請用此 Handle URI 來引用此文件：
http://tdr.lib.ntu.edu.tw/jspui/handle/123456789/89680完整後設資料紀錄
| DC 欄位 | 值 | 語言 |
|---|---|---|
| dc.contributor.advisor | 董致韡 | zh_TW |
| dc.contributor.advisor | Chih-Wei Tung | en |
| dc.contributor.author | 杜芸真 | zh_TW |
| dc.contributor.author | Yun-Chen Du | en |
| dc.date.accessioned | 2023-09-15T16:13:43Z | - |
| dc.date.available | 2023-09-16 | - |
| dc.date.copyright | 2023-09-15 | - |
| dc.date.issued | 2022 | - |
| dc.date.submitted | 2002-01-01 | - |
| dc.identifier.citation | Agostini, F., Zagalak, J., Attig, J., Ule, J. & Luscombe, N. M. (2021). Intergenic RNA mainly derives from nascent transcripts of known genes. Genome Biology 22(1): 136.
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| dc.identifier.uri | http://tdr.lib.ntu.edu.tw/jspui/handle/123456789/89680 | - |
| dc.description.abstract | 水稻 (Oryza sativa L.) 為世界重要糧食作物之一，而乾旱是氣候變遷下影響水稻產量的逆境之一，因此加速提升水稻乾旱耐受性至關重要。由於根系是植物汲取水分與養分的來源，透過改善根系結構可能有助於提升水稻乾旱耐受性。本研究目標在於，透過選擇性基因分型 (selective genotyping)、群集分離分析法 (bulk segregant analysis) 分析兩極端群體的 DNA 與 RNA 資訊，在減少時間與金錢成本的前提下，加速找到可能控制最大根長 (maximum root length, MRL) 之候選基因。一共有24個極端根長 (long and short) 的重組自交系 (recombinant inbred lines, RILs) 從 Nipponbare 與 IR64 雜交後的 F11 重組自交系族群中被篩選出來，分別稱作 Long (L) bulk (n=12) 與 Short (S) bulk (n=12)。首先，選擇性基因分型透過 general linear model (GLM) 偵測到 5、8、9 與 10 號染色體上皆有顯著的 SNP peak。其中，位於染色體 5 號的顯著單核甘酸多型性 (single nucleotide polymorphism, SNP) 位點 (S5_15750938) 可解釋70.20% 的外表型變異。接著群集分離分析之RNA 定序資料 (bulked segregant RNA-Seq, BSR-Seq) 則用於差異表現分析以及 RNA QTL-seq 分析。結果顯示，長根與短根兩個群集間共有 160 個差異表現基因 (differentially expressed genes, DEGs) 其中108個在 L bulk 是上調基因，52 個在 S bulk 為上調基因。這些基因共參與了13個生物途徑，其上游 2 kb 啟動子區域內共找到 14 種結合位點。另一方面，以 RNA 進行之 QTL-seq 分析，共偵測到 7 個候選區域分別位在染色體 5、8、9、10 與 12 號上。其中 8 號染色體尾端與 10 號染色體中段同時被 selective genotyping 與 QTL-seq 偵測到，因此我們認為重疊區域對最大根長的發育有重要的影響。另外，偵測到 155 顯著的 SNP/Indel 變異則透過 SnpEff 分析說明有 28 個基因帶有中度影響的變異，38 個基因帶有輕度影響的變異。本研究探勘之重要候選區域與候選基因可能控制根系長度的發育，將有助於未來透過調節根系結構以提升水稻耐旱性之目標。 | zh_TW |
| dc.description.abstract | Rice (Oryza sativa L.) is one of the most important edible food crops in the world. Drought stress under climate change is one of the major dilemmas for the final production of rice. Hence, it is necessary to accelerate the improvement of ricedrought tolerance to drought stressin rice. Due to the function of roots to absorb water and nutrients from the soil, root system architecture (RSA) was regarded as a promising factor to advance drought tolerance in plants. In this study, to accelerate the identification of candidate regions and genes controlling maximum root length (MRL), one of the RSA, selective genotyping, bulked segregant RNA sequencing (BSR-Seq), and RNA-based QTL-seq were adopted to analyze the DNA and RNA of two bulks with extreme phenotypes. phenotypes. A total of 24 recombinant inbred lines (RILs) with extremely long and short roots, called Long (L) bulk (n=12) and Short (S) bulk (n=12) were screened from an F11 RILs population derived from a cross between Nipponbare and IR64. Selective genotyping analysis was conducted with a general linear model (GLM) and revealed 4 four significant SNP peaks located in chromosomes 5, 8, 9, and 10. And the most significant peak (S5_15750938) is located on chromosome 5 explaining 70.20 % phenotypic variation. Second, BSR-Seq was used to identify the differentially expressed genes (DEGs) and conduct RNA-based QTL-seq. A total of 160 DEGs were found between 2 two bulks, containing 108 up-regulated genes in L bulk and 52 up-regulated genes in S bulk. Then, MapMan analysis reveals that 160 DEGs are involved in 13 pathways, and PlantCARE clarifies that a total of 14 types of the binding site are enriched in the 2k upstream sequence of 160 DEGs. RNA-based QTL-seq revealed 7 seven candidate regions on chromosomes 5, 8, 9, 10, and 12. Two candidate regions including the end of chr8 and the middle of chr10 overlapped between the results of selective genotyping and RNA-based QTL-seq, which elucidates the importance of these two regions on MRL development. QTL-seq revealed 155 significant SNPs with an ∆SNP-index greater than 0.8 at a significant level of 0.01. SnpEff revealed that 28 genes with moderate impact variants and 38 genes with low impact variants. In this study, we found important genomic regions and genes that might control the seedling MRL development. It is valuable for improving drought resistance by regulating RSA in rice. | en |
| dc.description.provenance | Submitted by admin ntu (admin@lib.ntu.edu.tw) on 2023-09-15T16:13:43Z No. of bitstreams: 0 | en |
| dc.description.provenance | Made available in DSpace on 2023-09-15T16:13:43Z (GMT). No. of bitstreams: 0 | en |
| dc.description.tableofcontents | 論文口試委員會審定書 I
摘要 II Abstract IV Content VI Index of Figures XI Index of Tables XIII Abbreviation XV Chapter 1. Introduction 1 Drought resistance mechanism 1 Genes and QTL controlling root system architecture in rice 3 Selective genotyping 5 Bulk segregant analysis and QTL-seq 6 Objective of this study 8 Chapter 2. Evaluation of seedling root traits and identification of QTLs by selective genotyping 9 Materials and Methods 9 Plant materials 9 Plant growth condition 9 Evaluation of maximum root length (MRL) 10 Unveiling the source of maximum root length and RSA 10 Root image analysis using EZ-Rhizo and RhizoVision Explorer 10 Single marker analysis with SNPs 11 Candidate genes mining 12 Results 12 Evaluating RILs with extreme root length trait 12 Seedling root development in two parents and 24 extreme root length RILs 13 Selective genotyping and single marker analysis 16 Candidate gene mining through four rice databases 16 Chapter 3. Bulked segregant RNA-Seq reveals differential expressed genes involved in regulating rice seedling root length 18 Materials and Methods 18 Plant materials 18 Plant growth 18 Extraction and isolation of bulked RNA (Figure 6) 18 RNA-Seq library construction and Sequencing (Figure 6) 19 Data cleaning and alignment process 19 Differential expressed gene analysis 20 MapMan analysis 21 Transcription factor searching through PlantPAN3.0 21 Cis-regulation elements detection in DEGs through PlantCARE databases 21 DE gene comparison between two parents and two bulks 22 Results 23 Quality control of RNA-Sequencing reads 23 Identification of differential expressed gene (DEGs) 23 MapMan analysis 24 Cis- and trans-regulation of the 160 DEGs 26 DE gene comparison between two parents and two bulks 27 Chapter 4. Bulked segregant RNA-based QTL-seq reveals significant SNP/Indel associated with rice seedling root length 31 Materials and Methods 31 Plant materials 31 Extraction and Isolation of bulked RNA 31 RNA-seq library construction and sequencing 31 Sequenced reads processing and alignment to reference genome 31 QTL-seq analysis: ∆SNP-index calculation, simulation, sliding window, and filtering 32 Validation of SNP/indel through three check data sets 34 SnpEff analysis 35 Results 36 QTL-seq: SNP-index, ∆SNP-index, confidence interval, and sliding window 36 Read coverage and depth 37 Significant SNP/Indel with opposite allele frequency between extreme bulks 38 Validation of SNPs/indels detected by HISAT2 and QTL-seq 38 Effect of the variant 39 Compare QTL-seq results to selective genotyping and BSR-Seq 40 Chapter 5. Discussion 42 Reproducibility of MRL in three independent experiments 42 Factors affect root image analysis 42 The phenotyping issue of RNA-Seq analysis 43 DE genes in six pairs of comparison 44 Selective genotyping, BSR-seq, and RNA-based QTL-Seq for detecting the candidate regions and genes controlling MRL in rice seedlings 45 Candidate regions and genes controlling seedling root development 47 Detection of intergenic SNPs in BSR-seq dataset 52 Conclusion and perspectives 54 Reference 55 Figures 68 Tables 84 Supplementary data 108 Supplemental figures 108 Supplemental tables 109 | - |
| dc.language.iso | en | - |
| dc.title | 透過選擇性基因分型與BSR-Seq探勘控制水稻幼苗根系發育之遺傳結構 | zh_TW |
| dc.title | Use selective genotyping and BSR-Seq to investigate genetic architecture controlling rice seedling root development | en |
| dc.type | Thesis | - |
| dc.date.schoolyear | 110-2 | - |
| dc.description.degree | 碩士 | - |
| dc.contributor.oralexamcommittee | 蔡育彰 | zh_TW |
| dc.contributor.oralexamcommittee | Kai-Yi Chen;Yu-Chang Tsai | en |
| dc.subject.keyword | 水稻,最大根長,選擇性基因分型,RNA 定序集群分離分析法,差異表現基因,數量性狀基因座定位,QTL-seq, | zh_TW |
| dc.subject.keyword | Rice,Maximum root length,Selective genotyping,Bulk segregant analysis RNA-Seq,Differentially expressed gene,QTL mapping,QTL-seq, | en |
| dc.relation.page | 110 | - |
| dc.identifier.doi | 10.6342/NTU202204044 | - |
| dc.rights.note | 同意授權(限校園內公開) | - |
| dc.date.accepted | 2022-09-28 | - |
| dc.contributor.author-college | 生物資源暨農學院 | - |
| dc.contributor.author-dept | 農藝學系 | - |
| dc.date.embargo-lift | 2024-09-30 | - |
| 顯示於系所單位： | 農藝學系 | |
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