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http://tdr.lib.ntu.edu.tw/jspui/handle/123456789/72340Full metadata record
| ???org.dspace.app.webui.jsptag.ItemTag.dcfield??? | Value | Language |
|---|---|---|
| dc.contributor.advisor | 張孟基 | |
| dc.contributor.author | Tsung-Yang Chen | en |
| dc.contributor.author | 陳宗暘 | zh_TW |
| dc.date.accessioned | 2021-06-17T06:36:23Z | - |
| dc.date.available | 2022-08-18 | |
| dc.date.copyright | 2018-08-18 | |
| dc.date.issued | 2018 | |
| dc.date.submitted | 2018-08-15 | |
| dc.identifier.citation | 邱燕欣 & 林詩舜 (2014). 淺談次世代定序技術（Next Generation Sequencing, NGS）發展與其應用. 種苗科技專訊 (88): 13-17.
陳依甄 (2012).水稻轉錄因子OsbHLH061和OsbHLH068在非生物逆境下基因表現及功能性分析. 臺灣大學農藝學研究所學位論文: 1-129. 廖珮君 (2014).轉錄因子OsbHLH068可促進植物鹽逆境耐受性. 臺灣大學農藝學研究所學位論文: 1-111. 謝謙謙 (2016).同源基因OsbHLH068和AtbHLH112參與阿拉伯芥鹽逆境耐受性及調控開花之研究. 臺灣大學農藝學研究所學位論文 1-107. Bedinger, P. A., Pearce, G. & Covey, P. A. (2010). RALFs. Plant Signaling & Behavior 5 (11): 1342-1346. Budde, C. O., Polenta, G., Pagani, A., Gabilondo, J., Fussi, M. & Murray, R. (2005).High temperature stress and exogenous applications of methyl jasmonate on peaches. 363-368: International Society for Horticultural Science (ISHS), Leuven, Belgium. Carvalhais Lilia, C., Dennis Paul, G., Fedoseyenko, D., Hajirezaei, M.-R., Borriss, R. & von Wirén, N. (2010). Root exudation of sugars, amino acids, and organic acids by maize as affected by nitrogen, phosphorus, potassium, and iron deficiency. Journal of Plant Nutrition and Soil Science 174 (1): 3-11. Celenza, J. L., Jr., Grisafi, P. L. & Fink, G. R. (1995). A pathway for lateral root formation in Arabidopsis thaliana. Genes Development 9 (17): 2131-2142. Che, J., Yamaji, N., Shen Ren, F. & Ma Jian, F. (2016). An Al-inducible expansin gene, OsEXPA10 is involved in root cell elongation of rice. The Plant Journal 88 (1): 132-142. Chen, H. C., Hsieh-Feng, V., Liao, P. C., Cheng, W. H., Liu, L. Y., Yang, Y. W., Lai, M. H. & Chang, M. C. (2017a). The function of OsbHLH068 is partially redundant with its homolog, AtbHLH112, in the regulation of the salt stress response but has opposite functions to control flowering in Arabidopsis. Plant Molecular Biology 94 (4-5): 531-548. Chen, S., Yang, W., Jia, Q., Wang, W., Zhang, N., Wang, X. & Wang, S. (2017b). Pleurotus ostreatus bHLH transcription factors regulate plant growth and development when expressed in Arabidopsis. Journal of Plant Interactions 12 (1): 542-549. Churko, J. M., Mantalas, G. L., Snyder, M. P. & Wu, J. C. (2013). Overview of high throughput sequencing technologies to elucidate molecular pathways in cardiovascular diseases. Circulation Research 112 (12): 1613-1623. Formentin, E., Sudiro, C., Perin, G., Riccadonna, S., Barizza, E., Baldoni, E., Lavezzo, E., Stevanato, P., Sacchi, G. A., Fontana, P., Toppo, S., Morosinotto, T., Zottini, M. & Lo Schiavo, F. (2018). Transcriptome and cell physiological analyses in different rice cultivars provide new insights into adaptive and salinity stress responses. Frontiers in Plant Science 9 (204). Fujino, K., Obara, M. & Sato, K. (2014). Diversification of the plant-specific hybrid glycine-rich protein (HyGRP) genes in cereals. Frontiers in Plant Science 5: 489. Fukaki, H. & Tasaka, M. (2009). Hormone interactions during lateral root formation. Plant Molecular Biology 69 (4): 437-449. Gao, S., Fang, J., Xu, F., Wang, W., Sun, X., Chu, J., Cai, B., Feng, Y. & Chu, C. (2014). A cytokinin oxidase/dehydrogenase gene OsCKX4 integrates cytokinin and auxin signaling to control rice crown root formation. Plant Physiology. 165: 1035–1046. Guilfoyle, T. J. (2015). The PB1 domain in auxin response factor and Aux/IAA proteins: a versatile protein interaction module in the auxin response. The Plant Cell 27 (1): 33. Haruta, M. & Constabel, C. P. (2003). Rapid Alkalinization Factors in Poplar Cell Cultures. Peptide Isolation, cDNA Cloning, and Differential Expression in Leaves and Methyl Jasmonate-Treated Cells. Plant Physiology 131 (2): 814-823. He, X. J., Mu, R. L., Cao, W. H., Zhang, Z. G., Zhang, J. S. & Chen, S. Y. (2005). AtNAC2, a transcription factor downstream of ethylene and auxin signaling pathways, is involved in salt stress response and lateral root development. Plant Journal 44 (6): 903-916. Higo, K., Ugawa, Y., Iwamoto, M. & Korenaga, T. (1999). Plant cis-acting regulatory DNA elements (PLACE) database: 1999. Nucleic Acids Research 27 (1): 297-300. Ivanchenko, M. G., Muday, G. K. & Dubrovsky, J. G. (2008). Ethylene-auxin interactions regulate lateral root initiation and emergence in Arabidopsis thaliana. Plant Journal 55 (2): 335-347. Jin, J., Tian, F., Yang, D. C., Meng, Y. Q., Kong, L., Luo, J. & Gao, G. (2017). PlantTFDB 4.0: toward a central hub for transcription factors and regulatory interactions in plants. Nucleic Acids Research 45 (D1): D1040-D1045. Jung, J. K. H. & McCouch, S. (2013). Getting to the roots of it: Genetic and hormonal control of root architecture. Frontiers in Plant Science 4: 186. Kanneganti, V. & Gupta, A. K. (2009). Isolation and expression analysis of OsPME1, encoding for a putative pectin methyl esterase from Oryza sativa (subsp. indica). Physiology and Molecular Biology of Plants 15 (2): 123-131. Khong, G., Richaud, F., Coudert, Y., Pati, P. K., Santi, C., Perin, C., Breitler, J. C., Meynard, D., Vinh do, N., Guiderdoni, E. & Gantet, P. (2008). Modulating rice stress tolerance by transcription factors. Biotechnology and Genetic Engineering Reviews 25: 381-403. Kiribuchi, K., Jikumaru, Y., Kaku, H., Minami, E., Hasegawa, M., Kodama, O., Seto, H., Okada, K., Nojiri, H. & Yamane, H. (2005). Involvement of the basic helix-loop-helix transcription factor RERJ1 in wounding and drought stress responses in rice plants. Bioscience Biotechnology Biochemistry 69 (5): 1042-1044. Kumar, V., Singh, A., Mithra, S. V., Krishnamurthy, S. L., Parida, S. K., Jain, S., Tiwari, K. K., Kumar, P., Rao, A. R., Sharma, S. K., Khurana, J. P., Singh, N. K. & Mohapatra, T. (2015). Genome-wide association mapping of salinity tolerance in rice (Oryza sativa). DNA Research 22(2): 133-145. Lee, D. K., Ahn, J. H., Song, S. K., Choi, Y. D. & Lee, J. S. (2003). Expression of an expansin gene is correlated with root elongation in soybean. Plant Physiology 131 (3): 985-997. Lee, T. I. & Young, R. A. (2000). Transcription of eukaryotic protein-coding genes. Annual Review of Genetics 34: 77-137. Li, J., Li, Y., Yin, Z., Jiang, J., Zhang, M., Guo, X., Ye, Z., Zhao, Y., Xiong, H., Zhang, Z., Shao, Y., Jiang, C., Zhang, H., An, G., Paek, N. C., Ali, J. & Li, Z. (2017). OsASR5 enhances drought tolerance through a stomatal closure pathway associated with ABA and H2O2 signalling in rice. Plant Biotechnology Journal 15 (2): 183-196 Li, M., Xiong, G., Li, R., Cui, J., Tang, D., Zhang, B., Pauly, M., Cheng, Z. & Zhou, Y. (2009). Rice cellulose synthase-like D4 is essential for normal cell-wall biosynthesis and plant growth. The Plant Journal 60 (6): 1055-1069. Li, X., Duan, X., Jiang, H., Sun, Y., Tang, Y., Yuan, Z., Guo, J., Liang, W., Chen, L., Yin, J., Ma, H., Wang, J. & Zhang, D. (2006). Genome-wide analysis of basic/helix-loop-helix transcription factor family in rice and Arabidopsis. Plant Physiology 141 (4): 1167-1184. Makkena, S. & Lamb, R. S. (2013). The bHLH transcription factor SPATULA regulates root growth by controlling the size of the root meristem. BMC Plant Biology 13: 1. Malamy, J. E. (2005). Intrinsic and environmental response pathways that regulate root system architecture. Plant Cell Environment 28 (1): 67-77. Marioni, J. C., Mason, C. E., Mane, S. M., Stephens, M. & Gilad, Y. (2008). RNA-Seq: an assessment of technical reproducibility and comparison with gene expression arrays. Genome Research 18 (9): 1509-1517. Marowa, P., Ding, A. & Kong, Y. (2016). Expansins: roles in plant growth and potential applications in crop improvement. Plant Cell Reports 35 (5): 949-965. Micheli, F. (2001). Pectin methylesterases: cell wall enzymes with important roles in plant physiology. Trends in Plant Science 6 (9): 414-419. Niu, Y. F., Chai, R. S., Jin, G. L., Wang, H., Tang, C. X. & Zhang, Y. S. (2013). Responses of root architecture development to low phosphorus availability: a review. Annals of Botany 112 (2): 391-408. Ogo, Y., Itai, R. N., Kobayashi, T., Aung, M. S., Nakanishi, H. & Nishizawa, N. K. (2011). OsIRO2 is responsible for iron utilization in rice and improves growth and yield in calcareous soil. Plant Molecular Biology 75 (6): 593-605. Passaia, G., Fonini, L. S., Caverzan, A., Jardim-Messeder, D., Christoff, A. P., Gaeta, M. L., de Araujo Mariath, J. E., Margis, R. & Margis-Pinheiro, M. (2013). The mitochondrial glutathione peroxidase GPX3 is essential for H2O2 homeostasis and root and shoot development in rice. Plant Science 208: 93-101. Pearce, G., Moura, D. S., Stratmann, J. & Ryan, C. A., Jr. (2001). RALF, a 5-kDa ubiquitous polypeptide in plants, arrests root growth and development. Proceedings of the National Academy of Sciences 98 (22): 12843-12847. Qiu, F., Zheng, Y., Zhang, Z. & Xu, S. (2007). Mapping of QTL associated with waterlogging tolerance during the seedling stage in maize. Annals of Botany 99 (6): 1067-1081. Salminen, T. A., Blomqvist, K. & Edqvist, J. (2016). Lipid transfer proteins: classification, nomenclature, structure, and function. Planta 244 (5): 971-997. Seo, E., Choi, D. & Choi (2015). Functional studies of transcription factors involved in plant defenses in the genomics era. Briefings in Functional Genomics 14 (4): 260-267. Seon-In, Y., Eunyoung, S., Sang-Keun, O., Woo, K. K. & Doil, C. (2012). A common plant cell-wall protein HyPRP1 has dual roles as a positive regulator of cell death and a negative regulator of basal defense against pathogens. The Plant Journal 69 (5): 755-768. Shankar, R., Bhattacharjee, A. & Jain, M. (2016). Transcriptome analysis in different rice cultivars provides novel insights into desiccation and salinity stress responses. Scientific Reports 6: 23719. Shannon, M. C., Rhoades, J. D., Draper, J. H., Scardaci, S. C. & Spyres, M. D. (1998). Assessment of salt tolerance in rice cultivars in response to salinity problems in California. Crop Science 38 (2): 394-398. Song, X. J., Huang, W., Shi, M., Zhu, M. Z. & Lin, H. X. (2007). A QTL for rice grain width and weight encodes a previously unknown RING-type E3 ubiquitin ligase. Nature Genetics 39 (5): 623-630. Sreevidya, V. S., Hernandez-Oane, R. J., Gyaneshwar, P., Lara-Flores, M., Ladha, J. K. & Reddy, P. M. (2010). Changes in auxin distribution patterns during lateral root development in rice. Plant Science 178 (6): 531-538. Szymanski, D. B., Lloyd, A. M. & Marks, M. D. (2000). Progress in the molecular genetic analysis of trichome initiation and morphogenesis in Arabidopsis. Trends Plant Science 5 (5): 214-219. Trapnell, C., Williams, B. A., Pertea, G., Mortazavi, A., Kwan, G., van Baren, M. J., Salzberg, S. L., Wold, B. J. & Pachter, L. (2010). Transcript assembly and abundance estimation from RNA-Seq reveals thousands of new transcripts and switching among isoforms. Nature biotechnology 28 (5): 511-515. Wang, Y., Hao, Y., Dai, J., Du, B., Zhang, J. & Chen, S. (2004). Improved tolerance of OsbHLH1 transgenic Arabidopsis to low temperature stress. Gaojishu tongxun 14 (4): 35-38. Wen, F., Zhu, Y. & Hawes, M. C. (1999). Effect of pectin methylesterase gene expression on pea root development. The Plant Cell 11 (6): 1129-1140. Weng, J., Gu, S., Wan, X., Gao, H., Guo, T., Su, N., Lei, C., Zhang, X., Cheng, Z., Guo, X., Wang, J., Jiang, L., Zhai, H. & Wan, J. (2008). Isolation and initial characterization of GW5, a major QTL associated with rice grain width and weight. Cell Research 18 (12): 1199-1209. Wu, W. & Cheng, S. (2014). Root genetic research, an opportunity and challenge to rice improvement. Field Crops Research 165: 111-124. Xu, J. & Hong, J. H. (2013).Root Development. In Genetics and Genomics of Rice, 297-316 (Eds Q. Zhang and R. A. Wing). New York, NY: Springer New York. Yoshida, S., Forno, D. A. & Cock, J. H. (1971). Laboratory manual for physiological studies of rice. Laboratory manual for physiological studies of rice. Yan, S., Tang, Z., Su, W. & Sun, W. (2005). Proteomic analysis of salt stress-responsive proteins in rice root. Proteomics 5 (1): 235-244. Yang, T., Hao, L., Yao, S., Zhao, Y., Lu, W. & Xiao, K. (2016). TabHLH1, a bHLH-type transcription factor gene in wheat, improves plant tolerance to Pi and N deprivation via regulation of nutrient transporter gene transcription and ROS homeostasis. Plant physiology and biochemistry 104: 99-113. Yang, Z., Wu, Y., Li, Y., Ling, H. Q. & Chu, C. (2009). OsMT1a, a type 1 metallothionein, plays the pivotal role in zinc homeostasis and drought tolerance in rice. Plant Molecular Biology 70 (1-2): 219-229. Yi, K., Wu, Z., Zhou, J., Du, L., Guo, L., Wu, Y. & Wu, P. (2005). OsPTF1, a novel transcription factor involved in tolerance to phosphate starvation in rice. Plant Physiology 138 (4): 2087-2096. Zenoni, S., Fasoli, M., Tornielli, G. B., Dal Santo, S., Sanson, A., de Groot, P., Sordo, S., Citterio, S., Monti, F. & Pezzotti, M. (2011). Overexpression of PhEXPA1 increases cell size, modifies cell wall polymer composition and affects the timing of axillary meristem development in Petunia hybrida. New Phytologist 191 (3): 662-677. Zhou, J., Li, F., Wang, J. L., Ma, Y., Chong, K. & Xu, Y. Y. (2009). Basic helix-loop-helix transcription factor from wild rice (OrbHLH2) improves tolerance to salt- and osmotic stress in Arabidopsis. Journal of Plant Physiology. 166 (12): 1296-1306. Zumajo-Cardona, C., Ambrose, B. A. & Pabón-Mora, N. (2017). Evolution of the SPATULA/ALCATRAZ gene lineage and expression analyses in the basal eudicot, Bocconia frutescens L. (Papaveraceae). EvoDevo 8: 5. | |
| dc.identifier.uri | http://tdr.lib.ntu.edu.tw/jspui/handle/123456789/72340 | - |
| dc.description.abstract | 轉錄因子可調控植物的生長、發育與面對逆境的反應。其中basic/helix-loop-helix (bHLH) 轉錄因子為一龐大水稻轉錄因子家族。目前水稻OsbHLHs基因如何參與水稻生長發育及非生物逆境耐受性所知不多。先前本實驗室分析公開微陣列資料庫與本身試驗的微陣列晶片資料結果，篩選出水稻受鹽逆境影響表現的基因 OsbHLH068，並開始對其功能進行了初步探討。研究結果指出於阿拉伯芥過量表現OsbHLH068能促使阿拉伯芥幼苗的根部延長並延遲其開花時間。而過量表現OsbHLH068之水稻則亦會促使水稻幼苗根部的延長，不過其調控的分子機制卻仍不清楚。為瞭解 OsbHLH068 如何影響水稻幼苗根部的生長發育，本試驗藉由RNA定序實驗進行轉錄體分析比較 TNG67 (野生型) 及過量表現水稻轉錄因子 OsbHLH068 轉殖株 (OsbHLH068 OE) 三葉齡幼苗根之基因表現圖譜 (Gene expression profiling) 的變化。結果顯示在兩個過量表現株 OsbHLH068 OE 8 和 OE 12 共同具有467個差異表現基因 (Differentially expressed genes, DEGs)，其中212個為表現量上調基因、255個則是表現量下調基因。經過基因富集分析 (Gene Ontology analysis) 與代謝路徑分析 (Kyoto Encyclopedia of Genes and Genomes pathway analysis)，得知差異表現基因的功能主要參與在逆境刺激反應、脂質的運輸、荷爾蒙訊息傳遞等的反應路徑，其中OsbHLH068可能參與Auxin、Cytokinin、Jasmonate訊息傳遞路徑來影響根長。另外經qPCR試驗證實OsPME1、OsEXPA7受到OsbHLH068正向調控，可能透過促使細胞壁的擴展來影響水稻胚根的延長。綜上所述，OsbHLH068不只參與了水稻非生物逆境耐受性之反應，亦在水稻根系發育上扮演調控角色。 | zh_TW |
| dc.description.abstract | Transcription factors regulate plant growth, development and response to various stresses. The basic/helix-loop-helix (bHLH) transcription factor belongs to a large rice transcription factor gene family. However, The functions of OsbHLHs gene involved in rice growth and development are not well studied. From public and laboratory microarray data, we picked up OsbHLH068 which is induced by salt for further study. Functional analysis of OsbHLH068 gene showed that heterologous over-expression OsbHLH068 in Arabidopsis thaliana, results in enhanced root elongation and delayed flowering time. Similar results were also obtained in overexpressed OsbHLH068 transgenic rice which displayed longer root phenotype. However, the regulation of OsbHLH068 in root elongation is not clear. To find out the possible molecular mechanism, we used RNA-sequencing technology and conducted transcriptome analysis of over-expressed transgenic rice root. The results showed that there are 467 differentially expressed genes (DEGs), including 212 up-regulated genes and 255 down-regulated genes. With assistance of Gene Ontology (GO) enrichment analysis and Kyoto Encyclopedia of Genes and Genome (KEGG), these genes can be categorized into various groups that mainly involved in stress stimulation reaction, lipid transport, and hormone signal transduction. From the results, root growth affected by OsbHLH068 may related to the regulation of Auxin, Cytokinin and Jasmonate signal transduction. Interestingly, RNA-Seq data and qPCR demonstrated that OsPME1 and OsEXPA7 genes were up-regulated in over-expressed OsbHLH068 rice. Taken together, this study showed that OsbHLH068 may not only involved in salinity stress response but also participate in regulating rice root growth. | en |
| dc.description.provenance | Made available in DSpace on 2021-06-17T06:36:23Z (GMT). No. of bitstreams: 1 ntu-107-R02621114-1.pdf: 1959803 bytes, checksum: 48d4e25b93e3aec30a753412fc8759e1 (MD5) Previous issue date: 2018 | en |
| dc.description.tableofcontents | 誌謝 I
中文摘要 II Abstract III 目錄 V 表目錄 VII 圖目錄 VII 附錄圖表 VIII 縮寫字對照表 IX 第一章 前言 1 第二章 前人研究 2 一、水稻轉錄因子家族 2 三、目前已知bHLH基因功能 4 四、植物根部生長發育的分子調控機制 4 五、次世代定序的發展與演進 5 六、次世代定序於農業生物研究上之應用 7 七、試驗目的 8 第三章 材料方法 9 一、植物材料與處理 9 二、OsbHLH068轉基因植株之篩選與分子鑑定 9 三、DNA之萃取和genomic PCR 10 四、RNA之萃取 10 五、cDNA的合成、RT-PCR與即時定量PCR (qPCR) 10 六、RNA定序 實驗流程和資料分析 10 (1) 實驗流程 11 (2) cDNA庫的備製與RNA定序 11 (2) 品質控制 13 (3) 基因參考序列的配對 (mapping to reference genome) 13 (4) 量化個別基因的表現量 (Quantification of gene expression level) 13 (5) 篩選差異表現基因分析 (Differential expression genes analysis) 14 七、基因本體分析 (Gene Ontology analysis, GO) 和 KEGG富集分析 14 八、差異表現基因的序列分析 14 第四章 結果 16 一、OsbHLH068轉殖株之篩選、分子鑑定及基因表現量分析 16 二、OsbHLH068過量表現對外表性狀之影響 16 三、探討OsbHLH068過量表現株之根部結構差異 17 四、利用RNA定序分析OsbHLH068過量表現株的轉錄體 17 五、OsbHLH068過量表現株之DEGs及基因表現趨勢分群 18 六、DEGs之富集分析 18 七、DEGs內可能影響水稻根長之基因 19 八、分析根長相關DEGs的順式作用元件序列 19 第五章 討論 20 一、OsbHLH068過量表現株根部發育與鹽逆境無關 20 二、過量表現OsbHLH068可增加水稻主根長度 20 三、OsbHLH068過量表現株的DEGs分群探討 23 四、OsbHLH068促進主根生長的可能機制 24 參考文獻 25 | |
| dc.language.iso | zh-TW | |
| dc.subject | ?稻 | zh_TW |
| dc.subject | 代謝路徑分析 | zh_TW |
| dc.subject | 次世代定序 | zh_TW |
| dc.subject | 轉錄體表現 | zh_TW |
| dc.subject | OsbHLH068 | zh_TW |
| dc.subject | OsbHLH068 | en |
| dc.subject | Japonica rice | en |
| dc.subject | Next generation sequencing | en |
| dc.subject | Transcriptome | en |
| dc.subject | pathway analysis | en |
| dc.title | 過量表現OsbHLH068水稻轉殖株之根部轉錄體分析 | zh_TW |
| dc.title | Root Transcriptome Analysis of Transgenic Rice Overexpressing OsbHLH068 Transcription Factor | en |
| dc.type | Thesis | |
| dc.date.schoolyear | 106-2 | |
| dc.description.degree | 碩士 | |
| dc.contributor.oralexamcommittee | 洪傳揚,蔡育彰,黃文理,侯新龍 | |
| dc.subject.keyword | OsbHLH068,?稻,次世代定序,轉錄體表現,代謝路徑分析, | zh_TW |
| dc.subject.keyword | OsbHLH068,Japonica rice,Next generation sequencing,Transcriptome,pathway analysis, | en |
| dc.relation.page | 55 | |
| dc.identifier.doi | 10.6342/NTU201803569 | |
| dc.rights.note | 有償授權 | |
| dc.date.accepted | 2018-08-16 | |
| 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 |
| Appears in Collections: | 農藝學系 | |
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|---|---|---|---|
| ntu-107-1.pdf Restricted Access | 1.91 MB | Adobe PDF |
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