TABLE OF CONTENTS

ACKNOWLEDGEMENTS...........................................................................I-II
ABSTRACT.....................................................................................................III
LIST OF TABLES..........................................................................................IV
LIST OF FIGURES........................................................................................V
LIST OF ABBREVIATIONS........................................................................VI
1. INTRODUCTION......................................................................................1-15
1.1 Rice......................................................................................................1
1.2 Rice landraces and genetic diversity....................................................1
1.3 DIVERSITY of Rice Landraces in Bangladesh..................................2
1.4. Diversity of deep-water Rice Landraces in Bangladesh.....................3
1.5. Genetic marker....................................................................................4
1.6. Molecular markers for fingerprinting.................................................5
1.7. Polymerase chain reaction (PCR).......................................................6
1.8. Simple sequence repeats (SSR)/microsatellite marker.......................7
1.9. DNA fingerprinting and genetic diversity analysis using
SSR marker.........................................................................................9
1.10. Submergence stress...........................................................................13
1.11. Machaism of SUB 1 gene action.......................................................13
1.12. Objectives of the study.....................................................................15
2. MATERIALS AND METHODS...............................................................16-31
2.1. Plant materials....................................................................................16
2.2. SSR markers.......................................................................................17
2.3. Genotyping protocol...........................................................................19
2.3.1. Collection of leaf sample............................................................19
2.3.2. Preparation of chemicals and working solutions for DNA
extraction..............................................................................................19
2.3.2.1. 1 M Tris (pH 8.0).............................................................20
2.3.2.2. 0.5M Stock Solution of EDTA (pH 8.0)..........................20
2.3.2.3. 5 M NaCl.........................................................................20
2.3.2.4. 10% Stock Solution of SDS.............................................21

2.3.2.5. Chloroform mix (24:1 mixture and isoamyl alcohol)......21

2.3.2.6. Ethanol.............................................................................21
2.3.2.7. DNA Extraction Buffer; this is a secondary chemical:. . .22
2.3.2.8. 1X TE Buffer; this is a secondary chemical....................22
2.3.3. Miniscale rice DNA extraction for PCR analysis.......................23
2.3.4. DNA Quantification....................................................................24
2.3.5. Preparation of working solution of DNA samples.....................24
2.3.6. Polymerase Chain Reaction (PCR).............................................25
2.3.7. Polyacraylamide Gel Electrophoresis (PAGE)...........................26
2.3.7.1. Assembly of the glass plate.............................................27
2.3.7.2. Preparation of Stock Solutions for Gel Electrophoresis. 27
2.3.7.2.1. 10X TBE Buffer (pH 8)........................................28
2.3.7.2.2. 10% APS (Ammonium per sulphate) preparation 28
2.3.7.2.3. Preparation of premix:..........................................28
2.3.7.3. Preparation of polyacrylamide gel..................................28
2.3.7.4. Casting Gel.....................................................................29
2.3.7.5. Ethidium bromide staining.............................................29
2.3.7.6. Visualization of gel.........................................................30
2.3.8. SSR Data Analysis......................................................................30
3. RESULTS....................................................................................................32-39
3.1. Overall SSR DNA marker diversity...................................................32
3.1.1. Number of alleles, allele size and frequency..............................32
3.1.2. Rare alleles..................................................................................34
3.1.3. Polymorphism information content (PIC) values.......................34
3.2. Genetic distance based analysis..........................................................37
3.2.2. UPGMA cluster analysis............................................................37
3.2.3. The pairwise genetic dissimilarity analysis................................39
4. DISCUSSION..............................................................................................40-42
5. SUMMARY AND CONCLUSION...........................................................43-44
6. REFERENCES...........................................................................................45-50
7. APPENDICES.............................................................................................VII- VIII