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| DC 欄位 | 值 | 語言 |
|---|---|---|
| dc.contributor.advisor | 董致韡(Chih-Wei Tung) | |
| dc.contributor.author | Che-Wei Hsu | en |
| dc.contributor.author | 許哲維 | zh_TW |
| dc.date.accessioned | 2021-06-17T03:40:18Z | - |
| dc.date.available | 2019-03-05 | |
| dc.date.copyright | 2018-03-05 | |
| dc.date.issued | 2018 | |
| dc.date.submitted | 2018-02-07 | |
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| dc.identifier.uri | http://tdr.lib.ntu.edu.tw/jspui/handle/123456789/70041 | - |
| dc.description.abstract | 植物的細胞質基因組是由兩種胞器的基因組所組成，分別為粒線體和葉綠體。在生化機制上，兩者於呼吸作用和光合作用中個別扮演著極其重要的角色。細胞質基因組有著與細胞核基因組不同的特性，為一單親本遺傳的單倍體基因組。因此細胞質基因組的遺傳訊息不會與來自另一親本的細胞質基因組進行重組而產生基因漸滲，換句話說，細胞質基因組的譜系歷史近似於單一基因且其來源為單一親本。這些特徵使其被廣泛應用於追溯族群的起源地與遷徙軌跡，而這種結合遺傳上親緣關係與地理學的研究被稱為親緣地理學 (phylogeography) 。本研究一共分析了 4140 種具遺傳多樣性的稻屬 (Oryza) 品系，包括了 3671 種亞洲栽培稻(Oryza sativa)、456 種亞洲野生稻 (Oryza rufipogon)、11 種澳洲野生稻 (Oryza meridionalis)、1 種非洲栽培稻 (Oryza glaberrima) 及 1 種非洲野生稻 (Oryza barthii)。透過分析4140 個稻種細胞質基因組的重定序 (resequencing) 資料，共分別於葉綠體和粒線體基因組中偵測到 665 和 882 個具高可信度的單一核苷酸多型性 (single nucleotide polymorphism, SNP) 。根據親緣分析 (phylogenetic analysis) 和主成分分析 (principle component analysis, PCA) 的結果，將4140 個稻種細胞質基因組分成15 個細胞質群 (cytogroup) ，並以此分群作為基準，描述細胞質基因組的遺傳歧異度和族群結構。親緣地理分析的結果顯示每個細胞質群都有獨特的地理分佈。本研究進一步利用歷史上的氣候資料進行野生稻生態棲位的模擬 (ecological niche modeling, ENM) ，探索野生稻族群於歷史上及地理上的消長，並由結果推論野生稻的歧異度中心（center of diversity ）為中南半島(SEA1)。依據考古證據，本研究假定野生稻最早被利用及馴化的地理區位於長江下游流域。透過建立不同族群的ENM，我們推論最早於長江下游流域被馴化的栽培稻為稉稻 (Oryza sativa spp. japonica) 。除了SNP 之外，本研究利用14 個已發表的水稻粒線體基因組開發出了9 個可代表序列間大片段插入和刪除（indels）的PAV (presence/absence variation) 分子標誌，能用於捕捉植物粒線體基因組所特有的大規模結構變異 (large-scale structural variation) ，而這些PAV分子標誌不僅提高了親緣地理分析的解析度，還與細胞質雄不稔 (cytoplasmic male sterility, CMS)有密切關聯。基因註解 (annotation) 與對偶基因頻度於不同細胞質群的分佈，暗示著細胞質群間功能上的差異。研究中發現 COX3 (cytochrome C oxidase 3) 和ATP6 (ATP synthase 6) 等組成呼吸作用中電子傳遞鏈 (electron transport chain, ETC) 的重要蛋白質，其替代等位基因 (alternative allele) 只存在於特定的細胞質群。這些等位基因很可能影響水稻於不同地理環境中的適應性。總結而言，本研究提供了水稻種原保護和利用的參考，以及進一步探究水稻的演化、細胞質核交互作用 (nucleo-cytoplasmic interaction) 和細胞質效應 (cytoplasmic effect) 的基石。 | zh_TW |
| dc.description.abstract | In plants, cytoplasmic genomes consist of genome from two organelles, chloroplast (cpDNA) and mitochondria (mtDNA). Each organelle plays a biochemically vital role in terms of photosynthesis and respiration. Cytoplasmic genomes have distinct characteristics from nuclear genome. Cytoplasmic genomes are inherited uniparentally as a haploid, which suggests that there is little adulteration of genetic information due to recombination or introgression from another parent. In other words, their genealogical history is analogous to that of a single gene. For reasons mentioned above, they are widely adopted to infer the geographical origins and migration events of populations. The approach utilizing both phylogenetics and geology is called phylogeography. In this research, 4140 diverse rice accessions were analyzed. Among 4140 accessions, there are 3671 Asian cultivated rice (Oryza sativa), 456 Asian wild rice (Oryza rufipogon), 11 Australian wild rice (Oryza meridionalis), 1 African cultivated rice (Oryza glaberrima) and 1 African wild rice (Oryza barthii). Through mining the resequencing data of these 4140 accessions, 665 and 882 high quality single nucleotide polymorphism (SNP) were identified in cpDNA and mtDNA respectively. 15 distinct cytogroups, which represent cytoplasmic genetic diversity and population structure, were then determined by both phylogenetic analysis and principle component analysis (PCA). Construction of phylogeography showed that each cytogroup had a unique geographical distribution. We further incorporated historical climate data to perform ecological niche modeling (ENM) of wild rice, which revealed demographic history of wild rice population across geographical regions. From the results, we deduced that center of diversity in wild rice was Indochina peninsula (SEA1). In this study, we assumed the region where the earliest wild rice cultivation and subsequent domestication occurred at lower Yangtze basin in China. By building ENMs of different populations, we suggested that the first cultivated subgroup being domesticated at lower Yangtze basin was japonica rice. In addition to SNP variation, complexed large-scale structural variation unique to plant mtDNA was captured by nine presence/absence variation (PAV) markers identified in 14 published de-novo assembled mtDNA sequences. These mitochondria-specific PAV markers represent large indel variation among genomes and some of them were associated with cytoplasmic male sterility (CMS). In addition, these PAV markers improved resolution of phylogeography of wild rice population. Distribution of allele frequency in annotated coding genes implied that functional differences could exist among cytogroups, alternative alleles of important electron transport chain (ETC) genes cytochrome c oxidase 3 (cox3) and ATP synthase 6 (atp6) were only found in specific cytogroups. These alternative alleles can be crucial for rice to adapt in diverse geographical environments. In summary, this research gave insights into germplasm conservation and management, and provided references for further investigation of rice evolution and how nucleo-cytoplasmic interaction and cytoplasmic effects affect rice adaptation. | en |
| dc.description.provenance | Made available in DSpace on 2021-06-17T03:40:18Z (GMT). No. of bitstreams: 1 ntu-107-R05621108-1.pdf: 33709816 bytes, checksum: d16e131de2667c79e0db727fde9bfe05 (MD5) Previous issue date: 2018 | en |
| dc.description.tableofcontents | 口試委員會審定書----------------------------------------------------------------------------------3
誌謝--------------------------------------------------------------------------------------------------4 摘要 Abstract --------------------------------------------------------------------------------------5 Figure index----------------------------------------------------------------------------------------10 Table index-----------------------------------------------------------------------------------------14 Abbreviation---------------------------------------------------------------------------------------15 Chapter 1. Genetic diversity and population structure of rice cytoplasmic genomes---16 Introduction---------------------------------------------------------------------------------16 Material and methods----------------------------------------------------------------------22 Results and discussion---------------------------------------------------------------------29 Chapter 2. Structural variation of rice mitochondrial genome-----------------------------40 Introduction---------------------------------------------------------------------------------40 Material and methods----------------------------------------------------------------------44 Results and discussion---------------------------------------------------------------------48 Chapter 3. Phylogeography and ecological niche modeling--------------------------------56 Introduction---------------------------------------------------------------------------------56 Material and methods----------------------------------------------------------------------59 Results and discussion---------------------------------------------------------------------61 Concluding remarks and perspectives---------------------------------------------------73 Reference-------------------------------------------------------------------------------------------76 Figure-----------------------------------------------------------------------------------------------87 Table-----------------------------------------------------------------------------------------------157 Supplementaries---------------------------------------------------------------------------------166 | |
| dc.language.iso | en | |
| dc.title | 水稻細胞質基因組之遺傳與親緣地理分析 | zh_TW |
| dc.title | Genetic and phylogeographic analysis of cytoplasmic genomes (mitochondria, chloroplast) in rice (Oryza) | en |
| dc.type | Thesis | |
| dc.date.schoolyear | 106-1 | |
| dc.description.degree | 碩士 | |
| dc.contributor.oralexamcommittee | 蔡育彰(Yu-Chang Tsai),李承叡(Cheng-Ruei Lee) | |
| dc.subject.keyword | 水稻,細胞質,粒線體,葉綠體,親緣地理學,生態棲位模擬,馴化,細胞質雄不稔,種原保護與探勘, | zh_TW |
| dc.subject.keyword | rice,cytoplasm,mitochondria,chloroplast,phylogeography,ecological niche modeling,domestication,CMS,germplasm conservation and management, | en |
| dc.relation.page | 166 | |
| dc.identifier.doi | 10.6342/NTU201800392 | |
| dc.rights.note | 有償授權 | |
| dc.date.accepted | 2018-02-08 | |
| dc.contributor.author-college | 生物資源暨農學院 | zh_TW |
| dc.contributor.author-dept | 農藝學研究所 | zh_TW |
| 顯示於系所單位： | 農藝學系 | |
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