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The Regulation of Leaf Thickness in Rice (Oryza Sativa L.)

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The Regulation of Leaf Thickness in Rice (Oryza Sativa L.) The regulation of leaf thickness in rice (Oryza sativa L.) A thesis submitted by Supatthra Narawatthana For the degree of Doctor of Philosophy Department of Animal and Plant Sciences The University of Sheffield July 2013 Abstract The regulation of leaf thickness in rice (Oryza sativa L.) S. Narawatthana One of the most important targets to improve crop yield is leaf photosynthetic capacity. Leaf thickness is one parameter closely associated with photosynthetic function and is strongly influenced by the level of irradiance. Generally, high light grown leaves are thicker, have higher light- saturated rates of photosynthesis, higher amounts of Rubisco and a higher chlorophyll a:b ratio than shade grown leaves. However, the developmental stage at which leaf thickness is set and how it is set are unclear. In this thesis I investigate the outcome on leaf thickness of changing irradiance level at specific points in the development of leaf 5 of rice plants via a series of transfer experiments from high light (HL) to low light (LL) at specific stages of leaf development. The results from these experiments show that the P2- to P4- stage of rice leaf development represents a developmental window during which final thickness can be altered via light regime. Analysis of photosynthetic capacity and gas exchange of the leaves from the transfer experiments indicated some correlation of leaf thickness with biochemical/physiological adaptation to the prevailing irradiance level. Interestingly, whilst HL induced the development of thicker rice leaves with a visibly larger mesophyll cell size, transferral of the leaves to LL conditions at any developmental stage led to a LL-acclimated photosynthetic response. To identify lead genes potentially involved in the growth response of young leaves to the prevailing light environment, I performed a microarray analysis of leaf primordia at P3-stage undergoing a leaf-thickness response to altered irradiance level. A number of lead genes were identified and a selection process based on independent expression analyses was performed to narrow the number of candidates for future functional analysis. An initial analysis of some of these genes is reported. ii Acknowledgements I was fortunate to have Prof. Andrew Fleming as my supervisor. His innovative attitude toward science and endless encouragement has been essential to finish the work. I am most grateful for your consistent support. I am grateful for other guidance available from Prof. Paul Quick who also gave me the opportunity to do my PhD. The financial support from Thailand Agricultural Research Development Agency (ARDA) is gratefully acknowledged. I was lucky to be a member of a very innovative research group, Dr. Asuka Kuwabara, Dr. Anna Kasprzewska, Dr. Jen Sloan and Marion Bouch generously gave their valuable time guidance and encouragement. My warmest thanks are to you. Special thanks to Majorie Lundgren for the helpful guidance on using the LI-COR and physiological works. Thanks to the lab manager, Bob Keen, for all the kind supports. I would also like to acknowledge Ramil Mauleon (IRRI) who did the microarray analysis. Many thanks to Dr. Stephen Rolfe and Julia Van Campen for their helps on the microarray result. The D59 member, Dr. Hoe Han Goh, Dr. Xiao Jia Yin, Dr. Phakpoom Phraprasert, Dr. Adam Hayes, Dr. Chloé Steel, Dr.Simon Wallace, Dr.Caspar Chater, Rachel George, Thomas Harcourt, Nazmin Yaapar and many others, deserves special thanks for making the day at the lab more enjoyable and memorable. In particular, I want to thank Nisa Patikarnmonton, Oratai Weeranantanapan, Dr.Natwadee Poomipark, Dr.Khanita Kamwilaisak, Dr.Patompon Wongtrakoongate, Dr.Rossukon Keawkaw, Dr.Chatchawal Phansopha, Dr.Sawaporn Siriphanthana, Chomchon Fusinpaiboon, Sujunya Boonpradit, and many other Thai friends for all kinds of support during these years. My life in Sheffield was made truly memorable. I would also like to thank Pattamapon Prachomrat, for always being there for me. I would like to thank my family for the endless love and unconditional supports. My parents, Pathawee and Arjin, my sisters, Ann, Koi, my niece Rida, and also my brother in-law have formed an excellent safety net which I could always rely on. My loving thanks are to you all. iii Abbreviations A Net carbon dioxide assimilation ANOVA Analysis of variance Chl a:b Chlorophyll a / chlorophyll b ratio Ci Substomatal carbon dioxide concentration CO2 Carbon dioxide DAS Days after sowing DIG Digoxigenin dNTPs Deoxynucleotide triphosphates EDTA Ethylenediaminetetraacetic acid FDR False discovery rate g Gram gm Mesophyll conductance gs Stomatal conductance HCl Hydrochloric acid HL High light condition (700 µmol m-2 s-1) HL-leaves Leaves grown under HL hr(s) Hour(s) IRRI International Rice Research Institute Jmax Maximum rate of electron transport LB Luria-Bertani medium LHC Light harvesting complex iv LL Low light condition (200 µmol m-2 s-1) LL-leaves Leaves grown under LL P1 P1-stage leaf P2 P2-stage leaf P3 P3-stage leaf P4 P4-stage leaf P5 P5-stage leaf PAR Photosynthetically active irradiance PBS Phosphate buffer saline Pmax Light saturated-rate of photosynthesis PPFD Photosynthetic photon flux density PSI Photosystem I PSII Photosystem II P-stage Leaf plastochron age Rd Dark respiration rate RQ Relative quantitation RT Room temperature Rubisco Ribulose-1,5-bisphosphate carboxylase oxygenase RuBP Ribulose-1,5-bisphosphate s Second Sc Chloroplast surface area Smes Mesophyll surface area v SAM Shoot apical meristem SDS-PAGE Sodium dodecyl sulphate- Polyacrylamide gel electrophoresis SSC Saline-sodiumcitrate buffer TAE Tris acetic acid EDTA buffer Tris Tris(hydroxymethyl) aminomethane v/ v Volume/ volume Vcmax Maximum rate of carboxylation of Rubisco w/v Weight/ volume vi Contents ABSTRACT II ACKNOWLEDGEMENTS III ABBREVIATIONS IV CHAPTER 1 | INTRODUCTION 1 1.1 Introduction 2 1.2 Leaf anatomy and morphology 3 1.2.1 Rice leaf anatomy 5 1.3 Leaf development 7 1.3.1 Leaf developmental landmarks 8 1.3.2 Cell division and leaf development 8 1.3.3 Molecular regulation of leaf development 10 1.3.4 Rice leaf development 12 1.4 Photosynthesis 15 1.4.1 Light reactions 16 1.4.2 Calvin cycle 18 1.4.3 Carbon dioxide supply for photosynthesis 19 1.5 Leaf thickness: current state of knowledge 21 1.6 Aims 24 1.7 Objectives 25 1.9 Hypotheses 25 CHAPTER 2 |MATERIALS AND METHODS 26 2.1 Materials 27 2.1.1 General chemicals 27 2.1.2 Plant materials and growth conditions 27 2.2 Methods in leaf morphological study 29 2.2.1 Analysis of leaf plastochron index 29 2.2.2 Measurement of leaf growth 29 2.2.3 Measurement of leaf thickness 30 2.2.4 Stomatal density 31 2.3 Methods in physiological study 31 2.3.1 RubisCO protein analysis 31 2.3.2 Chlorophyll analysis 32 2.3.3 Photosynthetic light response measurement 32 2.3.4 CO2 response measurement, The A/Ci curve 33 vii 2.3.5 Analysis of carbon isotope discrimination 34 2.4 Methods in gene expression analysis 35 2.4.1 RNA extraction 35 2.4.2 Microarray analysis 35 2.4.3 cDNA synthesis (Reverse transcription) 36 2.4.4 Quantitative polymerase chain reation (qPCR) 36 2.4.5 In Situ hybridisation analysis 39 CHAPTER 3 | RESPONSE OF RICE LEAF MORPHOLOGY TO IRRADIANCE 47 3.1 Introduction 48 3.2 Aims 52 3.3 Brief methodology 52 3.3.1 Leaf plastochron index 52 3.3.2 Leaf size 52 3.3.3 Leaf thickness 53 3.3.4 Stomatal density 53 3.3.5 Transfer experiments 53 3.4 Results 54 3.4.1 Rice leaf morphology and development 54 3.4.2 Using Lf3 length as a proxy for staging Lf5 development. 64 3.4.3 The response of leaf thickness to altered irradiance at different developmental stages of Lf5 68 3.4.4 Using transfer experiments to identify the developmental stage at which control of leaf thickness occurs 70 3.4.5 The response of stomatal patterning to altered irradiance at different developmental stages of Lf5 73 3.5 Discussion 77 CHAPTER 4 | DOES ALTERATION IN LEAF FORM EFFECT LEAF PERFORMANCE? 82 4.1 Introduction 83 4.2 Aims 85 4.3 Brief methodology 85 4.3.1 RubisCO protein analysis 85 4.3.2 Chlorophyll analysis 86 4.3.3 Light response measurement 86 4.3.4 CO2 response measurement, The A/Ci curve 87 4.3.5 Analysis of carbon isotope discrimination 88 4.4 Results 88 4.5 Discussion 97 CHAPTER 5 | HOW IS LEAF THICKNESS CONTROLLED BY CHANGING IRRADIANCE? 101 viii 5.1 Introduction 102 5.2 Aim 105 5.3 Brief methodology 105 5.3.1 RNA extraction 105 5.3.2 Microarray analysis 105 5.3.3 cDNA synthesis 106 5.3.4 Quantitative polymerase chain reaction (qPCR) 107 5.3.5 In Situ hybridisation analysis 108 5.4 Results 108 5.4.1 Change in gene expression following a transfer from HL to LL revealed by microarray analysis 108 5.4.2 Validation of microarray analysis results by qPCR 116 5.4.3 In Situ hybridisation analysis of lead genes 120 5.5 Discussion 124 CHAPTER 6 | GENERAL DISCUSSION 127 6.1 Response of rice leaf morphology to irradiance 128 6.2 Does alteration in leaf form effect leaf performance? 133 6.3 How is leaf thickness controlled by changing irradiance? 134 6.4 Concluding remarks and future perspectives 139 REFERENCES 142 APPENDIX 153 Appendix A 154 Appendix B 155 Appendix C 157 Appendix D 163 ix Figure contents Figure ‎1.1 Example of grass leaf morphology. Leaf morphology of Dichanthelium dichotomum. 4 Figure ‎1.2 Rice leaf morphology showing the 3 main parts; leaf blade, leaf sheath and the boundary between leaf blade and sheath composed of ligule and auricle.
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