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Genetic and Epigenetic Control of Soybean Agronomic Traits

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University of Tennessee, Knoxville TRACE: Tennessee Research and Creative Exchange Doctoral Dissertations Graduate School 12-2020 Genetic and Epigenetic Control of Soybean Agronomic Traits Daniel Niyikiza [email protected] Follow this and additional works at: https://trace.tennessee.edu/utk_graddiss Part of the Plant Breeding and Genetics Commons Recommended Citation Niyikiza, Daniel, "Genetic and Epigenetic Control of Soybean Agronomic Traits. " PhD diss., University of Tennessee, 2020. https://trace.tennessee.edu/utk_graddiss/6084 This Dissertation is brought to you for free and open access by the Graduate School at TRACE: Tennessee Research and Creative Exchange. It has been accepted for inclusion in Doctoral Dissertations by an authorized administrator of TRACE: Tennessee Research and Creative Exchange. For more information, please contact [email protected]. To the Graduate Council: I am submitting herewith a dissertation written by Daniel Niyikiza entitled "Genetic and Epigenetic Control of Soybean Agronomic Traits." I have examined the final electronic copy of this dissertation for form and content and recommend that it be accepted in partial fulfillment of the requirements for the degree of Doctor of Philosophy, with a major in Plants, Soils, and Insects. Tarek Hewezi, Major Professor We have read this dissertation and recommend its acceptance: Vince R. Pantalone, Carl E. Sams, Tom Gill, Tessa Burch-Smith Accepted for the Council: Dixie L. Thompson Vice Provost and Dean of the Graduate School (Original signatures are on file with official studentecor r ds.) Genetic and Epigenetic Control of Soybean Agronomic Traits A Dissertation Presented for the Doctor of Philosophy Degree The University of Tennessee, Knoxville Daniel Niyikiza December 2020 Copyright © 2020 by Daniel Niyikiza All rights reserved. ii DEDICATION To my wife Aline Josee U., our children Abba Shelby S. I. and Addy Davin N. N., without whom this dissertation would not have been completed. iii ACKNOWLEDGEMENTS My sincere gratitude and special appreciation go to Dr. Tarek Hewezi for having accepted me in his Lab and to serve as the major supervisor of my research project. His advice and guidance and incredible support were key determinants in the completion of this project. I would like to thank the co-supervisor of my research project, Dr. Vince Pantalone for his unequalled assistance throughout the course of the research project and dissertation. I will always remember that he initiated my first steps into the soybean breeding paths and technically accompanied me through this research journey. My heartfelt appreciation to the members of my committee, Dr. Tom Gill, Dr. Carl Sams, and Dr. Tessa Burch-Smith for enriching contribution to the quality of my dissertation. Your constructive advices were helpful. To Dr. Hewezi’s lab members: John Hollis Rice, Dr. Sarbottam Piya, Dr. Pratyush Routray, Dr. Aditi Rambani, Dr. Yin Fang, Dr. Valeria Lopes-Caitar, Dr. Long Miao, Morgan Bennet, and others I could not list here, and Dr. Pantalone’s lab members: Greyson Dickey, Rachel Fulton, Alison Willette, Dr. Chris Smallwood, Dr. Mia Cunicelli, Cris Wyman, Victoria Benelli, and many others not listed here, for your invaluable technical support. My sincere acknowledgement to Lisa A. Fritz and Susan T. Laired for their technical support for SCN screening assays. Much appreciation to The Borlaug for Higher Education and Agriculture Research and development (BHEARD) for granting me the scholarship and financial support to my project and The Tennessee Soybean Promotion Board (TSB) for financially co-supporting my research project. Special thanks, to my colleagues in Rwanda Agriculture Board, Aime Parfait G., Aimable I., Charles N., Francois S. and many others for their technical and logistics support. To Dr. Dave Ader and all my friends at UT for making my stay memorable And finally, my heartfelt gratitude to my friends, family members and colleagues for the encouragement along this resourceful experience. iv ABSTRACT Greater soybean productivity depends on the genetic improvement of yield components, epigenetic effects and the interactions with surrounding environment. We explored the possibility of soybean improvement by conventional biparental crossing of soybean lines, differing by seed quality, yield, and resistance to a range of pathogens, including soybean cyst nematode (SCN). We investigated the role of Resistance to Heterodera glycines (Rhg) 1 and 4 loci in soybean resistance to SCN, race 2 and 3. Further, we evaluated the adaptability of temperate-origin soybean lines in tropical environments of Rwanda. Lastly, we examined gene expression, RNA splicing, DNA methylation and their interactions in three distinct developmental stages of soybean nodules. Briefly, compared to the parental lines, the recombinant inbred lines (RILs) generated from the biparental cross, represented varying phenotypes for seed yield, protein and oil contents, with high broad-sense heritability scores. This suggests a possibility of selection of best individuals with potentially high genetic gain for each trait. Analysis of gene expression, nucleotide sequences, and copy number variation of Rhg1 and Rhg4 in a set of RILs revealed that resistance to race 2 is mediated independently of Rhg1 and Rhg4. Importantly, a QTL on chromosome 17, associated with resistance to SCN race 2 was identified, a finding that provides the foundation for cloning the underlying SCN resistance gene. Our data suggested a possibility to stack favorable SCN resistance alleles in high yielding cultivars as the yield of RILs harboring SCN resistance alleles to race 2, compared to the susceptible RILs, was not negatively impacted. Some US-developed soybean lines could adapt and double the current local yield potential. However, our data revealed a significant GXE interaction, implying their fitness in specific micro-climates of Rwanda. Amino acid profile and consequently seed storage protein can be improved through the manipulation of soybean nodulation. Our results revealed dynamic changes in gene expression, alternative splicing events and extensive DNA methylation reprogramming in the developing nodules. The results also revealed novel insights to the associations between the transcriptome, spliceome, and methylome of the developing soybean nodules and improved our understanding of the genetic and epigenetic mechanisms controlling soybean nodulation. v TABLE OF CONTENTS Chapter 1: General introduction and literature review ............................................................ 1 1. Introduction ............................................................................................................................... 2 1.1 The Implications of genetics and epigenetics in Soybean adaptation, agronomic and quality traits .............................................................................................................................. 2 1.2 The genetic basis of resistance and the importance of epigenetics in SCN control .... 10 1.3 Soybean nodulation: a biological process for seed yield and quality improvement ... 15 1.4 Soybean production in Rwanda: Challenges and opportunities .................................. 19 1.5 Organization of the Dissertation...................................................................................... 21 References .................................................................................................................................... 22 Chapter 2: Performance evaluation of TN09-029 x NCC05-1168 recombinant inbred lines (RIL) population of Soybean Glycines max (L) Merr. ......................................................... 41 Abstract ........................................................................................................................................ 42 1. Introduction ............................................................................................................................. 43 2. Results ...................................................................................................................................... 44 2.1 Agronomic traits ............................................................................................................... 44 2.2 Seed quality traits ............................................................................................................. 45 3. Discussion................................................................................................................................. 47 3.1 The agronomic performance improved .......................................................................... 47 3.2 Protein and oil content relatively increased ................................................................... 48 4. Conclusion ............................................................................................................................... 50 5. Materials and Methods ........................................................................................................... 50 5.1 Plant material .................................................................................................................... 50 5.2 Field experiments .............................................................................................................. 51 5.3 Agronomic traits ............................................................................................................... 51 5.4 Protein, Oil and Amino Acid Content ............................................................................
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