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| DC 欄位 | 值 | 語言 |
|---|---|---|
| dc.contributor.advisor | 林順福 | |
| dc.contributor.author | Ya-Ching Yang | en |
| dc.contributor.author | 楊雅淨 | zh_TW |
| dc.date.accessioned | 2021-06-08T05:29:35Z | - |
| dc.date.copyright | 2005-07-06 | |
| dc.date.issued | 2005 | |
| dc.date.submitted | 2005-07-06 | |
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| dc.identifier.uri | http://tdr.lib.ntu.edu.tw/jspui/handle/123456789/24527 | - |
| dc.description.abstract | 高等植物之葉綠體基因體在結構上一般區分為大單一拷貝(LSC)區域、小單一拷貝(SSC)區域與一組倒置重複序列(IRs)，而水稻葉綠體之基因體大小約為134.5-kb，目前已知至少包含4個rRNA基因、30個tRNA基因及超過100個具蛋白質功能的基因。本研究在整理及歸納前人有關限制酵素剪切所造成品種間之DNA長度多型性後，發現秈稉稻之間特定區域的葉綠體DNA序列確實存在長度及單一核苷酸的變異，又考量目前國際有關水稻葉綠體DNA變異之研究只採用三個品種互相比較，且其中兩個屬於稉稻另一為秈稻品種，無法深入探討亞種間或亞種內品種之DNA序列變異。因此，本研究以秈稻及稉稻各九個品種為材料，欲釐清秈稉稻亞種之間及亞種內特有的葉綠體DNA序列變異，並進一步探討這些變異可能影響之葉綠體基因，以及葉綠體DNA與粒線體DNA及核內DNA的演化關係。在總定序長度約576-kb內，共發現97個秈稉稻之間特有的變異，包括27個插入或缺失的片段(InDel)，以及70個單一核苷酸多型性(SNP)。亞種間變異中， LSC區域內發生InDel機率遠高於其他區域，有0.03％；而SNP的變異率則以SSC區域內最高，LSC區域次之。另外，在LSC區域內的76 kb附近也發現稉稻高雄139號獨有的一段35-bp的DNA序列插入；而嘉農秈6號、高雄秈2號、台中在來一號與台中秈17號的葉綠體基因體也存在兩個特有且相鄰的SNPs。因而亞種內的葉綠體DNA序列變異以秈稻品種間(6.6x10-3/kb)較稉稻品種間(8.3x10-4/kb)有較大之變異。由於發現所有秈稻與稉稻亞種間具有逆向互補序列存在，可知DNA序列倒置(Inversion)現象發生在兩個亞種分化之前；另外，僅有秈稻亞種內在葉綠體基因體不同區域發現逆向互補序列，可知DNA序列倒置亦發生在亞種分化後之秈稻品種。根據BLAST搜尋的結果，葉綠體具序列變異之DNA片段轉移至核內各染色體的平均事件約為6.42次，相近於轉移至粒線體基因體的7次，可以得知葉綠體DNA片段併入核內或粒線體基因體甚為頻繁。而葉綠體單一拷貝DNA序列內的變異區域轉移至核內基因體的平均次數為6.05，重複序列內變異區域的平均次數則為14.0，約為前者的兩倍，結果也顯示葉綠體DNA片段轉移至核內基因體的頻度大致上沒有區域性的偏好。本研究結果不但有助於瞭解水稻品種間葉綠體DNA之變異，亦有助於探討葉綠體基因與重要農藝性狀之關係。 | zh_TW |
| dc.description.abstract | Chloroplast genomes in higher plants generally contain two large inverted repeats (IRs), separated by a large single copy region (LSC) and a small single copy region (SSC). In rice, the chloroplast genome is about 134.5-kb in length and comprises at least four rRNA genes, 30 tRNA genes, and over 100 genes that encoding proteins. By summarizing previous studies on DNA polymorphisms resulted from restriction sites analysis in Oryza, the inter-subspecific length-polymorphisms and SNPs between the chloroplast genomes of Japonica and Indica rice were verified. The cpDNAs have been sequenced completely only in three varieties (the Japonica type, Nipponbare and PA64S; and the Indica type, 93-11), and the relative variation between/within subspecies is still unclear due to lack of more representive varieties. In this study, nine varieties of each subspecies were used to elucidate inter- or intra-subspecific chloroplast variations, the chloroplast genes related to these variations, and the evolutionary relationships among chloroplast, nuclear and mitochondrial DNA. In a total sequence of 576-kb in length, 97 variations in the rice chloroplast genomes between Japonica and Indica, including 27 InDels and 70 SNPs, were detected. In the inter-subspecific variations, the InDel rate in the LSC region (0.03%) was much higher than the other regions, and the highest SNP rate was in the SSC region, followed by the LSC region. In addition, an I-35 was found around the 76 kb in the LSC region existed in KS139 merely, and two adjacent SNPs specifically emerged in CHS6, KSS2, TCN1, and TCS17. And the frequency of variation among Indica varieties was 6.6x10-3 per kb larger than that among Japonica varieties (8.2x10-4 per kb). Based on the differences in reverse-complementary sequence variations between Indica and Japonica varieties, and within Indica varieties, the timings of inversion incidents could be traced back at pre- or post-differentiation stages of rice subspecies, respectively. According to the results from BLAST queries, the average number of cpDNA fragments integrated into the nuclear chromosomes was 6.42, which was near to the number of seven of cpDNA flux to the mitochondrial genome, and it appeared that the occurrence of cpDNA transferring to the nuclear or mitochondrial genomes was frequently. And the averaged transferring frequency for a single copy cpDNA fragment was 6.05, and the transferred frequency for cpDNA fragments in the inverted repeat regions was twice (14 on average) more than the single copy regions. It also indicated that the cpDNA fragments transferring to the nuclear genome were distributed evenly over the chloroplast genome. Results of this study not only contribute the information on chloroplast DNA variations among varieties, but also facilitate further researches on the relation between chloroplast genes and important agronomic traits of rice. | en |
| dc.description.provenance | Made available in DSpace on 2021-06-08T05:29:35Z (GMT). No. of bitstreams: 1 ntu-94-R92621114-1.pdf: 307340 bytes, checksum: d4d4747832ed294c7e05624ad031f935 (MD5) Previous issue date: 2005 | en |
| dc.description.tableofcontents | Abstract (Chinese)
Abstract (English) Introduction………………………………………………………01 Materials and methods.…………………………………………07 Results Chloroplast genomic variations between Japonica and Indica subspecies…………………………………………………………12 Inter-subspecific nucleotide length-polymorphisms………13 Inter-subspecific single nucleotide polymorphisms………19 Intra-subspecific variations…………………………………25 DNA transfer from chloroplasts to nucleus and mitochondria ………………………………………………………………………27 Discussion Inter-subspecific variations…………………………………30 Major and minor chloroplast genotypes within Japonica and Indica rice subspecies…………………………………………34 Occurrence of InDels and inversions…………………………35 Genes related to cpDNA sequence variations………………36 Intra-subspecific variations…………………………………38 cpDNA transfer……………………………………………………39 Conclusion…………………………………………………………40 Reference……………………………………………………………41 | |
| dc.language.iso | en | |
| dc.subject | 葉綠體基因體 | zh_TW |
| dc.subject | DNA序列倒置 | zh_TW |
| dc.subject | 重複序列 | zh_TW |
| dc.subject | 酸多型性 | zh_TW |
| dc.subject | 單一核苷 | zh_TW |
| dc.subject | 插入及缺失 | zh_TW |
| dc.subject | 亞種間（內）變異 | zh_TW |
| dc.subject | 秈稉 | zh_TW |
| dc.subject | inter- (intra-) subspecific variations between Japonica and Indica rice | en |
| dc.subject | DNA sequence inversion | en |
| dc.subject | repeat sequences | en |
| dc.subject | SNP | en |
| dc.subject | InDel | en |
| dc.subject | chloroplast genome | en |
| dc.title | 秈稻與稉稻品種間之葉綠體DNA序列變異 | zh_TW |
| dc.title | Chloroplast DNA Variation between and within Japonica and Indica Rice Subspecies | en |
| dc.type | Thesis | |
| dc.date.schoolyear | 93-2 | |
| dc.description.degree | 碩士 | |
| dc.contributor.oralexamcommittee | 黃懿秦,邢禹依,古新梅,鄭隨和 | |
| dc.subject.keyword | 葉綠體基因體,秈稉,亞種間（內）變異,插入及缺失,單一核苷,酸多型性,重複序列,DNA序列倒置, | zh_TW |
| dc.subject.keyword | chloroplast genome,inter- (intra-) subspecific variations between Japonica and Indica rice,InDel,SNP,repeat sequences,DNA sequence inversion, | en |
| dc.relation.page | 45 | |
| dc.rights.note | 未授權 | |
| dc.date.accepted | 2005-07-06 | |
| 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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