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完整後設資料紀錄
DC 欄位 | 值 | 語言 |
---|---|---|
dc.contributor.advisor | 鍾嘉綾(Chia-Lin Chung) | |
dc.contributor.author | Jui-Yu Liao | en |
dc.contributor.author | 廖睿瑜 | zh_TW |
dc.date.accessioned | 2021-07-11T14:47:00Z | - |
dc.date.available | 2023-08-08 | |
dc.date.copyright | 2013-09-06 | |
dc.date.issued | 2013 | |
dc.date.submitted | 2013-08-11 | |
dc.identifier.citation | 1. Alkan N, Fluhr R, Prusky D, 2012. Ammonium secretion during Colletotrichum coccodes infection modulates salicylic and jasmonic acid pathways of ripe and unripe tomato fruit. Molecular Plant-Microbe Interactions 25, 85-96.
2. Amil-Ruiz F, Blanco-Portales R, Munoz-Blanco J, Caballero JL, 2011. The strawberry plant defense mechanism: a molecular review. Plant and Cell Physiology 52, 1873-903. 3. Anders S, Huber W, 2010. Differential expression analysis for sequence count data. Genome Biology 11, R106. 4. Arroyo FT, Moreno J, Daza P, Boianova L, Romero F, 2007. Antifungal activity of strawberry fruit volatile compounds against Colletotrichum acutatum. Journal of Agricultural and Food Chemistry 55, 5701-7. 5. Asghari MRaB, M., 2009. Use of salicylic acid to increase strawberry fruit total antioxidant activity. In 6th International Postharvest Symposium, 8-12. 6. Babalar M, Asghari M, Talaei A, Khosroshahi A, 2007. Effect of pre- and postharvest salicylic on ethylene production, fungal decay acid treatment and overall quality of Selva strawberry fruit. Food Chemistry 105, 449-53. 7. Bent AF, 1996. Plant disease resistance genes: Function meets structure. Plant Cell 8, 1757-71. 8. Bringhurst RS, Voth V, Shaw D, 1990. University of California strawberry breeding. Hortscience 25, 834-44. 9. Brodersen P, Petersen M, Nielsen HB, et al., 2006. Arabidopsis MAP kinase 4 regulates salicylic acid- and jasmonic acid/ethylene-dependent responses via EDS1 and PAD4. Plant Journal 47, 532-46. 10. Cai X, Davis EJ, Ballif J, et al., 2006. Mutant identification and characterization of the laccase gene family in Arabidopsis. Journal of Experimental Botany 57, 2563-9. 11. Casado-Diaz A, Encinas-Villarejo S, Santos BDL, et al., 2006. Analysis of strawberry genes differentially expressed in response to Colletotrichum infection. Physiologia Plantarum 128, 633-50. 12. Chang, Puryear, Cairney, 1993. A simple and efficient method for isolating RNA from pine trees. Plant Molecular Biology Reporter 11, 113-6. 13. Chaudhuri RR, Yu L, Kanji A, et al., 2011. Quantitative RNA-seq analysis of the Campylobacter jejuni transcriptome. Microbiology 157, 2922-32. 14. Cheng GW, Breen PJ, 1991. Activity of phenylalanine ammonia-lyase (PAL) and concentrations of anthocyanins and phenolics in developing strawberry fruit. Journal of the American Society for Horticultural Science 116, 865-9. 15. Coquoz J-L, Buchala A, Metraux J-P, 1998. The biosynthesis of salicylic acid in potato plants. Plant Physiology 117, 1095-101. 16. Curry KJ, Abril M, Avant JB, Smith BJ, 2002. Strawberry anthracnose: Histopathology of Colletotrichum acutatum and C. fragariae. Phytopathology 92, 1055-63. 17. Darrow G, 1966. The Strawberry. History, Breeding and Physiology. Holt, Rinehart and Wilson, New York, USA. 18. Davis TM, Denoyes-Rothan B, Lerceteau-Koehler E, 2007. Genome mapping and molecular breeding in plants. Fruits and Nuts 4, 189-205. 19. Davis TM, Dimeglio LM, Yang R, Styan SMN, Lewers KS, 2006. Assessment of SSR marker transfer from the cultivated strawberry to diploid strawberry species: Functionality, linkage group assignment, and use in diversity analysis. Journal of the American Society for Horticultural Science 131, 506-12. 20. De Lorenzo G, Ferrari S, 2002. Polygalacturonase-inhibiting proteins in defense against phytopathogenic fungi. Current Opinion in Plant Biology 5, 295-9. 21. De Silva Pinto M, De Carvalho JE, Lajolo FM, Genovese MI, Shetty K, 2010. Evaluation of antiproliferative, anti-type 2 diabetes, and antihypertension potentials of ellagitannins from strawberries (Fragaria x ananassa Duch.) using in vitro models. Journal of Medicinal Food 13, 1027-35. 22. De Witt RN, 2012. Correlating metabolite and transcript profiles in transgenuc sugarcane lines. Master Thesis, University of Stellenbosch, Southern Africa. 23. Dean R, Van Kan JA, Pretorius ZA, et al., 2012. The top 10 fungal pathogens in molecular plant pathology. Molecular Plant Pathology 13, 414-30. 24. Denoyes-Rothan B, Guerin G, Lerceteau-Kohler E, Risser G, 2005. Inheritance of resistance to Colletotrichum acutatum in Fragaria x ananassa. Phytopathology 95, 405-12. 25. Dong J, Chen C, Chen Z, 2003. Expression profiles of the Arabidopsis WRKY gene superfamily during plant defense response. Plant Molecular Biology 51, 21-37. 26. Dubiellaa U, Seybolda H, Duriana G, et al., 2013. Calcium-dependent protein kinase/NADPH oxidase activation circuit is required for rapid defense signal propagation. Proceedings of the National Academy of Sciences 110, 8744-9. 27. Dubois A, Carrere S, Raymond O, et al., 2012. Transcriptome database resource and gene expression atlas for the rose. BMC Genomics 13, 638. 28. Encinas-Villarejo S, Maldonado AM, Amil-Ruiz F, et al., 2009. Evidence for a positive regulatory role of strawberry (Fragaria x ananassa) FaWRKY1 and Arabidopsis AtWRKY75 proteins in resistance. Journal of Experimental Botany 60, 3043-65. 29. Fedorova N, 1946. Crossability and phylogenetic relationa in the main European species of Fragaria. Comp. Rend. Acad. Sci. USSR 53, 545-7. 30. Feng J, Li J, Liu H, Gao Q, Duan K, Zou Z, 2013. Isolation and characterization of a calcium-dependent protein kinase gene, FvCDPK1, responsive to abiotic stress in woodland strawberry (Fragaria vesca). Plant Molecular Biology Reporter 31, 443-56. 31. Filippone MP, Diaz-Ricci JC, Castagnaro AP, Farias RN, 2001. Effect of fragarin on the cytoplasmic membrane of the phytopathogen Clavibacter michiganensis. Molecular Plant-Microbe Interactions 14, 925-8. 32. Filippone MP, Diaz Ricci J, Mamani De Marchese A, Farias RN, Castagnaro A, 1999. Isolation and purification of a 316 Da preformed compound from strawberry (Fragaria ananassa) leaves active against plant pathogens. FEBS Letters 459, 115-8. 33. Folta KM, 2013. Functionalizing the strawberry genome- a review. International Journal of Fruit Science 13, 162-74. 34. Folta KM, Clancy MA, Chamala S, et al., 2010. A transcript accounting from diverse tissues of a cultivated strawberry. The Plant Genome Journal 3, 90-105. 35. Folta KM, Davis TM, 2006. Strawberry genes and genomics. Critical Reviews in Plant Sciences 25, 399-415. 36. Fu ZQ, Yan S, Saleh A, et al., 2012. NPR3 and NPR4 are receptors for the immune signal salicylic acid in plants. Nature 486, 228-32. 37. Gorlach J, Raesecke H-R, Rentsch D, et al., 1995. Temporally distinct accumulation of transcripts encoding enzymes of the prechorismate pathways in elicitor-treated, cultured tomato cells. Proceedings of the National Academy of Sciences 92, 3166-70. 38. Grabherr MG, Haas BJ, Yassour M, et al., 2011. Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nature Biotechnology 29, 644-52. 39. Grellet-Bournonville CF, Martinez-Zamora MG, Castagnaro AP, Carlos Diaz-Ricci J, 2012. Temporal accumulation of salicylic acid activates the defense response against Colletotrichum in strawberry. Plant Physiology and Biochemistry 54, 10-6. 40. Gruenheit N, Deusch O, Esser C, Becker M, Voelckel C, Lockhart P, 2012. Cutoffs and k-mers: implications from a transcriptome study in allopolyploid plants. BMC Genomics 13, 92. 41. Guidarelli M, Carbone F, Mourgues F, et al., 2011. Colletotrichum acutatum interactions with unripe and ripe strawberry fruits and differential responses at histological and transcriptional levels. Plant Pathology 60, 685-97. 42. Hanhineva K, Kokko H, Siljanen H, Rogachev I, Aharoni A, Karenlampi SO, 2009. Stilbene synthase gene transfer caused alterations in the phenylpropanoid metabolism of transgenic strawberry (Fragaria x ananassa). Journal of Experimental Botany 60, 2093-106. 43. Haymes KM, Henken B, Davis TM, Van De Weg WE, 1997. Identification of RAPD markers linked to a Phytophthora fragariae resistance gene (Rpf1) in the cultivated strawberry. Theoretical and Applied Genetics 94, 1097-101. 44. Higgins J, Magusin A, Trick M, Fraser F, Bancroft I, 2012. Use of mRNA-seq to discriminate contributions to the transcriptome from the contituent genomes of the polyploid crop species Brassica napus. BMC Genomics 13, 247. 45. Hummer KE, Hancock J, 2009. Strawberry Genomics: Botanical History, Cultivation, Traditional Breeding, and New Technologies. 46. Hyde KD, Cai L, Mckenzie EHC, Yang YL, Zhang JZ, Prihastuti H, 2009. Colletotrichum: a catalogue of confusion. Fungal Diversity 39, 1-17. 47. Kasai K, Kanno T, Akita M, Ikejiri-Kanno Y, Wakasa K, Tozawa Y, 2005. Identification of three shikimate kinase genes in rice: characterization of their differential expression during panicle development and of the enzymatic activities of the encoded proteins. Planta 222, 438-47. 48. Kawahara Y, Oono Y, Kanamori H, Matsumoto T, Itoh T, Minami E, 2012. Simultaneous RNA-Seq analysis of a mixed transcriptome of rice and blast fungus interaction. PLoS One 7, e49423. 49. Kesarwani M, Yoo J, Dong X, 2007. Genetic interactions of TGA transcription factors in the regulation of pathogenesis-related genes and disease resistance in Arabidopsis. Plant Physiology 144, 336-46. 50. Khan AA, 2002. Characterization of chitinase activities, and cloning, analysis, and expression of genes encoding pathogenesis related proteins in strawberry. PhD Thesis Department of Biological Sciences Louisiana State University and Agricultural and Mechanical College, Louisiana. 51. Khan AA, Shih DS, 2004. Molecular cloning, characterization, and expression analysis of two class II chitinase genes from the strawberry plant. Plant Science 166, 753-62. 52. Khan AA, Wu J, Lackman P, Shih DS, 1999. Cloning and sequence analysis of a class III chitinase gene from Fragaria ananassa Dutch. Plant Physiology 120. 53. Langmead B, Salzberg SL, 2012. Fast gapped-read alignment with Bowtie 2. Nature Methods 9, 357-9. 54. Lebel E, Heifetz P, Thorne L, Uknes S, Ryals J, Ward E, 1998. Functional analysis of regulatory sequences controlling PR-1 gene expression in Arabidopsis. Plant Journal 16, 223-33. 55. Lemaire SD, 2004. The glutaredoxin family in oxygenic photosynthetic organisms. Photosynth Res. 79, 305-18. 56. Lerceteau-Kohler E, Guerin G, Laigret F, Denoyes-Rothan B, 2003. Characterization of mixed disomic and polysomic inheritance in the octoploid strawberry (Fragaria x ananassa) using AFLP mapping. Theoretical and Applied Genetics 107, 619-28. 57. Li J, Brader G, Palva ET, 2004. The WRKY70 transcription factor: A node of convergence for jasmonate-mediated and salicylate-mediated signals in plant defense. Plant Cell 16, 319-31. 58. Llop-Tous I, Dominguez-Puigjaner E, Vendrell M, 2002. Characterization of a strawberry cDNA clone homologous to calcium-dependent protein kinases that is expressed during fruit ripening and affected by low temperature. Journal of Experimental Botany 53, 2283-5. 59. Maas JL, Galletta GJ, Stoner GD, 1991. Ellagic acid, an anticarcinogen in fruits, especially in strawberries: a review. Hortscience 26, 10-4. 60. Martin JA, Wang Z, 2011. Next-generation transcriptome assembly. Nature Reviews Genetics 12, 671-82. 61. Martinez-Zamora MG, Abraham Z, Gambardella M, Echaide M, Carbonero P, Diaz I, 2005. The strawberry gene Cyf1 encodes a phytocystatin with antifungal properties. Journal of Experimental Botany 56, 1821-9. 62. Martinez Zamora MG, Castagnaro AP, Diaz Ricci JC, 2004. Isolation and diversity analysis of resistance gene analogues (RGAs) from cultivated and wild strawberries. Molecular Genetics and Genomics 272, 480-7. 63. Mauch-Mani B, Slusarenko AJ, 1996. Production of salicylic acid precursors is a major function of phenylalanine ammonia-lyase in the resistance of Arabidopsis to Peronospora parasitica. Plant Cell 8, 203-12. 64. Mehli L, Schaart JG, Kjellsen TD, et al., 2004. A gene encoding a polygalacturonase-inhibiting protein (PGIP) shows developmental regulation and pathogen-induced expression in strawberry. New Phytologist 163, 99-110. 65. Munoz C, Hoffmann T, Escobar NM, et al., 2010. The strawberry fruit Fra a allergen functions in flavonoid biosynthesis. Molocular Plant 3, 113-24. 66. Munoz C, Sanchez-Sevilla JF, Botella MA, Hoffmann T, Schwab W, Valpuesta V, 2011. Polyphenol composition in the ripe fruits of Fragaria species and transcriptional analyses of key genes in the pathway. Journal of Agricultural and Food Chemistry 59, 12598-604. 67. Ndamukong I, Al Abdallat A, Thurow C, et al., 2007. SA-inducible Arabidopsis glutaredoxin interacts with TGA factors and suppresses JA-responsive PDF1.2 transcription. Plant Journal 50, 128-39. 68. Nookaew I, Papini M, Pornputtapong N, et al., 2012. A comprehensive comparison of RNA-Seq based transcriptome analysis from reads to differential gene expression and cross-comparison with microarrays: a case study in Saccharomyces cerevisiae. Nucleic Acids Research 40, 10084-97. 69. Osorio S, Bombarely A, Giavalisco P, et al., 2011. Demethylation of oligogalacturonides by FaPE1 in the fruits of the wild strawberry Fragaria vesca triggers metabolic and transcriptional changes associated with defence and development of the fruit. Journal of Experimental Botany 62, 2855-73. 70. Osorio S, Castillejo C, Quesada MA, et al., 2008. Partial demethylation of oligogalacturonides by pectin methyl esterase 1 is required for eliciting defence responses in wild strawberry (Fragaria vesca). Plant Journal 54, 43-55. 71. Pedley KF, Martin GB, 2005. Role of mitogen-activated protein kinases in plant immunity. Current Opinion in Plant Biology 8, 541-7. 72. Pieterse CMJ, Leon-Reyes A, Van Der Ent S, Van Wees SCM, 2009. Networking by small-molecule hormones in plant immunity. Nature Chemical Biology 5, 308-16. 73. Pombo MA, Martinez GA, Civello PM, 2011. Cloning of FaPAL6 gene from strawberry fruit and characterization of its expression and enzymatic activity in two cultivars with different anthocyanin accumulation. Plant Science 181, 111-8. 74. Potter D, Luby JJ, Harrison RE, 2000. Phylogenetic relationships among species of Fragaria (Rosaceae) inferred from non-coding nuclear and chloroplast DNA sequences. Systemic Botany 25, 337-48. 75. Robinson J, Thorvaldsdottir H, Winckler W, et al., 2011. Integrative genome viewer. Nature Biotechnology 29, 24-6. 76. Rousseau-Gueutin M, Lerceteau-Kohler E, Barrot L, et al., 2008. Comparative genetic mapping between octoploid and diploid Fragaria species reveals a high level of colinearity between their genomes and the essentially disomic behavior of the cultivated octoploid strawberry. Genetics 179, 2045-60. 77. Rozen S, Skaletsky H, 2000. Primer 3 on the WWW for general users and for biologist programmers. In: Krawetz S, Misener S (eds) Bioinformatics methods and protocols: methods in molecular biology. Humana Press, Totowa, 365–86. 78. Sanseverino W, Roma G, De Simone M, et al., 2010. PRGdb: a bioinformatics platform for plant resistance gene analysis. Nucleic Acids Research 38, D814-D21. 79. Sargent DJ, Clarke J, Simpson DW, et al., 2006. An enhanced microsatellite map of diploid Fragaria. Theoretical and Applied Genetics 112, 1349-59. 80. Schaart JG, 2004. Towards consumer-friendly cisgenic strawberries which are less susceptible to Botrytis cinerea. Thesis, Wageningen University, Wageningen, The Netherlands. 81. Schaart JG, Mehli L, Schouten HJ, 2005. Quantification of allele-specific expression of a gene encoding strawberry polygalacturonase-inhibiting protein (PGIP) using pyrosequencing. Plant Journal 41, 493-500. 82. Schulz MH, Zerbino DR, Vingron M, Birney E, 2012. Oases: robust de novo RNA-seq assembly across the dynamic range of expression levels. Bioinformatics 28, 1086-92. 83. Senanayake YDA, Bringhurst RS, 1967. Origin of Fragaria polyploids. I. cytological analysis. American Journal of Botany 54, 221-8. 84. Shah J, 2003. The salicylic acid loop in plant defense. Current Opinion in Plant Biology 6, 365-71. 85. Shendure J, Ji H, 2008. Next-generation DNA sequencing. Nature Biotechnology 26, 1135-45. 86. Shirano Y, Kachroo P, Shah J, Klessig DF, 2002. A gain-of-function mutation in an Arabidopsis toll interleukin1 receptor-nucleotide binding site-leucine-rich repeat type R gene triggers defense responses and results in enhanced disease resistance. Plant Cell 14, 3149-62. 87. Shulaev V, Sargent DJ, Crowhurst RN, et al., 2011. The genome of woodland strawberry (Fragaria vesca). Nature 43, 109-16. 88. Sivasankar S, Sheldrick B, Rothstein SJ, 2000. Expression of allene oxide synthase determines defense gene activation in tomato. Plant Physiology 122, 1335-42. 89. Spoel SH, Johnson JS, Dong X, 2007. Regulation of tradeoffs between plant defenses against pathogens with different lifestyles. Proceedings of the National Academy of Sciences of the United States of America 104, 18842-7. 90. Spoel SH, Koornneef A, Claessens SMC, et al., 2003. NPR1 modulates cross-talk between salicylate- and jasmonate-dependent defense pathways through a novel function in the cytosol. Plant Cell 15, 760-70. 91. Stupar RM, Beaubien KA, Jin W, et al., 2006. Structural diversity and differential transcription of the patatin multicopy gene family during potato tuber development. Genetics 172, 1263-75. 92. Tada Y, Spoel SHP-M, K., Mou Z, et al., 2008. Plant immunity requires conformational charges of NPR1 via S-nitrosylation and thioredoxins. Science 321, 952-6. 93. Thorvaldsdottir H, Robinson JT, Mesirov JP, 2013. Integrative genomics viewer (IGV): high-performance genomics data visualization and exploration. Brief Bioinformatics 14, 178-92. 94. Townsend BJ, Poole A, Blake CJ, Llewellyn DJ, 2005. Antisense suppression of a (+)-delta-cadinene synthase gene in cotton prevents the induction of this defense response gene during bacterial blight infection but not its constitutive expression. Plant Physiology 138, 516-28. 95. Tzin V, Galili G, 2010. New insights into the shikimate and aromatic amino acids biosynthesis pathways in plants. Molecular Plant 3, 956-72. 96. Van Loon LC, Rep M, Pieterse CMJ, 2006. Significance of inducible defense-related proteins in infected plants. Annual Review of Phytopathology 44, 135-62. 97. Van Ooijen G, Van Den Burg HA, Cornelissen BJC, Takken FLW, 2007. Structure and function of resistance proteins in solanaceous plants. Annual Review of Phytopathology 45, 43-72. 98. Vlot AC, Dempsey DMA, Klessig, D. F., 2009. Salicylic acid, a multifaceted hormone to combat disease. Annual Review of Phytopathology 47, 177-206. 99. Wang D, Amornsiripanitch N, Dong X, 2006. A genomic approach to identify regulatory nodes in the transcriptional network of systemic acquired resistance in plants. PLoS Pathogens 2, 1042-50. 100. Wang L, Si Y, Dedow LK, Shao Y, Liu P, Brutnell TP, 2011. A low-cost library construction protocol and data analysis pipeline for Illumina-based strand-specific multiplex RNA-Seq. PLoS One 6, e26426. 101. Wiermer M, Feys BJ, Parker JE, 2005. Plant immunity: the EDS1 regulatory node. Current Opinion in Plant Biology 8, 383-9. 102. Wildermuth MC, Dewdney J, Wu G, Ausubel FM, 2001. Isochorismate syhthesis is required to synthesize salicylic acid for plant defense. Nature, 562-5. 103. Wu Y, Zhang D, Chu JY, et al., 2012. The Arabidopsis NPR1 protein is a receptor for the plant defense hormone salicylic acid. Cell Reports 1, 639-47. 104. Xu X, Chen C, Fan BF, Chen Z, 2006. Physical and functional interactions between pathogen-induced Arabidopsis WRKY18, WRKY40, and WRKY60 transcription factors. Plant Cell 18, 1310-26. 105. Yubero-Serrano EM, Moyano E, Medina-Escobar N, Munoz-Blanco J, Caballero JL, 2003. Identification of a strawberry gene encoding a non-specific lipid transfer protein that responds to ABA, wounding and cold stress. Journal of Experimental Botany 54, 1865-77. 106. Zhang J, Wang X, Yu O, et al., 2011. Metabolic profiling of strawberry (Fragaria x ananassa Duch.) during fruit development and maturation. Journal of Experimental Botany 62, 1103-18. 107. Zhang S, Zhang Z, Kang L, 2012. Transcriptome response analysis of Arabidopsis thaliana to leaf miner (Liriomyza huidobrensis). BMC Plant Biology 12, 234. 108. Zhang X, Chen S, Mou Z, 2010. Nuclear localization of NPR1 is required for regulation of salicylate tolerance, isochorismate synthase 1 expression and salicylate accumulation in Arabidopsis. J. Plant Physiol. 167, 144-8. 109. Zhang Y, 2006. Studies of pathogenesis-related proteins in the strawberry plant: partial purification of a chitinase-containing protein complex and analysis of an osmotin-like protein gene. Thesis, Louisiana State University and Agricultural and Mechanical College, Louisiana. 110. Zhang Y, Seeram NP, Lee R, Feng L, Heber D, 2008. Isolation and identification of strawberry phenolics with antioxidant and human cancer cell anti proliferative properties. Journal of Agricultural and Food Chemistry 56, 670-5. 111. Zhang Y, Shih DS, 2007. Isolation of an osmotin-like protein gene from strawberry and analysis of the response of this gene to abiotic stresses. Journal of Plant Physiology 164, 68-77. 112. Zhang Y, Tessaro MJ, Lassner M, Li X, 2003. Knockout analysis of Arabidopsis transcription factors TGA2, TGA5, and TGA6 reveals their redundant and essential roles in systemic acquired resistance. Plant Cell 15, 2647-53. | |
dc.identifier.uri | http://tdr.lib.ntu.edu.tw/jspui/handle/123456789/78231 | - |
dc.description.abstract | 草莓為高經濟及高營養價值之水果,因其基因體大小相對簡易且可快速繁殖,適
合做為薔薇科果樹研究的模式植物。適逢近年全球暖化,臺灣草莓育苗期亦因病 害嚴重而損失慘重 (如:炭疽病等),當前並無可完全抵禦之品系。為克服此一困 難,開發新穎性防治策略因應,須對草莓 (尤其本土栽培品種) 之抗感病機制有所 瞭解。我們選定對多種病害中度感病的臺灣本土栽培種「桃園三號」與日本強健 抗病品種「Superjumbo」為材料。為能完整解析草莓的防禦系統,本研究運用次世代定序技術,針對水楊酸在兩種草莓品系上所誘導之基因表現,以高通量方式進 行mRNA-seq whole-transcriptome analysis,以建構抗性相關基因資料庫。為確保定序樣品之防禦反應確實已被啟動,我們首先測定以水楊酸處理兩品種草莓之反應,結果證實可造成植株對炭疽病抗性增強及抗性途徑下游基因 (包含FaPR1、FaOLP2、和FaWRKY1) 之表現量增加。選定處理後6 hr、12 hr、24 hr 和48 hr 等時間點之RNA 樣品加以混合再進行定序,以獲取全面性資訊。考量栽培種草莓基因體,屬複雜之八倍體,因此本研究在基因組裝策略上,分別對de novo assembly 和gene annotation 進行策略評估。de novo assembly 部分,運用Trinity、Velvet/Oases 及CLC Bio 三種軟體,配合multiple k-mer 測試,結果指出Trinity 較可適用於八倍體草莓﹔gene annotation 部分,則分別依據二倍體草莓基因體資料庫及NCBI nr database 進行,結果顯示以二倍體草莓基因體資料庫進行註解可獲得較完整之資訊。依據Gene Ontology 及註解結果,我們總共於兩品種中篩選出近800 筆處理水楊酸後具差異性表現之基因,包括可能參與在水楊酸生合成、植物與病原交互作用、和防禦訊息傳導等重要功能之基因,以及數個具高度差異表現之新穎性未註解基因。透過quantitative real-time reverse transcription PCR (qRT-PCR),目前已驗證了資料庫中的17 個分屬於水楊酸抗病網路不同途徑之重要基因,包含genes encoding Resistance (R) protein、Shikimate dehydrogenase、Shikimate kinase、Chorismate mutase、Flavanone 3-dioxygenase、NPR1、FaWRKY1、WRKY70、WRKY51、TGA6、GrxC9、FaOLP2、FaPR1、Brassinosteroid insensitive 1-associated receptor kinase 1、Interleukin-7 receptor、Hyoscyamine 6-dioxygenase 和Patatin T5 等,確實可受到水楊酸誘導而引發表現量上升,並在兩品種間呈現表現時間之差 異性。此等基因透過次世代定序及qRT-PCR 測得之表現趨勢,與少數過去文獻相互比較印證後,可說明本研究所建構抗性資料庫之可信度。本研究為首度全面性深入探討栽培種草莓水楊酸誘導抗性網絡之研究,相關結果將有助於了解草莓受不同病原菌入侵時可能啟動之水楊酸抗性途徑,以利未來於抗病育種及防治策略開發等方面之運用。 | zh_TW |
dc.description.abstract | Cultivated strawberry, an economically important small fruit, has been considered a potential model system for Rosaceae plants. Pest damage and pesticide residue problems have always been major threats to strawberry cultivation in Taiwan. Aiming to develop novel disease control strategies, we used the Illumina next generation sequencing technology for high-throughput identification of genes up- and down-regulated by defense hormone- salicylic acid (SA), in two strawberry cultivars, Taoyuan 3 and Superjumbo. We verified the effectiveness of SA-treatment by evaluating anthracnose resistance and the expression of FaPR1, FaWRKY1, and FaOLP2, the hallmark genes downstream of the SA signaling pathway, in SA- or ddH2O-pretreated plants. After that, total RNA was extracted from samples of each cultivar collected 6, 12, 24, and 48 hours after SA- or ddH2O-treatment and then pooled
for sequencing. To tackle the complex octoploid genome, we adopted an assemble-then-align strategy. We first assessed Trinity, Velvet/Oases and CLC Bio in combination with multiple k-mer strategy for their efficiencies in de novo assembly. Trinity generated more full-length transcripts across a broad range of expression levels, with the assemblies exhibiting a higher similarity to the corresponding genes in a reference diploid strawberry genome. The result indicated that Trinity may be a better assembler for dealing with the homologous/homoeologous genes in the octoploid strawberry genome. As for gene annotation, we found that more transcripts could be better-annotated with the use of the diploid strawberry genome database. Overall, we identified about 800 genes that were significantly differentially expressed between SA-treated plants and the control. These included several novel genes and numerous genes likely involved in SA biosynthesis, plant-pathogen interactions, and defense signaling. We investigated the time-course expression profiling of a set of selected candidate genes using real-time quantitative RT-PCR. The expression of seventeen defense-related genes, encoding Resistance (R) protein, Shikimate dehydrogenase, Shikimate kinase, Chorismate mutase, Flavanone 3-dioxygenase, NPR, FaWRKY1, WRKY70, WRKY51, TGA6, GrxC9, FaOLP2, FaPR1, Brassinosteroid insensitive 1-associated receptor kinase 1, Interleukin-7 receptor, Hyoscyamine 6-dioxygenase, and Patatin T5, has been verified to be highly induced in response to SA. The expression patterns of these genes, quantified by RNAseq and qRT-PCR, were consistent with those previously reported in model plants and/or strawberry, suggesting that the defense database we constructed should be valid. This study is the first comprehensive investigation of the SA-mediated pathway in cultivated strawberry. The results will contribute to a better understanding of strawberry resistance mechanisms against the invasion of biotrophic/hemibiotropic pathogens. The identified defense-related genes can also be used as selection markers in strawberry resistance breeding. | en |
dc.description.provenance | Made available in DSpace on 2021-07-11T14:47:00Z (GMT). No. of bitstreams: 1 ntu-102-R00633018-1.pdf: 2633436 bytes, checksum: c6b5aefbc7d2bc1084d76c479511cdac (MD5) Previous issue date: 2013 | en |
dc.description.tableofcontents | 誌 謝..................................................ii
中文摘要..................................................iii ABSTRACT................................................v CONTENTS................................................vii LIST OF TABLES..........................................x LIST OF FIGURES.........................................xi LIST OF SUPPLEMENTARY DATA..............................xiii Chapter 1 Introduction............................1 Chapter 2 Literature Review.......................3 2.1 Strawberry and strawberry anthracnose...........3 2.1.1 Strawberry......................................3 2.1.2 Strawberry anthracnose..........................7 2.2 Defense mechanisms in strawberry................10 2.2.1 PAMP-triggered immunity - pattern recognition receptor (PRR)..........................................11 2.2.2 Effector-triggered immunity- Resistance protein (ETI receptor)...............................................12 2.2.3 Signal transduction of kinase pathway...........13 2.2.4 SA-biosynthesis.................................15 2.2.5 SA downstream signaling.........................18 2.2.6 Pathogenesis-related (PR) protein...............21 2.3 Application of transcriptome technology in polyploidy plants.......................................24 Chapter 3 Experimental Design.....................27 3.1 Plant materials.................................27 3.2 Salicylic acid treatment........................27 3.3 Evaluation of anthracnose resistance............28 3.4 RNA extraction and cDNA preparation.............29 3.5 Semiquantitative reverse transcription polymerase chain reaction (semiquantitative RT-PCR)................31 3.6 Quantitative real-time RT-PCR (qRT-PCR).........32 3.7 Primer Design...................................32 3.8 Messenger RNA (mRNA) sample preparation for next generation sequencing...................................33 3.9 Illumina sequencing.............................34 3.10 Data filtering and de novo assembly.............34 3.11 Differential expression analysis and mapping back to diploid strawberry......................................35 3.12 Annotation and pathway prediction...............36 Chapter 4 Results.................................37 4.1 SA-induced resistance...........................37 4.2 Marker gene verification........................37 4.3 Transcripts sequencing..........................38 4.4 De novo assembling..............................38 4.5 Gene ontology (GO) functional annotation........40 4.6 Selection of transcripts with significant differential expression.................................40 4.7 Gene annotation strategy........................41 4.8 Assessing quality of gene annotation............42 4.9 Differentially expressed genes involved in upstream of SA-related pathway...................................43 4.10 Defense-related genes involved in downstream of SA pathway.................................................44 4.11 R genes, PRR genes, and kinase genes............45 4.12 Verification of gene expression pattern.........46 4.13 Comparison of quantifying gene expression by qRT-PCR and RNA-seq.............................................47 Chapter 5 Discussion..............................48 5.1 Comprehensive investigation into strawberry defense mechanisms..............................................48 5.2 High-throughput transcripts level in Fragaria x ananassa................................................49 5.3 Difficulty in dealing with the complex polyploidy genome..................................................50 5.3.1 Profiling of assembly-then-alignment strategy...50 5.3.2 Summary in dealing with the homeologous / homologous genes...................................................51 5.3.3 Cutoff selection in differential expression analysis ........................................................51 5.4 Comparison of the downstream SA genes in Fragaria x ananasa.................................................52 5.4.1 Downstream marker genes.........................52 5.4.2 General defense related genes...................54 5.4.3 Genes encoding SA receptors/regulators..........55 5.5 Comparison of the upstream SA genes in Fragaria x ananasa.................................................56 5.5.1 Upstream of SA biosynthesis pathway.............56 5.5.2 Recognition and signaling transduction..........56 5.6 Comparison of SA treatments with other plants...58 5.6.1 Similarity between cultivated strawberry and model plants in SA-mediated defense responses.................58 5.6.2 Novel genes and new components of SA-mediated defense network.........................................59 5.7 Concluding remarks..............................61 REFERENCES..............................................62 FIGURES & TABLES........................................72 | |
dc.language.iso | en | |
dc.title | 探討栽培種草莓在水楊酸誘導下所引發之抗病防禦網絡 | zh_TW |
dc.title | Uncovering salicylic acid-mediated defense network in cultivated strawberry | en |
dc.type | Thesis | |
dc.date.schoolyear | 101-2 | |
dc.description.degree | 碩士 | |
dc.contributor.oralexamcommittee | 曾顯雄(Shean-Shong Tzean),葉信宏(Hsin-Hung Yeh),林乃君(Nai-Chun Lin) | |
dc.subject.keyword | Fragaria x ananasa,水楊酸,抗性網絡,轉錄體定序, | zh_TW |
dc.subject.keyword | Fragaria x ananasa,salicylic acid,defense network,transcriptome sequencing, | en |
dc.relation.page | 166 | |
dc.rights.note | 有償授權 | |
dc.date.accepted | 2013-08-12 | |
dc.contributor.author-college | 生物資源暨農學院 | zh_TW |
dc.contributor.author-dept | 植物病理與微生物學研究所 | zh_TW |
dc.date.embargo-lift | 2023-08-08 | - |
顯示於系所單位: | 植物病理與微生物學系 |
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