Development of dna extraction method of chemical, intensive chemical and transition soil and the effect of different soil on jasmine rice growth

THAI NGUYEN UNIVERSITY UNIVERSITY OF AGRICULTURE AND FORESTRY BUI THI THU PHUONG Topic title: DEVELOPMENT OF DNA EXTRACTION METHOD OF CHEMICAL, INTENSIVE CHEMICAL AND TRANSITION SOIL AND THE EFFECT OF DIFFERENT SOIL ON JASMINE RICE GROWTH BACHELOR THESIS Study Mode : Full-time Major : Biotechnology Faculty : Biotechnology and Food Technology Batch : 2014 – 2018 Thai Nguyen, 6/2018 THAI NGUYEN UNIVERSITY UNIVERSITY OF AGRICULTURE AND FORESTRY BUI THI THU PHUONG Topic title: DEVELOPMENT OF DNA EXTRACTION METHOD OF CHEMICAL, INTENSIVE CHEMICAL AND TRANSITION SOIL AND THE EFFECT OF DIFFERENT SOIL ON JASMINE RICE GROWTH BACHELOR THESIS Study Mode : Full-time Major : Biotechnology Faculty : Biotechnology and Food Technology Batch : 2014 – 2018 Supervisors : Dr Songsak Wattanachaisaereekul Assoc Prof Dr Duong Van Cuong Thai Nguyen, 6/2018 DOCUMENTATION PAGE WITH ABSTRACT Thai Nguyen University of Agriculture and Forestry Major Biotechnology Student name Bui Thi Thu Phuong Student ID DTN1453150017 Thesis title Development of DNA extraction method of chemical, intensive chemical and transition soil and the effect of different soil on Jasmine rice growth Supervisors Dr Songsak Wattanachaisaereekul Assoc Prof Dr Duong Van Cuong Msc Phimrak Khaokhajorn Abstract: Jasmine rice is a long grain variety of fragrant rice and it was officially named as Khao Dawk Mali 105, (KDML105) Jasmine rice has high nutritional value with nutritional substances: vitamin B1, B2, niacin, carbohydrates, protein, and minerals such as iron, calcium, and phosphorous Chemical soil, intensive chemical soil and transition soil with types of soil (silty, sandy and clay) were used for planting Jasmine rice plants were grown on total 27 soil samples for 10 weeks to observed rice growth The soil samples were also used to extract DNA by using different methods The result of rice growth observation was based on count tiller number In the average of tiller number, chemical soil is better than intensive chemical and transition soil after weeks of planting The result of DNA extraction was based on analysis on 0.8% agarose gels and measure nanodrop Transition soil group and group (clay) can’t extract by all methods Chemical soil (silty), intensive chemical soil (silty) and transition soil group (sandy) can extract and show good results of DNA quantity: chemical soil and transition soil group are more than 200 ng/µL; intensive chemical soil is more than 100 ng/µL All samples have low DNA quality Keywords Number of pages Develop, DNA extraction method, soil, Jasmine rice growth 29 i ACKNOWLEDGEMENT Firstly, I would like to express my sincere gratitude to my advisors Dr Songsak Wattanachaisaereekul and Msc Phimrak Khaokhajorn from the School of Bioresources and Technology, King Mongkut’s University of Technology Thonburi (KMUTT), Thailand, for providing me with all the necessary facilities for the research in their lab, helping and encouraging me in the past six months Their enthusiasm and guidance in all the time of research helped me to complete my dissertation possible I am also grateful to Assoc Prof Dr Duong Van Cuong from the Faculty of Biotechnology and Food Technology (FBFT) of Thai Nguyen University of Agriculture and Forestry (TUAF) who used to support me during this thesis implementation I would also like to express my sincere thanks to my teachers of the Faculty of Biotechnology and Food Technology (FBFT), TUAF who taught me a lot of useful knowledge through four years of university Last but not the least, I would like to thank my family and my friends for supporting me spiritually throughout writing this thesis and my life in general Thank you very much and best regards Student Bui Thi Thu Phuong ii TABLE OF CONTENT LIST OF FIGURES V LIST OF TABLES VIi LIST OF ABBREVIATIONS VII PART I INTRODUCTION 1.1 Background 1.1.1 Overview of Jasmine rice 1.1.2 Jasmine rice growing 1.1.2.1 Life cycle of the rice plant 1.1.2.2 Cultivation of Jasmine rice 1.1.3 Plant microbiota 1.1.3.1 Microbiota 1.1.3.2 Root microbiota 1.1.4 Microbita application for plant growth promotion 1.1.5 The characteristics of silty, sandy and clay soil 1.2 Objectives 1.3 Scope of study PART II MATERIALS AND METHODS 2.1 Equipment and materials 2.1.1 Equipment 2.1.2 Materials 2.1.2.1 Soils 2.1.2.2 Plant material 12 2.1.2.3 Lysis buffer 12 2.2 Methods 13 2.2.1 Preparing soil mixture for planting 13 2.2.2 Rice growing 14 2.2.3 Development of DNA extraction method 14 PART III RESULTS 17 iii 3.1 Compare the tiller number of the rice plant 17 3.2 Rice plants growth observation 19 3.3 Extraction of metagenomic DNA from different methods 21 PART IV CONCLUSIONS AND DISCUSSION 26 4.1 Growing Jasmine rice on different types of soil 26 4.2 DNA extraction methods suitable for three types of soil 26 REFERENCES 27 iv LIST OF FIGURES Figure 1.1 Long grain white Jasmine rice Figure 1.2 Growth phases and stages of the rice plant Figure 1.3 Root exudation in the rhizosphere Figure 1.4 Microbiome engineering improves plant growth Figure 1.5 Soil particle size (a) Sandy soil (b) Silty soil (c) Clay soil Figure 2.1 The seed of Jasmine rice 12 Figure 2.2 Three types of DNA extraction buffer 12 Figure 2.3 The process of germinating rice seeds 14 Figure 3.1 Averages of tiller number per pot in chemical soil 17 Figure 3.2 Averages of tiller number per pot in intensive chemical soil 18 Figure 3.3 Averages of tiller number per pot in transition soil 18 Figure 3.4 Averages of tiller number in three soil groups 19 Figure 3.5 Metagenomic DNA was extracted from transition soil (a) Method (b) Method (c) Method 23 Figure 3.6 Metagenomic DNA was extracted from intensive chemical soil group and group (a) Method (b) Method 24 Figure 3.7 Metagenomic DNA was extracted by method (a) Chemical soil group and group (b) Transition soil group 25 v LIST OF TABLES Table 2.1 Equipment of studies Table 2.2 samples of chemical soil Table 2.3 samples of intensive chemical soil 10 Table 2.4 samples of transition soil 11 Table 2.5 The real weight of the field soil samples for planting (g) 13 Table 2.6 Metagenomic DNA extraction from soils using sonication 15 Table 3.1 Rice plants growth in chemical soil 20 Table 3.2 Rice plants growth in intensive chemical soil 20 Table 3.3 Rice plants growth in transition soil 20 Table 3.4 Rice plants growth in three soil groups 21 Table 3.5 DNA quantity and quality by method for transition soil 21 Table 3.6 DNA quantity and quality by method for transition soil 22 Table 3.7 DNA quantity and quality by method for transition soil 22 Table 3.8 DNA quantity and quality by method for intensive chemical soil 23 Table 3.9 DNA quantity and quality by method for intensive chemical soil 24 Table 3.10 DNA quantity and quality by method for chemical soil and transition soil 25 vi LIST OF ABBREVIATIONS C1, C2, C3 Chemical soil group 1, Chemical soil group 2, Chemical soil group I1, I2, I3 Intensive chemical soil group 1, Intensive chemical group 2, Intensive chemical group T1, T2, T3 Transition soil group 1, Transition group 2, Transition group DNA Deoxyribonucleic acid mm Millimeter m2 Square meter % Percentage µL Microliter mL Milliliter g Gram kg Kilogram Minutes s Second ºC Degree centigrade or Celcius rpm Revolutions per minute ng Nanogram M Molar mass SDS Sodium dodecyl sulfate PEG Polyethylene glycol NEB New England BioLabs vii PART I INTRODUCTION 1.1 Background 1.1.1 Overview of Jasmine rice Jasmine rice is known as a most important aromatic rice originating in Thailand It was officially named as Khao Dawk Mali 105, (KDML105) [1] In 1945, the best Jasmine rice local variety was discovered by a farmer in Lam Pradoo district, Chonburi province, and in 1951, 199 panicles of the local variety were selected from a nearby district of Chachearngsoa province for pure line selection [2] Figure 1.1 Long grain white Jasmine rice (https://www.dreamstime.com/stockphoto-long-grain-uncooked-whitejasmine-rice-close-up-food-backgroundimage65134089) The origin of Jasmine rice was in Bang Khla District, Chachoengsao Province, which is an area of saline, sandy soil with no flooding Nowadays, this has been transformed into an industrial and residential area and the most famous and largest area of rice production in Northeast Thailand [3] The characteristics and size of the Jasmine rice grain: Jasmine rice grains shall possess the characteristics and size as follows: (1) General characteristic: long grain white; (2) Average length without breakage: not less than 7.0 mm; (3) Average width of the full grain rice without breakage: not less than 3.0 mm (Fig 1.1) Chemical Attributes: Jasmine rice shall contain not less than 12 percent and not more than 19 percent of amylose at the 14 percent humidity level [4] Its favorable properties have made this cultivar to be a frequent genetic resource for rice breeding [5] Jasmine rice is filled with nutritional substances: vitamin B1, B2, niacin, carbohydrates, protein, and minerals such as iron, calcium, and phosphorus [6] Jasmine rice can be consumed in many ways, for example, whole grain consumption Some Asian peoples cook their rice in an ample amount of water to obtain desirable texture whereas, in many western cultures, rice is boiled in excess water until the center of the grain is fully cooked [7] In Thailand, Jasmine rice is considered as a vital ... DTN1453150017 Thesis title Development of DNA extraction method of chemical, intensive chemical and transition soil and the effect of different soil on Jasmine rice growth Supervisors Dr Songsak Wattanachaisaereekul... UNIVERSITY OF AGRICULTURE AND FORESTRY BUI THI THU PHUONG Topic title: DEVELOPMENT OF DNA EXTRACTION METHOD OF CHEMICAL, INTENSIVE CHEMICAL AND TRANSITION SOIL AND THE EFFECT OF DIFFERENT SOIL ON JASMINE. .. better growth [33] 1.2 Objectives - To observe the effect of transition, chemical and intensive chemical soil to Jasmine rice growth - To develop DNA extraction method suitable for silty, sandy and