EFFECT OF WEEDY ( sativa L.)

ON THE YIELD OF CULTIVATED RICE ( L.) IN GREENHOUSE AND FIELD ENVIRONMENT

SALMAH BINTI TAJUDDIN

UNIVERSITI SAINS MALAYSIA 2014 EFFECT OF (Oryza sativa L.) ON THE YIELD OF CULTIVATED RICE (Oryza sativa L.) IN GREENHOUSE AND FIELD ENVIRONMENT

by

SALMAH BINTI TAJUDDIN

Thesis submitted in fulfilment of the requirements for the degree of

Master of Science

AUGUST 2014

ACKNOWLEDGEMENTS

My postgraduate (MSc) study at the Universiti Sains Malaysia (School of

Biological Sciences) was a great challenge. It was made possible with the kind assistance of many individuals, either directly or indirectly, to whom I am indebted, not all of whom are mentioned in this page.

First and foremost, my deepest appreciation goes to Prof. Mashhor Mansor for his strong support, unweary supervision and motivating guidance during the course of my study. In addition, I was also trained in writing scientific papers and had the opportunity to present scientific papers in seminars and conferences.

Other academicians had also given support through inspirational motivations and guidance, particularly Dr. Azmi Man, Prof. Nashriyah Mat and Dr. Asyraf

Mansor, my co-supervisors, to all of whom I am very grateful.

I wish to thank the staff of the Malaysian Meteorological Department Pulau

Pinang for providing me the necessary meteorological data needed for my thesis. The staff of MARDI (Seberang Perai) had been very helpful in my experimental work, especially En. Awang, En. Ebnil, En. Mustafa, Pn. Norhayati and Pn. Aqilah. The staff of USM for help me solve statistics analysis problems, particularly Dr. Zarul

Hazrin Hashim, En. Safian Bin Uda (The Advisory Statistician USM), and Dr. Nik

Fadzly Nik Rosely.

The grant of this study was provided Universiti Sains Malaysia under the TNC

Incentive and PRGS Grant. Universiti Sultan Zainal Abidin (UNISZA) provided the fellowship to enable me to do my postgraduate study at Universiti Sains Malaysia.

Last but not least, my heartfelt thanks go to members of my family who had given me continuous support an encouragement without which this study might not be completed. Cik Nur Diana Salihi, Cik Minah Muda, Dr. Fadzilah Hamzah, Cik

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Mastika Suhaila and all my family members that lended me a hand during my study.

Muhammad Fadzli (husband) and En. Tajuddin (father) had given me the strength and courage during those difficult times and to whom I am most grateful.

All names mentioned, I would like to add one more inspirational figure, my late beloved mother, Tom, who happened to have passed away during the course of my study.

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TABLE OF CONTENTS

Page

ACKNOWLEDGEMENTS ii TABLE OF CONTENTS iv LIST OF TABLES ix LIST OF FIGURES xiii LIST OF APPENDICES xix ABBREVIATIONS xxii ABSTRAK xxiv ABSTRACT xxv

CHAPTER 1 INTRODUCTION 1 1.1 Brief History of Weedy Rice Infestation in Rice Cultivation 1 1.2 The Malaysian Scenario 3 1.3 Current Issues 5 1.4 Problem Statement 5 1.5 The Need to Conduct the Study 6 1.6 Aim and Objectives 6 1.7 Hypotheses 7

CHAPTER 2 LITERATURE REVIEW 9 2.1 Basic Introduction to Rice Crop Science 9 2.2 General Background 10 2.2.1 Origins of Rice Culture 10 2.2.2 Classification, Species and Varieties 11 2.2.2.1 Classification of Oryza 11 2.2.2.2 Species and Varieties of Rice 12 2.2.2.3 Phylogentic Relationship 14 2.2.2.4 The International Rice Genebank 14 2.2.2.5 WR in General 14 2.2.2.6 WR in Peninsular Malaysia 17 2.2.2.7 Oryza rufipogon Griff. – A Wild Species of Rice 18

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2.2.2.8 CR Varieties 20 2.2.2.9 Yield of Malaysian (MARDI) Rice 22 2.2.2.10 General Statistics on Rice Industry in Malaysia 22 2.3 WR Phenomenon in Peninsular Malaysia 23 2.3.1 Characteristics of WR 24 2.3.1.1 Morphological and Anatomical Characters 24 2.3.1.2 Life-Cycle, Growth, and Dormancy 25 2.3.1.3 WR Accessions 26 2.3.1.4 Reduced Yield of CR due to WR 27 2.4 Previous Studies in Other Countries 29 2.4.1 General 29 2.4.2 Growth Studies 30 2.4.3 Yield Studies 33 2.4.4 Competition Between WR and CR 35

CHAPTER 3 METHODOLOGY 37 3.1 Introduction 37 3.2 Study Site 37 3.3 Germination Test 38 3.4 Selection of CR and WR Varieties 39 3.4.1 WR 39 3.4.2 Greenhouse Experiment – Competition Study 39 3.4.3 Field Experiment 41 3.5 Preparation for Planting Materials 41 3.5.1 Greenhouse Experiment 41 3.5.2 Field Experiment 43 3.6 Experimental Design 44 3.6.1 Overall Experiment Design 45 3.6.2 Additive Series and Replacement Series 46 3.6.3 Detailed Experiment Designs 47 3.6.3.1 Greenhouse Experiment 47 3.6.3.2 Field Experiment 50 3.7 Detailed Methodology 54 3.7.1 Methodology for Objectives 1 (Greenhouse) 55

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3.7.1.1 Planting Method 55 3.7.1.2 Agronomic Practice 58 3.7.1.3 Collection of Data 59 3.7.2 Methodology for Objectives 2 60 3.7.2.1 Planting Method 60 3.7.2.2 Agronomic Practice 60 3.7.2.3 Collection of Data 61 3.7.3 Methodology for Objectives 3 62 3.7.3.1 Planting Method 62 3.7.3.2 Agronomic Practice 62 3.7.3.3 Collection of Data 62 3.8 Analysis of Data 63 3.8.1 Analysis of Data for Objectives 1 63 3.8.2 Analysis of Data for Objectives 2 64 3.8.3 Analysis of Data for Objectives 3 66

CHAPTER 4 RESULTS 68 4.1 Introduction 68 4.2 Secondary Data (Meteorological Data) 68 4.3 Germination Test 69 4.4 Results for Objective 1 71 4.4.1 Relative Growth Rate for Greenhouse 71 4.4.2 Relative Growth Rate for Field 77 4.5 Results for Objective 2 82 4.5.1 Culm Height for Greenhouse 82 4.5.1.1 Additive Series 82 4.5.1.2 Replacement Series 83 4.5.2 Number of Tiller for Greenhouse 85 4.5.2.1 Additive Series 85 4.5.2.2 Replacement Series 87 4.5.3 Number of Filled Grain for Greenhouse 89 4.5.3.1 Additive Series 89 4.5.3.2 Replacement Series 91 4.5.4 Straw Weight (g) for Greenhouse 93

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4.5.4.1 Additive Series 93 4.5.4.2 Replacement Series 94 4.5.5 The Value of 1000 Grain Weight (g) for Greenhouse 96 4.5.5.1 Additive Series 96 4.5.5.2 Replacement Series 98 4.5.6 Yield per Hectare (tonnes/hectare) for Greenhouse 99 4.5.6.1 Additive Series 99 4.5.6.2 Replacement Series 103 4.5.6.3 Overall Results for Yield 106 4.5.7 Culm Height for Field 106 4.5.7.1 Additive Series: Season 1 106 4.5.7.2 Additive Series: Season 2 108 4.5.7.3 Replacement Series: Season 1 109 4.5.7.4 Replacement Series: Season 2 111 4.5.8 Number of Tiller for Field 112 4.5.8.1 Additive Series: Season 1 112 4.5.8.2 Additive Series: Season 2 114 4.5.8.3 Replacement Series: Season 1 115 4.5.8.4 Replacement Series: Season 2 116 4.5.9 Number of Filled Grain for Field 117 4.5.9.1 Additive Series: Season 1 117 4.5.9.2 Additive Series: Season 2 119 4.5.9.3 Replacement Series: Season 1 120 4.5.9.4 Replacement Series: Season 2 122 4.5.10 Straw Weight (g) for Field 123 4.5.10.1 Additive Series: Season 1 123 4.5.10.2 Additive Series: Season 2 124 4.5.10.3 Replacement Series: Season 1 126 4.5.10.4 Replacement Series: Season 2 127 4.5.11 The Value of 1000 Grain Weight (g) for Field 128 4.5.11.1 Additive Series: Season 1 128 4.5.11.2 Additive Series: Season 2 130 4.5.11.3 Replacement Series: Season 1 131 4.5.11.4 Replacement Series: Season 2 133

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4.5.12 Yield per Hectare (tonnes/hectare) for Field 134 4.5.12.1 Additive Series: Season 1 134 4.5.12.2 Additive Series: Season 2 137 4.5.12.3 Replacement Series: Season 1 139 4.5.12.4 Replacement Series: Season 2 142 4.6 Results for Objective 3 144 4.6.1 Prediction for CR Yield Model in Greenhouse 144 4.6.2 Prediction Model for CR Yields in Field 145

CHAPTER 5 DISCUSSIONS 147

CHAPTER 6 CONCLUSION 160

REFERENCES 163

APPENDICES 173

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LIST OF TABLES

Table 2.1: Species of rice (Oryza) in the world. 13

Table 2.2: List of rice in Peninsular Malaysia. 21

Table 2.3: Malaysia rice cultivars. 22

Table 2.4: Yield loss, density of CR and levels of infestation. 28

Table 2.5: Reduction of yield according to variety. 28

Table 3.1: Agronomic traits and origin of the selected cultivars. 40

Table 3.2: Planting pots used in the study (Ratio CR: WR [% WR 48 infested]).

Table 3.3: Additive series for CR-WR arrangement and seed rate 53 (density) used in Season 1.

Table 3.4: Replacement series for CR-WR arrangement and seed rate 53 (density) used in Season 1.

Table 3.5: Additive series for CR-WR arrangement and seed rate 54 (density) used in Season 2.

Table 3.6: Replacement series for CR-WR arrangement and seed rate 54 (density) used in Season 2.

Table 3.7: Fertiliser rate used on pots and plots. This rate was derived 59 from MARDI (2008).

Table 3.8: Summary of measurement characteristics. 61

Table 4.1: Culm height reduction (%) in competition by comparing 80 monoculture and mixture.

Table 4.1: (continue). 81

Table 4.2: Relative culm height (RYch) of CR and WR in the additive 83 series.

Table 4.3: Relative culm height (RYch) of CR and WR in the 84 replacement series.

Table 4.4: Relative number of tiller (RYt) of CR and WR in the 87 additive series.

Table 4.5: Relative number of tiller (RYt) of CR and WR in the 88

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replacement series.

Table 4.6: Relative number of filled grain (RYfg) of CR and WR in 90 the additive series.

Table 4.7: Relative number of filled grain (RYfg) of CR and WR in 92 the replacement series.

Table 4.8: Relative straw weight (RYsw) of CR and WR in the additive 93 series.

Table 4.9: Relative straw weight (RYsw) of CR and WR in the 96 replacement series.

Table 4.10: Relative 1000 grain weight (RY1000gw) of CR and WR in 97 the additive series.

Table 4.11: Relative 1000 grain weight (RY1000gw) of CR and WR in 98 the replacement series.

Table 4.12: Parameter estimates for the prediction of yield per hectare 101 (tonne) as a result of interferences of CR and WR in the additive series.

Table 4.13: Relative yield (RYyph) of CR and WR in the additive series. 102

Table 4.14: Parameter estimates for the prediction of yield per hectare 104 (tonne) as a result of interferences of CR and WR in the replacement series.

Table 4.15: Relative yield (RYyph) of CR and WR in the replacement 105 series.

Table 4.16: Relative culm height (RYch) of CR and WR in the additive 107 series for Season 1.

Table 4.17: Relative culm height (RYch) of CR in the additive series for 109 Season 2.

Table 4.18: Relative culm height (RYch) of CR and WR in the 110 replacement series for Season 1.

Table 4.19: Relative culm height (RYch) of CR in the replacement 112 series for Season 2.

Table 4.20: Relative number of tiller (RYt) of CR and WR in the 113 additive series for Season 1.

Table 4.21: Relative number of tiller (RYt) of CR in the additive series 115 for Season 2.

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Table 4.22: Relative number of tiller (RYt) of CR and WR in the 115 replacement series for Season 1.

Table 4.23: Relative number of tiller (RYt) of CR in the replacement 117 series for Season 2.

Table 4.24: Relative number of filled grain (RYfg) of CR and WR in 119 the additive series for Season 1.

Table 4.25: Relative number of filled grain (RYfg) of CR in the additive 119 series for Season 2.

Table 4.26: Relative number of filled grain (RYfg) of CR and WR in 121 the replacement series for Season 1.

Table 4.27: Relative number of filled grain (RYfg) of CR in the 123 replacement series for Season 2.

Table 4.28: Relative straw weight (RYsw) of CR and WR in the additive 124 series for Season 1.

Table 4.29: Relative straw weight (RYsw) of CR in the additive series 126 for Season 2.

Table 4.30: Relative straw weight (RYsw) of CR and WR in the 126 replacement series for Season 1.

Table 4.31: Relative straw weight (RYsw) of CR in the replacement 128 series for Season 2.

Table 4.32: Relative 1000 grain weight (RY1000gw) of CR and WR in 130 the additive series for Season 1.

Table 4.33: Relative 1000 grain weight (RY1000gw) of CR in the additive 130 series for Season 1.

Table 4.34: Relative 1000 grain weight (RY1000gw) of CR and WR in 132 the replacement series for Season 1.

Table 4.35: Relative 1000 grain weight (RY1000gw) of CR and WR in 134 the replacement series for Season 2.

Table 4.36: Parameter estimates for the prediction of yield per hectare 136 (tonne) as a result of interferences of CR and WR in the additive series for Season 1.

Table 4.37: Relative yield (RYyph) of CR and WR in the additive series 136 for Season 1.

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Table 4.38: Parameter estimates for the prediction of yield per hectare 139 (tonne) as a result of interferences of CR and WR in the additive series for Season 2.

Table 4.39: Relative yield (RYyph) of CR in the additive series for 139 Season 2.

Table 4.40: Parameter estimates for the prediction of yield per hectare 141 (tonne) as a result of interferences of CR and WR in the replacement series for Season 1.

Table 4.41: Relative yield (RYyph) of CR and WR in the replacement 141 series for Season 1.

Table 4.42: Parameter estimates for the prediction of yield per hectare 143 (tonne) as a result of interferences of CR and WR in the replacement series for Season 2.

Table 4.43: Relative yield (RYyph) of CR in the replacement series for 144 Season 2.

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LIST OF FIGURES

Figure 2.1: Life-history of CR (from Yoshida 1981). 9

Figure 2.2 Phylogenetic tree showing the AA genome in rice (after 15 Song Ge 1999).

Figure 2.3: Pattern in percentage reduction in yield for Malaysian CR 29 varieties with increased WR infestation (constructed from Table 2.5)

Figure 3.1: Seed germination test. 38

Figure 3.2: WR were planted for seed multiplication and to obtain 40 homogenous seed.

Figure 3.3: Planting pots - soil filled to 20 cm up the pot from bottom. 41

Figure 3.4: Tagging WR seedling. 43

Figure 3.5: Land preparation. 44

Figure 3.6: Overall diagram used to determine the influence of WR on 45 CR in term of RGR, yield components and yield per hectare.

Figure 3.6a: Chart used to determine RGR. 45

Figure 3.6b: Chart used to determine the yield components and yield per 46 hectare.

Figure 3.6c: Chart used to determine the influence of yield components 46 on yield per hectare (CR only).

Figure 3.7: Experimental design for greenhouse. 49

Figure 3.8: Pots arrangement in greenhouse. 50

Figure 3.9: Additive series and replacement series was employed to 51 elucidate findings on the effects of invasive WR on the RGR, yield components and yield per hectare of CR in field.

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Figure 3.10: Plot numbers arrangement in a RCBD with three blocks 52 (Block 1, Block 2, Block 3) in a field layout for Season 1.

Figure 3.11: Plot numbers arrangement in a RCBD with three replicates 52 (Block 1, Block 2, Block 3) in a field layout for Season 2.

Figure 3.12: Planting Method - blue circles represent CR, green circles 56 represent WR.

Figure 3.13: Planting lined for field experiment. Blue lines represent 57 CR, green lines represent WR.

Figure 3.14: Subplot used in the field study. 60

Figure 4.1: The bar chart and line graph for temperature and rainfall 69 respectively in 2011 (Malaysian Meteorological Department Pulau Pinang).

Figure 4.2: The bar chart and line graph for temperature and rainfall 69 respectively in 2012 (Malaysian Meteorological Department Pulau Pinang).

Figure 4.3: The germination rate for different types of CR and WR. 70

Figure 4.4: RGR value (cm cm−1 d−1) growth phase for culm height in 72 the additive series in CR and WR.

Figure 4.5: RGR value (cm cm−1 d−1) growth phase for culm height in 73 the replacement series in CR and WR.

Figure 4.6: RGR value (cm cm−1 d−1) is growth phase for culm height 78 in the additive series for Season 1.

Figure 4.7: RGR value (cm cm−1 d−1) growth phase for culm height in 79 the additive series for Season 2.

Figure 4.8: RGR value (cm cm−1 d−1) growth phase for culm height in 79 the replacement series for Season 1.

Figure 4.9: RGR value (cm cm−1 d−1) growth phase for culm height in 80 the replacement series for Season 2.

Figure 4.10: Culm height in the additive series measured at maturity. 83

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The vertical bars indicate standard deviation of the means.

Figure 4.11: Culm height in the replacement series measured at 85 maturity. The vertical bars indicate standard deviation of the means.

Figure 4.12: Number of tiller in the additive series measured at 86 maturity. The vertical bars indicate standard deviation of the means.

Figure 4.13: Number of tiller in the replacement series measured at 88 maturity. The vertical bars indicate standard deviation of the means.

Figure 4.14: Number of filled grain in the additive series measured at 90 maturity. The vertical bars indicate standard deviation of the means.

Figure 4.15: Number of filled grain in the replacement series measured 92 at maturity. The vertical bars indicate standard deviation of the means.

Figure 4.16: Straw weight in the additive series measured at maturity. 94 The vertical bars indicate standard deviation of the means.

Figure 4.17: Straw weight in the replacement series measured at 95 maturity. The vertical bars indicate standard deviation of the means.

Figure 4.18: The value of 1000 grain weight in the additive series 97 measured at maturity. The vertical bars indicate standard deviation of the means.

Figure 4.19: The value of 1000 grain weight in the replacement series 99 measured at maturity. The vertical bars indicate standard deviation of the means.

Figure 4.20: Yield per hectare (tonne) in the additive series measured at 102 maturity. The vertical bars indicate standard deviation of the means.

Figure 4.21: Yield per hectare (tonne) in the replacement series 105 measured at maturity. The vertical bars indicate standard deviation of the means.

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Figure 4.22: Culm height in the additive series for Season 1 measured at 107 maturity. The vertical bars indicate standard deviation of the means.

Figure 4.23: Culm height in the additive series for Season 2 measured at 108 maturity. The vertical bars indicate standard deviation of the means.

Figure 4.24: Culm height in the replacement series for Season 1 110 measured at maturity. The vertical bars indicate standard deviation of the means.

Figure 4.25: Culm height in the replacement series for Season 2 111 measured at maturity. The vertical bars indicate standard deviation of the means.

Figure 4.26: Number of tiller in the additive series for Season 1 113 measured at maturity. The vertical bars indicate standard deviation of the means.

Figure 4.27: Number of tiller in the additive series in Season 2 114 measured at maturity. The vertical bars indicate standard deviation of the means.

Figure 4.28: Number of tiller in the replacement series for Season 1 116 measured at maturity. The vertical bars indicate standard deviation of the means.

Figure 4.29: Number of tiller in the replacement series for Season 2 117 measured at maturity. The vertical bars indicate standard deviation of the means.

Figure 4.30: Number of filled grain in the additive series for Season 1 118 measured at maturity. The vertical bars indicate standard deviation of the means.

Figure 4.31: Number of filled grain in the additive series for Season 2 120 measured at maturity. The vertical bars indicate standard deviation of the means.

Figure 4.32: Number of filled grain in the replacement series for Season 121 1 measured at maturity. The vertical bars indicate standard deviation of the means.

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Figure 4.33: Number of filled grain in the replacement series for Season 122 2 measured at maturity. The vertical bars indicate standard deviation of the means.

Figure 4.34: Straw weight in the additive series for Season 1 measured 124 at maturity. The vertical bars indicate standard deviation of the means.

Figure 4.35: Straw weight in the additive series for Season 2 measured 125 at maturity. The vertical bars indicate standard deviation of the means.

Figure 4.36: Straw weight in the replacement series for Season 1 127 measured at maturity. The vertical bars indicate standard deviation of the means.

Figure 4.37: Straw weight in the replacement series for Season 2 128 measured at maturity. The vertical bars indicate standard deviation of the means.

Figure 4.38: The value of 1000 grain weight in the additive series for 129 Season 1 measured at maturity. The vertical bars indicate standard deviation of the means.

Figure 4.39: The value of 1000 grain weight in the additive series for 131 Season 2 measured at maturity. The vertical bars indicate standard deviation of the means.

Figure 4.40: The value of 1000 grain weight in the replacement series 132 for Season 1 measured at maturity. The vertical bars indicate standard deviation of the means.

Figure 4.41: The value of 1000 grain weight in the replacement series 133 for Season 2 measured at maturity. The vertical bars indicate standard deviation of the means.

Figure 4.42: Yield per hectare (tonne) in the additive series for Season 1 136 measured at maturity. The vertical bars indicate standard deviation of the means.

Figure 4.43: Yield per hectare (tonne) in the additive series for Season 2 138 measured at maturity. The vertical bars indicate standard deviation of the means.

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Figure 4.44: Yield per hectare (tonne) in the replacement series for 141 Season 1 measured at maturity. The vertical bars indicate standard deviation of the means.

Figure 4.45: Yield per hectare (tonne) in the replacement series for 143 Season 2 measured at maturity. The vertical bars indicate standard deviation of the means.

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LIST OF APPENDICES

Appendix 2.1: Trends in the number of tiller in five WR variants 173 (source: Chauhan and Johnson 2010).

Appendix 2.2: height after days of transplanting (after Munene et 174 al. 2008).

Appendix 2.3: Relative height growth rate (RGR) for the grass species 175 Piptocheatium napostaense and Poa ligularis (after Palaez et al. 2009).

Appendix 2.4: RGR (g g-1 d-1) for CR (after Hassanuzzaman et al. 176 2010).

Appendix 2.5: Relative yield for CR (IR64) and five type of WR 177 variaties from five Asian countries (after Chauhan and Johnson 2010).

Appendix 2.6: Reduction of yield due to infestation 178 (after Ottis et al. 2005).

Appendix 3.1: Rice Seed Standard by MARDI. 178

Appendix 4.1: Mean of culm height result in greenhouse. 179

Appendix 4.1: (continue). 180

Appendix 4.1: (continue). 181

Appendix 4.2: Summary of analysis of covariance (ANCOVA) results 182 for relative growth rates (RGR) of culm height in greenhouse.

Appendix 4.3: Summary of analysis of variance (ANOVA) results for 183 culm height in greenhouse.

Appendix 4.3: (continue). 184

Appendix 4.4: Summary of analysis of covariance (ANCOVA) results 185 for relative growth rates (RGR) of culm height in field.

Appendix 4.4: (continue). 186

Appendix 4.5: Mean of culm height result in field. 187

Appendix 4.5: (continue). 188

Appendix 4.6: Summary of analysis of variance (ANOVA) results for 189 culm height in greenhouse on maturity.

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Appendix 4.7: Summary of analysis of variance (ANOVA) results for 189 number of tiller in greenhouse.

Appendix 4.8: Summary of analysis of variance (ANOVA) results for 190 number of filled grain in greenhouse.

Appendix 4.9: Summary of analysis of variance (ANOVA) results for 190 straw weight in greenhouse.

Appendix 4.10: Summary of analysis of variance (ANOVA) results for 191 1000 grain weight in greenhouse

Appendix 4.11: Summary of analysis of variance (ANOVA) results for 191 yield per hectare in greenhouse.

Appendix 4.12: Summary of analysis of variance (ANOVA) results for 192 culm height in field.

Appendix 4.13: Summary of analysis of variance (ANOVA) results for 193 number of tiller in field.

Appendix 4.14: Summary of analysis of variance (ANOVA) results for 194 number of filled grain in field.

Appendix 4.15: Summary of analysis of variance (ANOVA) results for 195 straw weight in field.

Appendix 4.16: Summary of analysis of variance (ANOVA) results for 196 1000 grain weight in field.

Appendix 4.17: Summary of analysis of variance (ANOVA) results for 197 yield per hectare in field.

Appendix 4.18: Eigenvalues and proportions of variance for the two 198 components for CR in greenhouse.

Appendix 4.19: Results from the Principal Component Analysis variable 198 loadings for CR in greenhouse.

Appendix 4.20: Summary of analysis of linear regression analysis for 198 CR in greenhouse.

Appendix 4.21: Regressive model coefficients for CR in greenhouse. 198

Appendix 4.22: Summary of analysis of variance (ANOVA) results for 199 PCA (CR) in greenhouse.

Appendix 4.23: Eigenvalues and proportions of variance for the two 199 components for CR in field.

Appendix 4.24: Results from the Principal Component Analysis variable 199 loadings for CR in field.

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Appendix 4.25: Summary of analysis of linear regression analysis for 200 CR in field.

Appendix 4.26: Regressive model coefficients for CR in field. 200

Appendix 4.27 Summary of analysis of variance (ANOVA) results for 200 PCA (CR) in field.

Appendix 5.1: Field observation on 40 DAS. 201

Appendix 5.2: Field observation on 60 DAS WR overlapping the CR. 201 WR had overlay whole surface CR.

Appendix 5.3: Tall WR overshade short CR and CR type CL2 mature 202 earlier while WR in heading stage.

Appendix 5.4: Seed of WR shattered. 202

Appendix 5.5: WR growing higher than CR (CL2) on maturity stage in 203 field study.

Appendix 5.6: Comparison of WR and CR. 203

Appendix 5.7: Lodging WR at density ≥ 75kg/hectare WR infestation. 204

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ABBREVIATIONS

211 MR 211 220 MR 220 ANCOVA Analysis Covariate ANOVA Analysis of Variance B Regression coefficient CL1 MR 220 CL1 CL2 MR 220 CL2 cm Centimeter CR Cultivated rice/ rice/ cultivar d Day DAS Day of sowing et al. Et alii/ et aliae/ et alia/ and others e.g. For example f. Forma g Gram GRIN Germplasm Resources Information Network h Hour Ha Hectare i.e In other words or that is IRRI International Rice Research Centre IUCN International Union for Conservation of Nature Kg Kilogram LC Least Concern m Meter m2 Meter square m-2 Per meter square MARDI Malaysian Agricultural Research and Development Institute mm Milimeter MVSP Multivariate Statistical Package No. Number NPK Nitrogen Phospate Potassium fertilizer O. Oryza PC’s Principal Component

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PCA Principal Component Analysis R2 Sum of squares due to regression RGR Realtive Growth Rate RY Relative Yield

RYch Relative Yield Culm Height

RYt Relative Yield Number of Tiller

RYfg Relative Yield Number of Filled Grain

RY1000g Relative Yield 1000 Grain Weight

RYyph Relative Yield per Hectare S Setanjung Sect. Section Ser. Series Sig. Significant Sp. Species SPSS Statistical Package for the Social Sciences WR Weedy rice % Percentage > Larger than ∑ Sum % Percentage

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KESAN PADI ANGIN (Oryza sativa L.) TERHADAP HASIL PADI SAWAH (Oryza sativa L.) DI PERSEKITARAN RUMAH HIJAU DAN LAPANGAN

ABSTRAK

Kajian ini bertujuan untuk mengkaji keupayaan persaingan padi sawah (CR) terhadap padi angin (WR). Kajian ini yang telah dijalankan selama dua belas bulan dari Januari 2012 hingga Disember 2012 di persekitaran rumah hijau dan lapangan.

MR220, MR220 CL1, MR220 CL2, MR211, dan Setanjung adalah varieti yang telah dipilih bagi kajian rumah hijau. Kajian di lapangan dijalankan pada masa yang sama dengan menggunakan jenis variati CR yang sama dengan kajian rumah hijau.

Walaubagaimanapun, hanya satu jenis variati CR yang ditanam dikawasan lapangan kerana kekurangan masa, tempat dan tenaga pekerja. MR220 CL2 dipilih kerana keupayaan hasil tuaian yang lebih baik dan tempoh kematangan lebih pendek berbanding varieti CR yang lain. WR dan CR telah ditanam mengikut nisbah tertentu di dalam pasu untuk kajian rumah hijau dan plot di lapangan dengan mengunakan kaedah rekabentuk tambah siri dan penggantian siri. Keupayaan persaingan varieti

CR diukur berdasarkan Kadar Pertumbuhan Relatif (RGR), Hasil Relatif (RY) dan analisis regresi linear pada kepadatan serangan WR yang berlainan. Keputusan kaedah tambah siri dan penggantian siri telah menunjukkan bahawa varieti CR kurang kompetitif berbanding WR. Varieti CR yang berbeza menunjukkan kebolehan kompetitif yang berbeza. Kehadiran WR di CR menunjukkan penurunan hasil secara keseluruhan RGR, komponen hasil dan hasil tuaian. WR memberi kesan signifikan (P<0.05) kepada RGR, ketinggian batang, bilangan anak pokok, bilangan benih berisi, berat jerami, berat 1000 biji benih dan juga hasil tuaian varieti-varieti

CR. Variati CR baru (MR220 CL2) memberikan hasil tuaian lebih tinggi, tetapi ia kurang kompetitif kepada WR berbanding dengan variati CR lain.

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EFFECT OF WEEDY RICE (Oryza sativa L.) ON THE YIELD OF CULTIVATED RICE (Oryza sativa L.) IN GREENHOUSE AND FIELD ENVIRONMENT

ABSTRACT

This study aimed to investigate the competitive abilities of cultivated rice (CR) and weedy rice (WR). This study was performed over a period of twelve months from January 2012 to December 2012 in greenhouse and field environments.

MR220, MR220 CL1, MR220 CL2, MR211, and Setanjung were the selected CR varieties used in the greenhouse study. The field study was simultaneously conducted using the same selected CR varieties as in the greenhouse study. However, only one type of CR variety was planted in the field study because of time, space and labour constraints. MR220 CL2 was selected because of its high yields and short maturity period among all the CR varieties. Specific proportions of WR and CR were planted in pots for the greenhouse study and plots for the field study based on additive series and replacement series designs. The competitive abilities of CR varieties were measured based on the Relative Growth Rate (RGR), Relative Yield, and linear regression analysis under different infestation densities of WR. Results of additive series and replacement series designs indicate that CR varieties were less competitive than WR. Different CR varieties demonstrated various competitive abilities. The presence of WR in CR decreased overall RGR, yield components, and yield. WR significantly (P < 0.05) affected RGR, culm height, number of tiller, number of filled grain, straw weight, 1000 grain weight, and yield of CR varieties. The new CR variety (MR220 CL2) demonstrated high yield, but it was less competitive than WR and other old rice varieties.

xxv CHAPTER 1

INTRODUCTION

1.1 Brief History of Weedy Rice Infestation in Rice Cultivation

Weedy rice (WR) infestations were first reported from the Americas when red rice infestations were known to have occurred as early as 1846 (Allston, 1846).

Delouche et al. (2007) stated that it is generally believed that the red rice was introduced into the United States of America at a much earlier date as contaminants in imported seed rice.

Problems related to WR infestations in rice fields were said to have been reported from European countries since the 1970s (Tarditi and Verseci, 1993). The

WR phenomenon started when European farmers were cultivating the weak and semi-dwarf types of Oryza sativa var. indica (Tarditi and Verseci, 1993). In South-

East Asian countries, Azmi et al. (1998) reported that WR infestation started after the adoption of direct seeding practices in rice cultivation. This is in contrast to the traditional practice of transplanting seedlings from seedbeds to the paddy fields where WR infestation was relatively unknown. In Malaysia, the phenomenon is said to have started in the 1980s (Vaughan et al., 1993; Azmi and Karim, 2008).

Several theories have explained on the possible emergence or evolution of

WR. One theory states that WR was produced as a result of between cultivated rice (CR) species and their relatives in the wild or between different cultivars while other theories consider weedy species to be derived from natural mutations (Catling, 1992; Abdullah et al., 1996; Gressel, 1999; Federici et al., 2001).

One phenomenon related to WR is what is known as “volunteer seeding”. It is generally defined as seeds (usually of inferior quality) that are already present in

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the field that would germinate and grow into a crop, as opposed to those selected superior seeds of a crop which are sown to produce a good harvestable crop.

In terms of chromosome numbers, most of the different types of WR have the same genome as CR genome AA, 2n=24 (Azmi and Karim, 2008). Apparently, according to Azmi and Karim (2008) there are ten different genomic groups for

Oryza species, denoted as AA, BB, CC, BBCC, CCDD, EE, FF, GG, JJHH and

JJKK. Oka (1990), Gressel (1999), Lu et al. (2003) and Lu (2004) stated that species with different genomes are not compatible for intercrossing. The number of rice species from the various reports vary 22 to 26 (see Section 2.2.2).

In Malaysia, WR is of the same species as CR, Oryza sativa L., but the former is derived from inferior seed sources produced by CR as a result of unfavourable (drought) growing season as suggested by Watanabe et al. (2000). One of its main characteristics is its early shattering of mature seeds which accumulate at the ground level in the paddy fields while CR retain its seeds much longer and harvestable. Thus the seeds of WR would germinate and grow in the paddy fields after harvest season. Germination and growth of WR is much vigorous in the next rice planting season since growth conditions for the WR are made more favourable.

The WR will thus compete with the CR in terms of space and nutrients.

In general, rice species including WR are characterized by their capability to self-propagate and to produce seeds (Azmi and Karim, 2008). Apart from this, WR is also known to have the adaptability to withstand different weather conditions and thus it has an added advantage when competing with CR (Baki et al., 2000). On the other hand, Begum et al. (2005a, 2005b) had confirmed that WR populations could successfully colonize a CR field to such an extent that they would thus become the dominant weed species.

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1.2 The Malaysian Scenario

Baki et al. (2000) first reported on the occurrence of WR in paddy fields in the Projek Barat Laut Selangor (PBLS) since 1988 and its subsequent occurrence in the Muda rice scheme in Kedah in the 1990s. The report also stated that the emergence of WR in paddy fields might be attributed to severe droughts which occurred in Peninsular Malaysia in the 1980s. Subsequently, this had led to significant rice crop yield losses in the Malaysian rice production due to growth competition between the CR and the WR. It was also noted that WR had spread to other rice cultivation areas in all parts of Peninsular Malaysia.

Rice cultivation has undergone revolutionary advances especially with the introduction of machineries such as tractors and combine harvesters. These machines are often transported from place to place and they thus become carriers of WR seeds which are physically stuck to their body parts. This phenomenon has been observed and reported by Baki and Shakirin (2010) who specifically mentioned that the movement of farm machinery between granaries in different areas was a contributing factor to the WR infestation problems. On the other hand, Azmi et al. (2000) observed that the wide spread of WR in paddy fields throughout Peninsular Malaysia was also due to the shift of rice planting practice from the traditional method of transplanting rice seedlings (from seedbeds to the paddy fields) and to that of the modern practice of direct seeding.

Several factors are thought to cause the appearance of WR in rice fields.

Initially the retains its genetic makeup and grows as separate genepools apart from CR or “cultivars”. Gradually, the initial genetic materials of the WR become mixed with the genetic materials of the CR as a result of natural hybridization including . The mingling of genetic resources between

3

WR and the CR eventually produced new genetic strains of WR which are commonly referred to as the “new unwanted varieties” as mentioned by Azmi and

Karim (2008). These new unwanted varieties are also known as “padi angin” in

Malay (or “wind rice” in English) because of the early shattering characteristics and the lighter grains which are easily detached from the panicles when blown in the wind and thus these grains drop on the ground before rice harvesting.

Baki et al. (2000) and Azmi and Karim (2008) explained that the new unwanted varieties or “variants” (new strains of WR) could be triggered to grow competitively with CR as a result of external factors such as unpredictable weather conditions and lack of control in agricultural management. The unpredictability of weather conditions at times in Malaysia has increased the quantity of WR seeds embedded in natural seed bank sat the ground level as mentioned by Azmi and

Karim (2008). In addition, the absence of proper control of WR has allowed quick dispersal of WR seeds which is normally unknown to farmers in the field and thus would cause a possible major upsetting of the yield of the whole rice crop Azmi and

Karim (2008).

From available data gathered, it is known that at 35% level of WR infestation, the lost yield of CR is about 50-60% or 3.20-3.84 tonnes per hectare per season (Baki, 2004). In extreme cases, up to 75-100% lost yields have been recorded due to WR infestation (Azmi et al. unpublished data, in Baki 2004). These estimates are general information gathered by relevant authorities such MARDI based random surveys on rice production in certain rice paddy areas. However, detailed surveys on the effect of WR at different levels of infestation are seldom undertaken or very little known.

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1.3 Current Issues

At present Malaysia is only 72 percent self-sufficient in rice production

(Gomez, 2011; Zhi, 2011). Despite Malaysian Government’s efforts to boost its rice industry, rice production has not increased as expected. So much so Malaysia is still heavily dependent on rice imports. There was even a rice crisis in 2008 when rice exporting countries stopped exporting rice to Malaysia (Childs and Kiawu, 2009;

Vengedasalam, 2013), thus rice production is an important security issue in the country.

1.4 Problem Statement

Despite efforts to overcome problems caused by WR in the rice fields in

Peninsular Malaysia, the problems have persisted to the present day. Among the major issues faced by the rice industry is the indifferent attitude of rice farmers toward these problems. Some farmers prefer to use CR for seed stock, and do not consider WR as a weed. The lack of interaction and communication among agricultural agencies and insufficiency of integrated technologies to control WR have resulted in minimal attention being given to WR management in Peninsular

Malaysia. A group of farmers reportedly secured uncontaminated seed sources from the Pertubuhan Peladang Kawasan (“Regional Farmers Organization”), but seed contamination still occurs. During field inspection for certified seeds, off-type varieties cannot always be differentiated from WR. When differences can be distinguished, the maximum mixture of other varieties permitted is approximately

0.10%, which is equivalent to 0.15 kg per 150 kg CR rate. Little is known about seed contamination resulting from contaminated seed sources in actual rice fields, and information on actual levels of WR infestations in paddy fields throughout

5

Peninsular Malaysia is lacking. Given that this subject is becoming increasingly critical, more studies are necessary to supplement data.

1.5 The Need to Conduct the Study

Based on ISI Web of Knowledge Journal Citation Reports, there were about

146 studies on WR, which focused on various topics. Most of the studies were done on specifications of WR, while few were done on competition of WR. Only five studies recorded on WR competition by Burgos et al. (2006), Chauhan and Johnson

(2010), Lawton-Rauh and Burgos (2010) and Ziska et al. (2010). Based on the current state of knowledge on the effects of WR on CR production in Peninsular

Malaysia as mentioned above, a study of this nature is much needed in order to have better knowledge on the subject. This study is hoped to gather the much needed information especially on the effects of WR at different levels of infestation on the

CR.

1.6 Aim and Objectives

The aim of the study is to compare CR yields that are produced by CR at differing conditions, without and with the infestations at different levels of WR

(ratio) in cultivation. Three objectives have been identified in this study as follows:-

1. To determine the influence of WR on the Relative Growth Rate (RGR) of CR

by comparing CR monoculture with those of mixed culture at different ratios.

2. To determine the influence of WR on the yield components and yield of CR

by comparing CR monoculture with those of mixed culture at different ratios.

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3. To determine the influence of yield components on yields of CR by

comparing CR monoculture with those of mixed culture at different ratios.

1.7 Hypotheses

Based on the three objectives above, the following three hypotheses are formulated to test the statements of these objectives. The objectives and the hypotheses are the basis for the methodology adopted in this study as shown in

Chapter 3.

a) Hypothesis for Objective 1 (HA)

Null hypothesis: HA(0): WR does not affect RGR of CR even with increased levels of

infestation.

Alternative hypotheses: HA(1): WR does affect RGR of CR increasingly with

increased levels of infestation.

b) Hypothesis for Objective 2 (HB)

Null hypothesis: HB(0): WR does not affect the yield components and yield of CR

even with increased levels of infestation.

Alternative hypothesis: HB(1): WR does affect the yield components and yield of CR

increasingly with increased levels of infestation.

c) Hypothesis for Objective 3 (HC)

Null hypothesis: HC(0): Yield components does not affect yield of CR even with

increased levels of infestation.

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Alternative hypothesis: HC(1): Yield components does affect yield of CR increasingly

with increased levels of infestation.

8

CHAPTER 2

LITERATURE REVIEW

2.1 Basic Introduction to Rice Crop Science

Yoshida (1981) provided vital information pertaining to the fundamentals of rice crops science. Figure 2.1 shows the growth behaviour of the rice plant.

Figure 2.1: Life-history of CR (from Yoshida 1981).

The growth behaviour of the CR plant observed in this study would much refer to the established growth pattern such as the one shown above. Basically the annual CR takes about 3 to 4 months to complete its life-cycle. Based on a 120-day

(4-month) growth cycle, the vegetative growth lasts to about 90 days after which vegetative growth will be reduced significantly. Tillering usually starts at about 20

9

days after sowing and reaches maximum growth at about 60 days after sowing and after which tillering would remain constant or reduced (as shown in Figure 2.1).

Panicle initiation starts at about 80 plus days at the booting stage followed by grain filling at about 90 days after sowing. The rice plant should reach maturity in 120 days and after which growth will cease and the plant starts to undergo senescence.

2.2 General Background

A brief background information on rice is provided in this section. The subtopics under this section are those dealing with the origins of rice, taxonomic classification, and information on the species and cultivated varieties of rice in general.

2.2.1 Origins of Rice Culture

According to Zhimin (1999), the Asian-centered rice-planting culture has a wide distribution and a long history, with different hypotheses concerning its origin pointing to several regions including Assam, Yunnan, East Asian Crescent and middle and lower Yangtze River. Zhimin (1999) has also stated that, archaeologically, China has the earliest rice site with a rich culture, tracing both to the middle and lower Yangtze River, and thus subsequently its powerful influence on surrounding areas is well evidenced by Korean and Japanese findings.

The Chang-Watanabe hypothesis (Sato, 2000; History of Rice Cultivation), however, proposed that the Asian CR (O. sativa L.) emerged in an area stretching across Assam District of India, upper Myanmar, northen Thailand, northern Lao

(PDR), and the southwestern provinces of China.

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In the African continent, the species used for CR is , and the species has been long in cultivation in Africa before the arrival of the Europeans in the continent (Linares, 2002). However this species was gradually replaced by the

Asian Oryza sativa and according to Linares (2002) the Asian CR has replaced most of the native CR except in certain traditional areas. In the American continent, rice was introduced by the European settlers in the 17th century. Rice is not known to be native to the Americas.

2.2.2 Classification, Species and Varieties

2.2.2.1 Classification of Oryza

Oryza is a genus in the Graminae or family, or commonly known as the grass family. The grass family is the fourth largest family and contains about 11 000 species in 800 genera worldwide (Peterson 2001). Twenty- three genera contain 100 or more species or about half of all grass species, and almost half of the 800 genera are monotypic or diatypic, i.e. with only one or two species (Peterson, 2001).

APG 3 (Angiosperm Phylogenetic Group III) 2009 classifies rice or Oryza sativa L. as follows (also based on Gramene Oryza website; note the rank of

Subfamily is used based on GRIN and the rank of Tribe is used used after Tang et al,. 2010):-

Kingdom: Plantae - Plants Subkingdom: Tracheobionta - Vascular plants Superdivision: Spermatophyta - Seed plants Division: Magnoliophyta - Flowering plants Class: Liliopsida - Subclass: Commelinidae

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Order: Cyperales Family: Poaceae - Grass family [Subfamily: Ehrhartoideae] [Tribe: Oryzeae] Genus: Oryza L. – CR

2.2.2.2 Species and Varieties of Rice

Scientists are still divided on the of Oryza and the number of species quoted ranges from 21 to 26 species; 21 species (Delouche et al. 2007), 22 species (Brondani et al,. 2003; Jaiswal et al,. 2005; Mabilangan et al,. 2008), 23 species (American group – according to Gramene Oryza), 24 species (Jena, 2010;

Rice Bank Knowledge), 25 (GRIN database – see the list of species below) and 26 species listed by Gramene Oryza (based on survey of species names list). The list of species in Gramene Oryza is shown in Table 2.1.

A list of rice species based on GRIN database is given below (note: 67 taxa are listed in GRIN but only 25 have been extracted and regarded as valid species and listed here):-

1. Oryza alta Swallen (sect. Oryza ser. Latifoliae) 2. Oryza australiensis Domin (sect. Australiensis) 3. Oryza barthii A. Chev. (sect. Oryza ser. Oryza) 4. Oryza brachyantha A. Chev. & Roehr. (sect. Brachyantha) 5. Oryza eichingeri Peter (sect. Oryza ser. Latifoliae) 6. Oryza glaberrima Steud. (sect. Oryza ser. Oryza) 7. Oryza glumipatula Steud. (sect. Oryza ser. Oryza) 8. Oryza grandiglumis (Döll) Prodoehl (sect. Oryza ser. Latifoliae) 9. Oryza latifolia Desv. (sect. Oryza ser. Latifoliae) 10. Oryza longiglumis Jansen (sect. Padia ser. Ridleyanae) 11. Oryza longistaminata A. Chev. & Roehr. (sect. Oryza ser. Oryza) 12. Oryza malampuzhaensis Krishnasw. & 13. Oryza meridionalis Ng (sect. Oryza ser. Oryza) 14. Oryza meyeriana (Zoll. & Moritzi) Baill. 15. Oryza minuta J. Presl (sect. Oryza ser. Latifoliae) 16. Oryza neocaledonica Morat (sect. Padia ser. Meyerianae) 17. Oryza nivara S. D. Sharma & Shastry (sect. Oryza ser. Oryza)

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18. Oryza officinalis Wall. ex G. Watt (sect. Oryza ser. Latifoliae) 19. Oryza punctata Kotschy ex Steud. (sect. Oryza ser. Latifoliae) 20. Oryza rhizomatis D. A. Vaughan (sect. Oryza ser. Latifoliae) 21. Oryza ridleyi Hook. f. (sect. Padia ser. Ridleyanae) 22. Oryza rufipogon Griff. (sect. Oryza ser. Oryza) 23. Oryza sativa L. (sect. Oryza ser. Oryza) 24. Oryza schlechteri Pilg. (sect. Padia ser. Schlechterianae) 25. Oryza schweinfurthiana Prodoehl (sect. Oryza ser. Latifoliae)

Table 2.1: Species of rice (Oryza) in the world.

Oryza granulata Oryza alta Oryza latifolia Oryza australiensis Oryza officinalis Oryza longiglumis Oryza barthii Oryza perennis Oryza longistaminata (Oryza Oryza brachyantha Oryza punctata glumaepatula) Oryza coarctata Oryza rhizomatis Oryza malampuzhaensis Oryza eichingeri Oryza ridleyi Oryza meridionalis Oryza glaberrima Oryza rufipogon Oryza meyeriana Oryza glumipatula (Oryza Oryza sativa Oryza minuta glumaepatula) Oryza schlecteri Oryza nivara (Oryza sativa f. Data retrieved October 17, 2006 Oryza grandiglumis spontanea) (Note: Adapted from Gramene Oryza).

Up until now, the taxonomy of Oryza has not been fully resolved, but as for the cultivated species, most scientists accept two species; Oryza sativa and Oryza glaberrima as the world’s widely CR species. The rest of the species are considered wild although a few species of these so-called wild species might be in cultivation e.g. Oryza longistaminata or Red Rice which is cultivated in parts of traditional

Africa. The non-cultivated species may sometimes be referred to as “WR” (see subsection [e] below).

In Peninsular Malaysia, two species or rice are know to exist; Oryza rufipogon (the wild rice species) and Oryza sativa (cultivated species). Although

Oryza rufipogon is considered a wild species, it is however listed in IUCN Red Data

Book (or Red List) 2012 release under “Least Concern” (LC) or “Lowest risk”. In the

IUCN category of threatened species, this category denotes that a species does not

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qualify for a more “at risk” category. Widespread and abundant taxa are included in this category.

2.2.2.3 Phylogentic Relationship

Recently, there have been many studies on the phylogenetic relationships of

Oryza species by Song Ge et al. (1999), Sacks et al. (2006), Duan et al. (2007),

Zuccolo et al. (2007), Ammiraju et al. (2010), Tang et al. (2010) and Lawton-Rauh and Burgos (2010). The general concensus by scientists agrees that the two CR species Oryza sativa and Oryza glaberrima are both of genome AA together in the same clade (within the phylogenetic tree) with the non-cultivated species Oryza rufipogon, Oryza glumipatula, Oryza longistaminata, Oryza barthii, Oryza meridionalis and Oryza nivara as shown by Song Ge et al. (1999). It is generally believed that Oryza sativa is derived from Oryza rugifogon and that Oryza glaberrima is derived from Oryza nivara (Zuccolo et al. 2007).

2.2.2.4 The International Rice Genebank

IRRI (International Rice Research Institute) which is based in Los Banos,

Philippines holds more than 117,000 “types” of rice - the biggest collection of rice genetic diversity in the world. The genetic diversity of rice is used to new rice varieties (IRRI).

2.2.2.5 WR in General

This subject has been introduced earlier in Chapter 1 (Sections 1.2). As can be seen above, there are more than twenty species of rice, two of which are

14

cultivated, and all of which belong to the AA genome (Figure 2.2). There is the tendency for outcrossing, backcrossing and hybridization between populations of different species and varieties. As a result there would exist hybrids and outcrossed rice species and varieties that resemble closely with cultivated. These hybrids or varieties may infest rice fields though volunteer seeding or contaminated seeds.

Figure 2.2: Phylogenetic tree showing the AA genome in rice (after Song Ge 1999).

Begum et al. (2005a, 2005b) stated that existing weed vegetation could be drastically replaced by the WR of the Oryza sativa complex. WR, however, had not been listed as a dominant weed species before the emergence of the WR phenomenon in rice fields, but once it began to emerge in the rice fields, it then started to seriously infest the rice cultivars (Zainal, 2008). Baki et al. (2000)

15

postulated that the emergence of WR in rice fields was probably caused by severe droughts in Peninsular Malaysia in the 1980s.

Baki (2004) reported that WR had began to colonise the MADA rice cultivated areas in the early 1990s, followed by the Besut area (Terengganu) in 1995,

Sg. Manik and Kerian areas (Perak) in 1996, Seberang Perai (Pulau Pinang) in 1997, and Seberang Perak (Perak) and Kemubu (Kelantan) areas in 2001. It was also noted that about half of the 700 hectares of rice farm blocks in Selangor areas (Sekinchan,

Sungai Leman, Sungai Burong and Sungai Nipah) were infested by WR for Season 2 in 1993 (Baki, 2004).

According to Baki et al. (2000), owing to the sympatric occurrence of WR and commercial rice, the WR had the tendency to compete for space and the common pools of nutrients which were necessary for growth and survival. Baki et al. (2000) also reported that WR populations in the various rice cultivated areas in Selangor did not show distinct morphological variation.

Methods of WR control have been developed in Peninsular Malaysia to address the WR menace in rice fields such as better water management, application of suitable herbicides, and improved tilling method (Azmi and Karim, 2008). Despite efforts to reduce WR infestations in rice fields, the phenomenon had continued to persist. Baki et al. (2000) were of the opinion that the persistence or continued prevalence of WR over CR was an indication of better ecological adaptations by WR compared to the commercial rice varieties.

The use of herbicide-resistant rice cultivars has the potential to improve the efficiency of weed management in rice fields and to increase rice yields (MARDI,

2008). However, any new herbicide that is applied to the rice fields to protect a rice

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cultivar would consequently induce similar resistence in the WR found in the same area. This would happen through outcrossing (Busconi et al., 2012).

WR normally takes about 90-120 days to mature compared to the commercial variety which takes about 115 days to 120 days (Zainal, 2008). In addition, WR exhibits other advantageous characters over the commercial varieties such as taller plant height, faster growth rate, and earlier seed shattering. Some WR variants are known to have a life-cycle of less than 3 months, thus the seeds mature earlier and dropped into the natural seed banks and remain dormant until the next growing season. At the sametime, the dropped seeds of WR can also germinate and colonise abandoned rice fields after the harvest season.

WR can also originate from the natural hybrids between CR and WR through cross-pollination (Azmi and Karim, 2008; Grillo et al., 2009) as well through introgression (Baki et al., 2000). Introgression or introgressive hybridization is generally defined as the movement of a gene from one species into the gene pool of another by the repeated backcrossing of an interspecific with one of its parent species. The level of introgression can be determined by outcrossing (Baki et al., 2000). The rate of outcrossing affects the heterozygosity of populations which might also to contribute to the evolutionary potential of WR (Baki et al., 2000). For a non-specific crop, introgression is said to able to influence the genetic variation and possibly also the evolution of its co-existing WR populations (Baki, et al., 2000).

2.2.2.6 WR in Peninsular Malaysia

From personal study and observation, in Peninsular Malaysia, WR can be attributed to four factors were (i) volunteer seedling, (ii) seed contamination, (iii) outcrossing between Oryza rufipogon and Oryza sativa, (iv) outcrossing between

17

WR (which is a low quality variety of Oryza sativa) and CR (the high quality commercial variety) of the same species Oryza sativa. Azmi and Karim (2008) however regarded three factors that help to initiate the population growth of WR i.e.

(i) the existence of dormant seeds retained in the soil over crop seasons, (ii) the distribution of the WR seeds through contaminated seeds, and (iii) the return seeds from plants of the previous crop.

2.2.2.7 Oryza rufipogon Griff. – A Wild Species of Rice

Most of the following information was retrieved from the IUCN Red Data

List website (http://www.iucnredlist.org) on 29th August 2013. The plant description part (botanical description) was retrieved from the Rice Bank Knowledge website

(http://www.knowledgebank.irri.org) on 29th August 2013, and Ngu et al. (2010).

Oryza rufipogon is the wild species from which the CR, Oryza sativa, has been domesticated. It is wide spread in most of the world, being invasive in parts of

America. It is considered a weed in rice fields, as it easily crosses with the CR, reducing its market value. No serious threats have been reported for the species and hence it is included in the category Least Concern. It is important for the germplasm which has many resistant genes, and hence is collected and conserved in-situ and ex- situ in China.

Oryza rufipogon is a widely distributed tropical plant. It has been recorded in Asia (Afghanistan, Bangladesh, Cambodia, China, India, Indonesia, Iran, Iraq,

Korea, DPR, Republic of Korea, Laos, Malaysia, Myanmar, Nepal, Pakistan,

Philippines, Sri Lanka, Thailand, Vietnam), Africa (Egypt, Senegal, Swaziland,

Tanzania), North America (USA), Central America, South America (Brazil,

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Colombia, Ecuador, Guyana, Peru, Venezuela, Oceania), Australia (Australia,

Queensland, Papua New Guinea).

Native countries for Oryza rufipogon is native to these following countries:

Afghanistan; Australia; Bangladesh; Brazil; Cambodia; China (Guangdong, Guangxi,

Hunan, Jiangxi, Yunnan); Colombia; Ecuador; Egypt; Guyana; Hong Kong; India

(Andhra Pradesh, Assam, Bihar, Goa, Karnataka, Kerala, Madhya Pradesh,

Maharashtra, Orissa, Tamil Nadu, Uttar Pradesh, West Bengal); Indonesia (Irian

Jaya, Jawa, Kalimantan, Sulawesi); Iran, Islamic Republic of Iraq; Korea,

Democratic People's Republic of Korea, Republic of Lao People's Democratic

Republic; Malaysia; Myanmar; Nepal; Pakistan; Papua New Guinea; Peru;

Philippines; Senegal; Sri Lanka; Swaziland; Taiwan, Province of China; Tanzania,

United Republic of; Thailand; United States; Venezuela; Viet Nam.

The species is widely distributed and has invasive tendencies. The population trend is reported to be increasing. Oryza rufipogon grows in shallow water, irrigated fields, pools, ditches and sites with stagnant or slow, running water.

It occurs at altitudes from 0 to 1000 m and is suited to sites that support populations of CR. It is naturally found in terrestrial and freshwater swamp ecosystems.

Oryza rufipogon is perennial, tufted, and scrambling grass with nodal tillering; plant height variable (1-5 m) depending on the depth of water; panicles open; spikelets usually 4.5-10.6 mm long and 1.6-3.5 mm wide with awns usually 4-

10 cm long; anthers >3 mm reaching 7.4 mm long.

Oryza rufipogon were found growing in swamps, along river banks, irrigation canals and in or at margins of rice fields (Abdullah et al., 1991; Ngu et al.,

2010). However, this natural population Oryza rufipogon still can be found in

Peninsular Malaysia such as Seberang Perai of Pulau Pinang, Kedah, Kelantan and

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Terengganu. For Malaysia, this species can be found only in the northern part of

Peninsular Malaysia (Seberang Perai of Pulau Pinang, Kedah, Kelantan and

Terengganu), growing in swamps, along river banks, irrigation canals and in or at the margins of rice fields (Abdullah et al., 1991; Ngu et al., 2010). Oryza rufipogon is a perennial that lives in relatively a seasonal habitats and relies primarily on vegetative production; it is a short day plant that flowers near the end of the monsoon season

(October to March). It outcrosses at a much higher rate (7–56%) compared to Oryza sativa (1–2%) (Cao et al., 2007; Ngu et al., 2010) and has large, indehiscent and pendant anthers (Grillo et al., 2009; Ngu et al., 2010).

Since Oryza rufipogon is one of the most important gene pools for rice breeding, there is an urgent need for its conservation. The results of the present study on population structure of Oryza rufipogon can be helpful in designing methods for developing collection and conservation strategies for different populations of Oryza rufipogon in Malaysia (Ngu et al., 2010).

2.2.2.8 CR Varieties

Rice has been cultivated in China since ancient times and was introduced to

India before the time of the Greeks, and Chinese records of rice cultivation go back

4,000 years (IRRI website; Pearson Education website). Thus, the history of for rice a rather long one. To date, more than 117,000 types of rice

(cultivars) are kept in the International Rice Genebank at IRRI in the Philippines (see subsection [2.2.2.4] above).

In Peninsular Malaysia, at least forty cultivars have been recorded thus far by MARDI (MARDI 2011) as listed in Table 2.2 below.

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Table 2.2: in Peninsular Malaysia.

YEAR YEAR CR CR RELEASED RELEASED Malinja 1964 MR 81 1988 Mahsuri 1965 Pulut Hitam 9 PH9 1990 Ria (IR8) 1966 MR 103 1990 Bahagia 1968 MR 106 1990 Murni 1972 MR 123 1991 Masria Pulut 1972 MR 127 1991 Jaya (C4-63) 1973 MR 159 1995 Sri Malaysia I 1974 MR 167 1995 Pulut Malaysia I 1974 MR 185 1997 Sri Malaysia II 1974 MRQ 50 1999 Sekencang 1979 MR 211 1999 Setanjung 1979 MR 219 2001 Sekembang 1979 MR 220 2003 Kadaria 1981 Maswangi MRQ 74 2005 Pulut Siding 1981 MR 232 2006 Seberang 1984 MRM 16 2010 Manik 1984 MR220 CL1 2010 Muda 1984 MR220 CL2 2010 Makmur 1985 MR 253 2010 MR 84 1986 MR 263 2010

(Note: This table was constructed based on MARDI, 2011)

At present, majority of Peninsular Malaysia rice farmers are encouraged to use seeds of rice cultivars recommended by MARDI. However Chinese rice farmers in the Sekinchan area in Selangor prefer to use their own seed sources including those cultivars developed by selection and breeding conducted by these farmers.

Production from the Sekinchan paddy areas is usually higher compared to those areas using MARDI seeds. One such variety is the “Siraj” which is said to contribute about

200-300 % increase in rice yield.

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2.2.2.9 Yield of Malaysian (MARDI) Rice Cultivars

Table 2.3: Malaysia rice cultivars.

CR YIELD (kg/hectare) YEAR RELEASED JAYA 3500-5000 1973 MR1 (Setanjung) 4100-6000 1979 Kadaria 2900-5000 1981 MR 52 (Manik) 4000-5000 1984 MR 71 (Muda) 5000-5500 1984 MR 77 (Seberang) 5000-5500 1984 MR 73 (Makmur) 5500-6500 1985 MR 84 4057-6235 1986 MR 81 4200-6000 1989 MR 106 4500-7100 1990 PH 9 (Pulut hitam) 3800-4700 1990 MR 127 4831-7245 1991 MR 159 3500-5400 1995 MR 167 4000-6000 1995 MR 211 6000-9000 1999 MRQ 50 3500-4500 1999 MR 219 7000-10000 2001 MR 220 7000-10000 2003 MRQ 74 (Maswangi) 4500-5500 2005 MR 232 7000-10000 2006 MR 220 CL1 5740-9140 2009 MR 220 CL2 5840-9740 2009 MR253 5600-7000 2010 MR263 5500-7000 2010

(Note: Cultivars in bold are used in this study, compiled from information gathered from MARDI website).

2.2.2.10 General Statistics on Rice Industry in Malaysia

At present, nearly 690,000 hectare are currently under rice cultivation in

2011 in Malaysia (Department of Agriculture; Department of Statistics Malaysia).

Nearly 520,000 hectare are in Peninsular Malaysia which contribute to about 2.2 million tonnes of rice in 2001 (Department of Agriculture).

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For rice production in rice scheme areas with granaries, a total of nearly

390,000 hectare are under rice cultivation in 2011 with rice production is in the range of about 1.6 million tonnes to nearly 1.9 million tonnes from 2007 to 2011

(Department of Agriculture).

In terms of acreages, the area under rice cultivation for Malaysia does not show marked increase over the years. In 1970 rice cultivation covered about 533,400 hectare and in 2011 it covers about 690,000 hectare (Department of Statistics

Malaysia) showing about 30 % increase in over 40 years.

2.3 WR Phenomenon in Peninsular Malaysia

According to Azmi and Karim (2008) WR has been known to become a menace to the rice crop in Peninsular Malaysia since 1988. According to Azmi and

Baki (2007), on average about 10 % of the Muda rice scheme area was infected by

WR. Based on personal observation, about 5 to 50 % (in terms of area) of the rice field in the Muda rice scheme are infected by WR.

Outcrossing between WR and CR is said to have occurred in various rice cultivated areas in the granary schemes all over Malaysia (Abdullah et al., 1996;

Vaughan et al., 1995; Chin, 2001; Shakirin, 2009; Baki and Shakirin, 2010;

Zainuddin et al., 2010). This has led to the emergence of various new types of WR in rice field in Peninsular Malaysia. According to Watanabe et al. (2000), the WR has different genetic makeups for different areas meaning that they are part of the rice gene-pools of those specific areas and thus confined within such areas. At present, the in-depth study on WR is lacking in Peninsular Malaysia.

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2.3.1 Characteristics of WR

2.3.1.1 Morphological and Anatomical Characters

WR (weedy variety of Oryza sativa) some what resembles CR but with some minor observable differences. WR tends to be slightly more hardy and sometimes relatively taller than CR, and its internodes are relatively (slightly) longer.

A characteristic of WR is the presence of anthocyanin pigment in various parts of the plant including collar, ligule, grain apiculus, stigma and awns as mentioned by Azmi and Karim (2008). Awned WR has longer epidermal hairs (Zainal, 2008). The abaxial epidermis contains a higher number of stomata than the adaxial epidermis

(Arrieta-Espinoza et al., 2005; Zainal, 2008)

Baki et al. (2000) construed that the differences among the variants of WR could be determined based on the shape of fruit stalks (either compact or otherwise), the presence of reddish purple pigmentation, and the hairy characteristics of the seeds. In addition, differences in the length of rice stalks, the number of spikelets and empty seeds were also noted to occur from variant to variant. The name “Red Rice” as for some species and varieties is due to the pigmentation.

There are four important characters for WR in general; plant height, pigmented grain, easy shattering, and long awn. WR can occur as ecotypes depending on its environment and its morphological features are somewhat comparable to that of CR varieties from the seedling to the reproductive stage

(Zainal, 2008). According to Baki et al. (2000), most farmers in Peninsular Malaysia are able to differentiate WR from CR based on morphological characteristics.

In general, WR can be distinguished from rice cultivars in terms of height

(Zainal, 2008). Azmi and Baki (1995) studied several variants of WR from 18 different locations and it was discovered that some of the characteristic differences

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