department of plant molecular biology and biotechnilogy college of agriculture faculty of agriculture

213 Pages·2017·8.35 MB·English

“MAPPING QTL FOR TILLERING, NUMBER OF SPIKELETS AND GRAIN YIELD UNDER

WATER STRESS AND NON-STRESS CONDITIONS IN RICE (Oryza sativa L.)”

Ph.D. Thesis

by

Shubhnita Sahu

DEPARTMENT OF PLANT MOLECULAR BIOLOGY AND
BIOTECHNILOGY
COLLEGE OF AGRICULTURE
FACULTY OF AGRICULTURE
INDIRA GANDHI KRISHI VISHWAVIDYALAYA
RAIPUR (Chhattisgarh)
2016
“MAPPING QTL FOR TILLERING, NUMBER OF SPIKELETS AND GRAIN YIELD UNDER

WATER STRESS AND NON-STRESS CONDITIONS IN RICE (Oryza sativa L.)”

Thesis

Submitted to the

Indira Gandhi Krishi Vishwavidyalaya, Raipur

by

Shubhnita Sahu

IN PARTIAL FULFILMENT OF THE REQUIREMENTS
FOR THE DEGREE OF

Doctor of Philosophy

in

PLANT MOLECULAR BIOLOGY AND BIOTECHNOLOGY

Roll No. 16928 ID No. 118104068

JULY, 2016

Acknowledgement

After an intensive period of three & half years, today is the day: writing this note of
thanks is the finishing touch on my thesis. It has been a period of intense learning for me, not only
in the scientific arena, but also on a personal level. Writing this thesis has had a big impact on me.
I shall ever, remain thankfully indebted to all those learned souls, my present and former teachers,
known and unknown hands who directly or indirectly motivated me to achieve my goal and
enlightened me with the touch of their knowledge and constant encouragement. I feel this is an
extremely significant and joyous opportunity bestowed upon me by the goddess of learning, to
think about and thank all those persons.

I owe my heartfelt sincere gratitude to my major advisor,Dr. S. B. Verulkar, Professor,
Department of Plant Molecular Biology and Biotechnology, IGKV, Raipur whose encouragement,
supervision and support from the preliminary to the concluding level enabled me to develop an
understanding of the subject. Words could not express my indebtedness to you sir.

Most humbly and respectfully I wish to express my profound sense of gratitude to Dr.
Shubha Banarjee ma’m, Assistant Professor, Department Plant Molecular Biology and
Biotechnology, IGKV, Raipur for her valuable suggestions, motivation and perfect direction to my
thesis as well as personal life.

I am equally grateful to the another members of advisory committee Dr. Aarti Guhe
H.O.D of Department of Plant Physiology, Agricultural Biochemistry and MAPS for providing
me constant guidance and valuable suggestions, Dr. R. R. Saxsena Associate Professor,
Department of Statistics, for his supportive attitude.

My literal power is too less to express my thankfulness to respected teachers , Dr. Girish
Chandel, Professor; Dr.(Smt) Zenu Jha, Professor; Dr. (Smt.) Archana S. Prasad Assistant
Professor; Dr. (Smt.) Kanchan Bhan Assistant Professor, Department Plant Molecular Biology
and Biotechnology for their valuable suggestions critical comments and kind help rendered as and
when needed.

I wish to record my sincere thanks to Dr. S.K. Patil, Hon’ble Vice Chancellor, Dr. J. S.
Urkurkar Director Research Services and Dr. S. S. Shaw, Director of Instructions, Dr. S. S. Rao,
Dean and Dr. Madhav Pandey Librarian IGKV, Raipur for their help both administrative and
technical which facilitated my research work.

I wish to express my sincere thanks to all my dear friends Pushpanjali, Ojaswi, Priyanka,
Pritee, Ajit, Vinay, Swapnil and Manish for co-operation, help, encouragement and support. I feel
pleasure in expressing my thanks.

I extend my deepest thanks to my beloved seniors, colleagues Toshy ma’m, Mahima ma’m,
Renu ma’m, Sweta ma’m and Rashmi upadhyay and juniors, Roshni, Sujata, Anjali, Joyti ma’m,
Minakshi, Hemant, Datta, Swaraj, Pravin, shilpi, padmakshi and sashmita whose supports were
valuable and very helpful to my research work.
Unforgettable help and assistance throughout the course of this investigation by Mr.
Manish Makrand, Moti, Rajesh bhaiya, Drupati, bhujkumari didi and others also deserve my
sincere thanks.

i
At this inexplicable moment of joy, I deem it a proud privilege to recall all the cooperation
and the contribution, spirited guidance critical counsel and inspiration of my husband Dr.
Nemesh Kumar Sahu.

It is like a drop in the ocean of words that can never reach its mark to acknowledge
infinite love, blessings, sacrifices and constant encouragement of all my family members, my
especially to younger brothers Nitin and Piyush and Yogita bhabhi, and father and mother in-law
who have been the sole source of inspiration for me to proceed ahead in my life. I take this
opportunity to dedicate this work to my beloved parents Mr.Brijbhushan Lal Sahu and Mrs.
Dewhuti Sahu.

Last but not the least, I thank all the individuals who have in one any way been
associated with the completion of this work but have not been mentioned so far.

Place: Raipur (Shubhnita Sahu)
Date:

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CONTENTS

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ACNOWLEDGEMENT i
TABLE OF CONTENTS iii
LIST OF TABLES vii
LIST OF FIGURES ix
LIST OF PLATE xi
LIST OF APPENDICES xii
LIST OF ABBREVIATIONS xiii
ABSTRACT xv
I INTRODUCTION 1-4
II REVIEW OF LITERATURE 5-38
2.1 Phenotypic assessment of segregating population for 6
grain yield and yield related traits under drought and
irrigated condition.
2.2 Impact of drought on yield and yield contributing 8
characters
2.3 Genetic parameters for yield and yield related traits 9
2.3.1 Genetic variability 10
2.3.2 Heritability 12
2.3.3 Genetic advance 14
2.3.4 Correlation coefficients 15
2.3.5 Path analysis 18
2.4 Molecular approaches to improve grain yield 21
2.4.1 QTL mapping 21
2.4.1.1 Mapping population 21
2.4.1.2 Phenotyping of mapping population 22
2.4.1.3 High density linkage maps 22
2.4.1.4 Genetic map using microsatellites 25
2.4.1.5 Development of genotypic data based 26
on SSR marker
2.4.1.6 Statistical methods to detect QTLs 27
2.4.2 QTL x Environment interaction and common 29
QTLs across environments
2.4.3 Identification of QTL for grain yield and yield 29
component traits under irrigated and drought
Conditions
2.5 Phytohormones 38
III MATERIALS AND METHODS 40-61
3.1 Development and evaluation of F & F RIL mapping 40
14 15
population
3.1.1 Experimental Materials Characteristic features of 40

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parent
3.2 Methods 43
3.2.1 Field Studies 43
3.2.2 Role of the hormone to regulate tillering and 48
tiller dynamics of rice
3.2.3 Observations recorded 48
3.2.3.1 Observations under field condition 48
3.2.4 Statistical analysis 49
3.2.4.1 Analysis of variance 50
3.2.4.2.1 Mean 50
3.2.4.2.2 Range 51
3.2.5 Genetic analysis 51
3.2.5.1 Heritability 51
3.2.5.2 Standard deviation 51
3.2.5.3 Character association 52
3.2.5.3.1 Correlation coefficient 52
3.2.5.3.2 Genotypic and Phenotypic 52
Coefficient of Variation
3.2.5.3.3 Genetic advance 52
3.2.5.3.3.1 Expected Genetic Advance 52
3.2.5.3.3.2 Genetic Advance as 53
Percentage of Mean
3.2.6 Molecular studies 53
3.2.6.1 Genomic DNA isolation 53
3.2.6.2 Quantification of DNA 54
3.2.6.3 PCR amplification using HvSSR and 54
SSR markers
3.2.6.3.1 PCR reaction 54
3.2.6.3.2 Visualization of amplified 55
products in Polyacrylamide gel
electrophoresis
3.2.6.3.3 Assembling and pouring the gel 56
3.2.6.3.4 Electrophoresis 56
3.2.6.3.5 Visualization of bands 57
3.2.6.3.6 Detection of parental 57
polymorphism using highly variable
simple sequence repeats (HvSSR) and
simple sequence repeat (SSR) primers
3.2.6.3.7 Development of genotypic data of 57
population
3.2.6.3.8 Scoring of data 57
3.2.7 Reagents and solutions 58

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3.2.7.1 Reagents for PCR 58
3.2.7.2 Stock solutions 58
3.2.7.3 Solutions for electrophoresis 59
3.2.7.4 Stocks and solutions for PAGE 60
IV RESULTS AND DISCUSSION 62-139
4.1 Phenotypic observations 63
4.2 Variability 63
4.2.1 Analysis of variance 63
4.2.2 Mean and variability parameters 64
4.2.3 Genotypic coefficient and Phenotypic coefficient 75
4.2.4 Heritability 77
4.2.5 Phenotypic observation of BC F population 79
1 3
4.3 Genotypic and Phenotypic Correlation Coefficient of 81
Yield and its contributing traits under different

conditions

4.4 Path analysis of Yield and its contributing traits under 93
different conditions

4.5 Development of genotypic data using Danteshwari x 101
Dagad Deshi RIL population

4.5.1 Development of genotypic data based on HvSSR and 113

SSR markers

4.5.1.1 Parental polymorphism analysis using HvSSR and 113

SSR primers

4.5.2 Mapping of the molecular markers with QTLs 114
associated with yield related traits
4.5.2.1 Composite interval mapping 114
4.5.2.2 QTLs for grain yield 115
4.5.2.3 QTLs for total number of tiller 119
4.5.2.4 QTLs for Panicle per plant 121
4.5.2.5 QTLs for number of spikelets per panicle 122
4.5.2.6 QTLs for panicle length 124
4.5.2.7 QTLs for biological yield 126
4.5.2.8 QTLs for harvest index 127
4.5.2.9 QTLs for plant height 127
4.5.2.10 QTLs for days to flowering 129
4.6 Co-location of major effect QTLs contributing to grain 129
yield

4.7 Graphical genotyping of RILs using SSR and HvSSR 134
marker data

4.8 Effect of hormones on tillering ability of rice and grain 137
yield
V SUMMARY AND CONCLUSIONS 142-146

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REFERENCES 147-174
APPENDICES 175-186
RESUME 187
PUBLICATIONS

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