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研究生:陳昱齊
研究生(外文):Yu-Chi Chen
論文名稱:以抽穗期基因之序列多型性及表現變異進行臺灣原住民山地旱稻馴化之研究
論文名稱(外文):Domestication of Rice Land Races Collected in Taiwan Aboriginals Based on Sequence Polymorphism and Expression Variation of Heading Date Genes
指導教授:謝兆樞謝兆樞引用關係
指導教授(外文):Jaw-Shu Hsieh
學位類別:碩士
校院名稱:國立臺灣大學
系所名稱:農藝學研究所
學門:農業科學學門
學類:一般農業學類
論文種類:學術論文
論文出版年:2009
畢業學年度:97
語文別:中文
論文頁數:135
中文關鍵詞:水稻馴化抽穗期抽穗期基因山地品系序列分析TILLING
外文關鍵詞:Ricedomesticationheading dateheading date geneland raceDNA sequence analysisTILLING
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栽培稻 (Oryza sativa L.) 為亞洲主食之一,它為短日照植物,透過人類不斷選拔,造成適應溫帶或熱帶截然不同之氣候環境以及不同的栽培模式。過去經學者們藉由突變與染色體漫步方式方式找到許多與水稻抽穗期相關之基因,如本研究目標之六個水稻抽穗期基因,Heading date 3a (Hd3a) 基因、Heading date 1 (Hd1) 基因、Heading date 6 (Hd6) 基因、Photoperiodic sensitivity 5 (SE5) 基因、Early heading date 1 (Ehd1) 基因以及Early heading date 2 (Ehd2) 基因。
稻之抽穗期基因於自然界中存在許多變異,抽穗期日數上亦具有很大變異,本研究之材料為60種之臺灣山地旱稻品系,挑選其中抽穗期差異達60天之六個山地品系進行序列分析,發現Hd1、Hd3a、Hd6、Ehd1與Ehd2基因於序列上具有很多變異,並會造成胺基酸之改變甚或影響基因之表現,如Hd1基因之第一exon分別插入36 bp與123 bp,第二exon發現1901 bp之retrotransposon;Ehd2基因於第二intron發現具有長度變異之SSR (simple sequence repeats),以及諸多之SNP (single nucleotide polymorphism)等。
本實驗並進行TILLING (Targeting Induced Local Lesions in Genomes) 試驗,發現臺灣山地品系在此六個抽穗期基因具有極多之序列變異,分別存在於promoter、UTR、intron與exon上。日後可與其他地區之變異形式做一比較,並結合語言學、考古學與其他馴化基因之研究,或許可揭開臺灣水稻馴化史之神秘面紗。
Rice (Oryza sativa L.) is one of the major foods in Asia, and it is a short-day plant. During domestication by human selection had made it produced different adaption to the temperate or tropical climate zone and different cultivar types. Researchers had identified several genes responsible for heading date in rice through mutants and chromosome walking. Among those genes, Heading date 3a (Hd3a), Heading date 1 (Hd1), Heading date 6 (Hd6), Photoperiodic sensitivity 5 (SE5), Early heading date 1 (Ehd1), and Early heading date 2 (Ehd2) are the target genes in this study.
There are many natural variations in rice heading date gene sequences. In this study, six land races were selected from sixty rice land races collected from Taiwan aboriginals, with heading dates differed about sixty days.The study discovers many DNA sequence variations in these heading date genes among six land races, and some of them may result in amino acid variations. For instance, there are two types of insertions with 36 bp or 123 bp DNA fragments in the first exon of Hd1, and one type of insertions with the 1901bp (a retrotransposon) in the second exon of Hd1, in addition, many SNPs (single nucleotide polymorphism) were also observed.
In present study, TILLING (Targeting Induced Local Lesions in Genomes) analysis illustrates many variations in the six heading date related genes of the land races collected from Taiwan aboriginals. Those variations occur at the promoters, UTRs, introns and exons. In the future, we may compare the information with those obtained from land races in the nearby countries through international collaborations. Together with the efforts from archeologists and philologists, we should be able to reveal the rice cultivation of Taiwan during the pre-history period, including rice domestication.
誌謝 I

中文摘要 II

Abstract III

第一章、 前言 1

第二章、 研究目的 3

第三章、 前人研究 4
一、 水稻的馴化相關基因及過程 4
二、 抽穗時期對稻之分佈影響 6
三、 水稻抽穗期相關之數量性狀基因 7
四、 本論文研究之六個水稻抽穗期基因 8
(一)、 Heading date 3a (Hd3a) 8
(二)、 Heading date 1 (Hd1) 9
(三)、 Heading date 6 (Hd6) 10
(四)、 Photoperiodic sensitivity 5 (SE5) 11
(五)、 Early heading date 1 (Ehd1) 12
(六)、 Early heading date 2 (Ehd2) 14
五、 TILLING (Targeting Induced Local Lesions in Genomes) 16

第四章、 供試材料與研究方法大綱 17

第五章、 試驗方法 18
一、 植株材料種植方法 18
二、 群聚分析 (cluster analysis) 19
三、 序列分析 20
(一)、 序列分析之品系 20
(二)、 序列分析之抽穗期基因 20
(三)、 植株DNA之萃取 21
(四)、 Polymerase chain reaction反應 (PCR) 23
(五)、 PCR產物之純化 24
(六)、 進行次選殖,使用pGEM®-T Easy vector 24
(七)、 進行次選殖,使用CloneJET™ PCR Cloning Kit 26
(八)、 質體之抽取 27
(九)、 序列分析 27
四、 植株RNA之萃取 28
五、 RT-PCR 29
(一)、 cDNA合成 29
(二)、 PCR 29
六、 TILLING (Targeting Induced Local Lesions in Genomes) 31
(一)、 PCR 31
(二)、 CELⅠ酵素處理 32

第六章、 結果 33
一、 山地品系之外表型觀察 33
二、 山地品系抽穗期調查結果 34
三、 山地品系與栽培種以分子標誌進行群聚分析 (cluster analysis) 之結果 35
四、 序列分析 36
(一)、 Heading date 1 (Hd1) 基因 36
(二)、 Heading date 3a (Hd3a) 基因 38
(三)、 Heading date 6 (Hd6) 基因 38
(四)、 Photoperiodic sensitivity 5 (SE5) 基因 39
(五)、 Early heading date 1 (Ehd1) 基因 39
(六)、 Early heading date 2 (Ehd2) 基因 40
五、 水稻抽穗期相關基因於不同山地品系之Semi-quantitative RT-PCR結果 41
六、 TILLING分析之結果 42

第七章、 討論 44
一、 山地品系之外表型討論 44
二、 山地品系之抽穗期調查討論 46
三、 山地品系與栽培種以分子標誌進行群聚分析 (cluster analysis) 之討論 47
四、 六個抽穗期基因於序列分析之變異數與變異百分比 48
五、 六個抽穗期基因之個別討論 49
(一)、 SE5基因 49
(二)、 Hd6基因 49
(三)、 Ehd2基因 49
(四)、 Ehd1基因 50
(五)、 Hd1基因 51
(六)、 Hd3a基因 54
六、 TILLING之應用與侷限性 56

第八章、 結論與未來展望 57

第九章、 參考文獻 100

表次
表 1、本研究使用之植物材料對照表 59
表 2、Heading date 1基因於山地品系之序列變異對照表 62
表 3、Heading date 3a基因於山地品系之序列變異對照表 63
表 4、Heading date 6基因於山地品系之序列變異對照表 65
表 5、Photoperiodic sensitivity 5基因於山地品系之序列變異對照表 67
表 6、Early heading date 1基因於山地品系之序列變異對照表 68
表 7、Early heading date 2基因於山地品系之序列變異對照表 71
表 8、不同山地品系之抽穗期調查 76
表 9、六個抽穗期基因於序列分析之變異數與變異百分比 78

圖次
圖 1、本研究使用之山地品系稻株外觀 79
圖 2、本研究使用之山地品系稻穗外觀 80
圖 3、本研究使用之山地品系稻穗近觀 81
圖 4、本研究使用之部分山地品系種子外觀 82
圖 5、以RM164進行不同稻品種 (系) 之SSR分子標誌分析 83
圖 6、山地品系與栽培種以分子標誌進行群聚分析 (cluster analysis) 之結果 84
圖 7、不同山地品系於Heading date 1基因示意圖 85
圖 8、不同山地品系於Heading date 3a基因示意圖 86
圖 9、不同山地品系於Heading date 6基因示意圖 87
圖 10、不同山地品系於Photoperiodic sensitivity 5基因示意圖 88
圖 11、不同山地品系於Early heading date 1基因示意圖 89
圖 12、不同山地品系於Early heading date 2基因示意圖 90
圖 13、不同稻品種 (系) Hd1基因第二exon PCR產物之DNA電泳圖譜 91
圖 14、編號37山地品系之Hd1基因插入序列 (1901 bp) 之比對結果圖 92
圖 15、不同稻品種 (系) Hd1基因第一exon PCR產物之DNA電泳圖譜 93
圖 16、於Ehd2基因第二intron所發現具有長度變異之SSR 94
圖 17、Ehd2基因之第二intron的新SSR二級結構 95
圖 18、水稻抽穗期相關基因於不同山地品系之Semi-quantitative RT-PCR結果 96
圖 19、SE5基因於不同稻品種 (系) 之TILLING分析圖 97
圖 20、Hd1基因於不同稻品種 (系) 之TILLING分析圖 98
圖 21、Hd6基因於不同稻品種 (系) 之TILLING分析圖 99

附表次
附表 1、TILLING分析結果統整 109
附表 2、群聚分析使用之分子標誌 110
附表 3、本研究序列分析之引子 112
附表 4、六個抽穗期相關基因表現分析使用之引子 114

附圖次
附圖 1、阿拉伯芥與水稻於短日照及長日照環境下之開花機制圖 115
附圖 2、本研究之六個抽穗期基因之抽穗機制圖 116
附圖 3、水稻抽穗期相關基因之高解析度RFLP連鎖圖譜 117
附圖 4、Heading date 1基因之第一exon序列變異對照 118
附圖 5、Heading date 1基因之第一exon胺基酸序列變異對照 121
附圖 6、Heading date 1基因之第二exon序列變異對照 122
附圖 7、Heading date 1基因之第二exon胺基酸序列變異對照 123
附圖 8、Heading date 3a基因之第四exon序列變異對照 124
附圖 9、Heading date 3a基因之第四exon胺基酸序列變異對照 125
附圖 10、Heading date 6基因之第三exon序列變異對照 126
附圖 11、Heading date 6基因之胺基酸序列變異對照 127
附圖 12、Early heading date 1基因之第五exon序列變異對照 128
附圖 13、Early heading date 1基因之第五exon胺基酸序列變異對照 129
附圖 14、Early heading date 2基因之exon序列變異對照 130
附圖 15、Early heading date 2基因之胺基酸序列變異對照 133
附圖 16、Hd1基因插入序列 (1901 bp) 之電泳圖譜 134
附圖 17、不同稻品種 (系) 於ORF-100片段 PCR產物之DNA電泳圖譜 135
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