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Survey of Plant-Parasitic Nematodes in Pulse Crop Fields of the Canadian Prairies

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Survey of Plant-Parasitic Nematodes in Pulse Crop Fields of the Canadian Prairies Survey of Plant-Parasitic Nematodes in Pulse Crop Fields of the Canadian Prairies by Fernanda Gouvea Pereira A Thesis Submitted to the Faculty of Graduate Studies of The University of Manitoba in Partial Fulfillment of the Requirements for the Degree of MASTER OF SCIENCE Department of Soil Science University of Manitoba Winnipeg, Manitoba Copyright © December, 2018 ABSTRACT Gouvea Pereira, Fernanda. M.Sc., University of Manitoba, December, 2018. Survey of Plant- Parasitic Nematodes in Pulse Crop Fields of the Canadian Prairies. Advisor; Dr. Mario Tenuta. The current distribution of economically important plant parasitic nematodes is relatively unknown in the Canadian Prairies for pulse crops. The majority of previous surveys were done several decades ago and may now be suspect as a result of recent molecular identification methods; as has been the case with the quarantine pest Ditylenchus dipsaci (Kühn) Filipjev. The nematode species Ditylenchus dipsaci can constrain export markets for economically important crops, such as peas. However, a more recent study has revealed that previous identifications of D. dipsaci in yellow pea (Pisum sativum L.) exports have actually been the non-quarantine species Ditylenchus weischeri Chizhov, Borisov & Subbotin. To further our understanding of these issues, a survey was conducted in three major pulse crops growing regions of Canada (Alberta, Saskatchewan and Manitoba) to determine the occurrence of plant-parasitic nematodes associated with pea, chickpea (Cicer arietinum L.) and lentil (Lens culinaris L.). A total of 465 plant and soil samples of pea, chickpeas, lentils and creeping thistle (Cirsium arvense L.), plants from 93 fields were analysed. Recovered nematodes were identified to genus by morphological features. Molecular analysis by species-specific PCR, PCR-RFLP and sequencing of the ITS (ITS1 + 5.8S + ITS2) of the rRNA gene were also used to identify recovered nematodes to species. Twenty genera of plant-parasitic nematodes were recovered from the soil and (or) the plants of pea, chickpea, lentil and creeping thistle, including Anguina, Aphelenchoides, Ditylenchus, Helicotylenchus, Hoplolaimus, Longidorus, Merlinius, Paraphelenchus, Paratylenchus, Pratylenchus, Subanguina, Paratrichodorus, Tylenchorhynchus and Xiphinema. 1 Several fields had high density of plant-parasitic nematodes belonging to the genera Ditylenchus, Pratylenchus, Paratylenchus, Helicotylenchus and Tylenchorhynchus, which could be potentially problematic for the crops studied or for crops that are grown in rotation. Molecular analysis results indicate the recovery of D. weischeri, D. dipsaci, Pratylenchus neglectus (Rensch) Filipjev & Schuurmans-Stekhoven, Xiphinema rivesi Dalmasso and Paratylenchus nanus Cobb. Ditylenchus weischeri, a parasite of thistles and not crops, was recovered from 22 fields across Alberta, Saskatchewan and Manitoba. D. dipsaci was recovered from pods of one yellow pea field in Manitoba. These results confirm the high prevalence of D. weischeri on creeping thistle in pulse fields and the near absence of D. dipsaci. 2 ACKNOWLEDGMENTS To begin with, I would like to express my sincere gratitude to my advisor Dr. Mario Tenuta for his continuous support, guidance, and exceptional scientific knowledge. His dedication as an educator extends prior to my master’s studies, back when I was an undergraduate exchange student at the University of Manitoba. During this time, Dr. Tenuta took an hour per week out of his busy schedule to review the content he had taught in class with me, as I was often unable to understand the classes due to a language barrier. I am fortunate to have had the opportunity to learn from him. I would also like to thank Prof. Kateryn Rochon, who is on my thesis committee, for her insightful comments and encouragement, as well as Prof. Tee Boon Goh, who is also on my thesis committee. He taught me how to engage a class during a lecture and, together with his wife, he helped me troubleshoot the molecular data for this research. I thank our research partners Dale Risula and Dr. Michael Harding, the lab technician Jon Nielson, and the crop specialists Shannon Chant, Lyndon Hicks, John Ippolito, Kim Stonehouse, Cory Jacob, Kaeley Kindrachuk, Sherri Roberts, Shannon Friesen, Brian Olson, and Danielle Stephens for their passionate participation and hard work in helping with the sample collection. I gratefully acknowledge our project funders, without whom this research would not be possible: Alberta Pulse Growers (APG), Saskatchewan Pulse Growers (SPG), Manitoba Pulse Soybean Growers (MPSG), Pulse Canada, and Agriculture and Agri-Food Canada (AAFC). I also thank Jehn Francisco Gamurot, Ryan Orne-Zaluski, Idunno Ade-Ojo, Priscillar Wenyika, Nazanin Ghavami, and Terri Fairman for their help in the lab and for all the fun we had 3 working together. Special thanks to Abhishek Agarwal for his constant support and for always willing to help, whenever I needed him. I would like to express my appreciation to Dr. Francis Zvomuya, who always had a positive presence and an open office door. I would also like to thank our amazing lab technicians Rob Ellis, Mervin Bilous, and Brad Sparling for their assistance and everyone else in the Soil Department: It was great collaborating together, sharing a lab, helping each other, or just having coffee. Finally, I must express my most profound gratitude to both Cesar Nieto and Sonia Gouvea Nieto for providing me with unfailing support and continuous encouragement throughout my years of study. I owe it all to you. Thank you. I dedicate this thesis to my son, Thatcher Leopold. 4 TABLE OF CONTENTS Page ABSTRACT .................................................................................................................................... 1 ACKNOWLEDGMENTS .............................................................................................................. 3 TABLE OF CONTENTS ................................................................................................................ 5 LIST OF TABLES .......................................................................................................................... 8 LIST OF FIGURES ........................................................................................................................ 9 LIST OF ABBREVIATIONS ....................................................................................................... 10 1. GENERAL INTRODUCTION ................................................................................................ 12 1.1 Nematode Biology.......................................................................................................... 12 1.1.1 Survival Strategies ......................................................................................................... 12 1.1.2 Feeding Strategies .......................................................................................................... 13 1.1.3 Life Cycle ....................................................................................................................... 14 1.1.4 Plant Damage ................................................................................................................. 14 1.2 Nematode Identification ....................................................................................................... 16 1.2.1 Classical Morphology Identification .............................................................................. 17 1.2.2 Molecular Identification ................................................................................................. 19 1.3 Stem Nematodes (Ditylenchus spp.) .................................................................................... 22 1.3.1 Ditylenchus dipsaci ........................................................................................................ 22 1.4 Pulse Crops .......................................................................................................................... 25 1.5 Nematode Pests of Pulse Crops ........................................................................................... 26 1.6 Distribution of Plant-Parasitic Nematodes in Western Canada ........................................... 26 1.7 References ............................................................................................................................ 29 2 SURVEY OF PLANT-PARASITIC NEMATODES IN PULSE CROP FIELDS OF THE CANADIAN PRAIRIES .......................................................................................................... 33 5 2.1 Abstract ................................................................................................................................ 33 2.2 Introduction .......................................................................................................................... 35 2.3 Objectives............................................................................................................................. 38 2.4 Materials and Methods ......................................................................................................... 39 2.4.1 Soil and Plant Sampling ................................................................................................. 39 2.4.2 Extractions and Counting ............................................................................................... 40 2.4.3 Morphological Characterization ....................................................................................
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