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DEVELOPMENT of Liriodendron EST-SSR MARKERS and GENETIC COMPOSITION of TWO Liriodendron Tulipifera L

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DEVELOPMENT of Liriodendron EST-SSR MARKERS and GENETIC COMPOSITION of TWO Liriodendron Tulipifera L Clemson University TigerPrints All Theses Theses 12-2013 DEVELOPMENT OF Liriodendron EST-SSR MARKERS AND GENETIC COMPOSITION OF TWO Liriodendron tulipifera L. ORCHARDS Xinfu Zhang Clemson University, [email protected] Follow this and additional works at: https://tigerprints.clemson.edu/all_theses Part of the Genetics and Genomics Commons Recommended Citation Zhang, Xinfu, "DEVELOPMENT OF Liriodendron EST-SSR MARKERS AND GENETIC COMPOSITION OF TWO Liriodendron tulipifera L. ORCHARDS" (2013). All Theses. 1791. https://tigerprints.clemson.edu/all_theses/1791 This Thesis is brought to you for free and open access by the Theses at TigerPrints. It has been accepted for inclusion in All Theses by an authorized administrator of TigerPrints. For more information, please contact [email protected]. DEVELOPMENT OF Liriodendron EST-SSR MARKERS AND GENETIC COMPOSITION OF TWO Liriodendron tulipifera L. ORCHARDS A Thesis Presented to the Graduate School of Clemson University In Partial Fulfillment of the Requirements for the Degree Master of Science Genetics by Xinfu Zhang December 2013 Accepted by: Dr. Haiying Liang, Committee Chair Dr. Ksenija Gasic Dr. James Morris Dr. Alex Feltus ABSTRACT Liriodendron tulipifera L., commonly known as yellow-poplar, is a fast-growing hardwood tree species with great ecological and economic value and is native to eastern North America. Liriodendron occupies an important phylogenetic position as a basal angiosperm and has been used in studies of the evolution of flowering plants. Genomic resources, such as Expressed Sequence Taq (EST) databases and Bacterial Artificial Chromosome (BAC) libraries, have been developed for this species. However, no genetic map is available for Liriodendron, and very few molecular markers have been developed. In this study, a total of 119 informative genomic SSR markers suitable were identified for genetic linkage map construction with an F1 progeny from #UT108A × #UT23 cross, that have been developed. The full-sibship of 213 seedlings were validated. These informative SSR markers and full-sib seedlings are essential in construction of linkage maps. Linkage map will enable molecular breeding and quantitative trait locus (QTL) mapping, and provide framework for sequencing the Liriodendron genome. In addition we characterized 20 EST-SSR markers with 174 trees from two yellow-poplar seed orchards (residing in Knoxville, Tennesse, and Clemson, South Carolina, respectively), and the US National Arboretum, and provided a first look at the genetic diversity and allele richness among selections of this unique native species. Analysis revealed only one locus significantly deviating from Hardy-Weinberg proportions in the Clemson population, and 10 loci in Knoxville population (p>0.05). In addition, the Clemson orchard exhibited higher values of observed and effective number of alleles, ii observed heterozygosity, and Nei’s expected heterozygosity than the Knoxville orchard, revealing larger genetic diversity in the Clemson seed orchard. iii DEDICATION I dedicate this thesis to my family: my father, Hongyin Zhang, and my Mother, Jing Liu. They gave me positive encouragement during my graduate study. My family will always be the most important part of my life. iv ACKNOWLEDGMENTS Firstly, I would like to give my sincere thanks to my advisor, Dr. Haiying Liang, for her patient guidance, lasting assistance, and positive encouragement to me. Secondly, I would like to thank to Dr. Ksenija Gasic, Dr. James Morris, and Dr. Alex Feltus for serving on my committee, and for their sparkling wisdom, insightful feedback, and professional suggestions. I thank Jeanice Troutman, Christopher Saski, Xiaoxia Xia, and Margaret Staton in Clemson University Genome Institute (CUGI) for technical support in fragment analysis. I also thank Dr. Nannan Yang, a former Ph.D. student in Dr. Gasic’s lab, Dr. Jeanne Romero-Severson, and Tim McCleary in University of Notre Dame, who gave me professional suggestions about the whole work. I thank Dr. Scott Schlarbaum’s group in The University of Tennessee, who provided us plant materials. I also thank the former and current lab members in our lab, Dr. Haiying Liang, Dr. Shivegowda Thammannagowda, Dr. Yi Xu, Tao Xu, Dr. Tieguang He, Dr. Zhenkun Tian, and Ying Zhao. I thank the promising undergraduate students who worked with me, including Alanna Carlson, Christopher Saindon, and Jasmine Ruizyi in Clemson University, and Melany Moore from The University of Tennessee. Finally, I would like to thank all the faculty, staff, students, and visiting scholars in the Department of Genetics and Biochemistry. I am proud of being a member in this wonderful department. v TABLE OF CONTENTS Page TITLE PAGE .................................................................................................................... i ABSTRACT ..................................................................................................................... ii DEDICATION ................................................................................................................ iv ACKNOWLEDGMENTS ............................................................................................... v LIST OF TABLES ........................................................................................................ viii LIST OF FIGURES ........................................................................................................ ix CHAPTER 1. LITERATURE REVIEW ............................................................................................ 1 Liriodendron tulipifera L., a potential tree model research system for comparative genomics ................................................................................. 1 Applications of molecular markers in forest tree species ............................ 9 Project objectives ....................................................................................... 17 References .................................................................................................. 19 2. DEVELOPMENT OF FULL-SIB PROGENY AND INFORMATIVE SSR MARKERS FOR YELLOW-POPLAR GENETIC LINKAGE MAP CONSTRUCTION… ..................................................................................................... 46 Abstract ...................................................................................................... 46 Introduction ................................................................................................ 47 Materials and methods ............................................................................... 50 Results and discussion ............................................................................... 87 References .................................................................................................. 94 3. DETECTING GENETIC CONSTITUTION OF TWO LIRIODENDRON SEED ORCHARDS WITH EST-SSR MARKERS ................................................................. 99 Abstract ...................................................................................................... 99 Introduction .............................................................................................. 100 Materials and methods ............................................................................. 104 Results and disscussion ............................................................................ 109 References ................................................................................................ 121 vi CONCLUSION AND FUTURE DIRECTION ........................................................... 126 Conclusion ............................................................................................... 126 Future direction ........................................................................................ 128 APPENDICES ............................................................................................................. 129 Appendix I ............................................................................................... 129 Appendix II .............................................................................................. 131 Appendix III ............................................................................................. 133 vii LIST OF TABLES Table Page 1. Sixty-six polymorphic yellow-poplar EST-SSR markers that identified by Xu et al.....................................................................................................5-7 2. Putative EST-SSR markers from a comprehensive EST dataset…………………..53-85 3. Characteristics of 9 EST-SSR markers used for validation of full-sibship…………...86 4. Distribution of the 119 informative EST-SSR markers in the five groups……………91 5. Alleles at the nine SSR loci of the three parents used in genotype checking of #UT108A and #UT108B…………………………………………………....92 6. Characteristics of 20 EST-SSR loci………………………………………………….108 7. Statistics of the 15 markers analyzed by Cervus………………………………….…114 8. Genetic variation at six EST-SSR loci characterized in Clemson orchard……….….118 9. Genetic variation at six EST-SSR loci characterized in Knoxville orchard…….…...119 10. Nei's (1978) unbiased identity (above diagonal) and distance (below diagonal) ….120 viii LIST OF FIGURES Figure Page 1. PCR amplification success rate study with 112 chosen SSR markers ....................... 89 2. Liriodendron orchards ............................................................................................. 104 3. Examples of leaf shape of Liriodendron
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