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| DC 欄位 | 值 | 語言 |
|---|---|---|
| dc.contributor.advisor | 劉力瑜 | zh_TW |
| dc.contributor.advisor | Li-Yu Daisy Liu | en |
| dc.contributor.author | 莫貽婷 | zh_TW |
| dc.contributor.author | Yi-Ting Mo | en |
| dc.date.accessioned | 2024-03-04T16:14:37Z | - |
| dc.date.available | 2024-03-05 | - |
| dc.date.copyright | 2024-03-04 | - |
| dc.date.issued | 2024 | - |
| dc.date.submitted | 2024-02-06 | - |
| dc.identifier.citation | 1. Andersen, P., Kragelund, B. B., Olsen, A. N., Larsen, F. H., Chua, N. H., Poulsen, F. M., & Skriver, K. (2004). Structure and biochemical function of a prototypical Arabidopsis U-box domain. The Journal of biological chemistry, 279(38), 40053–40061. https://doi.org/10.1074/jbc.M405057200
2. Batina Roulston, M. S. (1999). Estimating the errors on measured entropy and mutual information. Physica D: Nonlinear Phenomena, 125(3), 285-294. 3. Batina, L., Gierlichs, B., Prouff, E., et al. (2011). Mutual Information Analysis: a Comprehensive Study. Journal of Cryptology, 24, 269-291. https://doi.org/10.1007/s00145-010-9084-8 4. Chanda, P., Costa, E., Hu, J., Sukumar, S., Van Hemert, J., & Walia, R. (2020). Information Theory in Computational Biology: Where We Stand Today. Entropy, 22, 627. https://doi.org/10.3390/e22060627 5. Chen, A. L., Liu, C. Y., Chen, C. H., Wang, J. F., Liao, Y. C., Chang, C. H., Tsai, M. H., Hwu, K. K., & Chen, K. Y. (2014). Reassessment of QTLs for late blight resistance in the tomato accession L3708 using a restriction site associated DNA (RAD) linkage map and highly aggressive isolates of Phytophthora infestans. PloS one, 9(5), e96417. https://doi.org/10.1371/journal.pone.0096417 6. Chen, S., Zhang, Y., Zhao, Y., Xu, W., Li, Y., Xie, J., & Zhang, D. (2020). Key Genes and Genetic Interactions of Plant-Pathogen Functional Modules in Poplar Infected by Marssonina brunnea. Molecular plant-microbe interactions : MPMI, 33(8), 1080–1090. https://doi.org/10.1094/MPMI-11-19-0325-R 7. Chunwongse, J., Chunwongse, C., Black, L., & Hanson, P. (2002). Molecular mapping of the Ph-3 gene for late blight resistance in tomato. The Journal of Horticultural Science and Biotechnology, 77(3), 281-286. https://doi.org/10.1080/14620316.2002.11511493 8. Dangl, J. L., & Jones, J. D. (2001). Plant pathogens and integrated defence responses to infection. Nature, 411(6839), 826–833. https://doi.org/10.1038/35081161 9. Della Coletta, R., Lavell, A. A., & Garvin, D. F. (2021). A Homolog of the Arabidopsis TIME FOR COFFEE Gene Is Involved in Nonhost Resistance to Wheat Stem Rust in Brachypodium distachyon. Molecular plant-microbe interactions : MPMI, 34(11), 1298–1306. https://doi.org/10.1094/MPMI-06-21-0137-R 10. Efron, B., & Tibshirani, R.J. (1994). An Introduction to the Bootstrap (1st ed.). Chapman and Hall/CRC. https://doi.org/10.1201/9780429246593 11. Foolad, M. R., Merk, H. L., & Ashrafi, H. (2008). Genetics, genomics and breeding of late blight and early blight resistance in tomato. Critical Reviews in Plant Sciences, 27(2), 75-107. https://doi.org/10.1080/07352680802147353 12. Fry W. (2008). Phytophthora infestans: the plant (and R gene) destroyer. Molecular plant pathology, 9(3), 385–402. https://doi.org/10.1111/j.1364-3703.2007.00465.x 13. Fry, W. E., Birch, P. R., Judelson, H. S., Grünwald, N. J., Danies, G., Everts, K. L., Gevens, A. J., Gugino, B. K., Johnson, D. A., Johnson, S. B., McGrath, M. T., Myers, K. L., Ristaino, J. B., Roberts, P. D., Secor, G., & Smart, C. D. (2015). Five Reasons to Consider Phytophthora infestans a Reemerging Pathogen. Phytopathology, 105(7), 966–981. https://doi.org/10.1094/PHYTO-01-15-0005-FI 14. Fushing, H., Liu, S. Y., Hsieh, Y. C., & McCowan, B. (2018). From patterned response dependency to structured covariate dependency: Entropy based categorical-pattern-matching. PloS one, 13(6), e0198253. https://doi.org/10.1371/journal.pone.0198253 15. Gangurde, S. S., Xavier, A., Naik, Y. D., Jha, U. C., Rangari, S. K., Kumar, R., Reddy, M. S. S., Channale, S., Elango, D., Mir, R. R., Zwart, R., Laxuman, C., Sudini, H. K., Pandey, M. K., Punnuri, S., Mendu, V., Reddy, U. K., Guo, B., Gangarao, N. V. P. R., Sharma, V. K., Wang, X., Zhao, C., & Thudi, M. (2022). Two decades of association mapping: Insights on disease resistance in major crops. Frontiers in Plant Science, 13, 1064059. https://doi.org/10.3389/fpls.2022.1064059 16. Goodwin, S. B., Smart, C. D., Sandrock, R. W., Deahl, K. L., Punja, Z. K., et al. (1998). Genetic change within populations of Phytophthora infestans in the United States and Canada during 1994 to 1996: Role of migration and recombination. Phytopathology, 88, 939-949. 17. Henderson, C. R., Kempthorne, O., Searle, S. R., & von Krosigk, C. M. (1959). The Estimation of Environmental and Genetic Trends from Records Subject to Culling. Biometrics, 15(2), 192–218. https://doi.org/10.2307/2527669 18. Hwang, C. F., & Williamson, V. M. (2003). Leucine-rich repeat-mediated intramolecular interactions in nematode recognition and cell death signaling by the tomato resistance protein Mi. The Plant journal : for cell and molecular biology, 34(5), 585–593. https://doi.org/10.1046/j.1365-313x.2003.01749.x 19. Ivanov, A. A., Ukladov, E. O., & Golubeva, T. S. (2021). Phytophthora infestans: An Overview of Methods and Attempts to Combat Late Blight. Journal of fungi (Basel, Switzerland), 7(12), 1071. https://doi.org/10.3390/jof7121071 20. Jupe, F., Pritchard, L., Etherington, G. J., Mackenzie, K., Cock, P. J., Wright, F., Sharma, S. K., Bolser, D., Bryan, G. J., Jones, J. D., & Hein, I. (2012). Identification and localisation of the NB-LRR gene family within the potato genome. BMC genomics, 13, 75. https://doi.org/10.1186/1471-2164-13-75 21. Kamoun, S., Furzer, O., Jones, J. D., Judelson, H. S., Ali, G. S., Dalio, R. J., Roy, S. G., Schena, L., Zambounis, A., Panabières, F., Cahill, D., Ruocco, M., Figueiredo, A., Chen, X. R., Hulvey, J., Stam, R., Lamour, K., Gijzen, M., Tyler, B. M., Grünwald, N. J., … Govers, F. (2015). The Top 10 oomycete pathogens in molecular plant pathology. Molecular plant pathology, 16(4), 413–434. https://doi.org/10.1111/mpp.12190 22. Kang, H. M., Zaitlen, N. A., Wade, C. M., Kirby, A., Heckerman, D., Daly, M. J., & Eskin, E. (2008). Efficient control of population structure in model organism association mapping. Genetics, 178(3), 1709–1723. https://doi.org/10.1534/genetics.107.080101 23. Kim, M. S., Kang, K. K., & Cho, Y. G. (2021). Molecular and Functional Analysis of U-box E3 Ubiquitin Ligase Gene Family in Rice (Oryzasativa). International journal of molecular sciences, 22(21), 12088. https://doi.org/10.3390/ijms222112088 24. Kuang, H., Wei, F., Marano, M. R., Wirtz, U., Wang, X., Liu, J., Shum, W. P., Zaborsky, J., Tallon, L. J., Rensink, W., Lobst, S., Zhang, P., Tornqvist, C. E., Tek, A., Bamberg, J., Helgeson, J., Fry, W., You, F., Luo, M. C., Jiang, J., … Baker, B. (2005). The R1 resistance gene cluster contains three groups of independently evolving, type I R1 homologues and shows substantial structural variation among haplotypes of Solanum demissum. The Plant journal : for cell and molecular biology, 44(1), 37–51. https://doi.org/10.1111/j.1365-313X.2005.02506.x 25. Li, J., Liu, L., Bai, Y., et al. (2011). Identification and mapping of quantitative resistance to late blight (Phytophthora infestans) in Solanum habrochaites LA1777. Euphytica, 179, 427-438. https://doi.org/10.1007/s10681-010-0340-7 26. Marone, D., Russo, M. A., Laidò, G., De Leonardis, A. M., & Mastrangelo, A. M. (2013). Plant nucleotide binding site-leucine-rich repeat (NBS-LRR) genes: active guardians in host defense responses. International journal of molecular sciences, 14(4), 7302–7326. https://doi.org/10.3390/ijms14047302 27. Mazumdar, P., Singh, P., Kethiravan, D., Ramathani, I., & Ramakrishnan, N. (2021). Late blight in tomato: insights into the pathogenesis of the aggressive pathogen Phytophthora infestans and future research priorities. Planta, 253(6), 119. https://doi.org/10.1007/s00425-021-03636-x 28. Nowicki, M., Foolad, M. R., Nowakowska, M., & Kozik, E. U. (2012). Potato and Tomato Late Blight Caused by Phytophthora infestans: An Overview of Pathology and Resistance Breeding. Plant disease, 96(1), 4–17. https://doi.org/10.1094/PDIS-05-11-0458 29. Panthee, D. R., Piotrowski, A., & Ibrahem, R. (2017). Mapping Quantitative Trait Loci (QTL) for Resistance to Late Blight in Tomato. International journal of molecular sciences, 18(7), 1589. https://doi.org/10.3390/ijms18071589 30. Sahu, P. K., Sao, R., Mondal, S., Vishwakarma, G., Gupta, S. K., Kumar, V., Singh, S., Sharma, D., & Das, B. K. (2020). Next Generation Sequencing Based Forward Genetic Approaches for Identification and Mapping of Causal Mutations in Crop Plants: A Comprehensive Review. Plants, 9(1355). https://doi.org/10.3390/plants9101355 31. Sanchez-Villarreal, A., Shin, J., Bujdoso, N., Obata, T., Neumann, U., Du, S. X., Ding, Z., Davis, A. M., Shindo, T., Schmelzer, E., Sulpice, R., Nunes-Nesi, A., Stitt, M., Fernie, A. R., & Davis, S. J. (2013). TIME FOR COFFEE is an essential component in the maintenance of metabolic homeostasis in Arabidopsis thaliana. The Plant journal : for cell and molecular biology, 76(2), 188–200. https://doi.org/10.1111/tpj.12292 32. Santner, A., Calderon-Villalobos, L. I., & Estelle, M. (2009). Plant hormones are versatile chemical regulators of plant growth. Nature chemical biology, 5(5), 301–307. https://doi.org/10.1038/nchembio.165 33. Sato, Y., Takeda, K., & Nagano, A. J. (2021). Neighbor QTL: an interval mapping method for quantitative trait loci underlying plant neighborhood effects. G3: Genes, Genomes, Genetics, 11(2), jkab017. https://doi.org/10.1093/g3journal/jkab017 34. Schapire, A. L., Valpuesta, V., & Botella, M. A. (2006). TPR Proteins in Plant Hormone Signaling. Plant signaling & behavior, 1(5), 229–230. https://doi.org/10.4161/psb.1.5.3491 35. Sharma, B., & Taganna, J. (2020). Genome-wide analysis of the U-box E3 ubiquitin ligase enzyme gene family in tomato. Scientific reports, 10(1), 9581. https://doi.org/10.1038/s41598-020-66553-1 36. Shin, J., Heidrich, K., Sanchez-Villarreal, A., Parker, J. E., & Davis, S. J. (2012). TIME FOR COFFEE represses accumulation of the MYC2 transcription factor to provide time-of-day regulation of jasmonate signaling in Arabidopsis. The Plant cell, 24(6), 2470–2482. https://doi.org/10.1105/tpc.111.095430 37. Su, C., Cui, J., Liu, Y., & Luan, Y. (2022). Genome-wide identification and characterization of the tomato F-box associated (FBA) protein family and expression analysis of their responsiveness to Phytophthora infestans. Gene, 821, 146335. https://doi.org/10.1016/j.gene.2022.146335 38. Sullenberger, M. T., Jia, M., Gao, S., Ashrafi, H., & Foolad, M. R. (2022). Identification of late blight resistance quantitative trait loci in Solanum pimpinellifolium accession PI 270441. The plant genome, 15(4), e20251. https://doi.org/10.1002/tpg2.20251 39. Sun, K., Wolters, A. M., Vossen, J. H., Rouwet, M. E., Loonen, A. E., Jacobsen, E., Visser, R. G., & Bai, Y. (2016). Silencing of six susceptibility genes results in potato late blight resistance. Transgenic research, 25(5), 731–742. https://doi.org/10.1007/s11248-016-9964-2 40. van der Vossen, E. A., Gros, J., Sikkema, A., Muskens, M., Wouters, D., Wolters, P., Pereira, A., & Allefs, S. (2005). The Rpi-blb2 gene from Solanum bulbocastanum is an Mi-1 gene homolog conferring broad-spectrum late blight resistance in potato. The Plant journal : for cell and molecular biology, 44(2), 208–222. https://doi.org/10.1111/j.1365-313X.2005.02527.x 41. Wang, G., Cai, G., Kong, F., Deng, Y., Ma, N., & Meng, Q. (2014). Overexpression of tomato chloroplast-targeted DnaJ protein enhances tolerance to drought stress and resistance to Pseudomonas solanacearum in transgenic tobacco. Plant physiology and biochemistry : PPB, 82, 95–104. https://doi.org/10.1016/j.plaphy.2014.05.011 42. Wang, G., Zhou, S., Luo, Y., Ma, C., Gong, Y., Zhou, Y., Gao, S., Huang, Z., Yan, L., Hu, Y., & Bian, Y. (2018). The heat shock protein 40 LeDnaJ regulates stress resistance and indole-3-acetic acid biosynthesis in Lentinula edodes. Fungal genetics and biology : FG & B, 118, 37–44. https://doi.org/10.1016/j.fgb.2018.07.002 43. Wang, Y., Li, C., Yan, S., Yu, B., Gan, Y., Liu, R., Qiu, Z., & Cao, B. (2022). Genome-Wide Analysis and Characterization of Eggplant F-Box Gene Superfamily: Gene Evolution and Expression Analysis under Stress. International journal of molecular sciences, 23(24), 16049. https://doi.org/10.3390/ijms232416049 | - |
| dc.identifier.uri | http://tdr.lib.ntu.edu.tw/jspui/handle/123456789/92041 | - |
| dc.description.abstract | 近期在遺傳科學領域，特別是定序技術方面的進步，大大提升了我們對基因或數量性狀基因座(QTL)與表型特徵之間關係的了解，這對植物育種研究有重要助益。次世代定序(NGS)技術使得更有效識別與作物病害抵抗等特性相關的基因和基因座成為可能。這對於對抗由Phytophthora infestans引起的晚疫病至關重要，該病害在全球範圍內對番茄和馬鈴薯造成顯著影響。
本研究脫離了傳統的線性模型，採用常用於類別型分析的卡方檢定(Chi-square test)對遺傳和表型數據進行分析，用以捕捉基因型與性狀表現之關係。此外，我們應用了源於信息理論的互條件熵(MCE)方法來幫助辨識與番茄晚疫病抗性相關的基因間交互作用。MCE方法強調基於計數的分析方式，特別著重於識別可能影響晚疫病抗性的遺傳因子組合。 我們利用美國國家生物技術資訊中心(NCBI)的局部相似性基本查詢工具(BLAST)將我們數據集中的序列與已知蛋白進行匹配，以驗證我們識別的遺傳標記是否與疾病抗性蛋白相關。本研究發現數個潛在的病害抗性相關基因，包括四個含多白胺酸重複(LRR)的蛋白質基因。值得注意的是，LRR是植物抗性蛋白中常見的結構。希望藉由持續的研究，並使用多樣的遺傳數據集，能評估這方法的有效性並驗證此研究的發現。 | zh_TW |
| dc.description.abstract | Recent advances in genetic science, especially sequencing technology, have greatly advanced our understanding of the relationship between genes or quantitative trait loci (QTL) and phenotypic traits, aiding plant breeding research. Next-generation sequencing (NGS) has enabled more efficient identification of genes and mapping of loci associated with traits like disease resistance in crops. This is crucial for combating Late blight, caused by Phytophthora infestans, which significantly affects tomatoes and potatoes worldwide.
This research diverged from traditional linear approaches, using categorical analysis like the Chi-square test for genetic and phenotypic data to reveal complex genotype-phenotype connections. We also applied Mutual Conditional Entropy (MCE), an information theory-based method, to identify the potential gene interactions related to tomato late blight resistance, focusing on interactive genetic factors that may affect this resistance. Utilizing Basic Local Alignment Search Tool (BLAST) provided by the National Center for Biotechnology Information (NCBI), we matched the sequences in our dataset with known proteins to verify if our identified markers are linked to disease resistance proteins. Our study highlighted the discovery of several significant resistance genes, including four Leucine-rich repeat (LRR) protein genes. LRR is a common structure in plant resistance proteins. Ongoing research, employing diverse genetic datasets, is vital to thoroughly evaluate the efficacy of this approach and validate our findings. | en |
| dc.description.provenance | Submitted by admin ntu (admin@lib.ntu.edu.tw) on 2024-03-04T16:14:37Z No. of bitstreams: 0 | en |
| dc.description.provenance | Made available in DSpace on 2024-03-04T16:14:37Z (GMT). No. of bitstreams: 0 | en |
| dc.description.tableofcontents | 口試委員審定書 i
誌謝 ii 摘要 iii ABSTRACT iv TABLE OF CONTENTS v LIST OF FIGURES vii LIST OF TABLES ix CHAPTER 1 INTRODUCTION 1 CHAPTER 2 MATERIALS 6 2.1 Plant Material and DSR Subgroups 6 2.2 Genetic Data 9 CHAPTER 3 METHODS 11 3.1 Data Preprocessing 11 3.1.1 Step 1: Data Removal 11 3.1.2 Step 2: Data Imputation 11 3.2 Cramer’s V Coefficient 12 3.3 Mutual Conditional Entropy 13 3.4 Chi-Square Test 18 3.5 Resampling Reliability Test 20 CHAPTER 4 RESULTS AND DISCUSSION 22 4.1 Data Preprocessing 22 4.1.1 Step 1: Data Removal 22 4.1.2 Step 2: Data Imputation 24 4.2 Merging Markers into Features 27 4.3 Mutual Conditional Entropy between Feature Pairs 32 4.4 Statistic Results of 1-Order Genetic Variable 36 4.4.1 Chi-Square Test Results of 1-Order Genetic Variable 36 4.4.2 Resampling Reliability Test Results of 1-Order Genetic Variable 41 4.6 Chi-Square Test Results of 2-Order Genetic Variables 43 4.7 Resampling Reliability Test Results of 2-Order Genetic Variables 47 4.8 Bioinformation of The Corresponding g-Marker Sequencies 48 4.8.1 1-Order g-Marker 48 4.8.2 2-Order g-Marker Pair 51 4.8.3 BLAST Result Comparison and Discussion 55 CHAPTER 5 CONCLUSION 59 REFERENCES 60 | - |
| dc.language.iso | en | - |
| dc.title | 類別資料探索分析用於番茄晚疫病中的基因作用 | zh_TW |
| dc.title | Categorical Exploratory Data Analysis for Discovering Gene Effects in Tomato Late Blight Disease | en |
| dc.type | Thesis | - |
| dc.date.schoolyear | 112-1 | - |
| dc.description.degree | 碩士 | - |
| dc.contributor.oralexamcommittee | 廖振鐸;歐尚靈;曾信嘉 | zh_TW |
| dc.contributor.oralexamcommittee | Chen-Tuo Liao;Shang-Ling Ou;Shinn-Jia Tzeng | en |
| dc.subject.keyword | 數量性狀基因座,類別型分析,番茄晚疫病,信息理論,互條件熵, | zh_TW |
| dc.subject.keyword | Quantitative Trait Loci,categorical analysis,tomato late blight,information theory,Mutual Conditional Entropy, | en |
| dc.relation.page | 67 | - |
| dc.identifier.doi | 10.6342/NTU202400489 | - |
| dc.rights.note | 同意授權(限校園內公開) | - |
| dc.date.accepted | 2024-02-07 | - |
| dc.contributor.author-college | 生物資源暨農學院 | - |
| dc.contributor.author-dept | 農藝學系 | - |
| dc.date.embargo-lift | 2029-02-02 | - |
| 顯示於系所單位： | 農藝學系 | |
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