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Investigations of Self-Incompatibility (SI) in Perennial Ryegrass (Lolium Perenne L.)

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Investigations of Self-Incompatibility (SI) in Perennial Ryegrass (Lolium Perenne L.) Investigations of self-incompatibility (SI) in perennial ryegrass (Lolium perenne L.) by Bicheng Yang A thesis submitted to The University of Birmingham for the degree of DOCTOR OF PHILOSOPHY School of Biosciences The University of Birmingham August 2009 1 University of Birmingham Research Archive e-theses repository This unpublished thesis/dissertation is copyright of the author and/or third parties. The intellectual property rights of the author or third parties in respect of this work are as defined by The Copyright Designs and Patents Act 1988 or as modified by any successor legislation. Any use made of information contained in this thesis/dissertation must be in accordance with that legislation and must be properly acknowledged. Further distribution or reproduction in any format is prohibited without the permission of the copyright holder. Abstract Perennial ryegrass (Lolium perenne L.) is one of the most economically and environmentally important grass species for the temperate zone. It maintains effective self-incompatibility (SI), which promotes outbreeding as well as limits the efficient production of inbred lines and hybrids. SI in L. perenne is controlled by the S and Z loci, mapping to linkage groups 1 and 2, respectively. None of the gene products has been identified so far. Comparative mapping has identified regions on rice chromosomes 5 (R5) and 4 with synteny to regions of L. perenne genome containing the S and Z loci, respectively. Markers were developed from the syntenic rice genomic region to refine the S and Z maps. The closest flanking markers had a map distance of 2 cM from S and 0.2 cM from Z. SI cDNA libraries were developed from in-vitro pollinated stigma subtracted with unpollinated stigma to identify SI components and SI response related genes. Through a BLAST search, candidates identified from the SI libraries that were orthologous to sequences on the S and Z flanking regions on rice R4 and R5 were the prime candidate SI genes. Altogether ten SI candidate genes were identified with incompatible response associated differentially expression pattern: a rapid increase in expression within two minutes after pollen-stigma contact and reaching a maximum between 2-10 minutes, implying their roles in the SI response. Attempts were carried out to determine the linkage relationships between the identified candidates and the S or Z loci. Large fine scale mapping populations were developed individually for the S and Z loci to generate high resolution maps of S and Z towards map-based cloning. Tightly linked markers were identified mapping at a distance of 1.4 cM from S and 0.9 cM from Z. The studies performed in this project have implications on both the underlying genetic control and the associated biochemical responses involved in L. perenne SI. The closely linked markers for S or Z could be applied in future marker assisted selection breeding programmes and map-based cloning. 2 Dedication This thesis is dedicated to my dearest parents, who give me endless love and support throughout my life. It is dedicated to my grandmother and grandparents, whose care and encouragement I am always indebted. It is also dedicated to my departed grandfather, whose love and trust is my forever inspiration. 3 Acknowledgements I would like to thank Teagasc (Ireland) for the Walsh fellowship, which provided me the possibility of undertaking this project. I would like to thank my supervisors Dr Susanne Barth (Teagasc), Dr Danny Thorogood (IBERS, Aberystwyth), Dr Ian Armstead (IBERS) and Professor Chris Franklin (University of Birmingham, UK), for their guidance and support during this project. I would also like to thank Dr Stephen Byrne (Teagasc) for all his advice. I would like to thank all the summer students who helped with the field work, DNA extraction and other lab works. I would like to thank all my friends in Teagasc Oak Park Crops Research Centre for providing a friendly and encouraging working environment. Especially thanks to my dear friends Kerstin Diekmann, Ulrike Anhalt and Celine Tomaszewski, for being my ‘family’, sharing thoughts and feelings, and making my life in Ireland so convenient and enjoyable. Finally, I would like to thank all my family, specially my parents, for their encouragement and support during the time of this study. 4 Contents Abstract Dedication Acknowledgements Table of contents List of figures List of tables Chapters Appendix List of references List of definitions and abbreviations 5 Table of contents CHAPTER 1 INTRODUCTION 1 1.1 General introduction 2 1.2 Introduction to self-incompatibility 3 1.3 Physiological features of SI 7 1.4 Molecular genetics of SI 9 1.4.1 Sporophytic self-incompatibility 9 1.4.2 Gametophytic self-incompatibility 13 1.4.2.1 S-RNase mechanism 14 1.4.2.2 Self-incompatibility in Papaver 18 1.5 Self-incompatibility in grasses 20 1.5.1 Physiological features 21 1.5.2 Genetics of self-incompatibility in grasses 23 1.5.3 Self-incompatibility in ryegrass 26 CHAPTER 2 MATERIALS AND METHODS 29 2.1. Comparative genetics approach for marker development and candidate SI gene identification 30 2.1.1 Plant material 30 2.1.2 Marker development based on comparative genetics 30 2.1.3 Genetic mapping 31 2.1.4 Identification of possible gene duplications in the S and Z regions of the rice genome 31 2.1.5 Molecular marker analysis 32 2.1.6 Lolium BAC library screening and BAC sequencing 32 2.1.6.1 PCR-based screening 32 2.1.6.2 BAC clones rows x columns minipreps 33 2.1.6.3 BAC clone midipreps 34 2.1.7 BAC and PCR products sequencing 36 2.2 Construction of subtracted SI cDNA libraries 36 2.2.1 In-vitro pollination method 36 2.2.2 Plant material 37 2.2.3 Total RNA extraction 37 2.2.3.1 Isolation of total RNA 37 2.2.3.2 DNase 1 treatment of total RNA 38 6 2.2.4 PCR cDNA synthesis 39 2.2.5 cDNA Subtraction by suppression PCR 40 2.2.5.1 Adaptor ligation 40 2.2.5.2 Ligation efficiency test 41 2.2.5.3 First Hybridization 42 2.2.5.4 Second Hybridization 43 2.2.5.5 PCR amplification 44 2.2.5.6 Subtraction efficiency test 45 2.2.6 Cloning of subtracted cDNAs 46 2.2.6.1 Purification of amplified cDNAs 46 2.2.6.2 Cloning into pGEM®-T Easy Vector and transformation 47 2.2.7 Differential screening of clones 48 2.2.7.1 cDNA insert analysis 48 2.2.7.2 Preparation of cDNA dot blots 49 2.2.7.3 Probe labelling and differential screening 49 2.2.8 DNA sequence analysis 50 2.2.9 Reverse transcriptase PCR 51 2.2.10 Full length cDNA amplification by rapid amplification of cDNA ends (RACE) 52 2.3 Real-time PCR analysis of candidate SI genes identified in the SI cDNA libraries 52 2.3.1 Plant materials and cDNA preparation 52 2.3.2 Primer design 53 2.3.3 Primer optimization 54 2.3.4 Quantitative Real-time PCR analysis 55 2.3.4.1 Real-time PCR assay 55 2.3.4.2 Determination of PCR amplification efficiency 55 2.3.4.3 Evaluation of normalization with reference genes 56 2.3.4.4 Calculation of relative quantities 57 2.4 Development of fine mapping populations for identification of tightly linked markers for the S and Z loci 57 2.4.1 Plant material 57 2.4.2 Genomic DNA preparation 58 2.4.2.1 CTAB method 58 2.4.2.2 Isolation of genomic DNA using the MagAttract 96 DNA plant kit with a robotic system 59 2.4.3 SSR markers analysis 61 2.4.4 Development of mapping markers 66 2.4.5 Linkage analysis 68 7 CHAPTER 3 COMPARATIVE MAPPING AND THE IDENTIFICATION OF CANDIDATE GENES FOR THE S AND Z LOCI 70 3.1 Introduction 71 3.1.1 Comparative genetics in the ‘Crop Circle’ 71 3.1.2 Comparative genetics in Lolium 72 3.1.3 ILGI mapping population of Lolium perenne 76 3.1.4 Aim of the study 77 3.2 Results and Discussion 78 3.2.1 Development and mapping of STS markers 78 3.2.2 Identification of a candidate SI gene 83 3.2.3 Lolium BAC library screening for SI candidate genes 89 CHAPTER 4 DEVELOPMENT OF SUBTRACTED SI cDNA LIBRARIES AND IDENTIFICATION OF DIFFERENTIALLY EXPRESSED GENES 91 4.1 Introduction 92 4.1.1 cDNA-AFLP technique 93 4.1.2 Suppression subtractive hybridization 94 4.1.2.1 Molecular basis of SSH 95 4.1.2.2 Differential screening 98 4.1.3 Confirmation of differential screening results 99 4.1.4 Aims 99 4.2 Results 100 4.2.1 Construction of SSH cDNA libraries 100 4.2.1.1 Development of SI SSH libraries 100 4.2.1.2 Differential screening and candidate sequence analysis 102 4.2.2 Pollen specific library 105 4.2.3 Library comparison for gene function analysis 106 4.2.3.1 Pollen-pistil interaction related genes 106 4.2.3.2 Stigma development related genes 109 4.2.3.3 Comparative genetics as a screen to select SI component candidates 110 4.2.4 Expression analysis of SI candidates with reverse transcriptase PCR 114 4.2.5 Gene structure analysis with full length cDNA sequence 116 4.3 Discussion 118 4.3.1 Pollen-pistil interaction related genes 120 4.3.2 Stigma development related genes 122 4.3.3 Involvement of protein kinases in Lolium SI response 123 8 4.3.4 Involvement of Ca2+ in SI responses 124 CHAPTER 5 EXPRESSION PATTERN ANALYSIS OF THE IDENTIFIED SI CANDIDATE GENES WITH REAL-TIME PCR 错误！未定义书签。 5.1 Introduction 128 5.1.1 Real-time PCR vs traditional PCR 129 5.1.2 Reverse Transcription 129 5.1.3 Detection of amplified products 130 5.1.4 Normalisation with reference genes 132 5.1.5 Quantification methods 133 5.1.6 Real-time RT-PCR data analysis 134 5.1.7 Aims 135 5.2 Results 135 5.2.1 Optimization of the annealing temperature for each primer pair 135 5.2.2 Determination of PCR amplification efficiency 136 5.2.3 Evaluation of reference genes 137 5.2.4 Relative quantification for expression pattern analysis 140 5.2.4.1 Expression pattern in a pollination time course 140 5.2.4.2 Differential expression between candidate genes 144 5.3.
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