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Strategies for Improving Brassica Napus Resistance to Leptosphaeria

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Strategies for Improving Brassica Napus Resistance to Leptosphaeria Strategies for improving Brassica napus resistance to Leptosphaeria maculans, a causal agent of blackleg disease in canola by Harunur Rashid A Thesis Submitted to the Faculty of Graduate Studies of The University of Manitoba in partial fulfilment of the requirements of the degree of DOCTOR OF PHILOSOPHY Department of Plant Science University of Manitoba Winnipeg Copyright©2018 by Harunur Rashid i ABSTRACT Rashid M. Harunur, PhD., The University of Manitoba, 2018. Strategies for improving Brassica napus resistance to Leptosphaeria maculans, a causal agent of blackleg disease in canola. Supervisor: Dr. W. G. Dilantha Fernando Canola (oilseed rape, Brassica napus L.) is a cash crop grown in different countries including Canada, the European Union, China and Australia. The production of this crop is threatened by blackleg disease caused by the fungus Leptosphaeria maculans (Desm.) Ces. & De Not. [anamorph: phoma-like (de Gruyter)]. In order to develop a more effective disease management strategy; there is a need to employ crop rotation, introgress new resistance (R) genes into elite cultivars, test the effectiveness of existing R genes, and predict the emergence of virulent isolates of L. maculans. In this study, sequenced characterised amplified region (SCAR) and derived-cleaved amplified polymorphic sequence (dCAPS) markers linked to the L. maculans resistance gene Rlm6 were developed and their segregation was confirmed by analysis of F2 and F3 progeny. In addition, chromosomal segment substitution lines (CSSLs) harbouring Rlm6 were developed through a combined approach of classical and marker-assisted backcross breeding. The field study suggested a potential effectiveness of a 2-year crop rotation, because of the reduction of disease severity at the end of the 4-year trial. By the end of the study, the R genes LepR1, LepR3, Rlm2, and Rlm4 were effective against L. maculans, whereas Rlm3 was moderately effective. Linear regression analysis suggests an order of effectiveness among the R genes tested: LepR3 > LepR1> Rlm2 > Rlm4 > Rlm3. Moreover, the decreased frequency of effector genes AvrLm2 and AvrLm4 in L. maculans isolates suggested the gaining of virulence toward Rlm2 and Rlm4 within a year. Results from sequencing of the AvrLm2 gene revealed a shift of AvrLm2 to avrLm2 allele due to the accumulation of point mutations. i Overall, CSSLs and DNA markers developed in this study may facilitate breeding B. napus varieties resistant to L. maculans in the future. It is predicted that rotation of Rlm2, Rlm3, Rlm4, and Rlm7 could be an opportunity to increase the effectiveness of those R genes under a 2-year crop rotation. However, these studies also suggest development of generic epidemiological models for the occurrence of complex molecular interactions in B. napus-L. maculans pathosystem, allowing plant breeders to select appropriate R genes in the proposed cultivar rotation strategies on the Prairies. ii ACKNOWLEDGEMENTS First and foremost, I would like to thank GOD, for His blessing and mercy. A special thanks to Dr. Dilantha Fernando, for providing the opportunity to work in his lab. I am honoured to work under his guidance and supervision. Without his support this work won’t be possible. I would like to thank my committee members, Dr. Brent McCallum, Dr. Georg Hausner, Dr. Hossein Borhan for their valuable comments and suggestions throughout the study period. I greatly appreciate Paula Parks for her great technical assistance throughout this study. My special thanks to Dr. Zhongwei Zou for his help especially developing DNA markers used in chapter 3 and 4 of this thesis. Lab colleagues Sakaria Liban and Xuehua Zhang are acknowledged for the initial set up of the experiment in the field in 2013. I wish to acknowledge Abdullah Zubaer for his help with the sequence analysis used in chapter 6 of this thesis. I would like to express my gratitude to greenhouse staff and technicians in the Department of Plant Science including Rob Visser, Cathy Bay, Alvin Iverson, and Lorne Adam, for their kind support in this research. I would like to thank my previous and present lab colleagues and summer students for their support during field, greenhouse and lab experiments. I would also like to acknowledge the support from fellow graduate students and people at general office, Department of Plant Science, University of Manitoba. Dr. Borhan’s lab, Agriculture and Agri-Food Canada (AAFC) Saskatoon Research Station, Saskatchewan is highly acknowledged for providing valuable plant materials utilized in this study. Finally, I pay my heartfelt thanks and gratitude to my family members and dear friends in Bangladesh and Canada. I would not be here and would not have been able to finish my study without love and motivation from my parents, my wife, my daughter, my parents in law, my brothers, and my sisters. I could not have finished my study without the iii encouragement and sacrifice from my wife Afrina M. Mousumi. She has always been incredibly supportive throughout the journey. Last, but not the least, I gratefully acknowledge SaskCanola, AAFC-Growing Forward 2 program, and National Sciences and Engineering Research Council (NSERC) for their financial support to this work. iv DEDICATION Dedicated to my BELOVED PARENTS v TABLE OF CONTENTS ABSTARCT…………………………………………..…………………………………….….i ACKNOWLEDGEMENT……….…………………………………………………………...iii DEDICATION……………………………………………………………………….….…….v TABLE OF CONTENTS……………………………………………………………….....….vi LIST OF TABLES……………………………………………………………………………xi LIST OF FIGURES……………………………………………………………………….....xii LIST OF APPENDICES………………………………………………...………….………xvii FORWARD…………………………………………………………………………….….xviii 1 GENERAL INTRODUCTION ............................................................................................... 1 2 LITERATURE REVIEW ....................................................................................................... 4 2.1 The host ............................................................................................................................. 4 2.1.1 Brassica species .......................................................................................................... 4 2.1.2 History of canola ......................................................................................................... 4 2.1.3 Economic importance of canola .................................................................................. 6 2.1.4 Cultivation environment .............................................................................................. 7 2.2 The pathogen – Leptosphaeria maculans ......................................................................... 7 2.2.1 Biology ........................................................................................................................ 7 2.2.2 Pathogenicity group (PG) and avirulence genes of Leptosphaeria maculans ............ 9 2.2.3 Evolution of virulence of Leptosphaeria maculans .................................................. 12 2.2.4 Life cycle and infection strategies ............................................................................. 12 2.2.5 Host range of Leptosphaeria maculans ..................................................................... 15 2.3 The disease – blackleg .................................................................................................... 16 2.3.1 Disease occurrence .................................................................................................... 16 2.3.2 Disease importance ................................................................................................... 17 2.3.3 Disease epidemiology ............................................................................................... 17 2.4 Blackleg disease control .................................................................................................. 19 2.4.1 Cultural control ......................................................................................................... 19 2.4.2 Chemical control ....................................................................................................... 21 2.4.3 Biological control ...................................................................................................... 21 2.4.4 Genetic control – host resistance ............................................................................... 23 2.5 Effectiveness of qualitative resistance ............................................................................ 26 2.6 Introgression of blackleg resistance ................................................................................ 28 vi 2.7 Molecular marker linked to blackleg resistance ............................................................. 30 2.8 Major objectives of the study .......................................................................................... 31 3 DEVELOPMENT OF MOLECULAR MARKERS LINKED TO THE LEPTOSPHAERIA MACULANS RESISTANCE GENE RLM6 AND INHERITANCE OF SCAR AND CAPS MARKERS IN B. NAPUS X B. JUNCEA INTERSPECIFIC HYBRIDS .............................. 34 3.1 Abstract ........................................................................................................................... 34 3.2 Introduction ..................................................................................................................... 34 3.3 Materials and Methods .................................................................................................... 37 3.3.1 Plant materials ..........................................................................................................
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