Gleason, Co-Major Professor Thomas C. Harrington, Co-Major Professor Jean C. Batzer Dennis V. Lavrov Nick Lauter Alison E. Robertson Leonor F. S. Leandro Iowa State University Ames, Iowa 2014 Copyright © Siti Izera Ismail, 2014. All rights reserved. ii DEDICATION I respectfully dedicate this dissertation to my family, Norha, Zaharah, Irina and Iradah, who have always supported me throughout my Ph.D journey at ISU. I could have never done this without your faith, continuous encouragement and prayers. I also dedicate this dissertation my husband, Ardian and our wonderful son, Danish Mikael for being there for me throughout the entire doctorate program. Thank for all the sacrifices made to get to this point. iii TABLE OF CONTENTS Page DEDICATION ........................................................................................................... ii ACKNOWLEDGEMENTS ....................................................................................... iv ABSTRACT ............................................................................................................... vi CHAPTER 1. GENERAL INTRODUCTION .......................................................... 1 Dissertation organization ..................................................................................... 1 Literature review .................................................................................................. 4 Dissertation objectives ......................................................................................... 21 References ............................................................................................................ 22 CHAPTER 2. PHENOLOGY OF INFECTION ON APPLE FRUIT BY SOOTY BLOTCH AND FLYSPECK SPECIES IN IOWA APPLE ORCHARDS ............... 32 Abstract ................................................................................................................ 32 Introduction .......................................................................................................... 33 Materials and methods ......................................................................................... 35 Results .................................................................................................................. 41 Discussion ............................................................................................................ 44 Acknowledgements .............................................................................................. 47 References ............................................................................................................ 48 Table .................................................................................................................... 52 Figures.................................................................................................................. 57 CHAPTER 3. PHYLOGENETIC ANALYSIS TO ASSESS THE EVOLUTIONARY ORIGINS OF SOOTY BLOTCH AND FLYSPECK FUNGI ON APPLE .............. 61 Abstract ................................................................................................................ 62 Introduction .......................................................................................................... 62 Materials and methods ......................................................................................... 66 Results .................................................................................................................. 71 Discussion ............................................................................................................ 75 Acknowledgements .............................................................................................. 79 References ............................................................................................................ 79 Table .................................................................................................................... 83 Figures.................................................................................................................. 87 CHAPTER 4. GENERAL CONCLUSIONS ............................................................. 91 APPENDIX ............................................................................................................ 93 iv ACKNOWLEDGEMENTS I would like to express my gratitude to Dr. Mark Gleason, my major advisor, for his guidance, patience, and the excellent mentorship support he always demonstrated during my time at ISU. Thank you for admitting me into the graduate program. I also would like to express my sincere thanks and appreciations to Dr. Thomas Harrington, my co-major advisor, for his expert feedback and advice throughout my Ph.D studies. Without your persistent help and ongoing support, this dissertation would have never been possible. I am extremely grateful to Dr. Jean Batzer, for her valuable insights and advice throughout my research project. Thank you from the bottom of my heart. I would also like to thank Dr. Dennis Lavrov for your advice throughout my program. Your expert feedback was important for the completion of my evolution study. Your teachings in molecular phylogenetics will always have an impact in my career as plant pathologist. I would also like to thank the other of my POS committee, Dr. Nick Lauter, Dr. Alison Robertson, Dr. Leonor Leandro, for all their meaningful feedback and guidance throughout the course of my study. Your time and effort is sincerely appreciated. I am thankful to my friends, colleagues, department faculty and staff for making my graduate student life at ISU a wonderful experience. Thank you to Erika, Xiaoyu, Qian, Sally, Gang, Ataur, Hafizi, Nenad, Ashley and Yeganeh, for being there throughout my journey. You are the best friends I could ask for. Thank you to my Malaysian friends, Zanariah, Irma and Hidayah for your incredible friendship. You are the source of my strength for success during the completion of my Ph.D studies. v I also thank everyone who has worked in the Gleason lab and Harrington lab for their help and time dedicated for my research. Finally, I would like to acknowledge Ministry of Higher Education Malaysia and Universiti Putra Malaysia for the Skim Latihan Akademik Bumiputera (SLAB) scholarship that funded my Ph.D studies. vi ABSTRACT The sooty blotch and flyspeck (SBFS) complex is comprised of more than 80 species of fungi which colonize the surface of apple fruit. The dark blotches caused by SBFS species result in economically significant damage to apple in humid production regions worldwide. Despite rapid progress in clarifying the taxonomy and ecology of SBFS fungi, there is no information available about species-specific patterns in the timing of fruit infection. A motivation for obtaining this knowledge is that it may set the stage for development of more efficient SBFS management practices, since the species that are prevalent in apparent orchards vary among geographic regions. The first objective of this study was therefore to determine whether there are species-specific patterns in the timing of SBFS infection on apple fruit. To answer this question, an experiment was conducted in six commercial apple orchards in central Iowa in 2009 and 2010. Beginning 10-21 days after petal fall, apples were covered individually by fruit bags. A subsample of apples (cv. Golden Delicious) was exposed for each of seven consecutive 2-week-long exposure periods, and then rebagged from the end of the exposure period until harvest. All individual colonies that were visible at harvest were identified using a PCR-RFLP protocol. A total of 15 species were identified. The results provided the first evidence that some SBFS species differ significantly from others in the timing of fruit infection, and found that seven SBFS species displayed the same general temporal pattern: in each species, fruit infections that resulted in formation of visible colonies