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研究生:曾意雯
研究生(外文):Yi-Wen Tseng
論文名稱:建立利用PTGS及TGS與CRISPR/Cas9系統抗番茄黃化捲葉泰國病毒與番茄捲葉台灣病毒之轉基因抗病植物暨台灣新病毒與植物菌質體病害之鑑定
論文名稱(外文):Development of crops with broader resistance against begmoviruses, TYLCTHV and ToLCTV, via PTGS combined with TGS and CRISPR/Cas9 systems, and identification of new virus and phytoplasma diseases in Taiwan
指導教授:詹富智
指導教授(外文):Fuh-Jyh Jan
口試委員:蔡文錫王惠亮張宗仁陳煜焜
口試日期:2023-07-31
學位類別:博士
校院名稱:國立中興大學
系所名稱:植物病理學系所
學門:農業科學學門
學類:植物保護學類
論文種類:學術論文
論文出版年:2023
畢業學年度:111
語文別:英文
論文頁數:181
中文關鍵詞:基因靜默CRISPR/Cas9豆金黃嵌紋病毒屬番茄捲葉泰國病毒番茄捲葉臺灣病毒假馬鞭番茄捲葉宿霧病毒咸豐草斑紋病毒軟枝黃蟬嵌紋病毒植物菌質體
外文關鍵詞:gene silencingCRISPR/Cas9BegomovirusTYLCTHVToLCTVStachytarpheta jamaicensisToLCCeVBiMoVAllaMVphytoplasma
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番茄捲葉泰國病毒 (tomato yellow leaf curl Thailand virus, TYLCTHV) 與番茄捲葉臺灣病毒 (tomato leaf curl Taiwan virus, ToLCTV) 為番茄栽種上的限制因子。因豆金黃嵌紋病毒屬 (Begomovirus) 病毒常發生基因重組與變異,對於此屬病毒病害難以傳統育種的方式進行防治。於前人研究分析ToLCTV全基因體序列的抗病研究結果發現,在其基因間區段 (intergenic region; IR)、C2C3基因重疊區域 (C2C3 overlapping) 及C1基因3'端的序列片段可觸發較高的轉錄後基因沉寂機制 (PTGS) 提供植物抗性。為了提供轉基因植物對此兩種DNA 病毒之抗性,擬將以基因靜默的方式與CRISPR/Cas (clustered regularly interspaced short palindromic repeats/CRISPR-associated proteins) 系統應用於抗病植株的生產與抗病能力的分析。在基因靜默抗病的系統,利用TYLCTHV的IR序列構築成髮夾結構 (hairpin) 插入內含子 (intron) 的序列中,利用mRNA修飾時內含子被剪切 (splicing) 的機制,將hairpin IR留在細胞核中誘發TGS導致病毒DNA甲基化 (methylation) 並選序列保留性較高的AC1-AC2-AC3及TSWV之L基因片段連結於內含子之上下游,經RNA修飾後,AC1-AC2-AC3與TSWV之L基因的嵌合體片段可送至細胞質誘發PTGS。抗病評估結果顯示,以SeRDR1 intron 3建立之系統抗病效果最佳,且以亞硫酸鹽定序之方式分析轉基因植物中DNA甲基化的情形,發現在抗病株系中IR區域發生DNA甲基化之情形比感病株系來得高,且多集中於能形成雙股結構之序列上,顯示此構築可進行TGS抗病,而此連結多個病毒基因片段的系統,可提供植物抗多種病毒的能力。另外在CRISPR/Cas9抗病研究的部分,總共建立了6個單一gRNA與2個連結多個gRNA的構築並進行抗病能力的評估,在抗性分析結果顯示,兩個連結多個gRNA的構築可提供菸草與番茄較高的抗病能力,在indel分析也可看到對於兩個目標病毒的基因片段上進行了突變。此外,本研究進行了在假馬鞭上三種新興病毒 (番茄捲葉宿霧病毒、咸豐草斑紋病毒與軟枝黃蟬嵌紋病毒) 病害與植物菌質體在四種不同植物 (長梗紫麻、木藍、七里香與菊花) 上造成病害的鑑定,而這些病原可能對於這些作物與其相關產業具有潛在的危害。
Tomato yellow leaf curl Thailand virus (TYLCTHV) and tomato leaf curl Taiwan virus (ToLCTV) are the major barriers to the tomato industry in Taiwan. Since high frequency of interspecies recombination and mutation of begomoviruses, it is difficult to control the diseases via traditional breeding methods. Previous studies reported that intergenic region (IR), C2C3 gene overlapping, and 3'-end of C1 gene of ToLCTV could be targeted to induce viral resistance in transgenic plants via post-transcriptional gene silencing (PTGS). In order to generate stable resistant plants against the two begomoviruses, simultaneously induce both transcriptional gene silencing (TGS) and PTGS strategy and the genome editing method, CRISPR/Cas9, were used and the resistance of the generated plants was evaluated in this study. In the PTGS combined with TGS resistant strategy, the SeRDR1 intron 3 gave better splicing activity and more siRNA accumulation. In the bisulfite sequencing analysis, it showed that the high level of DNA methylation on IR region is associated with the TYLCTHV resistance in the transgenic plants, indicating the resistance is mediated through TGS. The results showed promise for the development of resistance against multiple plant viruses, e.g., TYLCTHV, TSWV, and ToLCTV. In the genome editing method, via CRISPR/Cas9, 8 constructs were constructed, including 6 single guide RNAs (sgRNAs) and 2 multiplex gRNAs so far. After being challenged with the target begomoviruses, the transgenic tobacco and tomato, respectively, the results revealed that CRISPR/Cas9 systems could target viral genome and introduce mutations within the target sequence of viral genome to reduce the symptoms severity caused by TYLCTHV and ToLCTV. Especially the two multiple-linking gRNA constructs that promote and allow plants to establish better and sufficient tolerance against the begomoviruses. Furthermore, in this study, three viruses, i.e., tomato leaf curl Cebu virus (ToLCCeV), bidens mottle virus (BiMoV), and Allamanda mosaic virus (AllaMV) were identified on diseased Stachytarpheta jamaicensis and four phytoplasma-associated diseases on Oreocnide pedunculate, Indigofera suffruticosa, Murraya exotica, and Chrysanthemum morifolium plants were identified and classified in Taiwan. Those viruses and phytoplasmas may potentially become a threat to other related crops and industries in Taiwan.
Abbreviations i
摘要 iii
Abstract v
Contents vii
Table contents xii
Figure contents xiv
Chapter 1. Introduction literature review 1
The importance of tomato and the pathogens 2
The characteristic and economical importance of Begomovirus 2
Tomato-infecting begomoviruses in Taiwan 3
Management of viral pathogen on plants 4
Transgenic resistance strategy to the viral diseases 5
(1) Pathogen-derived resistance to tomato leaf curl disease 5
1. Protein-mediated resistance 5
2. RNA-mediated resistance 6
(2) Genome editing strategy to develop plants that can resist virus infection 8
1. Introduction of CRISPR/Cas9 8
2. CRISPR/Cas9-mediated viral interference in plants 9
Characterization of phytoplasmas and their transmission manners 10
Phytoplasma diseases in Taiwan 10
Control of phytoplasmas and their vectors 11
Objectives 12
References 13
Chapter 2. Development and evaluation of tomato resistance to tomato yellow leaf curl Thailand virus, tomato spotted wilt virus, and tomato leaf curl Taiwan virus using gene interference strategies, PTGS and TGS 23
Abstract 24
Introduction 26
Characteristics of tomato yellow leaf curl Thailand virus (TYLCTHV) and tomato leaf curl Taiwan virus (ToLCTV) and their management 26
Characteristics of tomato spotted wilt virus and the control strategy 27
Transgenic resistance to TSWV 28
Transformation of marker-free transgenic plants system 29
Materials and Methods 31
Construction of multiple genes-linking vectors 31
Plant transformation and regeneration 31
(1) Tobacco transformation and regeneration 31
(2) Tomato transformation and regeneration 32
Screening for TYLCTHV, TSWV, and ToLCTV resistance 33
(1) Inoculation of TYLCTHV and ToLCTV 33
(2) Inoculation of TSWV 33
Total DNA extraction and virus detection 34
Total RNA extraction and reverse transcription-polymerase chain reaction (RT-PCR) 34
Progeny segregation analysis 35
DNA bisulfite analysis 35
Results 36
Establish the regenerated transgenic plants and the resistance evaluation 36
(1) Transgenic tobacco plants 36
(2) Transgenic tomato plants 37
Marker-free plants analysis 37
DNA bisulfite analysis 38
Discussion 38
References 43
Appendix 51
Chapter 3. Development of a broad viral resistance to two tomato-infecting begomoviruses, TYLCTHV and ToLCTV, through CRISPR/Cas9 68
Abstract 69
Introduction 70
The characteristics of Begomovirus 70
CRISPR/Cas9-mediated viral interference in plants 71
Materials and Methods 72
The putative sgRNA target site selection and the sgRNA vector construction 72
Construction of multiple sgRNA-linking vectors 72
Analysis of the resistance of each CRISPR/Cas9 construct by agrobacterium transient expression 72
Plant transformation 73
(1) Tobacco transformation and regeneration 73
(2) Tomato transformation and regeneration 74
Challenge the transgenic plants with viruses 75
Total RNA extraction and reverse transcription-polymerase chain reaction (RT-PCR) 75
Total DNA extraction and polymerase chain reaction (PCR) 76
Analysis of the viral accumulation in the transient expression plants 77
Mutation evaluation 77
Results 77
SgRNA target site selection and resistant efficiency of CRISPR/Cas9 constructs in transient assay 77
Construction of multiple sgRNA-linking vectors and their resistant efficiency in transient assay 78
Viruses interference assay on transgenic plants 79
(1) Analysis on transgenic tobacco plants 79
(2) Analysis on transgenic tomato plants 80
(3) Viruses interference assays of the progeny plants 80
Double strand breaks (DSB) and the indel analysis in the transgenic plants 81
Discussion 81
References 84
Appendix 89
Chapter 4. Identification and characterization of three novel viruses on Stachytarpheta jamaicensis 106
Abstract 107
Introduction 109
Stachytarpheta jamaicensis and the application 109
The reported pathogens on S. jamaicensis 109
Characteristics and criteria of Potyvirus 110
Characteristics and criteria of Begomovirus 111
Materials and Methods 113
Samples collection 113
Nuclei acid extraction 113
(1) Total DNA extraction 113
(2) Total RNA extraction 113
Reverse transcription-polymerase chain reaction (RT-PCR) and PCR amplification 114
Negative staining and transmission electronic microscope (TEM) operation 114
Infectious clone construction 115
Back inoculation by mechanical inoculation and agro-inoculation 115
(1) Mechanical inoculation 115
(2) Agro-inoculation 115
Virus purification and antiserum production 116
Western blotting 117
Results 117
Virus detection 117
Potyvirus isolation and back inoculation 119
Confirmation of the infectivity of ToLCCeV-stachy isolate infectious clones 120
Transmission electron microscopy observation 120
BiMoV-antiserum preparation and western blotting 120
Discussion 120
References 124
Appendix 130
Chapter 5. Identification and characterization of four phytoplasmas associated with plant diseases in Taiwan 135
Abstract 136
Introduction 138
Current phytoplasma taxonomy and classification based on the 16S ribosomal RNA (rRNA) gene (16Sr groups) 138
Available multilocus sequence analysis (MLSA) of phytoplasmas 138
(1) Ribosomal protein (rp) operon genes 138
(2) Tuf gene 139
(3) SecA gene 139
(4) SecY gene 139
Oreocnide pedunculate and the pathogens 140
Indigofera suffruticosa and the phytoplasma-associated diseases 141
Murraya excortica (orange jasmine) and the pathogens 141
Chrysanthemum morifolium and the pathogens 142
Materials and Methods 143
Occurrence, symptoms and plant sample collection 143
Nuclei acid extraction 143
Polymerase chain reaction (PCR) amplification of multilocus genes 144
(1) Nested PCR for 16S rRNA amplification 144
(2) SecY gene amplification 144
(3) Ribosomal protein (rpl23-rpl16) gene amplification 144
Sequence cloning and the sequence analysis of the amplicons 145
Identification and classification of phytoplasmas based on the 16S rDNA 145
Phylogenetic analyses on multilocus genes 146
Transmission electron microscopy (TEM) 146
Results 147
Plant total DNA extraction and the 16S rDNA analysis 147
Phylogenetic tree construction based on 16S rDNA 149
Multilocus genes analysis 150
Transmission electron microscopy (TEM) observation 151
Discussion 151
References 154
Appendix 162
Chapter 6. Conclusion 178
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Chapter 5
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