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Identification and Characterization of Stress Responsive Genes in Soybean and Sunflower Surendra Neupane South Dakota State University

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Identification and Characterization of Stress Responsive Genes in Soybean and Sunflower Surendra Neupane South Dakota State University South Dakota State University Open PRAIRIE: Open Public Research Access Institutional Repository and Information Exchange Electronic Theses and Dissertations 2019 Identification and Characterization of Stress Responsive Genes in Soybean and Sunflower Surendra Neupane South Dakota State University Follow this and additional works at: https://openprairie.sdstate.edu/etd Part of the Agriculture Commons, Agronomy and Crop Sciences Commons, Biology Commons, Plant Biology Commons, and the Plant Breeding and Genetics Commons Recommended Citation Neupane, Surendra, "Identification and Characterization of Stress Responsive Genes in Soybean and Sunflower" (2019). Electronic Theses and Dissertations. 3249. https://openprairie.sdstate.edu/etd/3249 This Dissertation - Open Access is brought to you for free and open access by Open PRAIRIE: Open Public Research Access Institutional Repository and Information Exchange. It has been accepted for inclusion in Electronic Theses and Dissertations by an authorized administrator of Open PRAIRIE: Open Public Research Access Institutional Repository and Information Exchange. For more information, please contact [email protected]. IDENTIFICATION AND CHARACTERIZATION OF STRESS RESPONSIVE GENES IN SOYBEAN AND SUNFLOWER BY SURENDRA NEUPANE A dissertation submitted in partial fulfillment of the requirements for the Doctor of Philosophy Major in Biological Sciences Specialization in Molecular Biology South Dakota State University 2019 iii This dissertation is dedicated to my parents Ram Prasad Neupane and Chandra Kala Neupane and to my siblings Deepak Neupane, Sarita Neupane, and Deepa Neupane. I am immensely indebted to them for their infinite encouragement, support and unwavering trust without which there is nothing in my ability to succeed. iv ACKNOWLEDGMENTS I extend my deepest gratitude to my Ph.D. advisor, Dr. Madhav Nepal for valuable guidance, timely suggestion, words of encouragement, constructive remarks and dynamic supervision throughout this study and dissertation preparation. I am grateful to co-advisor Dr. Adam Varenhorst for his guidance in greenhouse experiments. The opportunity to work with him and Dr. Febina Mathew led my strong passion of integrating plant genomics to entomology and pathology. I would like to acknowledge other advisory committee members Drs. Christine Larson, R. Neil Reese, and Yajun Wu, who have assisted especially in giving me constructive feedback throughout my program. Thanks are also extended to those who assisted directly and indirectly in carrying out this study especially, Ethan Andersen, Achal Neupane, Sarah Schweitzer, Alyssa Vachino, Paul Okello, Pawan Basnet, Philip Rozeboom for their help throughout the lab work, greenhouse experiments, and data analysis. I would like to thank Dr. Anne Fennell, Dr. Ruanbao Zhou, and Dr. Emmanuel Byamukama for valuable suggestions during manuscript preparation and greenhouse experiments. I am thankful to the Department of Biology and Microbiology for providing me with the support for the completion of the graduate program. I would also like to acknowledge the funding agencies, USDA National Institute of Food and Agriculture (Hatch projects SD00H469-13 and SD00H659-18), South Dakota Soybean Research and Promotion Council (SDSRPC-SA1800238), and the Agriculture Experiment Station at South Dakota State University. v I was blessed and lucky to be surrounded with many friends during my stay in Brookings. Especially, I am thankful to Deepak Raj Joshi, Subash Acharya, Krishna Ghimire, Bimal Paudel and Reshma Thapa for their care and support. vi TABLE OF CONTENTS LIST OF ABBREVIATIONS ........................................................................................... xii LIST OF FIGURES ........................................................................................................ xvii LIST OF TABLES ......................................................................................................... xxiv ABSTRACT ................................................................................................................... xxvi CHAPTER 1: LITERATURE REVIEW ............................................................................ 1 1.1 Soybean ............................................................................................................. 1 1.2. Sunflower ......................................................................................................... 2 1.3. Resistance (R) Genes ....................................................................................... 3 1.4. Mitogen Activated Protein Kinase (MAPK) Genes ......................................... 3 1.5. Aphis glycines Matsumura ............................................................................... 5 1.5.1 Life Cycle of A. glycines .................................................................... 5 1.5.2. Aphid Effectors ................................................................................. 7 1.5.3. Aphis glycines Biotypes .................................................................. 10 1.5.4. Soybean Cultivars Exhibiting Antibiosis, Antixenosis, and Tolerance as a Resistance Response to Soybean Aphids .......................... 11 1.5.5. Rag Genes in Soybean Cultivars Provide Resistance to A. glycines ................................................................................................................... 12 1.5.6. GWAS Studies on A. glycines Resistance in Soybean Expanding to a Number of QTLs .................................................................................... 17 1.5.7. Rag Gene Pyramiding Provides Resistance to all A. glycines biotypes ..................................................................................................... 18 1.5.8. Transcriptomic Studies on Soybean-A. Glycines Interaction: Jasmonic Acid (JA) and Abscisic Acid (ABA) Signaling Pathway Plays a Crucial Role in Plant Resistance ............................................................... 18 vii 1.6. Heterodera glycines Ichinohe ........................................................................ 20 1.6.1. Origin and Distribution of SCN .......................................... 21 1.6.2. Life Cycle of SCN .............................................................. 21 1.6.3. SCN Effectors ..................................................................... 23 1.6.4. Rhg1 and Rhg4 as Major QTLs for SCN Resistance .......... 26 1.6.5. LRR-RLK Genes were Considered as the Resistance Genes against H. glycines ........................................................................ 27 1.6.7. Role of GmSNAP18 (Rhg1) and GmSHMT08 (Rhg4) Uncovered for SCN Resistance .................................................... 28 1.6.8. Minor QTLs/Genes for SCN Resistance ............................. 34 1.6.9. GWAS Study in SCN Resistance Expands other QTLs on SCN ............................................................................................... 36 1.7. Plant-aphid Interactions ................................................................................. 39 1.8. Plant-nematode Interactions ........................................................................... 42 1.9. Plant-aphid-nematode Interactions ................................................................ 43 1.10. Induced Susceptibility .................................................................................. 46 References ............................................................................................................. 51 CHAPTER 2: EVOLUTIONARY DIVERGENCE OF TNL DISEASE-RESISTANCE PROTEINS IN SOYBEAN (GLYCINE MAX) AND COMMON BEAN (PHASEOLUS VULGARIS)....................................................................................................................... 73 2.1. Introduction .................................................................................................... 74 2.2. Materials and Methods ................................................................................... 79 2.2.1. Hidden Markov Model (HMM) Search and TNL Gene Identification ................................................................................................................... 79 2.2.2. Phylogenetic Analysis ..................................................................... 80 2.2.3. Chromosomal Locations, Clustering and Syntenic Analysis .......... 81 2.2.4. Expression and microRNA (miRNA) Analysis .............................. 81 2.3. Results ............................................................................................................ 82 viii 2.3.1. Identification of TNL Genes in Soybean and Common Bean ........ 82 2.3.2. Gene Clustering and Structural Variation ....................................... 84 2.3.4. Ks Values ......................................................................................... 85 2.3.5. Phylogenetic and Syntenic Relationships ....................................... 86 2.3.6. Expression and miRNA Analysis ................................................... 89 2.4. Discussion ...................................................................................................... 92 2.4.1. Diversity of TNL Genes .................................................................. 92 2.4.2. Gene Clustering and Structural Variation ....................................... 96 2.4.3. Ks Values as a Proxy of Gene Duplication History ........................ 97 2.4.4. Phylogenetic Relationships of Identified TNL Genes and Their Orthologs..................................................................................................
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