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Diversity Among Isolates of Phytophthora Cinnamomi from Ornamental Plants in South Carolina

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Diversity Among Isolates of Phytophthora Cinnamomi from Ornamental Plants in South Carolina Clemson University TigerPrints All Theses Theses 8-2013 DIVERSITY AMONG ISOLATES OF PHYTOPHTHORA INNC AMOMI FROM ORNAMENTAL PLANTS IN SOUTH CAROLINA Simon Schreier Clemson University, [email protected] Follow this and additional works at: https://tigerprints.clemson.edu/all_theses Part of the Plant Pathology Commons Recommended Citation Schreier, Simon, "DIVERSITY AMONG ISOLATES OF PHYTOPHTHORA IC NNAMOMI FROM ORNAMENTAL PLANTS IN SOUTH CAROLINA" (2013). All Theses. 1761. https://tigerprints.clemson.edu/all_theses/1761 This Thesis is brought to you for free and open access by the Theses at TigerPrints. It has been accepted for inclusion in All Theses by an authorized administrator of TigerPrints. For more information, please contact [email protected]. DIVERSITY AMONG ISOLATES OF PHYTOPHTHORA CINNAMOMI FROM ORNAMENTAL PLANTS IN SOUTH CAROLINA A thesis Presented to the Graduate School of Clemson University In Partial Fulfillment of the Requirements for the Degree Master of Science Plant and Environmental Sciences by Simon Gabriel Isaac Schreier August 2013 Accepted by: Dr. Steven N. Jeffers, Committee Chair Dr. Julia L. Kerrigan Dr. Saara J. DeWalt ABSTRACT Phytophthora cinnamomi is a devastating pathogen that can attack over 900 hosts. It is the most common species of Phytophthora isolated from woody ornamental crops in South Carolina but little is known about variability among isolates of P. cinnamomi that attack these plants. Therefore, 142 isolates of P. cinnamomi recovered from diseased plant samples submitted to the Clemson University Plant Problem Clinic between 1995 and 2011 were characterized for mycelium growth habit, growth rate, mefenoxam sensitivity, mating type, and sporangium morphology. Mycelium growth habit on PARPH-V8 selective medium was classified as aerial, appressed, or dwarf; 87% of isolates had the aerial mycelium growth habit. Isolates with different growth habits had significantly different growth rates. All isolates were uniformly sensitive to the fungicide mefenoxam at 100 ppm. The population was composed of 129 isolates that were mating type A2 and 13 isolates that were mating type A1, with six of these A1 isolates recovered from Camellia spp. All isolates with the aerial and appressed mycelium growth habits, which were most of the isolates in the study, produced few sporangia from clarified V8 juice agar plugs immersed in non-sterile soil extract for 1 to 4 days under continuous fluorescent light; however, the two isolates with the dwarf mycelium growth habit and a single isolate of P. cinnamomi var. parvispora produced abundant sporangia under these same incubation conditions. Isolates in this population originated from plant samples sent from 27 counties in South Carolina, two counties in Virginia, and one county in Georgia. The 142 isolates were found associated with 56 known species and 16 unspecified ii species in 46 genera and 31 families. Thirty-three previously unreported host plant associations were discovered. The genetic diversity of this population was measured by sequencing DNA for several loci and building phylogenies based on these data. The ITS region was sequenced for all isolates in the population. There was a high degree of genetic uniformity in the ITS region for this population. Four other loci—β-tub, cox1, cox2, and rps10—were sequenced for a set of 59 isolates representative of the population. Two isolates, Pc40 (mating type A2) and Pc138 (mating type A1) from avocado trees in California, were incorporated into this study group as standards for comparison. Mating types were distinguishable at the β-tub locus, and both mating types and mycelium growth habit types were genetically distinct at the rps10 locus. Cluster analysis of the genotypes at each locus revealed seven distinct groups. Strong correlations were observed between cluster analysis groups and phenotypes of the isolates. This is the first study to find significant correlations between genotype and phenotypic characters other than mating type in P. cinnamomi. iii DEDICATION To everyone who helped me along the way; teachers, mentors, and friends. Especially to Mom, Pops, and Max, I am here because of you. iv ACKNOWLEDGMENTS Dr. Steven Jeffers: for guiding me through three enlightening years of graduate school and advising me on science, life, and everything in between, and whose help I could not have succeeded without. Dr. Julia Kerrigan and Dr. Saara DeWalt: for their role on my committee. I truly appreciate your support, assistance, and patience. Dr. Jaesoon Hwang and Inga Meadows: who helped get my research feet on the ground. Lynn Luszcz: who pulled isolates, ordered materials, told stories, shared music, and (on occasion) fed me. This project would have been impossible without her help. Dr. Frank Martin, USDA-ARS Research Station, Salinas, CA: who provided intellectual guidance and support. Meg Williamson and the Clemson University Plant Problem Clinic: who received diseased plant samples from which most of the isolates used in this study were obtained. Dr. William Bridges: for help and guidance with statistical analyses. The people at the Clemson University Genomics Institute (CUGI): who expertly and efficiently handled sequencing for this project. The staff of the former Department of Entomology, Soils, and Plant Sciences: who opened up a new world of plant pathology through classes, seminars, and conversation. My fellow students: who have been supportive, informative, adventurous, and—above all else—friends. v TABLE OF CONTENTS Page TITLE PAGE ....................................................................................................................... i ABSTRACT ........................................................................................................................ ii DEDICATION ................................................................................................................... iv ACKNOWLEDGMENTS ...................................................................................................v LIST OF TABLES ........................................................................................................... viii LIST OF FIGURES ........................................................................................................... ix CHAPTERS I. LITERATURE REVIEW AND INTRODUCTION .........................................1 The Impact of Phytophthora cinnamomi on Ornamental Crops ..................1 Phytophthora species and the Ornamental Plant Industry ...........................2 Phytophthora cinnamomi: Diseases, Biology, and Ecology ........................6 Description and Ecology of Phytophthora cinnamomi ................................8 Current Understanding of the Diversity of Phytophthora cinnamomi .......13 Research Project.........................................................................................20 Literature Cited ..........................................................................................22 II. PHENOTYPIC DIVERSITY AMONG AND HOST PLANT ASSOCIATIONS FOR ISOLATES OF PHYTOPHTHORA CINNAMOMI FROM ORNAMENTAL PLANTS IN SOUTH CAROLINA....................................................................................33 Abstract ......................................................................................................33 Introduction ................................................................................................34 Materials and Methods ...............................................................................40 Results ........................................................................................................50 Discussion ..................................................................................................56 Literature Cited ..........................................................................................66 III. GENETIC DIVERSITY AMONG ISOLATES OF PHYTOPTHORA CINNAMOMI FROM ORNAMENTAL PLANTS IN SOUTH CAROLINA....................................................................................90 vi Table of Contents (continued) Page Abstract ......................................................................................................90 Introduction ................................................................................................91 Materials and Methods ...............................................................................98 Results ......................................................................................................103 Discussion ................................................................................................110 Literature Cited ........................................................................................117 IV. SUMMARY OF FINDINGS AND FUTURE RESEARCH .........................134 APPENDICES .................................................................................................................136 A: List of all isolates used in this study: Geographic information .....................137 B: List of all isolates used in this study: Morphological and physiological characters ...........................................................................149 C: List of all isolates used in this study: Molecular characters and species identification (far right column) ..................................................155 D: Alternative β-tub phylogenetic tree incorporating isolate 05-0798 ...............164 E: List of the subset of isolates used for phylogenetic analysis:
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