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Characterization of Rutabaga for Genetic Diversity and As a Source of Clubroot Resistance

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Characterization of Rutabaga for Genetic Diversity and As a Source of Clubroot Resistance Characterization of rutabaga for genetic diversity and as a source of clubroot resistance by Zhiyu Yu A thesis submitted in partial fulfillment of the requirements for the degree of Master of Science in Plant Science Department of Agricultural, Food and Nutritional Science University of Alberta © Zhiyu Yu, 2019 Abstract Rutabaga (Brassica napus ssp. napobrassica (L.) Hanelt) is widely grown as a vegetable crop and animal fodder, and is reported to be an excellent source of clubroot (Plasmodiophora brassicae) resistance genes. In this study, the genetic diversity and clubroot resistance of 124 rutabaga accessions from the Nordic countries (Norway, Sweden, Finland, Denmark, and Iceland) were assessed using a 15K Brassica single nucleotide polymorphism (SNP) array. Filtering was done to remove markers that did not amplify genomic DNA, and monomorphic and low coverage site markers. Allelic frequency statistics calculated with the retained 6861 SNP markers indicated that the rutabaga accessions from Norway, Sweden, Finland and Denmark were not genetically different from each other. In contrast, accessions from these countries were significantly different from the Icelandic accessions (P < 0.05). The rutabaga accessions were also evaluated in the greenhouse for their reaction to five single-spore isolates representing P. brassicae pathotypes 2F, 3H, 5I, 6M, and 8N and 12 field isolates representing pathotypes 2B, 3A, 3O, 5C, 5G, 5K, 5L, 5X (two isolates, L-G2 and L-G3), 8E, 8J and 8P. The rutabaga accessions exhibited differential reactions to the 17 isolates with 0.8-46.4% resistant (R), 4.0- 20.0% moderately resistant (MR) and 32.8-93.6% susceptible (S). Nine accessions with broad- spectrum (R + MR) resistance also were identified. The rutabaga accessions were genotyped with 63 PCR-based primers linked to previously identified clubroot resistance genes. Genome- wide association studies (GWAS) using the genotypic (SNP + PCR-based markers) and phenotypic data identified 45 SNPs (36 on the A-genome and 9 on the C-genome or scaffolds) and 4 PCR-based markers that were associated strongly with resistance to isolates representing 13 pathotypes (2F, 3H, 5I, 6M, 8N, 2B, 3A, 3O, 5C, 5G, 5K, 5L and 8P). The SNPs identified in this study will be important for marker-assisted breeding (MAS) of clubroot resistant cruciferous crops. ii Preface This thesis is an original work by me, Zhiyu Yu, who conducted all of the experiments and wrote the first drafts of all chapters. My Supervisor Dr. Stephen Strelkov reviewed and revised all chapters of this thesis. My Supervisory Committee member Dr. Rudolph Fredua-Agyeman helped with the data analysis and contributed to the revisions of Chapters 2 and 3. Dr. Robert Conner (Agriculture and Agri-Food Canada) also reviewed Chapter 2 and provided suggestions for improvements. Once the draft thesis was complete, Dr. Strelkov and my co-supervisor Dr. Sheau-Fang Hwang approved the dissertation to go to defense. The Brassica napus ssp. napobrassica accessions used in this thesis were obtained from Nordic Genetic Resource Center (Nordgen, Sweden) in 2015. The Plasmodiophora brassicae isolates in Chapter 3 were provided by Drs. Strelkov and Hwang. Dr. Fredua-Agyeman provided guidance and suggestions on experimental design and statistical analysis for Chapters 2 and 3. Mr. Chris Sehn and Ms. Yixiao Wang (University of Alberta) provided assistance with plant and DNA sampling and PCR genotyping in Chapters 2 and 3. Staff and students from the University of Alberta Plant Pathology Lab assisted with the greenhouse inoculation experiments described in Chapter 3. Financial support was provided by grants to Dr. Fredua-Agyeman from the Alberta Crop Industry Development Fund (ACIDF) and to Drs. Strelkov and Hwang from the Canadian Agricultural Partnership (Agriculture and Agri-Food Canada and the Canola Council of Canada). I also acknowledge the in-kind support provided by Alberta Agriculture and Forestry and the University of Alberta, including access to greenhouse facilities and related laboratory infrastructure. iii Acknowledgements I would like to acknowledge my supervisor Dr. Stephen Strelkov, co-supervisor Dr. Sheau-Fang Hwang and my committee member Dr. Rudolph Fredua-Agyeman for their kind guidance and support throughout my M.Sc. program. I would also like to thank Dr. Robert Conner for critically reviewing Chapter 2. I gratefully appreciate the technical help I received from Dr. Qixing Zhou and Mr. Heting Fu (Alberta Agriculture and Forestry), along with the help from the summer students at the University of Alberta Plant Pathology Lab. I would like to thank Dr. Boyd Mori for serving as the arm’s-length examiner on my defense and providing suggestions for this thesis. My sincere, heartfelt gratitude goes to Drs. Strelkov and Hwang for inspiring me in plant pathology and leading me to the door of scientific research. I also gratefully thank Dr. Fredua- Agyeman for his kind guidance and help on my projects. I address my special thanks to my colleague and dearest friend Ms. Yixiao Wang for her support and help during this entire process, who walked me through the darkest moments. Lastly, I would like to thank my parents Mr. Jiankun Yu and Ms. Qiufang Lin for their encouragement and support over the years and my late grandmother Lanhua Yan who always expected me to step forward and be strong. I would like to acknowledge the financial support from the Alberta Crop Industry Development Fund (ACIDF) and the Canadian Agricultural Partnership (Agriculture and Agri- Food Canada and the Canola Council of Canada). I also thank Alberta Agriculture and Forestry and University of Alberta for their generous in-kind support. iv Table of Contents Chapter 1: Introduction and Literature Review.........................................................................1 1.1 Clubroot ..................................................................................................................................1 1.1.1 Introduction to clubroot ..................................................................................................1 1.1.2 Importance of clubroot ....................................................................................................1 1.1.3 History of clubroot ..........................................................................................................2 1.1.4 Taxonomy .......................................................................................................................3 1.1.5 Life cycle ........................................................................................................................3 1.1.6 Epidemiology and host range ..........................................................................................4 1.1.7 Physiologic specialization ...............................................................................................5 1.2 Management of Clubroot ......................................................................................................7 1.2.1 Background ......................................................................................................................7 1.2.2 Cultural control ...............................................................................................................7 1.2.3 Chemical control .............................................................................................................9 1.2.4 Biocontrol .....................................................................................................................11 1.2.5 Resistance and breeding ................................................................................................12 1.2.5 Marker-based techniques for the identification of clubroot-resistant genes .................15 1.3 Rutabaga as a source of clubroot resistance for canola .......................................................16 1.3.1 Background ...................................................................................................................16 1.3.2 Rutabaga .......................................................................................................................17 1.3.3 Clubroot resistance in rutabaga .....................................................................................18 1.4 Research objectives and hypotheses ...................................................................................19 1.5 Figures .................................................................................................................................20 v Chapter 2: Genetic diversity and population structure of rutabaga accessions from Nordic countries .......................................................................................................................................22 2.1 Introduction .........................................................................................................................22 2.2 Materials and Methods ........................................................................................................24 2.2.1 Plant Material ...............................................................................................................24 2.2.2 SNP genotyping and filtering .......................................................................................24 2.2.3 Allele frequency-based population structure analyses .................................................24 2.2.4 Distance-based population structure analyses ..............................................................25
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