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VIETNAM NATIONAL UNIVERSITY OFAGRICULTURE FACULTY OF BIOTECHNOLOGY -------oOo------- GRADUATION THESIS TOPIC: “POLYMORPHISM OF PARTIAL D-LOOP MITOCHONDRIAL DNA REGION AND PHYLOGENETICS IN FIVE DUCK BREEDS IN VIETNAM” HA NOI - 2023
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VIETNAM NATIONAL UNIVERSITY OFAGRICULTURE FACULTY OF BIOTECHNOLOGY -------oOo------- GRADUATION THESIS TOPIC: “POLYMORPHISM OF PARTIAL D-LOOP MITOCHONDRIAL DNA REGION AND PHYLOGENETICS IN FIVE DUCK BREEDS IN VIETNAM” Student : Bui Binh An Code : 637401 Class : K63CNSHE Instructor : MSc. Nguyen Quoc Trung HA NOI - 2023
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COMMITMENT The work contained in this thesis has not been previously submitted for a degree or diploma at any other undergraduate education institution. I hereby declare that all results of the thesis were done by me. To the best of my knowledge and belief, the thesis contains no material previously published or written by another person except where reference is made. Hanoi, February 10th, 2023 Bui Binh An i
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ACKNOWLEDGEMENT First of all, I would like to express my gratitude to the Board of Directors of Vietnam National University of Agriculture, the Dean of the Faculty and all the teachers in the Faculty of Biotechnology for creating a great learning environment and provided me the valuable knowledge throughout four and a half academic years. Additionally, I would like to thank Dr. Nguyen Hoang Thinh, Faculty of Animal Science. Dr. Nguyen Thi Thuy Hanh, Dr. Dinh Truong Son, Faculty of Biotechnology supported my thesis. I also express my heartfelt respect, gratitude and sincere appreciation to Msc. Nguyen Quoc Trung, Department of Molecular Biology and Applied Biotechnology, Vietnam National University of Agriculture for his scholastic guidance, constructive criticisms and constant inspiration during the entire period of the study as well as the research, for your time to help me in writing and for provide me the opportunity to carry out my thesis in the laboratory of Department of Molecular Biology and Applied Biotechnology. I would like to thank all professors from Department of Molecular Biology and Applied Biotechnology, who encouraged me to enhance my knowledge and help me get the orientation of thesis. Along with my supervisor, I would like to thank Cao Thi Thu Thuy and Nguyen Duc Hoang, two of my lab-mates, for all of their assistance throughout the experiment. I appreciated their enthusiastic guidance as I conducted my research and wrote this thesis. Last but not least, I want to express my thanks to my dear parents, family members, and friends for their support, blessings, inspiration, and unwavering sacrifice during the entirety of my academic career. With warm and regards! Hanoi, February 10th, 2023 Bui Binh An ii
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TABLE OF CONTENTS COMMITMENT ............................................................................................................i ACKNOWLEDGEMENT ...........................................................................................iv LIST OF TABLE ...........................................................................................................v LIST OF FIGURE ........................................................................................................vi LIST OF ABBREVIATIONS ................................................................................... viii ABTRACT.....................................................................................................................ix CHAPTER I. INTRODUCTION .................................................................................1 1.1. Introduction ...........................................................................................................1 1.2. Objective ...............................................................................................................2 1.2.1. Objective.............................................................................................................2 1.2.2. Specific objectives..............................................................................................2 CHAPTER II. LITERATURE REVIEWS .................................................................3 2.1. Duck status in the world. ..........................................................................................3 2.2. The importance of duck in Vietnam.........................................................................5 2.3. Diversity of Vietnamese duck ..................................................................................6 2.4. Mitochondrial DNA as a tool for assessing the genetic diversity. ...........................9 2.5. General information of the five duck breeds in this study .....................................12 2.5.1. General characteristics.........................................................................................12 2.5.2. Co duck................................................................................................................12 2.5.3. Co Lung duck .....................................................................................................12 2.5.4. Na Tau duck.........................................................................................................13 2.5.5. Troi duck..............................................................................................................14 2.5.6. Dom duck ............................................................................................................15 CHAPTER III. MATERIALS AND METHODS ....................................................16 3.1. Material...................................................................................................................16 3.2. Place and time of study...........................................................................................17 3.2.1. Place of study ......................................................................................................17 3.2.2. Time of study.......................................................................................................17 3.3. Method....................................................................................................................18 3.3.1. Sample collection ................................................................................................18 iii
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3.3.2. DNA isolation......................................................................................................18 3.3.3. PCR amplification and sequencing .....................................................................20 3.3.4. Data Analysis.......................................................................................................21 CHAPTER IV. RESULTS AND DISCUSSION.......................................................23 4.1. Results of DNA extraction .....................................................................................23 4.2. Amplification of D-loop region and sequencing ....................................................23 4.2.1. PCR results ..........................................................................................................23 4.2.2. Sequence identification .......................................................................................24 4.3. Phylogenetic analysis and distribution of haplotypes of all 5 duck breeds in Vietnam ............................................................................................................25 4.3.1. Polymorphism and genetic diversity ...................................................................25 4.3.2. Distribution of haplotypes of 84 samples belonging to 5 duck breeds ...............27 4.3.3. Phylogenetic analysis of 84 samples belonging to 5 duck breeds.......................29 4.4. Phylogenetic analysis and distribution of haplotypes of each breed......................30 4.4.1. Phylogenetic analysis and distribution of haplotypes of Co breed .....................30 4.4.2. Phylogenetic analysis and distribution of haplotypes of Co Lung breed ............32 4.4.3. Phylogenetic analysis and distribution of haplotypes of Na Tau breed ..............34 4.4.4. Phylogenetic analysis and distribution of haplotypes of Troi breed ...................35 4.4.5. Phylogenetic analysis and distribution of haplotypes of Dom breed ..................37 4.5. Discussion...............................................................................................................39 CHAPTER V. REFERENCES...................................................................................42 APPENDIX...................................................................................................................44 iv
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LIST OF TABLE Table 2.1. Price of duck products in Vietnam on 06/09/2022.........................................6 Table 3.1. Sample condition and total number of samples ...........................................16 Table 3.2. Primers used for PCR amplification.............................................................21 Table 4.1. Diversity indices and neutrality test results based on the genetic analysis of mtDNA D-loop sequence fragments for the five duck populations studied* .....................................................................................25 Table 4.2. Haplotype distribution table in all 5 duck breeds in Vietnam......................27 Table 4.3. Polymorphic analysis from partial sequencing of the mitochondrial D- loop gene segment of 5 duck breeds in Vietnam .........................................28 Table 4.4. Haplotype distribution table in Co duck ......................................................30 Table 4.5. Polymorphic analysis from partial sequencing of the mitochondrial D- loop gene segment of Co breed....................................................................31 Table 4.6. Haplotype distribution table in Co Lung duck .............................................32 Table 4.7. Polymorphic analysis from partial sequencing of the mitochondrial D- loop gene segment of Co Lung breed ..........................................................33 Table 4.8. Haplotype distribution table in Na Tau duck ...............................................34 Table 4.9. Polymorphic analysis from partial sequencing of the mitochondrial D- loop gene segment of Na Tau breed ............................................................34 Table 4.10. Haplotype distribution table in Troi duck ..................................................36 Table 4.11. Polymorphic analysis from partial sequencing of the mitochondrial D- loop gene segment of Troi breed..................................................................36 Table 4.12. Haplotype distribution table in Dom duck .................................................37 Table 4.13. Polymorphic analysis from partial sequencing of the mitochondrial D- loop gene segment of Dom breed ................................................................38 v
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