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Population Variability of Rotylenchulus Reniformis in Cotton Agroecosystems Megan Leach Clemson University, [email protected]

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Population Variability of Rotylenchulus Reniformis in Cotton Agroecosystems Megan Leach Clemson University, Mleach@Clemson.Edu Clemson University TigerPrints All Dissertations Dissertations 12-2010 Population Variability of Rotylenchulus reniformis in Cotton Agroecosystems Megan Leach Clemson University, [email protected] Follow this and additional works at: https://tigerprints.clemson.edu/all_dissertations Part of the Plant Pathology Commons Recommended Citation Leach, Megan, "Population Variability of Rotylenchulus reniformis in Cotton Agroecosystems" (2010). All Dissertations. 669. https://tigerprints.clemson.edu/all_dissertations/669 This Dissertation is brought to you for free and open access by the Dissertations at TigerPrints. It has been accepted for inclusion in All Dissertations by an authorized administrator of TigerPrints. For more information, please contact [email protected]. POPULATION VARIABILITY OF ROTYLENCHULUS RENIFORMIS IN COTTON AGROECOSYSTEMS A Dissertation Presented to the Graduate School of Clemson University In Partial Fulfillment of the Requirements for the Degree Doctor of Philosophy Plant and Environmental Sciences by Megan Marie Leach December 2010 Accepted by: Dr. Paula Agudelo, Committee Chair Dr. Halina Knap Dr. John Mueller Dr. Amy Lawton-Rauh Dr. Emerson Shipe i ABSTRACT Rotylenchulus reniformis, reniform nematode, is a highly variable species and an economically important pest in many cotton fields across the southeast. Rotation to resistant or poor host crops is a prescribed method for management of reniform nematode. An increase in the incidence and prevalence of the nematode in the United States has been reported over the last two decades. However it is not clear whether the observed increase is related to the emergence of novel populations that are more aggressive or have a higher fitness or shifts in host availability or susceptibility. The objectives of this research were to determine the variability of the species by studying the effect of crop rotations on the genotype of reniform nematode populations, the effect of temperature on the embryonic development of reniform nematode populations from the southeastern United States, and to determine the genetic diversity of R. reniformis populations representing cotton-growing areas in the United States. We used AFLPs (Amplified Fragment Length Polymorphisms) to determine changes in population structure due to rotations. Six rotation schemes were used that included susceptible cotton and soybean, resistant soybean, and non-host corn during four planting cycles. Distinct changes in genotype were observed following rotations with resistant soybean or corn. Rotations involving reniform nematode resistant and susceptible soybean cultivars had the most distinct effect on population structure. To determine variability of populations in the absence of a host, embryogenesis was compared among three geographic reniform nematode populations at 20, 25, 30, and 35ºC. The greatest differences among populations occurred at 20 and 35ºC. Results at the intermediate ii temperatures (25 and 30oC) were similar for the three populations. Reniform nematode may have the ability to increase its distribution range through variants able to reproduce in a wider temperature range, but genetic variability of isolates needs to be determined. To determine the genetic variability of individual reniform nematodes we developed and optimized 10 polymorphic microsatellite loci and tested loci on 160 individual reniform nematodes to determine informative genetic variation of isolates from the Southeastern United States, Colombia, and Japan and R. parvus isolated from a field in Arizona. Most isolates exhibited significant genotypic differentiation and moderate to very high genetic differentiation based on FST analysis. The most consistently differentiated isolates were found reproducing parthenogenetically in Japan. Understanding the adaptive potential of this species is crucial for the development of durable management strategies, and our results indicate a need for an standardized method to genetically characterize R. reniformis variants and monitor variation. iii DEDICATION This dissertation is dedicated to everyone who has loved and supported me while I worked on obtaining my PhD, especially my family. My family is the driving force in my life that has led to me wanting to learn more and achieve more. Without their love and support, none of this would have been possible. I would like to make a special dedication to my parents. If it was not for their love and financial support, I would not have had enough faith in myself to be so successful in life. I look forward to many more years of health, happiness, and love. iv ACKNOWLEDGMENTS I wish to especially thank my advisor, Dr. Paula Agudelo who was brave enough to allow me to be her first Doctoral Student. It has been a wonderful path full of opportunities to learn something exciting and new. I would also like to thank all of my committee members: Dr. Halina Knap, Dr. John Mueller, Dr. Amy Lawton-Rauh, and Dr. Emerson Shipe. It has been an honor to have you as committee members and to have the opportunity to learn from each of you. I was truly fortunate to have such a supportive committee that helped me to become a confident researcher. I would like to thank Dr. Wheeler and Dr. DeWalt from the Biological Sciences Department at Clemson University for the opportunity to be a Teaching Assistant for Biology of Plants. It was an excellent opportunity to learn and I enjoyed the experience greatly. I wish to also thank all of the members of the Clemson University Nematology Lab past, present, and future. I will always be proud to be associated with Clemson University and a lab headed by Dr. Paula Agudelo. No matter where life leads everyone, this common thread will always be there to connect us. Finally, I would like to thank the faculty, staff, and students of the Department of Entomology, Soils, and Plant Sciences and the Plant and Environmental Sciences Program. It was an honor to represent both during my graduate career. v TABLE OF CONTENTS Page TITLE PAGE .................................................................................................................... i ABSTRACT ..................................................................................................................... ii DEDICATION ................................................................................................................ iv ACKNOWLEDGMENTS ............................................................................................... v LIST OF TABLES ........................................................................................................ viii LIST OF FIGURES ........................................................................................................ ix CHAPTER I. EFFECT OF CROP ROTATIONS ON ROTYLENCHULUS RENIFORMIS POPULATION STRUCTURE ................................................................ 1 Materials and Methods ............................................................................. 3 Results ...................................................................................................... 5 Discussion .............................................................................................. 10 II. EFFECT OF TEMPERATURE ON THE EMBRYOGENESIS OF GEOGRAPHIC POPULATIONS OF ROTYLENCHULUS RENIFORMIS ....................................................................................... 17 Materials and Methods ........................................................................... 19 Results .................................................................................................... 20 Discussion .............................................................................................. 22 III. TEN POLYMORPHIC MICROSATELLITE LOCI FOR RENIFORM NEMATODE, ROTYLENCHULUS RENIFORMIS .................................................... 31 IV. GENETIC VARIABILITY OF ROTYLENCHULUS RENIFORMIS ...................................................................................... 38 vi Materials and Methods ........................................................................... 41 Results .................................................................................................... 45 Discussion .............................................................................................. 50 V. CONCLUSIONS AND FUTURE RESEARCH ......................................... 65 REFERENCES .............................................................................................................. 69 vii LIST OF TABLES Table Page 1.1 Six rotation schemes used to determine host selection pressure on Rotylenchulus reniformis, rotation abbreviation, number of distinct clusters (K) from population structure analysis from STRUCTURE V 2.3, and log probability(lnP(D)) of results from STRUCTURE V 2.3 analysis ................................................................ 14 2.1 Average days to eclosion for three geographic populations (Huxford, Alabama (AL), Glendora, Mississippi (MS), and St. Matthews, South Carolina (SC)) at four incubation temperatures (20, 25, 30, 35ºC), with average rates, median, mode, range, standard deviation, and number of replicates at each temperature ............................................................................................ 27 2.2 Normal low and high temperatures for the locations from where the three populations included in this study were isolated ................................................................................. 28 3.1 Primer sequences
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