香蕉為台灣最具經濟重要性之果樹，自五零年代起每年均穩定外銷創造可觀之產值。香蕉之栽培容易受到各種病害的危害，導致產量與品質的損失。特別是幾種能夠造成系統性感染之病害，包括鐮刀菌引起之黃葉病及幾種病毒病害，會藉由帶病親本垂直感染，防治難度高，對香蕉之栽培威脅最大。已知的病毒病害中香蕉萎縮病毒（Banana bunchy top virus, BBTV）、胡瓜嵌紋病毒（Cucumber mosaic virus, CMV）及香蕉苞葉嵌紋病毒（Banana bract mosaic virus, BBrMV）都可以藉由組織培養過程而全面垂直傳染至後代種苗，因此此等病害之防除必須在組培繁殖前檢定其種原，確認無病毒後方能進行複製繁殖。過去產業界通常利用傳統之 ELISA 或 PCR 技術執行香蕉病毒檢測，但因為有多重病毒感染之疑慮，必須分別進行多次單一病毒之檢測，時間與成本並不經濟。故本研究嘗試研發生物晶片檢測系統，期於單次檢測流程中即可完成多種病毒的檢測，以節省成本提升檢測效率。本研究室已完成 CMV 與 potyvirus 之生物晶片檢測系統，本研究將針對 BBTV 研發其生物晶片，並整合構築能夠同時檢測上述三種病毒之生物晶片系統。由於台灣尚未發生 BBrMV，故本研究目前所為之檢測試驗均以與 BBrMV 同屬 potyvirus 屬之蕪菁嵌紋病毒 （Turnip mosaic virus, TuMV）作為測試標的進行模擬，並且在設計 PCR 引子時乃以可廣效性增幅所有 potyviruses 之策略進行。目前測試結果已確認引子對 C511 可穩定檢測各種不同胡瓜嵌紋病毒分離株，獲得 511 bp 大小之 DNA 產物。而 P374 引子對則可穩定增幅至少 20 種不同的 potyviruses，獲得一個 374 bp 之增幅產物。針對 BBTV 則分別就其 DNA 1 與 DNA 3 基因區域分別設計 B313 及 B251 二組引子對，結果均證實分別可以獲得 313 bp 與 251 bp 之增幅產物。但後續針對上述 PCR 產物之序列，設計專一性探針並進行晶片雜合反應測試時，發現針對 B251 產物序列所設計的超過十組以上探針均因會產生非特異性雜合反應而不適合後續晶片系統之應用。但針對 313 bp 產物序列所設計之二組探針（B-pb-2 及 B-pb-3）則可產生理想之雜合反應。另外針對 CMV 與 BBrMV 之增幅產物則分別選出兩個專一性探針（Cpb-2 與 Ppb-ci2）可獲得理想的雜合反應。測試所選出的三組引子對證實可以組合成為多目標型（multiplex RT-PCR）增幅系統，且增幅之產物可以與所選出的各組探針產生專一性雜合反應，但不與非對應之探針發生非專一性雜合。且針對上述三種病毒單獨或複合感染之情況下，此一 multiplex 系統均能有效將單獨或複合感染病毒檢測出來。對於無病毒感染之健康香蕉或組培苗樣品均不產生非專一性增幅產物，或於晶片雜合反應中出現非專一性訊號。此一檢測系統除可應用於田間香蕉植株樣品之檢測外，也適用於組織培養苗之病毒檢測。面對台灣各地所採集之20株以上之不同 BBTV 與 CMV 病毒分離株，此系統亦均能獲得穩定無差異之檢測結果。由於 BBTV 屬於 DNA 病毒與 CMV 及 potyviruses 之 RNA 病毒不同。傳統上進行 此二病毒之多目標增幅時香蕉組織樣品必須分別以DNA 與 RNA 套組純化總量核酸，流程較為繁複且成本較高。本研究已證實應用過去文獻已報導之緩衝溶液與快速組織萃取流程，可適用於本檢測系統同時穩定檢測出 BBTV 及 CMV 兩種不同基因體病毒。此一簡速流程與傳統分別應用DNA 與 RNA 核酸純化套組以萃取全量核酸之病毒檢測結果並無差異。另外我們也發現利用一種商用磁珠套組亦可同時純化香蕉組織之全量 DNA 與RNA 樣品並且獲得無差異之多目標型病毒增幅與晶片探針雜合結果。經由此等全量核酸萃取流程，確實可在不影響最終晶片檢測的結果下，提升檢測效率降低成本。

Banana is ranked the most economically important fruit crops in Taiwan. It is exported consistently to foreign countries and evident output value has been created annually since 1950s. During cultivation, banana was always suffered to various diseases and resulted significant loss on yield and quality. Among the diseases that threaten banana’s cultivation, those causing systemic infection such as Panama and virus diseases are the most devastating ones due to the difficulty of control and easiness to transmit from infected mother plants to young progenies. Banana viruses include Cucumber mosaic virus (CMV), Banana bunchy top virus (BBTV) and Banana bract mosaic virus (BBrMV) can vertically infect all tissue culture propagated growing materials, therefore banana mother plants need to be indexed for virus infection before tissue culture cloning process. Traditionally banana industry applied ELISA or PCR-based techniques to detect banana viruses. Due to multiple virus infection possibility, banana mother stocks should separately indexed by different virus probes or techniques. This process is vital but time and labor consuming and also cost ineffective. The purpose of this research is to develop a biochip DNA microarray system that can detect all three banana viruses simultaneously so that the efficiency of virus indexing will be increased and therefore the cost can be reduced. Currently we have successfully designed and selected three pairs of PCR primers respectively specific to CMV, BBTV and BBrMV. Due to BBrMV is now considered as quarantine pest in Taiwan, its live cultures are not available for testing. Therefore, we took an approach by designing a Potyvirus genera specific PCR primer pair that could amplify at least more than 20 different potyvirus species, so that the amplification spectrum could theoretically cover BBrMV. During testing period, we consistently used another potyvirus, Turnip mosaic virus (TuMV), as model to test the feasibility of the detection system. Our result showed the primer pair, namely C511, could specifically amplify more than 10 CMV isolates collecting from different crops including banana and resulted a 511 bp PCR product. The primer pair, P374, could successfully amplify at least 20 different potyviruses and all producing a 374 bp amplicon. As for BBTV, we designed and selected two primer pair, i.e. B313 and B251, specific respectively to sequences in DNA 1 and 3 of the virus that could obtain respectively 313 bp and 251 bp PCR products. However in the next stage when oligonucleotide probes were designed to hybridize with their corresponding amplicon, more than 10 probes designed from the 251 bp amplicon sequences were unsuccessful for hybridization. Therefore, the further testing of BBTV detection by primer pair B251 was terminated. Fortunately, two probes, Bpb-2 and Bpb-3, designed for capturing the 313 bp amplicon were found highly dependable, therefore they were chosen to combine with another two oligonucleotide probes (Cpb-2 and Ppb-ci2) specific respectively to CMV and BBrMV into an integrated DNA microarray system to hybridize with PCR products amplified by multiplex primer pairs of C511, P374 and B313 mixture. Our result showed that these four selected oligo-probes when immobilized on biochip could consistently react with its corresponding amplicon specifically and gave no non-specific signals against each other. Using this multiplex detection microarray system, we were able to demonstrate either single or mixed infection of these three banana viruses could consistently be detected and differentiated. Not only field collected banana plants but also small plantlets during tissue culture stage could be used as targets in this detection system. Moreover, the system is highly specific that no signal was resulted in reaction to healthy uninfected banana plant samples and tissue cultured plantlets. In this study we have tested more than twenty isolates each of BBTV and CMV and found all isolates were uniformly detected by the system. Furthermore, due to BBTV is a DNA virus different from the RNA genome of CMV and BBrMV, the preparation of total nucleic acids from sample tissue in the first step of PCR reaction is traditionally different. In the beginning of our experiment, we always applied separate commercial DNA or RNA nucleic acid purification kits to extract DNA from BBTV and RNAs from CMV or BBrMV infected tissues. These separate procedures were apparently costly and labor intensive. In order to reduce the cost and increase efficiency, we tested the possibility of using a literature cited buffer and extraction protocol for quick extraction of both RNA and DNA from plant tissue before PCR amplification. The result indicated that the same buffer and extraction procedure was feasible in our multiplex banana virus detection system as a one-step total nucleic acid extraction before PCR. We also found that a commercial total nucleic acid (DNA plus RNA) purification system using magnetic beads could also be applied in our detection system for one-step nucleic acid extraction. There was no difference found in the final biochip result between either the two quick extraction systems or those traditional extraction protocols.

目錄
書名頁
碩士論文授權書
論文口試委員審定書（中文版）
論文口試委員審定書（英文版）
中文摘要 I
英文摘要 IV
誌謝 VII
表目錄 IX
圖目錄 X
目錄 XIII
壹、緒論 1
貳、前人研究 5
一、感染香蕉植物之病毒種類 5
（一）香蕉萎縮病（Banana bunchy top disease） 5
（二）香蕉嵌紋病（Banana mosaic disease） 12
（三）香蕉條紋病（Banana streak disease） 17
（四）香蕉苞葉嵌紋病（Banana bract mosaic disease） 21
二、生物晶片檢測系統 24
（一）生物晶片定義與類型 24
（二）生物晶片於植物病毒檢測發展與應用 26
（三）香蕉病毒檢測用生物晶片構築策略 27
參、材料與方法 29
一、罹病香蕉植株樣品來源，採集與保存方法 29
（一）田間樣品 29
（二）組織培養苗 29
二、香蕉病毒之檢測 31
（一）總量核酸之萃取 31
（二）專一性引子對之設計與 multiplex RT-PCR 系統之構築 35
（三）瓊脂電泳分析 38
（四）PCR 產物之分析與選殖 39
（五）生物晶片系統 45
（六）晶片檢測 49
肆、結果 51
一、香蕉組織培養苗之建立 51
（一）感染 BBTV 之香蕉組培苗 51
（二）感染 CMV 之香蕉組培苗 51
（三）無病毒感染之香蕉組培苗 52
二、PCR 引子對之設計與 multiplex RT-PCR 系統 52
（一）針對 BBTV DNA 3 區域設計引子對之增幅反應 52
（二）針對 BBTV DNA 1 序列區域設計引子對之增幅反應 54
（三）引子對 B251、B313 測試 56
（四）CMV 專一性引子對檢測 56
（五）Potyvirus 廣效性引子對檢測 57
（六）Multiplex RT-PCR 系統檢測 58
三、生物晶片雜合反應 59
（一）BBTV-PCR 產物之晶片雜合反應 59
（二）CMV-PCR 產物之晶片雜合反應 60
（三）Potyvirus-PCR 產物之晶片雜合反應 60
（四）三種香蕉病毒檢測用晶片之雜合反應系統整合 60
四、香蕉樣品組織之總量核酸萃取方式之比較 61
（一）快速萃取加熱法 61
（二）比較快速萃取加熱、商用磁珠與試劑套組三種不同總量核酸萃取方式之檢測結果 62
五、組織培養苗之晶片檢測 62
（一）感染 BBTV 之組培苗晶片檢測 62
（二）感染 CMV 之組培苗晶片檢測 63
伍、討論 64
陸、參考文獻 73
表、 97
圖、 106

表目錄

表一、 本研究所使用誘導香蕉組織培養苗之培養基配方………….. 97
表二、 本研究利用 P374 廣效性引子對所檢測 20 種不同的 potyviruses，其病毒名之縮寫、全名………………….……… 98
表三、 香蕉萎縮病毒（Banana bunch top virus, BBTV）朝陽分離株（CY1）之鞘蛋白基因之核苷酸與胺基酸序列與 NCBI GenBank 上已登錄之 17 項相關 BBTV 序列比對相同度之結果………………………………………………………….. 99
表四、 利用引子對 B251 增幅香蕉萎縮病毒（Banana bunch top virus, BBTV）所獲得之 251 bp 產物之核苷酸序列與 NCBI GenBank 中所登錄之BBTV DNA 3 序列進行比對之結果... 100
表五、 香蕉萎縮病毒（Banana bunch top virus, BBTV）朝陽分離株（CY2）之 replication initiation protein 基因之核苷酸與胺基酸與 NCBI GenBank 上已登錄之 16 項相關 BBTV 序列比對相同度之結果………………………………………….. 101
表六、 利用引子對 B313 增幅香蕉萎縮病毒（Banana bunch top virus, BBTV）CY2朝陽分離株所獲得 313 bp 產物之核苷酸序列與 NCBI GenBank 中所登錄之 BBTV DNA 1 相對應序列進行比對之結果……………………………………….. 102
表七、 對應胡瓜嵌紋病毒（Cucumber mosaic virus, CMV）專一性引子對C511所增幅之核苷酸序列與 GenBank 中所登錄之 15 種不同來源 CMV 分離株之相對應序列之相同度比較... 103
表八、 利用potyvirus廣效性引子對（P374）增幅蕪菁嵌紋病毒（Turnip mosaic virus, TuMV）所獲之序列與GenBank中登錄之20 種不同來源potyviruses之相對應序列之相同度比較……………………………………………………………….. 104
表九、 本研究所設計與使用的寡核苷酸探針種類及其序列……….. 105


圖目錄

圖一、 田間感染香蕉萎縮病毒（Banana bunch top virus, BBTV）之香蕉植株外觀與葉片病徵圖………………………………….. 106
圖二、 田間感染胡瓜嵌紋病毒（Cucumber mosaic virus, CMV） 之香蕉植株外觀與葉片病徵圖……………………………...... 107
圖三、 本研究所使用之生物晶片檢測原理圖解…………………….. 108
圖四、 感染病毒與健康無病毒香蕉組織培養苗不同階段之發育情形………………………………………...................................... 109
圖五、 對應胡瓜嵌紋病毒（Cucumber mosaic virus, CMV）之專一性引子對 C511，其增幅 CMV 基因體 RNA 3 之序列範圍圖示…………………………………………………………….. 111
圖六、 利用胡瓜嵌紋病毒（Cucumber mosaic virus, CMV）專一性引子對 C511 針對 8 個感染 CMV 之樣品進行 RT-PCR 檢測之電泳分析結果………………………………………….. 112
圖七、 對應蕪菁嵌紋病毒（Turnip mosaic virus, TuMV）之廣效性引子對 P374，其增幅 potyvirus 基因體 cylindrical inclusion（CI）protein gene之相對應序列範圍圖示…………………. 113
圖八、 利用過去本實驗室所設計之馬鈴薯 Y 屬病毒 Potyvirus 廣效性引子對（P374）針對 20 個不同種 potyviruses 樣品進行檢測之電泳分析結果……………………………………….. 114
圖九、 利用對應香蕉萎縮病毒（Banana bunch top virus, BBTV）全長鞘蛋白基因之引子對（BBTV-up/dw）進行病毒PCR 增幅獲得 1023 bp 產物之結果……………………………….. 116
圖十、 利用引子對 BBTV-up/dw 增幅香蕉萎縮病毒（Banana bunch top virus, BBTV）所獲得 1023 bp 產物之定序結果…. 117
圖十一、 針對香蕉萎縮病毒（Banana bunch top virus, BBTV）鞘蛋白基因區域內設計三組專一性 PCR 增幅引子對，所增幅之相關區域與產物大小圖解……………………………….. 118
圖十二、 利用電泳分析經B167、B461及B251 引子對檢測香蕉萎縮病毒（Banana bunch top virus, BBTV）之結果……..…. 119
圖十三、 利用引子對 B251 增幅香蕉萎縮病毒（Banana bunch top virus, BBTV）所獲得 251 bp 產物之定序結果…………… 121
圖十四、 利用 B861 引子對檢測香蕉萎縮病毒（Banana bunch top virus, BBTV）之電泳分析結果…………………………...… 122
圖十五、 利用 B861 引子對增幅香蕉萎縮病毒（Banana bunch top virus, BBTV之replication initiation protein gene所獲產物之定序結果………………………………………………….. 123
圖十六、 針對香蕉萎縮病毒（Banana bunch top virus, BBTV）replication initiation protein 基因區域內設計專一性 PCR 增幅引子對B313，所增幅之相關區域與產物大小圖解…... 124
圖十七、 利用針對香蕉萎縮病毒（Banana bunch top virus, BBTV）DNA 1之replication initiation protein 基因區域所設計之 B313 引子對進行PCR 檢測田間香蕉感病樣品之電泳分析結果……………………………………………………….. 125
圖十八、 利用香蕉萎縮病毒（Banana bunch top virus, BBTV）專一性引子對 B313 針對 18 個來自不同地區之BBTV感染樣品進行PCR檢測之電泳分析結果………………………. 126
圖十九、 利用設計之引子對 B251 與 B313 針對香蕉萎縮病毒（Banana bunch top virus, BBTV）病株不同葉片部位進行PCR檢測之結果……………………………………….……. 128
圖二十、 利用兩組香蕉萎縮病毒（Banana bunch top virus, BBTV）專一性引子對 （B251 及 B313） 所整合之多目標型 PCR系統檢測田間感病香蕉樣品之電泳分析結果……….. 129
圖二十一、 利用胡瓜嵌紋病毒（Cucumber mosaic virus, CMV）專一性引子對 C511 進行 RT-PCR 檢測香蕉樣品之電泳分析結果……………………………………………….. 130
圖二十二、 利用過去本實驗室所設計之馬鈴薯 Y 屬病毒 Potyvirus 廣效性引子對（P374）模擬檢測感染於香蕉之蕪菁嵌紋病毒（Turnip mosaic virus, TuMV）之電泳分析結果………………………………………………….. 131
圖二十三、 利用 C511、P374、B313 三組引子對所整合而成之多目標型 RT-PCR系統檢測三種不同香蕉病毒組合之電泳分析結果…………………………………………….. 132
圖二十四、 針對香蕉萎縮病毒（Banana bunch top virus, BBTV）以 B251 引子對所增幅之序列區域，設計 14 組寡核苷酸探針（編號2-15）進行雜合反應之測試結果…………. 134
圖二十五、 不同香蕉萎縮病毒（Banana bunch top virus, BBTV）經B313 引子對增幅之產物以B-pb-2和B-pb-3探針進行晶片雜合反應之結果…………………………………….. 135
圖二十六、 胡瓜嵌紋病毒（Cucumber mosaic virus, CMV）以C511 引子對進行RT-PCR 所增幅產物以 Cpb-2 探針進行晶片雜合反應之結果…………………………………….. 137
圖二十七、 不同馬鈴薯Y屬病毒經P374廣效性引子對所增幅之產物與 Ppb-ci2 探針進行晶片雜合反應之結果…………. 138
圖二十八、 利用可同時檢測三種香蕉病毒包括胡瓜嵌紋病毒（CMV）、蕪菁嵌紋病毒（TuMV）及香蕉萎縮病毒（BBTV）之多目標型晶片病毒檢測系統模擬測試單獨與複合感染不同病毒樣品之結果……………………….. 140
圖二十九、 香蕉病毒整合型生物晶片系統檢測靈敏度測試之結果.. 142
圖三十、 比較利用快速萃取加熱法及傳統試劑套組萃取法萃取植物組織內總量核酸，再以 RT-PCR 檢測三種感染香蕉之胡瓜嵌紋病毒（CMV）、蕪菁嵌紋病毒（TuMV）及香蕉萎縮病毒（BBTV）之電泳分析結果……………………… 144
圖三十一、 田間複合感染胡瓜嵌紋病毒（Cucumber mosaic virus, CMV）與香蕉萎縮病毒（Banana bunch top virus, BBTV）之香蕉植株……………………………………………….. 146
圖三十二、 三種總量核酸萃取法應用於香蕉病毒晶片檢測系統之比較……………………………………………………….. 147
圖三十三、 利用香蕉病毒晶片系統檢測感染香蕉萎縮病毒（BBTV）之香蕉組培苗之結果…………………………. 149
圖三十四、 利用香蕉病毒晶片系統檢測感染胡瓜嵌紋病毒（CMV）之香蕉組培苗之結果…………………………………….. 151

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