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Association Genetics for Agronomic Traits in Rice and Cloning of ALS Louisiana State University LSU Digital Commons LSU Doctoral Dissertations Graduate School 2006 Association Genetics for Agronomic Traits in Rice and Cloning of ALS Herbicide Resistant Genes from Coreopsis Tinctoria Nutt Nengyi Zhang Louisiana State University and Agricultural and Mechanical College, [email protected] Follow this and additional works at: https://digitalcommons.lsu.edu/gradschool_dissertations Recommended Citation Zhang, Nengyi, "Association Genetics for Agronomic Traits in Rice and Cloning of ALS Herbicide Resistant Genes from Coreopsis Tinctoria Nutt" (2006). LSU Doctoral Dissertations. 3847. https://digitalcommons.lsu.edu/gradschool_dissertations/3847 This Dissertation is brought to you for free and open access by the Graduate School at LSU Digital Commons. It has been accepted for inclusion in LSU Doctoral Dissertations by an authorized graduate school editor of LSU Digital Commons. For more information, please [email protected]. ASSOCIATION GENETICS FOR AGRONOMIC TRAITS IN RICE AND CLONING OF ALS HERBICIDE RESISTANT GENES FROM COREOPSIS TINCTORIA NUTT. A Dissertation Submitted to the Graduate Faculty of the Louisiana State University and Agricultural and Mechanical College in partial fulfillment of the requirements for the degree of Doctor of Philosophy In The Department of Agronomy and Environmental Management By Nengyi Zhang B.S., Hangzhou University, 1991 M.S., Zhejiang Agricultural University, 1994 August 2006 This work is dedicated to my father, Xingjian Zhang and my mother, Fengnu Zhang ii ACKNOWLEDGEMENTS I wish to express my profound gratitude to Dr. James Oard, my major professor, for his support, encouragement, guidance and useful suggestions throughout the period of this research. Without his help, it would be impossible for me to complete any portion of this work. I am greatly thankful to my committee members, Drs. Gerald Myers, Don Labonte, Charles Johnson, and Seth Johnson for their contributions to my studies and research. I gratefully appreciate the contributions from our collaborators Drs. Yunbi Xu and Susan McCouch from Cornell University and Dr. Dearl Sanders from Louisiana State University Agricultural Center. I am grateful for Dr. Svetlana Oard and my brother, Dr. Nenggang Zhang for their useful discussion and suggestions. I am greatly thankful to Louisiana State University Agricultural Center who provided the Fellowship of Biotechnology Education for Students and Teachers (BEST) for this degree and funding for the research. I want to express my sincere acknowledgement to the head and staff of the Department of Agronomy and Environmental Management for making it possible for me to study here. I thank my colleagues, Muhanad Akash, Gabriel Aluko, Dawen Liu, Alicia Ryan, Baogong Jiang, Joohyun Lee, Weiqiang Zhang, Suresh Kadaru, Samuel Ordonez, Suman Andru, Sredhar Alwala, Niranjan Baisakh and others for their assistance. Finally, my deepest thanks will go to my dear wife, Zhifang Cheng and our son, Jack for their love, understanding, supporting and encouragement during my study. iii TABLE OF CONTENTS DEDICATION ................................................................................................................................ii ACKNOWLEDGEMENTS ...........................................................................................................iii LIST OF TABLES .........................................................................................................................vi LIST OF FIGURES ......................................................................................................................vii ABSTRACT ................................................................................................................................viii CHAPTER 1: INTRODUCTION ...................................................................................................1 1.1 Rapid Identification of Candidate Markers Associated with Agronomic Traits among Inbred Lines of Rice Using Association Genetics ......................................1 1.2 Genetic Studies of Mutants of Coreopsis tinctoria Nutt. .................................................7 1.3 References .......................................................................................................................12 CHAPTER 2: IDENTIFICATION OF CANDIDATE MARKERS ASSOCIATED WITH AGRONOMIC TRAITS IN RICE USING DISCRIMINANT ANALYSIS ....................22 2.1 Introduction .....................................................................................................................22 2.2 Materials and Methods …................................................................................................24 2.3 Results and Discussion ....................................................................................................26 2.4 Conclusions .....................................................................................................................35 2.5 References .......................................................................................................................36 CHAPTER 3: STEPWISE, LEAST ANGLE AND LASSO REGRESSION MODELS FOR MARKER-TRAIT ASSOCIATIONS AMONG INBRED LINES OF RICE ........................................................................................................................................41 3.1 Introduction .....................................................................................................................41 3.2 Materials and Methods ....................................................................................................44 3.3 Results and Discussion ....................................................................................................45 3.4 Conclusions .....................................................................................................................54 3.5 References .......................................................................................................................55 CHAPTER 4: CLONING AND PHYLOGENETIC ANALYSIS OF GENES ENCODING ACETOLACTATE SYNTHASE FROM COREOPSIS TINCTRIA NUTT. FOR RESISTANCE TO SULFONYLUREA AND IMIDAZOLINONE HERBICIDES ................................................................................................................................57 4.1 Introduction .....................................................................................................................57 4.2 Materials and Methods ....................................................................................................64 4.3 Results .............................................................................................................................65 4.4 Discussion .......................................................................................................................67 4.5 References .......................................................................................................................68 CHAPTER 5: SUMMARY AND CONCLUSIONS …................................................................77 iv APPENDIX: LETTER OF PERMISSION ...................................................................................80 VITA .............................................................................................................................................82 v LIST OF TABLES Table 2.1. Mean values of agronomic traits of US and Asian rice lines, 1996-1997, Alvin, Texas. ............................................................................................27 Table 2.2. Percent correct classification of 218 inbred rice lines assigned to defined groups of early and late heading date as training samples using a k-nearest neighbor algorithm with and without consideration of population structure, 1996-1997, Alvin, Texas. ............................................................................................30 Table 2.3. SSR/RFLP alleles identified by DA from 1 SD, 2 SD and 3 SD training samples among 218 US and Asian inbred rice lines. ..................................................31 Table 3.1. SSR/RFLP alleles identified by discriminant analysis (1 SD), stepwise forward regression, and LASSO/LAR regression with R2 values in rice. ..................46 Table 3.2. Epistatic loci and R2 values determined for twelve rice traits derived from modified stepwise forward and LASSO/LAR regression methods with or without consideration of population structure. …...................................................50 Table 3.3. Goodness of fit of two different models in explaining phenotypic variation for twelve rice traits. ....................................................................................52 vi LIST OF FIGURES Fig. 2.1. Chromosomal locations of markers identified by discriminant analysis (DA) and quantitative trait loci (QTL) mapping for plant height, maturity, and tiller number in rice. Solid, empty, and striped boxes represent QTLs detected in previous research using standard IM/CIM methods for plant height, heading date, and tiller number, respectively. DA-selected SSR or RFLP markers associated with plant height are underlined. DA-selected SSR or RFLP markers associated with heading date are labeled with an asterisk. DA-selected SSR or RFLP markers with no label are associated with tiller number. .........................................................................................................32 Fig. 3.1. Chromosomal locations of markers identified by discriminant analysis
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