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Delineating Root System Architecture in Rapeseed/Canola (Brassica

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DELINEATING ROOT SYSTEM ARCHITECTURE IN RAPESEED/CANOLA (BRASSICA NAPUS L.) THROUGH MOLECULAR AND TRANSCRIPTOMIC APPROACHES A Dissertation Submitted to the Graduate Faculty of the North Dakota State University of Agriculture and Applied Science By Muhammad Arif Uz Zaman In Partial Fulfillment of the Requirements for the Degree of DOCTOR OF PHILOSOPHY Major Department: Plant Sciences October 2018 Fargo, North Dakota North Dakota State University Graduate School Title DELINEATING ROOT SYSTEM ARCHITECTURE IN RAPESEED/CANOLA (BRASSICA NAPUS L.) THROUGH MOLECULAR AND TRANSCRIPTOMIC APPROACHES By Muhammad Arif Uz Zaman The Supervisory Committee certifies that this disquisition complies with North Dakota State University’s regulations and meets the accepted standards for the degree of DOCTOR OF PHILOSOPHY SUPERVISORY COMMITTEE: Dr. Mukhlesur Rahman Chair Dr. Phillip E. McClean Dr. David P. Horvath Dr. Luis del Rio-Mendoza Approved: 11/14/2018 Dr. Rich Horsley Date Department Chair ABSTRACT Root system architecture of plant plays a key role in water and nutrient uptake from the soil, provides anchorage and acts as a storage organ. In this current research, we have focused on the molecular and physiological basis of root system variation in canola (Brassica napus L.). Genome wide association mappings in a diverse canola germplasm panel with ~37,500 and ~30,200 single nucleotide polymorphism (SNP) markers were conducted under greenhouse and field conditions, respectively. A total of 52 significant SNP markers associated with different root architectural traits were identified in the greenhouse study. Majority of the markers were distributed on five chromosomes, A01, A02, A04, C03 and C06, of B. napus. Twenty-two candidate genes related to root growth and development were detected within 50 kbp upstream and downstream of the significant markers. Three of these candidate genes, P-glycoprotein 6 (PGP6), Tetraspanin 7 (TET7) and ARABIDILLO-2, were co-localized with three markers on chromosome C03, A01 and A04, respectively. In the field study, 31 significant SNP markers associated with different root traits were detected. A total of 15 root related candidate genes were identified within 100 kbp upstream and downstream of different significant markers. We also analyzed and compared the transcriptomes from the root systems of spring (weak root system) and winter (vigorous root system) growth habits at two different time points, 30 and 60 days. A total of 169,646 transcripts were analyzed, of which, 582 and 555 transcripts were found to be significantly differentially expressed between spring and winter types at 30 and 60 days, respectively. Several cytokinin and gibberellin associated genes and genes sets were found to be upregulated in spring type compared to winter type at 60 days. Cytokinin has proven inhibitory effect on root system architecture in different crops, whereas, gibberellin promote root iii elongation but inhibit lateral root growth. Therefore, we suggest that cytokinin and gibberellin may play an important role in root system variation between spring and winter growth habits. Significant marker loci, candidate genes and transcriptome profile identified in this research will assist future research to understand the root system variation in rapeseed/canola. iv ACKNOWLEDGEMENTS First, I would like to thank the Almighty, Allah, the most merciful and benevolent, for showing me the right path and leading me towards my dream. I would like to express my deepest appreciation and gratitude to my committee chair and adviser Dr. Mukhlesur Rahman, for his constant guideline, valuable suggestions and continuous support in conducting this research and writing this manuscripts. Without his persistent help, this dissertation would not have been possible. My heartfelt thanks to the members of my advisory committee Dr. Phillip McClean, Dr. David Horvath and Dr. Luis del Rio for their assistance, valuable suggestions and for their time in reviewing this manuscript. Special thanks to Dr. David Horvath for his support, technical assistance and guiding me during data analyses of the transcriptomics study. I am immensely grateful to Dr. Sujan Mamidi, Dr. Zahirul Talukdar, and Dr. Atena OladzadAbbasabadi for their valuable suggestions at various stages of data analyses. I would like to extend my sincere thanks to Andrew Ross (Canola and Flax breeding and genetics group), Rian Lee (McClean’s lab), and Laura Kelly (Horvath’s lab) for their extraordinary help in conducting the research is the field, greenhouse and laboratory. I would also like to thank all the current and former graduate students in Canola & Flax Breeding and Genetics group for their help and mental support during my time in NDSU. I gratefully acknowledge the funding sources of this research, NDSU Center of Excellence for Agbiotechnology, National institute of Food and Agriculture (NIFA) and Northern Canola Growers Association. v Lastly, I would like to express my heartiest gratitude to my Mother and late Father for incorporating the thirst of knowledge and wisdom in my early age. It would not be possible for me to continue my higher study without the unconditional support, wise guidance, continuous encouragements and inspirations of my Mother. Special thanks to my younger brother Mohammad Tarik Uz Zaman for always being by my side whenever I need him. I am forever in debt with my loving wife Sanzida Rahman for her continuous support and encouragement. Her immensely supportive behaviors and understanding made my graduate student life lots easier. vi DEDICATION I would like to dedicate this dissertation to my late father Muhammad Shamsuzzaman, whose prime concern was to provide me good educational facility despite of having so many limitations, and, to my beloved mother, Rokhsana Akter for all the sacrifices she has made to raise me; and inspire me always to go for higher education vii TABLE OF CONTENTS ABSTRACT ................................................................................................................................... iii ACKNOWLEDGEMENTS ............................................................................................................ v DEDICATION .............................................................................................................................. vii LIST OF TABLES ....................................................................................................................... xvi LIST OF FIGURES ................................................................................................................... xviii LIST OF APPENDIX TABLES .................................................................................................. xxi CHAPTER 1: GENERAL INTRODUCTION ............................................................................... 1 CHAPTER 2: LITERATURE REVIEW ........................................................................................ 6 2.1. Canola/Rapeseed .................................................................................................................. 6 2.1.1. Brassica ......................................................................................................................... 6 2.1.2. Brassica U triangle ........................................................................................................ 6 2.1.3. Brassica napus ............................................................................................................... 7 2.1.4. Origin and domestication of B. napus ........................................................................... 7 2.1.5. Taxonomy and botany ................................................................................................... 8 2.1.6. Development of canola/rapeseed ................................................................................... 8 2.1.7. Canola oil health benefit ................................................................................................ 9 2.2. Root system architecture in plants ..................................................................................... 10 2.2.1. Root system architecture ............................................................................................. 10 2.2.2. Role and function of root system architecture in plants .............................................. 11 2.2.3. Correlation between root system architecture and yield in different crops ................. 12 2.2.4. Correlation between root system architecture and yield in Brassica species .............. 14 2.3. Breeding for root architectural traits .................................................................................. 14 2.3.1. Selection for root traits and challenges........................................................................ 14 viii 2.3.2. High throughput phenotyping for root traits................................................................ 15 2.3.3. Marker assisted selection/breeding for root architectural traits ................................... 16 2.3.4. Genome wide association mapping ............................................................................. 18 2.3.5. Genome wide association mapping on root architectural traits in different crops ...... 19 2.4. Differential gene expression study ..................................................................................... 21 2.4.1. Transcriptomics ........................................................................................................... 21
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