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 Luan van 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. Duong Van Cuong Thai Nguyen, 6/2018 Luan van DOCUMENTATION PAGE WITH ABSTRACT Thai Nguyen University of Agriculture and Forestry Major Biotechnology Student name Bui Thi Thu Phuong Student ID DTN1453150017 Development of DNA extraction method of chemical, Thesis title intensive chemical and transition soil and the effect of different soil on Jasmine rice growth 1. Songsak Wattanachaisaereekul Supervisors 2.
Duong Van Cuong 3. 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 3 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 8 weeks of planting.
The result of DNA extraction was based on analysis on 0.8% agarose gels and measure nanodrop. Transition soil group 1 and group 3 (clay) can’t extract by all methods. Chemical soil (silty), intensive chemical soil (silty) and transition soil group 2 (sandy) can extract and show good results of DNA quantity: chemical soil and transition soil group 2 are more than 200 ng/µL; intensive chemical soil is more than 100 ng/µL. All samples have low DNA quality.
Develop, DNA extraction method, soil, Jasmine rice Keywords growth. Number of pages 29 i Luan van (Luan.growth 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. 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 Luan van (Luan.growth TABLE OF CONTENT LIST OF FIGURES. V LIST OF TABLES.VIi LIST OF ABBREVIATIONS. Overview of Jasmine rice.
Jasmine rice growing. Life cycle of the rice plant. Cultivation of Jasmine rice. Microbita application for plant growth promotion.
The characteristics of silty, sandy and clay soil. Scope of study. MATERIALS AND METHODS. Equipment and materials.
Preparing soil mixture for planting. Development of DNA extraction method. 17 iii Luan van (Luan. Compare the tiller number of the rice plant.
Rice plants growth observation. Extraction of metagenomic DNA from different methods. CONCLUSIONS AND DISCUSSION. Growing Jasmine rice on different types of soil.
DNA extraction methods suitable for three types of soil. 27 iv Luan van (Luan.growth LIST OF FIGURES Figure 1. Long grain white Jasmine rice. Growth phases and stages of the rice plant.
Root exudation in the rhizosphere. Microbiome engineering improves plant growth. Soil particle size. The seed of Jasmine rice.
Three types of DNA extraction buffer. The process of germinating rice seeds. Averages of tiller number per pot in chemical soil. Averages of tiller number per pot in intensive chemical soil.
Averages of tiller number per pot in transition soil. Averages of tiller number in three soil groups. Metagenomic DNA was extracted from transition soil. Metagenomic DNA was extracted from intensive chemical soil group 2 and group 3.
Metagenomic DNA was extracted by method 3. (a) Chemical soil group 1 and group 3. (b) Transition soil group 2. 25 v Luan van (Luan.growth LIST OF TABLES Table 2.
Equipment of studies. 9 samples of chemical soil. 9 samples of intensive chemical soil. 9 samples of transition soil.
The real weight of the field soil samples for planting (g). Metagenomic DNA extraction from soils using sonication. Rice plants growth in chemical soil. Rice plants growth in intensive chemical soil.
Rice plants growth in transition soil. Rice plants growth in three soil groups. DNA quantity and quality by method 1 for transition soil. DNA quantity and quality by method 2 for transition soil.
DNA quantity and quality by method 3 for transition soil. DNA quantity and quality by method 2 for intensive chemical soil. DNA quantity and quality by method 3 for intensive chemical soil. DNA quantity and quality by method 3 for chemical soil and transition soil 25 vi Luan van (Luan.growth LIST OF ABBREVIATIONS C1, C2, C3 Chemical soil group 1, Chemical soil group 2, Chemical soil group 3 I1, I2, I3 Intensive chemical soil group 1, Intensive chemical group 2, Intensive chemical group 3 T1, T2, T3 Transition soil group 1, Transition group 2, Transition group 3 DNA Deoxyribonucleic acid mm Millimeter m2 Square meter % Percentage µL Microliter mL Milliliter g Gram kg Kilogram min 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 Luan van (Luan.
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, Figure 1. Long grain white Jasmine rice 199 panicles of the local variety were selected (https://www.com/stock- photo-long-grain-uncooked-white- from a nearby district of Chachearngsoa jasmine-rice-close-up-food-background- province for pure line selection [2].
image65134089) 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. 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 1 Luan van (Luan.growth crop for domestic consumers and a primary export commodity for economic growth [8]. It was produced annually at approximately 9.4 M ton of paddy rice from 4. The annual export quantities of aromatic rice were as high as 1.45 million tons, which represented 20–27% of Thailand’s total rice export [10]. Jasmine rice growing 1.
Life cycle of the rice plant Figure 1. Growth phases and stages of the rice plant (https://nature-and- farming.com/2014/10/rice-production-chapter-2-growth-stages.html) The growth duration of the rice plant is 3-6 months, depending on the variety and the environment under which it is grown. During this time, rice completes three distinct growth phases: vegetative, reproduction and ripening (Fig. The vegetative phase is subdivided into germination, early seedling growth, and tillering; the reproductive phase is subdivided into the time before and after heading, that is, panicle exsertion.
The time after heading is better known as the ripening period. The vegetative phase is characterized by active tillering, a gradual increase in plant height, and leaf emergence at regular intervals. The reproductive growth phase is characterized by culm elongation (which increases plant height), a decline in tiller number, emergence of the flag leaf (the last leaf), booting, heading, and flowering of the spikelets. Ripening follows fertilization and can be subdivided into milky, dough, 2 Luan van (Luan.growth yellow ripe, and maturity stages.
These terms are primarily based on the texture and color of the growing grains. The length of ripening varies among varieties from about 15 to 40 days [11]. Cultivation of Jasmine rice Jasmine rice has a tall, lanky, floppy architecture. The average plant height at harvest is approximately 140 cm.
Jasmine rice is a photo-sensitive variety which could be grown only one a year [12]. Due to photoperiod sensitivity, Jasmine rice can be grown during August–December [13]. The growing of Jasmine rice should be grown in December. It has the best growth and yield.
Planted in December has produced paddy grain that meets the standard of quality [14]. Currently, the best Hom Mali rice in Thailand is grown in the Northeast. The plantation area of Thai jasmine rice is about 7.6 million acres and its yield is only 1125–1500 kg/acre [15]. Microbiota Microbiota: the set of microorganisms present in a given environment [16].
It appears everywhere on Earth, include in the soil, in the ocean, in the atmosphere, in the body that anywhere the body comes into contact with the outside world. Microbiota is so important for life on Earth because it has a close relationship with human, animal and plant health. The human microbiota affects host physiology to a great extent. There are a lot of microbes colonize in the human body, including bacteria, archaea, viruses, and eukaryotic microbes [17].
Studies have suggested that the microbiota is primarily involved in promoting the maturation of immune cells and the normal development of immune functions [18]. However, not all microbiota lead to health benefits. Studies have revealed the human microbiota has a close relationship with diseases of different systems, such as infection, liver diseases, respiratory diseases and autoimmune diseases [19]. The animal microbiota, such as those in and on the gut, oral cavity, and skin, communicate among themselves and exchange signals with the animal’s organ systems, participating in the body’s homeostasis [20].
Microorganisms colonizing 3 Luan van (Luan.growth plant surfaces and inner tissues play an eminent role in the shaping of the planet - from natural vegetation to intense agricultural production systems up to human health.