screening of rice landraces for salt tolerance through ...

SCREENING OF RICE LANDRACES FOR SALT TOLERANCE THROUGH BIOCHEMICAL AND MORPHO MOLECULAR CHARACTERIZATION

MS THESIS

MD. TAHJIB-UL-ARIF

DEPARTMENT OF BIOCHEMISTRY AND MOLECULAR BIOLOGY BANGLADESH AGRICULTURAL UNIVERSITY MYMENSINGH-2202

JUNE 2015

SCREENING OF RICE LANDRACES FOR SALT TOLERANCE THROUGH BIOCHEMICAL AND MORPHO MOLECULAR CHARACTERIZATION

A Thesis Submitted to Bangladesh Agricultural University, Mymensingh In Partial Fulfillment of the Requirements for the degree of

MASTER OF SCIENCE IN BIOCHEMISTRY AND MOLECULAR BIOLOGY By MD. TAHJIB-UL-ARIF Roll No. 14 BMB JJ 01 M Registration No. 36361 Session: 2009-2010

Department of Biochemistry and Molecular Biology Bangladesh Agricultural University Mymensingh-2202

JUNE 2015

SCREENING OF RICE LANDRACES FOR SALT TOLERANCE THROUGH BIOCHEMICAL AND MORPHO MOLECULAR CHARACTERIZATION A Thesis Submitted to Bangladesh Agricultural University, Mymensingh In Partial Fulfillment of the Requirements for the Degree of MASTER OF SCIENCE IN BIOCHEMISTRY AND MOLECULAR BIOLOGY

By MD. TAHJIB-UL-ARIF Roll No. 14 BMB JJ 01 M Registration No. 36361 Session: 2009-2010 Approved as to style and contents by

............…….……………….......

……………………………..........

(Prof. Dr. M. Afzal Hossain)

(Dr. Mirza Mofazzal Islam)

Supervisor

Co-supervisor

…………………………………… (Dr. Mohammad Anowar Hossain) Chairman, Examination Committee And Head, Biochemistry and Molecular Biology Bangladesh Agricultural University Mymensingh-2202 JUNE 2015

ACKNOWLEDGEMENTS All praises are due to “Almighty Allah” the great, gracious, merciful, the Creator and the Sustainer of the universe for bestowing mercy upon me and for imbibing confidence on me to complete the research work and thesis successfully for the degree of Master of Science in Biochemistry and Molecular Biology. The author takes the opportunity to express his heart-felt respect, deep sense of gratitude and profound appreciation to his reverend research supervisor, Dr. M. Afzal Hossain, Professor, Department of Biochemistry and Molecular Biology, Bangladesh Agricultural University, Mymensingh who undertook to act as the supervisor despite his many other professional commitments. His keen interest, scholastic supervision, innovative suggestions, constructive criticism, constant encouragement and provisions of facilities and infrastructural supports during the entire tenure of the research work and during writing up this thesis are gratefully acknowledged. The Author would like to express sincere appreciation, gratefulness and deep indebtedness to his reverend co-supervisor Dr. Mirza Mofazzal Islam, Chief Scientific Officer and Head, Biotechnology Division, Bangladesh Institute of Nuclear Agriculture (BINA), Mymensingh, for his kind Cooperation, excellent advice, affection, constructive comments, valuable suggestions and encouragement throughout this research work. The author is especially grateful to Dr. Mohammad Anowar Hossain, Associate Professor and Head, Department of Biochemistry and Molecular Biology, BAU, Mymensingh, for his keen interest, valuable suggestions throughout the research. The author is extremely happy expressing his recognition and gratefulness to Prof. Nilofar Newaz, Prof. Bishan Lal Das Chowdhury, Prof. Dr. Md. Golam Mortuza, Prof. Dr. Md. Tofazzal Hossain, Associate Prof. Mr. Muhammad Javidul Haque Bhyiyan, Associate Prof. Dr. Md. Abdul Hannan, Assistant Prof. Md. Rezwanul Haque and Assistant Prof. Shayla Sarmin, Dept. of Biochemistry and Molecular Biology, BAU, Mymensingh, for their encouragement, sincere cooperation, frequent suggestions and valuable guidance. The author is also grateful and says many thanks to Manosh Kanti Saha, for his cordial help during the course of research work. The author feels much pleasure to convey the profound thanks to his friends and well-wishers for their cooperation, encouragement and help during the ongoing of the research. He is particularly thankful to Sonya Afrin for her constant inspiration throughout the research work. Finally, the author owes a debt of gratitude to his beloved parents, sisters, grandfather and all other relatives for their blessings, constant source of inspiration, all out sacrifice and moral support throughout the entire period of his academic life. The Author

SCREENING OF RICE LANDRACES FOR SALT TOLERANCE THROUGH BIOCHEMICAL AND MORPHO MOLECULAR CHARACTERIZATION MD. TAHJIB-UL-ARIF ABSTRACT This experiment was conducted to find out potential salt tolerant rice landraces. Twenty five rice genotypes were used to screen out salt tolerant rice genotypes at germination and seedling stage based on morphological (shoot length, root length, total dry weight), biochemical (sodium and potassium uptake) and molecular parameters. At germination stage 0 dSm-1 and 12dSm-1 salinity was imposed in rice genotypes. Ward’s cluster analysis divided rice genotypes into three clusters (susceptible, moderately tolerant & tolerant) based on the physiological indices (GSI, SLSI, SDSI, RLSI & RDSI) at germination stage. The tolerant rice landraces were Sona Toly, Nakraji, Komol Bhog. At seedling stage screening was performed following IRRI standard protocol at 12 dSm-1 salinity. Initial and final scoring for visual salt injury using the IRRI Standard Evaluation System (SES) were done 10 and 16 days after salinization. Based on 1-9 scale scoring after 16 days after salinization, only one rice landrace (Komol Bhog) was identified as highly tolerant, five rice landraces (Bolonga, Sona Toly, Dud Sail, Tal Mugur and Nakraji) were found salt tolerant. Based on the performances on each parameter at seedling stage, genotypes were scored and categorized as highly tolerant (score 1), tolerant (score 3), moderately tolerant (score 5), susceptible (score 7) and highly susceptible (score 9). Considering sodium and potassium uptake (Na+/K+ratio), Nakraji and Komol Bhog were highly tolerant, Tal Kapor, Tal Mugur, Gajor Goria and Sona Toly were tolerant landrace rice genotypes. On the basis of MSTS one landrace (Komol Bhog) was highly tolerant, 5 (Nakraji, Bolonga, Sona Toly, Tal Kapor, Gajor Goria) were tolerant (score 3), 5 were moderately tolerant (score 5) and rest of them were susceptible. Molecular characterization was also performed using two SSR markers viz. RM121, RM337 to screen out the genotypes for salt tolerance. Utilizing the polymorphisms as detected by two SSR markers (RM121 & RM337) through genetic similarity in dendrogram, 25 rice genotypes were distributed into four clusters. Cluster I represented susceptible genotypes which includes Tal Mugur, Patnai Balam, Kolmilota, Dud Sail, Konkacur, Sona Anjul and Vushiara rice landraces. On the other hand cluster II, III & IV represented tolerant genotypes which were Bolonga, Til Kapor, Panbra, Sona Toly, Beto, Bina Sail, Komol Bhog, Nakraji, Tilkapur, Gajor Goria and Gota. This study is expected to be a good use for breeding program to develop salt tolerant high yielding rice varieties.

CONTENTS TITLE

PAGE NO.

ACKNOWLEDGEMENTS

i

ABSTRACT

ii

CONTENTS

iii

LIST OF TABLES

vii

LIST OF FIGURES

ix

LIST OF PHOTOGRAPHS

x

LIST OF APPENDICES

xi

ABBREVIATIONS

xii

CHAPTER 1: INTRODUCTION

1

CHAPTER 2: REVIEW OF LITERATURE

5

2.1

Concept of salinity

5

2.2

Present status of salinity

6

2.3

Impact of salinity on plants

7

2.4

Salinity tolerance and its varietal differences

8

2.5

Effects of salinity on the growth and development of rice

11

2.6

Salinity tolerance in rice

12

2.7

Physiological basis of salt tolerance

13

2.8

Mechanism of salinity tolerance in rice

14

2.9

Molecular mechanism of salt tolerance in rice

16

2.10

Salinity induced limitations in rice

18

2.11

Screening for salinity tolerance of rice

18

2.12

Screening based on phenotypic performances

19

2.13

Biochemical basis of varietal difference

22

2.14

Molecular characterization of salt tolerant rice genotypes

23

CHAPTER 3: MATERIALS AND METHODS

28

3.1 3.2 3.3 3.4

28 28 28 30

Experimental site Experimental period Collection of rice genotypes Screening of salt tolerant rice genotypes using physiological indices at germination stage 3.4.1 Salinity treatments iii

30

TITLE

3.5

3.6

3.7

PAGE NO.

3.4.2 Germination test 3.4.3 Data collection 3.4.4 Physiological indices Phenotypic screening of rice genotypes for salt tolerance at seedling stage 3.5.1 Reagents and instruments needed 3.5.2 Experimental setup 3.5.3 Evaluation of salt stress symptoms 3.5.4 Data collection Biochemical characterization

30 30 31 31

3.6.1 Determination of tissue Na+ and K+ tolerance 3.6.2 Reagents and instruments needed 3.6.3 Methodology 3.6.4 Quantitative measurement of Na+ and K+ uptake DNA fingerprinting of rice germplasms using SSR markers 3.7.1 Collection of leaf samples for DNA extraction 3.7.2 Genomic DNA extraction 3.7.3 Materials required 3.7.4 Reagent preparation for DNA extraction 3.7.5 Procedure of genomic DNA isolation 3.7.6 Confirmation of DNA samples 3.7.7 DNA conformation using agarose gel electrophoresis 3.7.8 Quantification of DNA by spectrophotometer 3.7.9 Preparation of working solution (25 ng µl-1) of DNA samples 3.7.10 Procedure involved in SSR marker analysis

35 35 35 36 37 37 37 37 38 40 41 41 43 45 45

3.7.10.1

Primer selection for SSR

45

3.7.10.2

Polymerase chain reaction (PCR)

45

3.7.10.3

Components of PCR cocktail

46

3.7.10.4

Preparation of dNTPs (400 ml)

46

3.7.10.5

Preparation of PCR Cocktail for SSR Analysis (For Each Sample) PCR amplification profile

46

3.7.10.6 3.7.10.7 3.7.11 3.7.12

31 32 34 34 35

Polyacrylamide gel electrophoresis (PAGE) Data analysis at foreground selection Analysis of SSR data

iv

47 48 50 51

TITLE

PAGE NO.

CHAPTER 4: RESULTS

53

4.1

53

4.2

4.3 4.4 4.5

Screening of salt tolerant rice genotypes using physiological indices at germination stage 4.1.1 Germination stress tolerance index (GSI) 4.1.2 Shoot length stress tolerance index (SLSI) 4.1.3 Root length stress tolerance index (RLSI) 4.1.4 Shoot dry biomass stress tolerance index (SDSI) 4.1.5 Root dry biomass stress tolerance indices (RDSI) 4.1.6 Cluster analysis based on physiological indices Phenotypic screening of rice genotypes for salt tolerance at seedling stage 4.2.1 Screening based on SES score 4.2.2 Shoot length 4.2.3 Root length 4.2.4 Total dry weight Biochemical characterization 4.3.1 Sodium and potassium uptake Mean salinity tolerance score (MSTS) DNA fingerprinting of rice germplasms using SSR markers 4.5.1 Visual comparison of genotypic performances 4.5.2 Allelic and loci variation within the genotypes 4.5.3 Size and frequency of alleles 4.5.4 Number of alleles per locus 4.5.5 Rare alleles per locus 4.5.6 Null allele per locus 4.5.7 Allele size range 4.5.8 PIC (Polymorphism Information Content) values 4.5.9 Major allele 4.5.10 Genetic diversity 4.5.11 Analysis based on genetic distance 4.5.12 Genetic similarity analysis using UPGMA

5.2

5.3 5.4

66 66 72 75 78 81 81 84 87 87 89 92 92 92 92 93 93 94 94 94 96 99

CHAPTER 5: DISCUSSION 5.1

53 56 58 60 62 64

Screening of salt tolerant rice genotypes using physiological indices at germination stage Phenotypic screening of rice genotypes for salt tolerance at seedling stage 5.2.1 Screening based on SES score 5.2.2 Plant growth Biochemical characterization 5.3.1 Sodium and potassium uptake DNA fingerprinting of rice germplasms using SSR markers v

99 101 101 102 103 103 104

TITLE

PAGE NO.

CHAPTER 6: SUMMARY

107

CHAPTER 7: CONCLUSIONS

112

CHAPTER 8: REFERENCES

114

CHAPTER 9: APPENDICES

133

vi

LIST OF TABLES TITLE 1 2

PAGE NO. List of germplasms used for this study List of reagents and apparatus needed for phenotypic study of rice Modified standard evaluation score (SES) of visual salt injury at seedling stage List of essential requirement for determination of tissue Na+ and K+ content DNA quantification of 24 rice germplasms. Summary of microsatellite (SSR) markers used for molecular study Components of PCR cocktail Steps of Polymerase Chain reaction (PCR) Ratio of the components of the polyacrylamide gel Germination stress tolerance index (GSI) of various rice genotypes

29 32

11

Shoot length stress tolerance index (SLSI) of various rice genotypes

57

12

Root length stress tolerance index (RLSI) of various rice genotypes Shoot dry biomass stress tolerance index (SDSI) of various rice genotypes Root dry biomass stress tolerance index (RDSI) of various rice genotypes Cluster analysis of rice genotypes at germination stage SES score of different rice genotypes at different salinity stress at 10 and 16 days after salinization Categories of rice genotypes based on SES scoring as affected by 12 dSm-1 of salinity after 16 days of salinization Shoot length of different rice genotypes at different salinity stress at seedling stage. Categories of rice genotypes based on shoot length as affected by 12 dSm-1 of salinity Root length of different rice genotypes at different salinity stress at seedling stage Categories of rice genotypes based on root length as affected by 12 dSm-1 of salinity Total dry weight of different rice genotypes at different

59

3 4 5 6 7 8 9 10

13 14 15 16 17 18 19 20 21 22

vii

34 36 44 45 47 47 49 55

61 63 64 68 69 73 75 76 78 79

TITLE 23 24 25 26

27 28

29 30

31 32 33 34

PAGE NO. salinity stress at seedling stage Categories of rice genotypes based on total dry weight as affected by 12 dSm-1 of salinity Sodium and potassium content of rice genotypes under salt stress at seedling stage Categories of rice genotypes based on Na-K ratio as affected by 12 dSm-1 of salinity Mean salinity tolerance score of different growth and biochemical parameters 25 rice genotypes under 12 dSm-1 salinity stress at seedling stage Comparison of genotypic performances of 25 selected rice genotypes against 2 SSR markers for saline tolerance Summary of the genotypic performances comparison of 25 selected rice genotypes against 2 SSR markers for saline tolerance Categorization of 25 rice genotypes based on the visual comparison of genotypic performances for two SSR markers Number of allele of different sizes with frequency, variance, standard deviation found at 2 SSR loci across 25 rice varieties Molecular analysis results found in 25 rice genotypes for 2 SSR markers Size and frequency of alleles and diversity index at 2 SSR loci across 25 rice genotypes Summary of Nei’s (1973) genetic distance values between 25 selected rice genotypes for all loci List of rice genotypes into four clusters

viii

81 83 84 85

88 89

89 92

93 93 95 98

LIST OF FIGURES TITLE PAGE NO. 1 Dendrogram using physiological indices showing three 65 clusters at germination stage

2 3

Effect of salinity on SES score of rice genotypes Percent reduction of shoot length of 25 rice genotypes compare to their respective control Percent reduction of root length of 25 rice genotypes compare to their respective control Percent reduction of plant dry weight of 25 rice genotypes compare to their respective control

67 74

86

8

Percent increment of sodium potassium ratio of 25 rice genotypes compare to their respective control Comparative salinity tolerance ranking of 25 rice genotypes at seedling stage Microsatellite profiles of 25 rice genotypes at loci RM121

9

Microsatellite profiles of 25 rice genotypes at loci RM337

97

10

UPGMA Dendrogram based on Nei’s (1973) genetic distance, summarizing data on differentiation among 25 rice genotypes according to SSR analyses (Sub cluster was cut at 50% of average Nei’s genetic distance 0.3288)

97

4 5 6 7

ix

80 82

91 91

LIST OF PHOTOGRAPHS TITLE

PAGE NO.

Photo 1 Photographs showing the visual appearance of rice plant under salinity at seedling stage ( 10 days after salinization) Photo 2 Photographs showing the visual appearance of rice plant under salinity at seedling stage ( 16 days after salinization)

70

x

71

LIST OF APPENDICES TITLE 9.1

PAGE NO. Temporal increase in magnitude and extent of soil salinity

133

in Bangladesh 9.2

ANOVA table of GSI at germination stage

134

9.3

ANOVA table of SLSI at germination stage

134

9.4

ANOVA table of SDSI at germination stage

134

9.5

ANOVA table of RLSI at germination stage

134

9.6

ANOVA table of RDSI at germination stage

134

9.7

ANOVA table of shoot length reduction at 12dSm-1 in

134

seedling stage 9.8

ANOVA table of root length reduction at 12dSm-1 in

135

seedling stage 9.9

ANOVA table of total dry weight reduction at 12dSm-1 in seedling stage

xi

135

ABBREVIATIONS AEZ ANOVA App. BAU BINA bp BRRI CTAB CV ddH 2 O dH 2 O dSm-1 EC GSI Ha PAGE PIC RDSI RLSI SDSI SE SES SLSI SRDI SSR MSTS TBE TE UPGMA μl

Agro-ecological zone Analysis of variance Appendix Bangladesh Agricultural University Bangladesh Institute of Nuclear Agriculture Base Pair Bangladesh Rice Research Institute Cetyl Trimethyl Ammonium Bromide Coefficient of Variation Double Distilled Water Distilled Water Desi semens par meter Electrical Conductivity Germination stress tolerance index Hectare Polyacrylamide Gel Electrophoresis polymorphism information content Root dry biomass stress tolerance index Root length stress tolerance index Shoot dry biomass stress tolerance index Standard error Standard evaluation score Shoot length stress tolerance index Soil Resource Development Institute Simple Sequence Repeat Mean Salinity Tolerant Score Tris Boric EDTA Tris EDTA Unweighted Pair Group Method of Arithmetic Means Micro liter

xii

Dedicated To My Beloved Parents and Sisters

CHAPTER I INTRODUCTION

CHAPTER II REVIEW OF LITERATURE

CHAPTER III MATERIALS AND METHODS

CHAPTER IV RESULTS

CHAPTER V DISCUSSION

CHAPTER VI SUMMARY

CHAPTER VII CONCLUSIONS

CHAPTER VIII REFERENCES

CHAPTER IX APPENDICES

CHAPTER 1: INTRODUCTION

CHAPTER I INTRODUCTION

Rice (Oryza sativa L.) is the most important and extensively cultivated cereal crops in Bangladesh. Rice has been considered as staple food of the Bangladeshi people; about 80 % of the total cultivated lands in Bangladesh are used for rice cultivation and its total production is 33.83 million metric tons (BBS, 2013). Rice supplies more than 70 % of calories (Khush, 2008) and more than 50 % proteins (Islam, 2009) as well as contributes 95 % of the cereals consumed in Bangladesh. Rice (Oryza sativa L.), belongs to the family Gramineae. It in one of the most important food crop grown worldwide and is the staple food for half of the world population (Sasaki and Burr, 2000). This crop is being cultivated in at least 95 countries throughout the world and is the second agricultural crop plant in the world (FAO, 2004). This staple food ranked first position by production among all cereals in Bangladesh (BBS, 2014). Total rice cultivated area 282288 thousand acres (BBS, 2013). The contribution of the crop sector to GDP is 12.57 % rice alone contributes of about 8.99%.i.e. about 71% of the total contribution of the crop sector (BBS, 2014). Rice production is affected by many biotic and abiotic stresses throughout the world. These abiotic stresses contribute about 50% of the total yield losses. Among the abiotic stresses salinity is considered as one of the major and prevalent stresses limiting rice production in the world (Ren et al., 2010). Approximately 30 % of the total irrigated land worldwide is salt-affected (Rengasamy, 2006) and that limits the total rice production in the world. At present, salinity is the second most widespread soil problem in rice growing countries after drought and is considered as a serious constraint to increase rice production worldwide (Gregorio et al., 1997).

1

CHAPTER 1: INTRODUCTION

The coastal areas of Bangladesh cover more than 30% of the cultivable lands of the country (SRDI, 2010). Out of 2.85 million hectares of coastal and offshore land, about 1.5 million hectares are affected by varying degrees of salinity. The coastal saline soils are distributed unevenly in 64 Upazila of 13 District, covering portions of eight agro-ecological zones (AEZ) of the country (Seraj and Salam, 2000). Agricultural land use in those areas is very poor, which is much lower than country’s average cropping intensity (Petersen and Shireen, 2001). The severity of salinity problem in Bangladesh increases due to climate change and the desiccation of the soil. On the other hand, Bangladesh needs to increase its rice production by more than 50% in the next 15 years to keep up with its population growth. With its high population density, there is no scope of new agricultural lands being used for the increased production of rice that is needed. One alternative is to use unfavorable land, which remains fallow, for most of the year such as the salt-affected coastal areas in the south of Bangladesh. But, modern rice cultivars tolerant to saline soils are few in number. Only crop grown in these areas is local transplant Aman rice with low yields. Therefore, development of salt tolerant varieties has been considered as one of the strategies to sustain food security by increasing rice production in saline prone coastal areas. But progress of developing salt tolerant varieties has been hampered due to several factors viz., limited knowledge on the genetics of salt tolerance, lack of understanding on the mechanism of salt tolerance, low selection efficiency, inadequate screening techniques, and poor understanding of the interactions of salinity and environments (Akbar, 1986). So there is a need to determine the salt induced change in agronomical (shoot length, root length & dry weight) and biochemical (sodium and potassium uptake) parameters so as to provide plant breeders to use these characteristics as selection criteria for salt tolerance for individual species rather than generalized for all species (Ashraf, 2004). One of the common means of development of new varieties is conventional breeding. But it is time consuming and depends on environmental conditions. It 2

CHAPTER 1: INTRODUCTION

takes 8-12 years to develop a variety through this breeding approach. However, DNA markers seem to be the best candidate for efficient evaluation and selection of plant material. Recent progress and technical advances in DNA marker technology permit reduction of time and accuracy of breeding. Marker assisted backcrossing can be used for speedy incorporation of saltol gene into modern high yielding and popular varieties. To do that marker assisted backcrossing firstly we should have some potential identified salt tolerant genotypes from which we can transfer gene into modern varieties. So to find out salt tolerant varieties screening is obligatory and landraces could be the potential source of salt tolerant gene. Because landraces provided “adaptability genes” for specific environmental conditions (Tang et al., 2002). The screening can be done based on agronomical and biochemical parameters as well as by molecular markers. SSR markers are playing an important role to identify gene for salt tolerance that can be helpful for plant breeders to develop new cultivars (Moniruzzaman et al., 2012). Screening of rice germplasms for salt tolerance at seedling stage based on agronomical and biochemical parameters readily acceptable as it is based on a simple criterion of selection, it provides rapid screening of large number of materials and the results are reproducible. Screening under controlled condition has the benefit of reduced environmental effects and the hydroponic system is free from the difficulty associated with soil related stress factors. To screen the salt tolerant variety reliable technique is needed. IRRI standard protocol (Gregorio et al, 1997) for salinity screening is very effective. On the other hand, SSR or microsatellite markers are proved to be ideal for making genetic maps (Islam, 2004; Niones, 2004), assisting selection (Bhuiyan, 2005) and studying genetic diversity in genotypes. Microsatellite marker analysis is promising to identify major gene locus for salt tolerance that can be helpful for biotechnologist and plant breeders to develop new variety.

3

CHAPTER 1: INTRODUCTION

The present study was therefore designed to screen out a wide range of rice genotypes based on their tolerance to different levels of salinity and to characterize these using molecular markers. The research was undertaken with the following objectives: •

To screen out saline tolerant rice genotypes at germination stage based on physiological indices.

•

To screen out saline tolerant rice genotypes at seedling stages based on agronomical and biochemical parameters.

•

To identify salt tolerant rice genotypes using microsatellite markers.

4

CHAPTER 2: REVIEW OF LITERATURE

CHAPTER II REVIEW OF LITERATURE

Bangladesh is an agriculture based country and rice is the staple food of the people of this country. A large area in the coastal region can’t be utilized for high yielding rice cultivation due to salinity problem and now it becomes a major concern for the scientists to develop salinity tolerant high yielding rice varieties to cultivate in the saline prone areas of Bangladesh. To develop a salt tolerant variety it is essential to understand rice, salinity, its effect on rice and the mechanism of salt tolerance properly. We must identify the sources of salt tolerant germplasms and then utilize it. A number of investigations have been done on the effect of salinity on the growth, sodium potassium uptake of rice and identification of salt tolerant genotypes of rice in different parts of the world. In Bangladesh, research works in this respect are a few. The following section describes the findings observed by different researchers in the past related to the present study. 2.1 Concept of Salinity: The term “salinity” represents all the problems of the soil accumulating excessive salts over long periods of time. Such soil can be categorized into sodic (or alkaline) and saline soils (IRRI, 2011). Sodic soils having a poor soil structure, generally spread over arid and semi-arid regions, retaining high concentrations of Na+ at the exchangeable site of clay particles in the soil, which shows high pH (greater than 8.5) with a high exchangeable sodium percentage (ESP >15) (IRRI, 2011). Saline soils can be generally found in arid regions, estuaries, and coastal fringes, which are dominated by Na+ ions with electrical conductivity of the extract (EC) more than 4 dS m-1 or that corresponds to approximately 40 mM NaCl and generates an osmotic pressure of approximately 0.2 MPa (IRRI, 2011; Munns and Tester, 2008) or gives an EC exceeding 4 mmhos cm-1 at 25ºC, in the water-saturated soil paste extract. Moreover, saline soils exhibit ESP of