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Characterization of Quantitative Traits Using Association Genetics Louisiana State University LSU Digital Commons LSU Doctoral Dissertations Graduate School 2010 Characterization of quantitative traits using association genetics tetraploid and genetic linkage mapping in diploid cotton (Gossypium spp.) Ashok Badigannavar Louisiana State University and Agricultural and Mechanical College, [email protected] Follow this and additional works at: https://digitalcommons.lsu.edu/gradschool_dissertations Recommended Citation Badigannavar, Ashok, "Characterization of quantitative traits using association genetics tetraploid and genetic linkage mapping in diploid cotton (Gossypium spp.)" (2010). LSU Doctoral Dissertations. 2207. https://digitalcommons.lsu.edu/gradschool_dissertations/2207 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]. CHARACTERIZATION OF QUANTITATIVE TRAITS USING ASSOCIATION GENETICS IN TETRAPLOID AND GENETIC LINKAGE MAPPING IN DIPLOID COTTON (GOSSYPIUM SPP.) 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 School of Plant, Environmental, and Soil Sciences By Ashok Badigannavar BSc (Agri), University of Agricultural Sciences, Dharwad, India, 1997 MSc (Agri), University of Agricultural Sciences, Dharwad, India, 1999 May 2010 This dissertation is dedicated in memory of my late father….. ii ACKNOWLEDGEMENTS I would like to express my sincere gratitude to my major professor Dr.Gerald O Myers for his valuable guidance and advice throughout my dissertation. The freedom he has provided during the course of study is commendable. My appreciation is also extended to the committee members; Dr.Rajasekharan, Dr.Collins Kimbeng, Dr. C. Knott and Dean nominee, Dr. Fangneng Huang. I am indebted to all my committee members for their incredible help and guidelines in the dissertation research, analysis and writing. I would like to thank Dr. Oard for his valuable suggestions in formulating the research proposal and Dept. Head and staff for their encouragement and support. The financial support provided by the research sponsor, Cotton Incorporated is greatly appreciated. I would extend my sincere gratitude to Dr. A. H. Paterson for providing seeds of the diploid mapping population, Dr. F. Bourland, for providing the Arkansas genotypes, various public breeders and private seed companies allowing me to use their varieties, Dr. M. Ulloa for providing SSR markers, the LSU AgCenter, Cotton Fiber Lab for fiber sample analysis and to Dr. C.Kimbeng for their cooperation. The public breeders of the RBTN trials are acknowledged for providing the multistate cotton phenotypic data. I am extremely grateful to Computational Biology Unit, Microsoft High Performance Computing Facility, Cornell University for allowing me to use clusters for simulation studies. I would like to thank my fellow colleagues, Jimmy Zumba, Tyson, Sreedhar, Suman, Samuel, Reddy, Rakesh, Charanjit and Marvellous for their help during the course of study. I am also thankful to Dr. N. Baisakh for his valuable suggestions during the course of study. I would also like to thank my mother, brother, mama and niece for their love, continuous encouragement and being my motivational force. My heartfelt thanks are also extended to all my Indian and International friends without whom I would have missed the fun and wonderful life in Baton Rouge. iii TABLE OF CONTENTS DEDICATION………………………………………………………………………………... ii ACKNOWLDGEMENTS…………………………………………………………………… iii LIST OF TABLES……………………………………………………………………………. vi LIST OF FIGURES…………………………………………………………………………... ix LIST OF ABBREVIATIONS………………………………………………………………… xii ABSTRACT…………………………………………………………………………………... xiii CHAPTER 1 GENERAL INTRODUCTION………………………………………………… 1 1.1 Genetic Linkage Mapping and QTL Analysis of Fiber Traits in Diploid Cotton Using AFLP-SSR-TRAP Markers………………………………….. 3 1.2 Association Mapping of Fiber Traits in Upland Cotton Using Molecular Markers……………………………………………………………………… 5 1.3 Characterization and Marker Trait Associations of Seed Quality Traits in Upland Cotton (Gossypium hirsutum L.)……………………………………. 8 1.4 Characterization of Upland Cotton Genotypes for Molecular Diversity and Marker Trait Associations…………………………………………………... 10 1.5 References…………………………………………………………………... 12 CHAPTER 2 GENETIC LINKAGE MAPPING AND QTL ANALYSIS IN DIPLOID COTTON USING AFLP-SSR-TRAP MARKERS………………………… 15 2.1 Introduction…………………………………………………………………. 15 2.2 Materials and Methods……………………………………………………... 19 2.3 Results……………………………………………………………………… 26 2.4 Discussion…………………………………………………………………... 41 2.5 Conclusion………………………………………………………………….. 44 2.6 References………………………………………………………………….. 44 CHAPTER 3 GENETIC ASSOCIATION MAPPING OF QUANTITATIVE TRAITS IN UPLAND COTTON………………………………………………………... 49 3.1 Introduction…………………………………………………………………. 49 3.2 Materials and Methods ……………………………………………………... 54 3.3 Results and Discussion…..………………………………………………….. 64 3.4 Conclusion.…………………………………………………………………. 88 3.5 References…………………………………………………………………... 89 CHAPTER 4 CHARACTERIZATION OF UPLAND COTTON GENOTYPES FOR MOLECULAR DIVERSITY AND MARKER TRAIT ASSOCIATIONS... 95 4.1 Introduction………………………………………………………………… 95 4.2 Materials and Methods……………………………………………………… 97 4.3 Results………………………………………………………………………. 102 iv 4.4 Discussion.………………………….………………………………………. 113 4.5 Conclusion………………………………………………………………….. 115 4.6 References…………………………………………………………………... 115 CHAPTER 5 CHARACTERIZATION AND MARKER TRAIT ASSOCIATIONS OF SEED QUALITY TRAITS IN UPLAND COTTON (Gossypium hirsutum). 120 5.1 Introduction…………………………………………………………………. 120 5.2 Materials and Methods……………………………………………………… 122 5.3 Results………………………………………………………………………. 129 5.4 Discussion…………………………………………………………………... 141 5.5 Conclusion and Future Work……………………………………………….. 145 5.6 References…………………………………………………………………... 146 CHAPTER 6 SUMMARY AND CONCLUSIONS………………………………………….. 150 VITA…………………………………………………………………………………………. 153 v LIST OF TABLES 2.1a Adapters and primers of AFLP marker system used for pre and selective amplification in diploid F2 population………………………………………………………………… 21 2.1b Forward and reverse primer sequences of TRAP markers used in diploid F2 population………………………………………………………………………………. 23 2.2 Univariate analysis of FL, UNI, SFI, FS, ELO and SI characters in parental and 26 diploid F2 population…………………………………………………………………… 2.3 Pearson correlation coefficients among fibber traits of diploid F2 population………… 28 2.4 Summary of AFLP primers used and the number of polymorphic loci identified by each combination………………………………………………………………………. 29 2.5 Number of genetic loci per LG, estimated LG length and average distance in the diploid linkage map…………………………………………………………………….. 33 2.6 Discriminant analyses selected markers for petal color, seed fuzziness and petal spot in a diploid F2 population of cotton…………………………………………………… 36 2.7 Composite Interval Mapping for fiber traits using F2 diploid cotton population from a cross between G. arboreum and G. herbaceum. QTLs are listed traitwise along with 38 their position on LG, LOD, additive and dominant effects…………………………….. 2.8 Significant markers selected using PROC GLMSELECT for fiber traits in diploid F2 mapping population…………………………………………………………………….. 39 3.1a List of genotypes selected from five growing regions utilized for cotton association mapping………………………………………………………………………………… 55 3.1b Cotton Microsatellite Database (CMD) - a standardized Panel of cotton genotypes used to compare with association mapping genotypes (www.cottonmarker.org)........... 56 3.2 Adapters and primers of AFLP markers system used for pre and selective amplification in cotton association mapping…………………………………………… 57 3.3 Mixed models designed for association mapping in cotton using TASSEL software…. 62 3.4 Phenotypic variation for yield and fiber traits in CAM panel…………………………. 64 3.5 Correlations between lint yield and major HVI fiber properties in upland cotton…….. 65 3.6 Population genetic parameters for the inferred six clusters of cotton association mapping panel………………………………………………………………………….. 66 vi 3.7 Nei’s genetic diversity estimates for the inferred six clusters in cotton association mapping panel. X axis: PIC values, Y axis: frequency………………………………… 67 3.8 Allele frequency divergence among inferred subpopulations in cotton association genotypes……………………………………………………………………………….. 68 3.9 Analysis of Molecular Variance (AMOVA) among and within inferred groups……… 69 3.10 Pairwise FST values between six inferred groups of cotton association genotypes…… 69 3.11 Quantitative trait alleles identified by the MTIK mixed model using TASSEL. Based 2 on the high adj.R and significant P value, the QTAs were identified for each trait in 79 cotton association mapping panel……………………………………………………… 3.12a Significant QTLs selected from MLM-MMR based models for fiber elongation…….. 82 3.12b Significant QTLs selected from MLM-MMR based models for Lint yield…………... 83 3.12c Significant QTLs selected from MLM-MMR based models for Lint percentage…….. 83 3.12d Significant QTLs selected from MLM-MMR based models for fiber strength……….. 84 3.12e Significant QTLs selected from MLM-MMR based models for fiber length………… 85 3.12f Significant QTLs selected from MLM-MMR based models for Micronaire…………. 85 3.12g Significant QTLs selected by MLM-MMR based
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