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Rust Resistance in the Guatemalan Climbing Bean Germplasm Collection

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Rust Resistance in the Guatemalan Climbing Bean Germplasm Collection RUST RESISTANCE IN THE GUATEMALAN CLIMBING BEAN GERMPLASM COLLECTION A Thesis Submitted to the Graduate Faculty of the North Dakota State University of Agriculture and Applied Science By Luz de Maria Albertina Montejo Domínguez In Partial Fulfillment of the Requirements for the Degree of MASTER OF SCIENCE Major Department: Plant Sciences July 2017 Fargo, North Dakota North Dakota State University Graduate School Title RUST RESISTANCE IN THE GUATEMALAN CLIMBING BEAN GERMPLASM COLLECTION By Luz de Maria Albertina Montejo Domínguez The Supervisory Committee certifies that this disquisition complies with North Dakota State University’s regulations and meets the accepted standards for the degree of MASTER OF SCIENCE SUPERVISORY COMMITTEE: Ph.D. Juan M. Osorno Chair Ph.D. Phillip McClean Ph.D. Samuel Markell Ph.D. Elias Elias Approved: August 2, 2017 Ph.D. Richard Horsley Date Department Chair ABSTRACT Common bean is the main source of protein, fiber, and iron for Guatemalan's poorest households; however, bean rust can cause up to 100% yield losses. There is limited information about bean rust in Guatemala, especially at mid-altitude highlands. During 2015, 23 bean rust samples were collected in the Western Guatemalan Highlands and 17 isolates where characterized, as a result, races 63-1 and 31-1 were identified. Those were used to evaluate rust resistance by using 372 Guatemalan climbing beans. In total, 82% of accessions were resistant to race 63-1, 86% to race 31-1, and 90% to race 20-3. Based on GWAS results (78,754 SNPs) the Pv02 (38.13 Mb-38.22Mb) and Pv04 (379 kb) regions were associated with resistance to race 20- 3. The Pv10 (10.71-10.68 Mb and 11.09 Mb) and Pv04 (1.42 MB) regions control resistance to race 63-1. And, the Pv04 (39.28 Mb) and Pv02 (35.92 Mb) control resistance to race 31-1. iii ACKNOWLEDGEMENTS I would like to thank Dr. Juan M. Osorno for his guidance, opportunities and support during my career. I would also like to express my gratitude to my committee members: Dr. Elias, Dr. McClean and Dr. Markell for their help. I would like to give special thanks to Dr. Steadman from Plant Pathology Department at University of Nebraska, Lincoln for his support in my whole research. I will not forget the kindness and help from the staff of the Dry Bean Breeding Program at NDSU, Jody VanderWal, Mike Klobendanz, Stephan Schroder, Ali Soltani, Katelynn Walker, Carlos Maldonado, and Federico Velasquez as well as Gabriela Tobar from the bean molecular genetics group. In addition, I would like to thank Serena McCoy and Becky Higgins from the Plant Pathology Department at UNL, Nebraska, for their support and warmness. I have great appreciation for The USAID Legume Innovation Lab project, ICTA - Guatemala and the Department of Plant Sciences at North Dakota State University. Without their support, this opportunity would not have been available. Most importantly, to all my family members for their support, cheers and encouraging me to pursuit my goals. Finally, thanks to all my friends who supported me during this journey. iv DEDICATION To my parents Luz Dominguez and Benjamin Montejo v TABLE OF CONTENTS ABSTRACT ................................................................................................................................... iii ACKNOWLEDGEMENTS ........................................................................................................... iv DEDICATION ................................................................................................................................ v LIST OF TABLES ....................................................................................................................... viii LIST OF FIGURES ....................................................................................................................... ix LIST OF APPENDIX TABLES ..................................................................................................... x LIST OF APPENDIX FIGURES................................................................................................... xi INTRODUCTION .......................................................................................................................... 1 LITERATURE REVIEW ............................................................................................................... 5 The Importance of Common Bean .............................................................................................. 5 Relevance of Climbing Beans in Latin America ......................................................................... 8 Bean Rust: A Biotic Constrain .................................................................................................. 11 Genome Wide Association Study (GWAS) in Common Bean ................................................. 18 MATERIALS AND METHODS .................................................................................................. 21 Rust Collection in Guatemala ................................................................................................... 21 Pathogen Characterization ......................................................................................................... 22 Germplasm Greenhouse Evaluation .......................................................................................... 25 Genome Wide Association Analysis ......................................................................................... 28 RESULTS ..................................................................................................................................... 31 Pathogen Characterization ......................................................................................................... 31 Germplasm Greenhouse Evaluation .......................................................................................... 34 Genome –Wide Association Studies ......................................................................................... 35 DISCUSSION ............................................................................................................................... 41 Pathogen Characterization ......................................................................................................... 41 vi Germplasm Greenhouse Evaluation .......................................................................................... 42 Genome–Wide Association Studies .......................................................................................... 44 REFERENCES ............................................................................................................................. 50 APPENDIX ................................................................................................................................... 56 vii LIST OF TABLES Table Page 1. Common bean differential cultivars set used to characterize isolates of U. appendiculatus. ................................................................................................................. 14 2. Description of infection types of U. appendiculatus isolates on 1-6, based on pustule diameter. ............................................................................................................... 14 3. Samples of U. appendiculatus in beans collected at Western highlands of Guatemala ......................................................................................................................... 22 4. Quantitative scores for 1 to 6 infection types to U. appendiculatus. ................................ 28 5. Infection types for the standard set of 12 differential bean cultivars to U. appendiculatus isolates collected from Guatemala, and races based on the binary system at the seedling stage .............................................................................................. 32 6. Virulence phenotype of bean rust races 63-1, 31-1 and 20-3* to P. vulgaris differential cultivars for rust resistance............................................................................. 33 7. Analysis of Variance with fixed effects for rust diseases reactions in 372 climbing bean accessions. ................................................................................................................ 35 8. Percentage of resistant and susceptible genotypes by race, maximum and minimum infection type scores. ........................................................................................ 35 9. Mean Square Deviation (MSD) of each GWAS Statistical Model with Continuous and Binary Data. ............................................................................................................... 36 10. SNPs markers (0.01%) significantly associated with rust resistance to race 20-3 on the Guatemalan climbing bean collection, sorted by the lowest P-value. ................... 37 11. SNPs markers (0.01%) significantly associated with rust resistance to race 63-1 on the Guatemalan climbing bean collection, sorted by the lowest P-value. ................... 38 12. SNPs markers (0.01%) significantly associated with rust resistance to race 31-1 on the Guatemalan climbing bean collection, sorted by the lowest P-value. ................... 40 viii LIST OF FIGURES Figure Page 1. Bean rust life cycle............................................................................................................ 13 2. Inoculation of pinto UI-114 with bean rust spore samples collected from Guatemala, for spores increasing. ....................................................................................
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