探究徒長病對水稻苗期轉錄體之影響

Exploring the Transcriptome of Rice Seedlings Affected by Bakanae Disease

10.6342/NTU201800550

鄭安伯

水稻徒長病 ； 轉錄體分析 ； 防禦機制 ； CRISPR/Cas9 ； bakanae disease ； transcriptome analysis ； defense-related mechanisms ； CRISPR/Cas9

臺灣大學植物病理與微生物學研究所學位論文

2018年

碩士

鍾嘉綾

英文

水稻徒長病 (bakanae disease) 為Fusarium fujikuroi所引起的種子及土壤傳播性真菌病害，其侵染水稻後會造成植株徒長及/或葉片夾角加大等不正常生理現象，嚴重時可導致植株死亡或穀粒不充實。據報導，水稻徒長病曾在許多大規模水稻種植國家如日本、印度、泰國等地造成嚴重損失；臺灣近年則於東部有較嚴重發病之情形。由於水稻抵禦徒長病菌的相關機制目前研究甚少，本研究利用Illumina次世代定序技術，分析水稻抗病品系Tainung 67 (TNG67)及感病品系Zerawchanica karatals (ZK) 之幼苗基部受徒長病菌感染7天後之轉錄體，透過比對水稻與阿拉伯芥資料庫進行基因功能預測，探討與賀爾蒙及防禦相關之基因表現變化。結果顯示，F. fujikuroi接種後有顯著表現差異之基因 (differential expression genes, DEGs)，在抗病品系TNG67有118個 [包括WRKY、plant pattern recognition receptor (PRR)及peroxidase]，在感病品系ZK有169個 (包括cytochrome P450、WRKY、PRR、glycoside hydrolase、thaumatin-like protein及peroxidase)。檢視賀爾蒙相關之基因網路，發現吉貝素生合成、茉莉酸生合成、茉莉酸訊號傳遞路徑於接種前後並無整體上升或下降趨勢；而在抗性品系TNG67中，參與吉貝素訊號傳遞之OsGID1 (吉貝素受體；促進DELLA蛋白之降解) 表現量下降、OsSLR1 (DELLA蛋白；吉貝素訊息傳遞抑制因子) 則顯著上升，顯示抗病品種對吉貝素有負調控的現象。針對16個被註解為抗性相關之DEGs，利用real-time qRT-PCR測定額外三次獨立實驗中，TNG67與ZK兩品種接種7、14、21天後之基因表現，其中八個基因在接種後7天與轉錄體分析結果具有一致性，且於不同次獨立實驗之趨勢一致。本研究選擇以CRISPR/Cas9技術進行基因功能喪失驗證，首先以實驗室前人研究所得之三個抗稻熱病候選基因為對象，建立水稻CRISPR/Cas9系統，再應用於四個抗徒長病候選基因之突變。上述候選基因之single guide RNA (sgRNA) 質體，經T7核酸內切酶I進行水稻原生質體短暫表現之突變體檢測後，篩選出sgRNA突變率超過10%者，繼續進行水稻轉殖株之建立。目前已獲得其中一個基因之五個T0轉殖品系，經基因型測定後，確認有四個品系於目標序列被成功突變。期望透過本研究瞭解水稻對徒長病之抗性網路及有潛力的抗性基因，為水稻育種及病害防治找到新的發展方向。

Bakanae disease is a seedborne and soilborne fungal disease caused by Fusarium fujikuroi. The plants infected with the pathogen show symptoms such as abnormal stem elongation and/or wider angle of the leaf with the stem. Severe infection can cause seedling blight and sterile grains. In rice-growing countries such as Japan, India, and Thailand, there are reports on bakanae disease causing yield losses and great impact on rice production. In recent years, outbreaks of bakanae disease were observed in Taiwan, particularly in the eastern areas. Since little is known about the mechanisms involved in rice against F. fujikuroi, the research focuses on applying Illumina next-generation sequencing technology to analyze the transcriptome profiles of a resistant cultivar Tainung 67 (TNG67) and a susceptible cultivar Zerawchanica karatals (ZK), using the basal stems of rice seedlings collected after 7 days post inoculation (dpi) of F. fujikuroi. Genes were annotated according to the reference databases of Oryzae sativa (MSU7) and Arabidopsis thaliana (TAIR10). Expression profiles of genes associated with phytohormones and defense responses were examined. There were 118 differential expression genes (DEGs) in the resistant TNG67 [including WRKYs, plant pattern recognition receptor (PRR), and peroxidases] and 169 DEGs in the susceptible ZK (including cytochrome P450, WRKY, PRR, glycoside hydrolase, thaumatin-like protein, and peroxidase). For phytohormone biosynthesis and signaling pathways, overall up- or down-regulations were not observed in gibberellin (GA) biosynthesis, jasmonic acid (JA) biosynthesis, and JA signaling pathways. In TNG67, the GA signaling pathway seemed to be suppressed according to the down-regulation of OsGID1 (gibberellin receptor; induced degradation of DELLA proteins) and up-regulation of OsSLR1 (DELLA protein; GA-insensitive gene homolog) after F. fujikuroi inoculation. Real-time quantitative RT-PCR was conducted to evaluate the expression levels of 16 defense-related DEGs at 7, 14, and 21 dpi in additional three independent inoculation trials. A set of 8 candidate genes, with 7-dpi expression patterns similar to the transcriptome data and consistency among different replicated trials, were selected for loss-of-function verification using CRISPR/Cas9 system. Three blast-resistance candidate genes identified in our another study were used as targets to set up CRISPR/Cas9 system, which was subsequently applied to four candidate genes associated with bakanae resistance. Mutation efficiencies of single guide RNA (sgRNA) vectors were tested in rice protoplasts using T7 endonuclease I (T7E1) assay, and the constructs showed mutation efficiencies of >10% were sent for generating transgenic rice plants. Currently five T0 mutant lines for one candidate gene were obtained. These lines have been genotyped and four lines were successfully mutated at the target site. Uncovering potential resistance-related genes and mechanisms will provide new insights into resistance breeding and disease control of bakanae disease.

1. Amatulli, M., Spadaro, D., Gullino, M., and Garibaldi, A. 2010. Molecular identification of Fusarium spp. associated with bakanae disease of rice in Italy and assessment of their pathogenicity. Plant Pathology 59:839-844.
   連結：
2. Anders, S., and Huber, W. 2010. Differential expression analysis for sequence count data. Genome Biology 11:R106.
   連結：
3. Athwal, D. 1971. Semidwarf rice and wheat in global food needs. The Quarterly Review of Biology 46:1-34.
   連結：
4. Belhaj, K., Chaparro-Garcia, A., Kamoun, S., and Nekrasov, V. 2013. Plant genome editing made easy: targeted mutagenesis in model and crop plants using the CRISPR/Cas system. Plant Methods 9:39.
   連結：
5. Boatwright, J. L., and Pajerowska‐Mukhtar, K. 2013. Salicylic acid: an old hormone up to new tricks. Molecular Plant Pathology 14:623-634.
   連結：
6. Bogdanove, A. J., and Voytas, D. F. 2011. TAL effectors: customizable proteins for DNA targeting. Science 333:1843-1846.
   連結：
7. Boller, T., and He, S. Y. 2009. Innate immunity in plants: an arms race between pattern recognition receptors in plants and effectors in microbial pathogens. Science 324:742-744.
   連結：
8. Bostock, R. M. 2005. Signal crosstalk and induced resistance: straddling the line between cost and benefit. Annual Review of Phytopathology 43:545-580.
   連結：
9. Britt, A. B., and May, G. D. 2003. Re-engineering plant gene targeting. Trends in Plant Science 8:90-95.
   連結：
10. Cao, A., Jin, J., Li, S., and Wang, J. 2017. Integrated analysis of mRNA and miRNA expression profiling in rice backcrossed progenies (BC2F12) with different plant height. PLoS ONE 12:e0184106.
    連結：
11. Carroll, D. 2011. Genome engineering with zinc-finger nucleases. Genetics 188:773-782.
    連結：
12. Carter, L., Leslie, J., and Webster, R. 2008. Population structure of Fusarium fujikuroi from California rice and water grass. Phytopathology 98:992-998.
    連結：
13. Cermak, T., Doyle, E. L., Christian, M., Wang, L., Zhang, Y., Schmidt, C., Baller, J. A., Somia, N. V., Bogdanove, A. J., and Voytas, D. F. 2011. Efficient design and assembly of custom TALEN and other TAL effector-based constructs for DNA targeting. Nucleic Acids Research 39:e82-e82.
    連結：
14. Chang, W.-B. 2015. Identification of quantitative trait loci for blast resistance in Taiwan rice variety Tainung 84. National Taiwan University.
    連結：
15. Chen, K., and Gao, C. 2013. TALENs: customizable molecular DNA scissors for genome engineering of plants. Journal of Genetics and Genomics 40:271-279.
    連結：
16. Chen, S. Y., Huang, K. J., Kuo, Y. F., Lai, M. H., Chen, Y. C., and Chung, C. L. 2015. Three modified methods for evaluation of bakanae disease resistance in rice seedlings. Plant Pathology Bulletin 24:201-210.
    連結：
17. Chen, X., and Ronald, P. C. 2011. Innate immunity in rice. Trends in Plant Science 16:451-459.
    連結：
18. Chen, Y.-C., Lai, M.-H., Wu, C.-Y., Lin, T.-C., Cheng, A.-H., Yang, C.-C., Wu, H.-Y., Chu, S.-C., Kuo, C.-C., and Wu, Y.-F. 2016. The genetic structure, virulence, and fungicide sensitivity of Fusarium fujikuroi in Taiwan. Phytopathology 106:624-635.
    連結：
19. Chern, M., Fitzgerald, H. A., Canlas, P. E., Navarre, D. A., and Ronald, P. C. 2005. Overexpression of a rice NPR1 homolog leads to constitutive activation of defense response and hypersensitivity to light. Molecular Plant-Microbe Interactions 18:511-520.
    連結：
20. Chittoor, J. M., Leach, J. E., and White, F. F. 1997. Differential induction of a peroxidase gene family during infection of rice by Xanthomonas oryzae pv. oryzae. Molecular Plant-Microbe Interactions 10:861-871.
    連結：
21. De Vleesschauwer, D., Gheysen, G., and Höfte, M. 2013. Hormone defense networking in rice: tales from a different world. Trends in Plant Science 18:555-565.
    連結：
22. De Vleesschauwer, D., Xu, J., and Höfte, M. 2014. Making sense of hormone-mediated defense networking: from rice to Arabidopsis. Frontiers in Plant Science 5:1-15.
    連結：
23. De Vleesschauwer, D., Yang, Y., Cruz, C. V., and Höfte, M. 2010. Abscisic acid-induced resistance against the brown spot pathogen Cochliobolus miyabeanus in rice involves MAP kinase-mediated repression of ethylene signaling. Plant Physiology 152:2036-2052.
    連結：
24. Deltcheva, E., Chylinski, K., Sharma, C. M., Gonzales, K., Chao, Y., Pirzada, Z. A., Eckert, M. R., Vogel, J., and Charpentier, E. 2011. CRISPR RNA maturation by trans-encoded small RNA and host factor RNase III. Nature 471:602-607.
    連結：
25. Derksen, H., Rampitsch, C., and Daayf, F. 2013. Signaling cross-talk in plant disease resistance. Plant Science 207:79-87.
    連結：
26. Dill, A., Jung, H.-S., and Sun, T.-p. 2001. The DELLA motif is essential for gibberellin-induced degradation of RGA. Proceedings of the National Academy of Sciences 98:14162-14167.
    連結：
27. Du, Z., Zhou, X., Ling, Y., Zhang, Z., and Su, Z. 2010. agriGO: a GO analysis toolkit for the agricultural community. Nucleic Acids Research 38:W64-W70.
    連結：
28. Eizenga, G. C., Ali, M., Bryant, R. J., Yeater, K. M., McClung, A. M., and McCouch, S. R. 2014. Registration of the rice diversity panel 1 for genomewide association studies. Journal of Plant Registrations 8:109-116.
    連結：
29. Fu, X., Richards, D. E., Ait-Ali, T., Hynes, L. W., Ougham, H., Peng, J., and Harberd, N. P. 2002. Gibberellin-mediated proteasome-dependent degradation of the barley DELLA protein SLN1 repressor. The Plant Cell 14:3191-3200.
    連結：
30. Glazebrook, J. 2005. Contrasting mechanisms of defense against biotrophic and necrotrophic pathogens. Annual Reviews Phytopathology 43:205-227.
    連結：
31. Gomi, K., and Matsuoka, M. 2003. Gibberellin signalling pathway. Current Opinion in Plant Biology 6:489-493.
    連結：
32. Grant, M. R., and Jones, J. D. 2009. Hormone (dis)harmony moulds plant health and disease. Science 324:750-752.
    連結：
33. Grennan, A. K. 2006. Gibberellin metabolism enzymes in rice. Plant Physiology 141:524-526.
    連結：
34. Gutjahr, C., and Paszkowski, U. 2009. Weights in the balance: jasmonic acid and salicylic acid signaling in root-biotroph interactions. Molecular Plant-Microbe Interactions 22:763-772.
    連結：
35. Hamberger, B., and Bak, S. 2013. Plant P450s as versatile drivers for evolution of species-specific chemical diversity. Philosophical Transactions of the Royal Society B: Biological Sciences 368:20120426.
    連結：
36. Haq, M., Mia, M. T., Rabbi, M., and Ali, M. 2010. Incidence and severity of rice diseases and insect pests in relation to climate change. Pages 445-457 in: Climate Change and Food Security in South Asia. Springer.
    連結：
37. Hedden, P. 2003. The genes of the Green Revolution. TRENDS in Genetics 19:5-9.
    連結：
38. Heitz, T., Widemann, E., Lugan, R., Miesch, L., Ullmann, P., Désaubry, L., Holder, E., Grausem, B., Kandel, S., and Miesch, M. 2012. Cytochromes P450 CYP94C1 and CYP94B3 catalyze two successive oxidation steps of plant hormone jasmonoyl-isoleucine for catabolic turnover. Journal of Biological Chemistry 287:6296-6306.
    連結：
39. Helliwell, E. E., Wang, Q., and Yang, Y. 2013. Transgenic rice with inducible ethylene production exhibits broad‐spectrum disease resistance to the fungal pathogens Magnaporthe oryzae and Rhizoctonia solani. Plant Biotechnology Journal 11:33-42.
    連結：
40. Hilaire, E., Young, S. A., Willard, L. H., McGee, J. D., Sweat, T., Chittoor, J., Guikema, J. A., and Leach, J. E. 2001. Vascular defense responses in rice: peroxidase accumulation in xylem parenchyma cells and xylem wall thickening. Molecular Plant-Microbe Interactions 14:1411-1419.
    連結：
41. Hsieh, W., Smith, S., and Snyder, W. 1977. Mating groups in Fusarium moniliforme. Phytopathology 67:1041-1043.
    連結：
42. Hsu, C. C., Huang, J. W., and Chen, C. Y. 2013. The cause of rice bakanae disease in Taiwan. Plant Pathology Bulletin 22:279-289.
    連結：
43. Ikeda, A., Ueguchi-Tanaka, M., Sonoda, Y., Kitano, H., Koshioka, M., Futsuhara, Y., Matsuoka, M., and Yamaguchi, J. 2001. slender rice, a constitutive gibberellin response mutant, is caused by a null mutation of the SLR1 gene, an ortholog of the height-regulating gene GAI/RGA/RHT/D8. The Plant Cell 13:999-1010.
    連結：
44. Inoue, H., Hayashi, N., Matsushita, A., Xinqiong, L., Nakayama, A., Sugano, S., Jiang, C.-J., and Takatsuji, H. 2013. Blast resistance of CC-NB-LRR protein Pb1 is mediated by WRKY45 through protein–protein interaction. Proceedings of the National Academy of Sciences 110:9577-9582.
    連結：
45. Itoh, H., Ueguchi-Tanaka, M., Sato, Y., Ashikari, M., and Matsuoka, M. 2002. The gibberellin signaling pathway is regulated by the appearance and disappearance of SLENDER RICE1 in nuclei. The Plant Cell 14:57-70.
    連結：
46. Izzati Mohd Zainudin, N., Razak, A., and Salleh, B. 2008. Bakanae disease of rice in Malaysia and Indonesia: etiology of the causal agent based on morphological, physiological and pathogenicity characteristics. Journal of Plant Protection Research 48:475-485.
    連結：
47. Ji, Z., Zeng, Y., Liang, Y., Qian, Q., and Yang, C. 2016. Transcriptomic dissection of the rice–Fusarium fujikuroi interaction by RNA-Seq. Euphytica 211:123-137.
    連結：
48. Jinek, M., Chylinski, K., Fonfara, I., Hauer, M., Doudna, J. A., and Charpentier, E. 2012. A programmable dual-RNA–guided DNA endonuclease in adaptive bacterial immunity. Science 337:816-821.
    連結：
49. Kanehisa, M., and Goto, S. 2000. KEGG: kyoto encyclopedia of genes and genomes. Nucleic Acids Research 28:27-30.
    連結：
50. Kanehisa, M., Sato, Y., Kawashima, M., Furumichi, M., and Tanabe, M. 2016. KEGG as a reference resource for gene and protein annotation. Nucleic Acids Research 44:D457-D462.
    連結：
51. Kanehisa, M., Furumichi, M., Tanabe, M., Sato, Y., and Morishima, K. 2017. KEGG: new perspectives on genomes, pathways, diseases and drugs. Nucleic Acids Research 45:D353-D361.
    連結：
52. Khush, G. S. 1999. Green revolution: preparing for the 21st century. Genome 42:646-655.
    連結：
53. Konishi, H., Ishiguro, K., and Komatsu, S. 2001. A proteomics approach towards understanding blast fungus infection of rice grown under different levels of nitrogen fertilization. Proteomics 1:1162-1171.
    連結：
54. Kurosawa, E. 1926. Experimental studies on the nature of the substance secreted by the" bakanae" fungus. Natural History Society of Formosa 16:213-227.
    連結：
55. Kyozuka, J. 2007. Control of shoot and root meristem function by cytokinin. Current Opinion in Plant Biology 10:442-446.
    連結：
56. La Camera, S., Gouzerh, G., Dhondt, S., Hoffmann, L., Fritig, B., Legrand, M., and Heitz, T. 2004. Metabolic reprogramming in plant innate immunity: the contributions of phenylpropanoid and oxylipin pathways. Immunological Reviews 198:267-284.
    連結：
57. Langmead, B., and Salzberg, S. L. 2012. Fast gapped-read alignment with Bowtie 2. Nature Methods 9:357-359.
    連結：
58. Leslie, J. F. 1995. Gibberella fujikuroi: available populations and variable traits. Canadian Journal of Botany 73:282-291.
    連結：
59. Li, T., Liu, B., Spalding, M. H., Weeks, D. P., and Yang, B. 2012. High-efficiency TALEN-based gene editing produces disease-resistant rice. Nature Biotechnology 30:390-392.
    連結：
60. Lin, S., Staahl, B., Alla, R. K., and Doudna, J. A. 2014. Enhanced homology-directed human genome engineering by controlled timing of CRISPR/Cas9 delivery. Elife 3:e04766.
    連結：
61. Liu, L.-Y. D., Tseng, H.-I., Lin, C.-P., Lin, Y.-Y., Huang, Y.-H., Huang, C.-K., Chang, T.-H., and Lin, S.-S. 2014. High-throughput transcriptome analysis of the leafy flower transition of Catharanthus roseus induced by peanut witches’-broom phytoplasma infection. Plant and Cell Physiology 55:942-957.
    連結：
62. Liu, X., Bai, X., Wang, X., and Chu, C. 2007. OsWRKY71, a rice transcription factor, is involved in rice defense response. Journal of Plant Physiology 164:969-979.
    連結：
63. Liu, X., Li, F., Tang, J., Wang, W., Zhang, F., Wang, G., Chu, J., Yan, C., Wang, T., and Chu, C. 2012. Activation of the jasmonic acid pathway by depletion of the hydroperoxide lyase OsHPL3 reveals crosstalk between the HPL and AOS branches of the oxylipin pathway in rice. PLoS ONE 7:e50089.
    連結：
64. Lyons, R., Manners, J. M., and Kazan, K. 2013. Jasmonate biosynthesis and signaling in monocots: a comparative overview. Plant Cell Reports 32:815-827.
    連結：
65. Mahmood, T., Jan, A., Kakishima, M., and Komatsu, S. 2006. Proteomic analysis of bacterial‐blight defense‐responsive proteins in rice leaf blades. Proteomics 6:6053-6065.
    連結：
66. Malamy, J., and Klessig, D. F. 1992. Salicylic acid and plant disease resistance. The Plant Journal 2:643-654.
    連結：
67. Manandhar, H., Mathur, S., Smedegaard-Petersen, V., and Thordal-Christensen, H. 1999. Accumulation of transcripts for pathogenesis–related proteins and peroxidase in rice plants triggered by Pyricularia oryzae, Bipolaris sorokiniana and uv light. Physiological and Molecular Plant Pathology 55:289-295.
    連結：
68. Manosalva, P. M., Davidson, R. M., Liu, B., Zhu, X., Hulbert, S. H., Leung, H., and Leach, J. E. 2009. A germin-like protein gene family functions as a complex quantitative trait locus conferring broad-spectrum disease resistance in rice. Plant Physiology 149:286-296.
    連結：
69. Mao, Y., Zhang, H., Xu, N., Zhang, B., Gou, F., and Zhu, J.-K. 2013. Application of the CRISPR–Cas system for efficient genome engineering in plants. Molecular Plant 6:2008.
    連結：
70. Matić, S., Bagnaresi, P., Biselli, C., Carneiro, G. A., Siciliano, I., Valé, G., Gullino, M. L., and Spadaro, D. 2016. Comparative transcriptome profiling of resistant and susceptible rice genotypes in response to the seedborne pathogen Fusarium fujikuroi. BMC Genomics 17:608.
    連結：
71. Matsushita, A., Inoue, H., Goto, S., Nakayama, A., Sugano, S., Hayashi, N., and Takatsuji, H. 2013. Nuclear ubiquitin proteasome degradation affects WRKY45 function in the rice defense program. The Plant Journal 73:302-313.
    連結：
72. Mei, C., Qi, M., Sheng, G., and Yang, Y. 2006. Inducible overexpression of a rice allene oxide synthase gene increases the endogenous jasmonic acid level, PR gene expression, and host resistance to fungal infection. Molecular Plant-Microbe Interactions 19:1127-1137.
    連結：
73. Miller, J. C., Holmes, M. C., Wang, J., Guschin, D. Y., Lee, Y.-L., Rupniewski, I., Beausejour, C. M., Waite, A. J., Wang, N. S., and Kim, K. A. 2007. An improved zinc-finger nuclease architecture for highly specific genome editing. Nature Biotechnology 25:778-785.
    連結：
74. Monaghan, J., and Zipfel, C. 2012. Plant pattern recognition receptor complexes at the plasma membrane. Current Opinion in Plant Biology 15:349-357.
    連結：
75. Mur, L. A., Kenton, P., Atzorn, R., Miersch, O., and Wasternack, C. 2006. The outcomes of concentration-specific interactions between salicylate and jasmonate signaling include synergy, antagonism, and oxidative stress leading to cell death. Plant Physiology 140:249-262.
    連結：
76. Nahar, K., Kyndt, T., De Vleesschauwer, D., Höfte, M., and Gheysen, G. 2011. The jasmonate pathway is a key player in systemically induced defense against root knot nematodes in rice. Plant Physiology 157:305-316.
    連結：
77. Navarro, L., Bari, R., Achard, P., Lisón, P., Nemri, A., Harberd, N. P., and Jones, J. D. 2008. DELLAs control plant immune responses by modulating the balance of jasmonic acid and salicylic acid signaling. Current Biology 18:650-655.
    連結：
78. Niewoehner, O., Jinek, M., and Doudna, J. A. 2013. Evolution of CRISPR RNA recognition and processing by Cas6 endonucleases. Nucleic Acids Research 42:1341-1353.
    連結：
79. Norman-Setterblad, C., Vidal, S., and Palva, E. T. 2000. Interacting signal pathways control defense gene expression in Arabidopsis in response to cell wall-degrading enzymes from Erwinia carotovora. Molecular Plant-Microbe Interactions 13:430-438.
    連結：
80. Ohira, K., Ojima, K., and Fujiwara, A. 1973. Studies on the nutrition of rice cell culture I. A simple, defined medium for rapid growth in suspension culture. Plant and Cell Physiology 14:1113-1121.
    連結：
81. Ou, S. 1984. Exploring tropical rice diseases: a reminiscence. Annual Review of Phytopathology 22:1-11.
    連結：
82. Pan, C., Ye, L., Qin, L., Liu, X., He, Y., Wang, J., Chen, L., and Lu, G. 2016. CRISPR/Cas9-mediated efficient and heritable targeted mutagenesis in tomato plants in the first and later generations. Scientific Reports 6:24765.
    連結：
83. Park, W.-S., Choi, H.-W., Han, S.-S., Shin, D.-B., Shim, H.-K., Jung, E.-S., Lee, S.-W., Lim, C.-K., and Lee, Y.-H. 2009. Control of bakanae disease of rice by seed soaking into the mixed solution of procholraz and fludioxnil. Research in Plant Disease 15:94-100.
    連結：
84. Passardi, F., Cosio, C., Penel, C., and Dunand, C. 2005. Peroxidases have more functions than a Swiss army knife. Plant Cell Reports 24:255-265.
    連結：
85. Peng, J., Carol, P., Richards, D. E., King, K. E., Cowling, R. J., Murphy, G. P., and Harberd, N. P. 1997. The Arabidopsis GAI gene defines a signaling pathway that negatively regulates gibberellin responses. Genes & Development 11:3194-3205.
    連結：
86. Pieterse, C. M., Leon-Reyes, A., Van der Ent, S., and Van Wees, S. C. 2009. Networking by small-molecule hormones in plant immunity. Nature Chemical Biology 5:308-316.
    連結：
87. Pinot, F., and Beisson, F. 2011. Cytochrome P450 metabolizing fatty acids in plants: characterization and physiological roles. The Federation of European Biochemical Societies Journal 278:195-205.
    連結：
88. Qin, X., Liu, J. H., Zhao, W. S., Chen, X. J., Guo, Z. J., and Peng, Y. L. 2013. Gibberellin 20-oxidase gene OsGA20ox3 regulates plant stature and disease development in rice. Molecular Plant-Microbe Interactions 26:227-239.
    連結：
89. Qiu, D., Xiao, J., Xie, W., Cheng, H., Li, X., and Wang, S. 2009. Exploring transcriptional signalling mediated by OsWRKY13, a potential regulator of multiple physiological processes in rice. BMC Plant Biology 9:74.
    連結：
90. Qiu, D., Xiao, J., Xie, W., Liu, H., Li, X., Xiong, L., and Wang, S. 2008. Rice gene network inferred from expression profiling of plants overexpressing OsWRKY13, a positive regulator of disease resistance. Molecular Plant 1:538-551.
    連結：
91. Qiu, D., Xiao, J., Ding, X., Xiong, M., Cai, M., Cao, Y., Li, X., Xu, C., and Wang, S. 2007. OsWRKY13 mediates rice disease resistance by regulating defense-related genes in salicylate-and jasmonate-dependent signaling. Molecular Plant-Microbe Interactions 20:492-499.
    連結：
92. Ray, A., and Langer, M. 2002. Homologous recombination: ends as the means. Trends in Plant Science 7:435-440.
    連結：
93. Reuber, T. L., Plotnikova, J. M., Dewdney, J., Rogers, E. E., Wood, W., and Ausubel, F. M. 1998. Correlation of defense gene induction defects with powdery mildew susceptibility in Arabidopsis enhanced disease susceptibility mutants. The Plant Journal 16:473-485.
    連結：
94. Riemann, M., Riemann, M., and Takano, M. 2008. Rice JASMONATE RESISTANT 1 is involved in phytochrome and jasmonate signalling. Plant, Cell & Environment 31:783-792.
    連結：
95. Riemann, M., Haga, K., Shimizu, T., Okada, K., Ando, S., Mochizuki, S., Nishizawa, Y., Yamanouchi, U., Nick, P., and Yano, M. 2013. Identification of rice Allene Oxide Cyclase mutants and the function of jasmonate for defence against Magnaporthe oryzae. The Plant Journal 74:226-238.
    連結：
96. Robert-Seilaniantz, A., Grant, M., and Jones, J. D. 2011. Hormone crosstalk in plant disease and defense: more than just jasmonate-salicylate antagonism. Annual Review of Phytopathology 49:317-343.
    連結：
97. Roberts, W. K., and Selitrennikoff, C. P. 1990. Zeamatin, an antifungal protein from maize with membrane-permeabilizing activity. Microbiology 136:1771-1778.
    連結：
98. Ross, C. A., Liu, Y., and Shen, Q. J. 2007. The WRKY gene family in rice (Oryza sativa). Journal of Integrative Plant Biology 49:827-842.
    連結：
99. Sakamoto, T., Miura, K., Itoh, H., Tatsumi, T., Ueguchi-Tanaka, M., Ishiyama, K., Kobayashi, M., Agrawal, G. K., Takeda, S., and Abe, K. 2004. An overview of gibberellin metabolism enzyme genes and their related mutants in rice. Plant Physiology 134:1642-1653.
    連結：
100. Sallaud, C., Meynard, D., Van Boxtel, J., Gay, C., Bes, M., Brizard, J.-P., Larmande, P., Ortega, D., Raynal, M., and Portefaix, M. 2003. Highly efficient production and characterization of T-DNA plants for rice (Oryza sativa L.) functional genomics. Theoretical and Applied Genetics 106:1396-1408.
     連結：
101. Sampson, T. R., Saroj, S. D., Llewellyn, A. C., Tzeng, Y.-L., and Weiss, D. S. 2013. A CRISPR/Cas system mediates bacterial innate immune evasion and virulence. Nature 497:254-257.
     連結：
102. Santiago-Sotelo, P., and Ramirez-Prado, J. 2012. prfectBLAST: a platform-independent portable front end for the command terminal BLAST+ stand-alone suite. BioTechniques 53:299.
     連結：
103. Sapranauskas, R., Gasiunas, G., Fremaux, C., Barrangou, R., Horvath, P., and Siksnys, V. 2011. The Streptococcus thermophilus CRISPR/Cas system provides immunity in Escherichia coli. Nucleic Acids Research 39:9275-9282.
     連結：
104. Schneider, C. A., Rasband, W. S., and Eliceiri, K. W. 2012. NIH Image to ImageJ: 25 years of image analysis. Nature Methods 9:671-675.
     連結：
105. Shan, Q., Wang, Y., Li, J., and Gao, C. 2014. Genome editing in rice and wheat using the CRISPR/Cas system. Nature Protocols 9:2395-2410.
     連結：
106. Shan, Q., Wang, Y., Chen, K., Liang, Z., Li, J., Zhang, Y., Zhang, K., Liu, J., Voytas, D. F., and Zheng, X. 2013a. Rapid and efficient gene modification in rice and Brachypodium using TALENs. Molecular Plant 6:1365-1368.
     連結：
107. Shan, Q., Wang, Y., Li, J., Zhang, Y., Chen, K., Liang, Z., Zhang, K., Liu, J., Xi, J. J., and Qiu, J.-L. 2013b. Targeted genome modification of crop plants using a CRISPR-Cas system. Nature Biotechnology 31:686-688.
     連結：
108. Sharma, R., Cao, P., Jung, K.-H., Sharma, M. K., and Ronald, P. C. 2013. Construction of a rice glycoside hydrolase phylogenomic database and identification of targets for biofuel research. Frontiers in Plant Science 4.
     連結：
109. Shen, X., Liu, H., Yuan, B., Li, X., Xu, C., and Wang, S. 2011. OsEDR1 negatively regulates rice bacterial resistance via activation of ethylene biosynthesis. Plant, Cell & Environment 34:179-191.
     連結：
110. Shimono, M., Sugano, S., Nakayama, A., Jiang, C.-J., Ono, K., Toki, S., and Takatsuji, H. 2007. Rice WRKY45 plays a crucial role in benzothiadiazole-inducible blast resistance. The Plant Cell 19:2064-2076.
     連結：
111. Shimono, M., Koga, H., Akagi, A., Hayashi, N., Goto, S., Sawada, M., Kurihara, T., Matsushita, A., Sugano, S., and JIANG, C. J. 2012. Rice WRKY45 plays important roles in fungal and bacterial disease resistance. Molecular Plant Pathology 13:83-94.
     連結：
112. Shukla, V. K., Doyon, Y., Miller, J. C., DeKelver, R. C., Moehle, E. A., Worden, S. E., Mitchell, J. C., Arnold, N. L., Gopalan, S., and Meng, X. 2009. Precise genome modification in the crop species Zea mays using zinc-finger nucleases. Nature 459:437-441.
     連結：
113. Siciliano, I., Amaral Carneiro, G., Spadaro, D., Garibaldi, A., and Gullino, M. L. 2015. Jasmonic acid, abscisic acid, and salicylic acid are involved in the phytoalexin responses of rice to Fusarium fujikuroi, a high gibberellin producer pathogen. Journal of Agricultural and Food Chemistry 63:8134-8142.
     連結：
114. Silverman, P., Seskar, M., Kanter, D., Schweizer, P., Metraux, J.-P., and Raskin, I. 1995. Salicylic acid in rice (biosynthesis, conjugation, and possible role). Plant Physiology 108:633-639.
     連結：
115. Silverstone, A. L., Jung, H.-S., Dill, A., Kawaide, H., Kamiya, Y., and Sun, T.-p. 2001. Repressing a repressor gibberellin-induced rapid reduction of the RGA protein in Arabidopsis. The Plant Cell 13:1555-1566.
     連結：
116. Sinkunas, T., Gasiunas, G., Waghmare, S. P., Dickman, M. J., Barrangou, R., Horvath, P., and Siksnys, V. 2013. In vitro reconstitution of Cascade‐mediated CRISPR immunity in Streptococcus thermophilus. The EMBO Journal 32:385-394.
     連結：
117. Sorek, R., Lawrence, C. M., and Wiedenheft, B. 2013. CRISPR-mediated adaptive immune systems in bacteria and archaea. Annual Review of Biochemistry 82:237-266.
     連結：
118. Sugano, S., Jiang, C.-J., Miyazawa, S.-I., Masumoto, C., Yazawa, K., Hayashi, N., Shimono, M., Nakayama, A., Miyao, M., and Takatsuji, H. 2010. Role of OsNPR1 in rice defense program as revealed by genome-wide expression analysis. Plant Molecular Biology 74:549-562.
     連結：
119. Sun, T.-p. 2011. The molecular mechanism and evolution of the GA–GID1–DELLA signaling module in plants. Current Biology 21:R338-R345.
     連結：
120. Symington, L. S., and Gautier, J. 2011. Double-strand break end resection and repair pathway choice. Annual Review of Genetics 45:247-271.
     連結：
121. Taheri, P., and Tarighi, S. 2010. Riboflavin induces resistance in rice against Rhizoctonia solani via jasmonate-mediated priming of phenylpropanoid pathway. Journal of Plant Physiology 167:201-208.
     連結：
122. Takatsuji, H., Jiang, C.-J., and Sugano, S. 2010. Salicylic acid signaling pathway in rice and the potential applications of its regulators. Japan Agricultural Research Quarterly: JARQ 44:217-223.
     連結：
123. Takeuchi, K., Gyohda, A., Tominaga, M., Kawakatsu, M., Hatakeyama, A., Ishii, N., Shimaya, K., Nishimura, T., Riemann, M., and Nick, P. 2011. RSOsPR10 expression in response to environmental stresses is regulated antagonistically by jasmonate/ethylene and salicylic acid signaling pathways in rice roots. Plant and Cell Physiology 52:1686-1696.
     連結：
124. Tamaoki, D., Seo, S., Yamada, S., Kano, A., Miyamoto, A., Shishido, H., Miyoshi, S., Taniguchi, S., Akimitsu, K., and Gomi, K. 2013. Jasmonic acid and salicylic acid activate a common defense system in rice. Plant Signaling & Behavior 8:e24260.
     連結：
125. Tanaka, N., Matsuoka, M., Kitano, H., Asano, T., Kaku, H., and Komatsu, S. 2006. gid1, a gibberellin‐insensitive dwarf mutant, shows altered regulation of probenazole‐inducible protein (PBZ1) in response to cold stress and pathogen attack. Plant, Cell & Environment 29:619-631.
     連結：
126. Taniguchi, S., HOSOKAWA‐SHINONAGA, Y., Tamaoki, D., Yamada, S., Akimitsu, K., and Gomi, K. 2014. Jasmonate induction of the monoterpene linalool confers resistance to rice bacterial blight and its biosynthesis is regulated by JAZ protein in rice. Plant, Cell & Environment 37:451-461.
     連結：
127. Tao, Z., Liu, H., Qiu, D., Zhou, Y., Li, X., Xu, C., and Wang, S. 2009. A pair of allelic WRKY genes play opposite roles in rice-bacteria interactions. Plant Physiology 151:936-948.
     連結：
128. Terns, M. P., and Terns, R. M. 2011. CRISPR-based adaptive immune systems. Current Opinion in Microbiology 14:321-327.
     連結：
129. Thaler, J. S., Humphrey, P. T., and Whiteman, N. K. 2012. Evolution of jasmonate and salicylate signal crosstalk. Trends in Plant Science 17:260-270.
     連結：
130. Thomma, B. P., Penninckx, I. A., Cammue, B. P., and Broekaert, W. F. 2001. The complexity of disease signaling in Arabidopsis. Current Opinion in Immunology 13:63-68.
     連結：
131. Tian, T., Liu, Y., Yan, H., You, Q., Yi, X., Du, Z., Xu, W., and Su, Z. 2017. agriGO v2. 0: a GO analysis toolkit for the agricultural community, 2017 update. Nucleic Acids Research.
     連結：
132. Tong, X., Qi, J., Zhu, X., Mao, B., Zeng, L., Wang, B., Li, Q., Zhou, G., Xu, X., and Lou, Y. 2012. The rice hydroperoxide lyase OsHPL3 functions in defense responses by modulating the oxylipin pathway. The Plant Journal 71:763-775.
     連結：
133. Townsend, J. A., Wright, D. A., Winfrey, R. J., Fu, F., Maeder, M. L., Joung, J. K., and Voytas, D. F. 2009. High-frequency modification of plant genes using engineered zinc-finger nucleases. Nature 459:442-445.
     連結：
134. Untergasser, A., Cutcutache, I., Koressaar, T., Ye, J., Faircloth, B. C., Remm, M., and Rozen, S. G. 2012. Primer3—new capabilities and interfaces. Nucleic Acids Research 40:e115-e115.
     連結：
135. Vigers, A. J., Roberts, W. K., and Selitrennikoff, C. P. 1991. A new family of plant antifungal proteins. Molecular Plant-Microbe Interactions 4:315-323.
     連結：
136. Vlot, A. C., Dempsey, D. M. A., and Klessig, D. F. 2009. Salicylic acid, a multifaceted hormone to combat disease. Annual Review of Phytopathology 47:177-206.
     連結：
137. Vogt, T. 2010. Phenylpropanoid biosynthesis. Molecular Plant 3:2-20.
     連結：
138. Voigt, K., Schleier, S., and Brückner, B. 1995. Genetic variability in Gibberella fujikuroi and some related species of the genus Fusarium based on random amplification of polymorphic DNA (RAPD). Current Genetics 27:528-535.
     連結：
139. Vouillot, L., Thélie, A., and Pollet, N. 2015. Comparison of T7E1 and surveyor mismatch cleavage assays to detect mutations triggered by engineered nucleases. G3: Genes, Genomes, Genetics 5:407-415.
     連結：
140. Wang, L., Shen, R., Chen, L. T., and Liu, Y. G. 2014. Characterization of a novel DUF1618 gene family in rice. Journal of Integrative Plant Biology 56:151-158.
     連結：
141. Wiedenheft, B., Sternberg, S. H., and Doudna, J. A. 2012. RNA-guided genetic silencing systems in bacteria and archaea. Nature 482:331-338.
     連結：
142. Wollenweber, H. W. 1931. Fusarium-Monographie. Parasitology Research 3:269-516.
     連結：
143. Woo, J. W., Kim, J., Kwon, S. I., Corvalán, C., Cho, S. W., Kim, H., Kim, S.-G., Kim, S.-T., Choe, S., and Kim, J.-S. 2015. DNA-free genome editing in plants with preassembled CRISPR-Cas9 ribonucleoproteins. Nature Biotechnology 33:1162-1164.
     連結：
144. Xie, K., and Yang, Y. 2013. RNA-guided genome editing in plants using a CRISPR–Cas system. Molecular Plant 6:1975-1983.
     連結：
145. Yamada, S., Kano, A., Tamaoki, D., Miyamoto, A., Shishido, H., Miyoshi, S., Taniguchi, S., Akimitsu, K., and Gomi, K. 2012. Involvement of OsJAZ8 in jasmonate-induced resistance to bacterial blight in rice. Plant and Cell Physiology 53:2060-2072.
     連結：
146. Yan, H., Saika, H., Maekawa, M., Takamure, I., Tsutsumi, N., Kyozuka, J., and Nakazono, M. 2007. Rice tillering dwarf mutant dwarf3 has increased leaf longevity during darkness-induced senescence or hydrogen peroxide-induced cell death. Genes & Genetic Systems 82:361-366.
     連結：
147. Yang, D.-L., Li, Q., Deng, Y.-W., Lou, Y.-G., Wang, M.-Y., Zhou, G.-X., Zhang, Y.-Y., and He, Z.-H. 2008. Altered disease development in the eui mutants and Eui overexpressors indicates that gibberellins negatively regulate rice basal disease resistance. Molecular Plant 1:528-537.
     連結：
148. Ye, M., Luo, S. M., Xie, J. F., Li, Y. F., Xu, T., Liu, Y., Song, Y. Y., Zhu-Salzman, K., and Zeng, R. S. 2012. Silencing COI1 in rice increases susceptibility to chewing insects and impairs inducible defense. PLoS ONE 7:e36214.
     連結：
149. Ying, J., Zhao, J., Hou, Y., Wang, Y., Qiu, J., Li, Z., Tong, X., Shi, Z., Zhu, J., and Zhang, J. 2017. Mapping the N-linked glycosites of rice (Oryza sativa L.) germinating embryos. PLoS ONE 12:e0173853.
     連結：
150. Yuan, Y., Zhong, S., Li, Q., Zhu, Z., Lou, Y., Wang, L., Wang, J., Wang, M., Li, Q., and Yang, D. 2007. Functional analysis of rice NPR1‐like genes reveals that OsNPR1/NH1 is the rice orthologue conferring disease resistance with enhanced herbivore susceptibility. Plant Botechnology Journal 5:313-324.
     連結：
151. Zhou, G., Qi, J., Ren, N., Cheng, J., Erb, M., Mao, B., and Lou, Y. 2009. Silencing OsHI‐LOX makes rice more susceptible to chewing herbivores, but enhances resistance to a phloem feeder. The Plant Journal 60:638-648.
     連結：
152. Zipfel, C. 2008. Pattern-recognition receptors in plant innate immunity. Current Opinion in Immunology 20:10-16.
     連結：
153. Zipfel, C. 2014. Plant pattern-recognition receptors. Trends in Immunology 35:345-351.
     連結：
154. Zulfugarov, I. S., Tovuu, A., Kim, C.-Y., Vo, K. T. X., Ko, S. Y., Hall, M., Seok, H.-Y., Kim, Y.-K., Skogstrom, O., and Moon, Y.-H. 2016. Enhanced resistance of PsbS-deficient rice (Oryza sativa L.) to fungal and bacterial pathogens. Journal of Plant Biology 59:616-626.
     連結：
155. Amatulli, M., Spadaro, D., Gullino, M., and Garibaldi, A. 2010. Molecular identification of Fusarium spp. associated with bakanae disease of rice in Italy and assessment of their pathogenicity. Plant Pathology 59:839-844.
     連結：
156. Anders, S., and Huber, W. 2010. Differential expression analysis for sequence count data. Genome Biology 11:R106.
     連結：
157. Athwal, D. 1971. Semidwarf rice and wheat in global food needs. The Quarterly Review of Biology 46:1-34.
     連結：
158. Belhaj, K., Chaparro-Garcia, A., Kamoun, S., and Nekrasov, V. 2013. Plant genome editing made easy: targeted mutagenesis in model and crop plants using the CRISPR/Cas system. Plant Methods 9:39.
     連結：
159. Boatwright, J. L., and Pajerowska‐Mukhtar, K. 2013. Salicylic acid: an old hormone up to new tricks. Molecular Plant Pathology 14:623-634.
     連結：
160. Bogdanove, A. J., and Voytas, D. F. 2011. TAL effectors: customizable proteins for DNA targeting. Science 333:1843-1846.
     連結：
161. Boller, T., and He, S. Y. 2009. Innate immunity in plants: an arms race between pattern recognition receptors in plants and effectors in microbial pathogens. Science 324:742-744.
     連結：
162. Bostock, R. M. 2005. Signal crosstalk and induced resistance: straddling the line between cost and benefit. Annual Review of Phytopathology 43:545-580.
     連結：
163. Britt, A. B., and May, G. D. 2003. Re-engineering plant gene targeting. Trends in Plant Science 8:90-95.
     連結：
164. Cao, A., Jin, J., Li, S., and Wang, J. 2017. Integrated analysis of mRNA and miRNA expression profiling in rice backcrossed progenies (BC2F12) with different plant height. PLoS ONE 12:e0184106.
     連結：
165. Carroll, D. 2011. Genome engineering with zinc-finger nucleases. Genetics 188:773-782.
     連結：
166. Carter, L., Leslie, J., and Webster, R. 2008. Population structure of Fusarium fujikuroi from California rice and water grass. Phytopathology 98:992-998.
     連結：
167. Cermak, T., Doyle, E. L., Christian, M., Wang, L., Zhang, Y., Schmidt, C., Baller, J. A., Somia, N. V., Bogdanove, A. J., and Voytas, D. F. 2011. Efficient design and assembly of custom TALEN and other TAL effector-based constructs for DNA targeting. Nucleic Acids Research 39:e82-e82.
     連結：
168. Chang, W.-B. 2015. Identification of quantitative trait loci for blast resistance in Taiwan rice variety Tainung 84. National Taiwan University.
     連結：
169. Chen, K., and Gao, C. 2013. TALENs: customizable molecular DNA scissors for genome engineering of plants. Journal of Genetics and Genomics 40:271-279.
     連結：
170. Chen, S. Y., Huang, K. J., Kuo, Y. F., Lai, M. H., Chen, Y. C., and Chung, C. L. 2015. Three modified methods for evaluation of bakanae disease resistance in rice seedlings. Plant Pathology Bulletin 24:201-210.
     連結：
171. Chen, X., and Ronald, P. C. 2011. Innate immunity in rice. Trends in Plant Science 16:451-459.
     連結：
172. Chen, Y.-C., Lai, M.-H., Wu, C.-Y., Lin, T.-C., Cheng, A.-H., Yang, C.-C., Wu, H.-Y., Chu, S.-C., Kuo, C.-C., and Wu, Y.-F. 2016. The genetic structure, virulence, and fungicide sensitivity of Fusarium fujikuroi in Taiwan. Phytopathology 106:624-635.
     連結：
173. Chern, M., Fitzgerald, H. A., Canlas, P. E., Navarre, D. A., and Ronald, P. C. 2005. Overexpression of a rice NPR1 homolog leads to constitutive activation of defense response and hypersensitivity to light. Molecular Plant-Microbe Interactions 18:511-520.
     連結：
174. Chittoor, J. M., Leach, J. E., and White, F. F. 1997. Differential induction of a peroxidase gene family during infection of rice by Xanthomonas oryzae pv. oryzae. Molecular Plant-Microbe Interactions 10:861-871.
     連結：
175. De Vleesschauwer, D., Gheysen, G., and Höfte, M. 2013. Hormone defense networking in rice: tales from a different world. Trends in Plant Science 18:555-565.
     連結：
176. De Vleesschauwer, D., Xu, J., and Höfte, M. 2014. Making sense of hormone-mediated defense networking: from rice to Arabidopsis. Frontiers in Plant Science 5:1-15.
     連結：
177. De Vleesschauwer, D., Yang, Y., Cruz, C. V., and Höfte, M. 2010. Abscisic acid-induced resistance against the brown spot pathogen Cochliobolus miyabeanus in rice involves MAP kinase-mediated repression of ethylene signaling. Plant Physiology 152:2036-2052.
     連結：
178. Deltcheva, E., Chylinski, K., Sharma, C. M., Gonzales, K., Chao, Y., Pirzada, Z. A., Eckert, M. R., Vogel, J., and Charpentier, E. 2011. CRISPR RNA maturation by trans-encoded small RNA and host factor RNase III. Nature 471:602-607.
     連結：
179. Derksen, H., Rampitsch, C., and Daayf, F. 2013. Signaling cross-talk in plant disease resistance. Plant Science 207:79-87.
     連結：
180. Dill, A., Jung, H.-S., and Sun, T.-p. 2001. The DELLA motif is essential for gibberellin-induced degradation of RGA. Proceedings of the National Academy of Sciences 98:14162-14167.
     連結：
181. Du, Z., Zhou, X., Ling, Y., Zhang, Z., and Su, Z. 2010. agriGO: a GO analysis toolkit for the agricultural community. Nucleic Acids Research 38:W64-W70.
     連結：
182. Eizenga, G. C., Ali, M., Bryant, R. J., Yeater, K. M., McClung, A. M., and McCouch, S. R. 2014. Registration of the rice diversity panel 1 for genomewide association studies. Journal of Plant Registrations 8:109-116.
     連結：
183. Fu, X., Richards, D. E., Ait-Ali, T., Hynes, L. W., Ougham, H., Peng, J., and Harberd, N. P. 2002. Gibberellin-mediated proteasome-dependent degradation of the barley DELLA protein SLN1 repressor. The Plant Cell 14:3191-3200.
     連結：
184. Glazebrook, J. 2005. Contrasting mechanisms of defense against biotrophic and necrotrophic pathogens. Annual Reviews Phytopathology 43:205-227.
     連結：
185. Gomi, K., and Matsuoka, M. 2003. Gibberellin signalling pathway. Current Opinion in Plant Biology 6:489-493.
     連結：
186. Grant, M. R., and Jones, J. D. 2009. Hormone (dis)harmony moulds plant health and disease. Science 324:750-752.
     連結：
187. Grennan, A. K. 2006. Gibberellin metabolism enzymes in rice. Plant Physiology 141:524-526.
     連結：
188. Gutjahr, C., and Paszkowski, U. 2009. Weights in the balance: jasmonic acid and salicylic acid signaling in root-biotroph interactions. Molecular Plant-Microbe Interactions 22:763-772.
     連結：
189. Hamberger, B., and Bak, S. 2013. Plant P450s as versatile drivers for evolution of species-specific chemical diversity. Philosophical Transactions of the Royal Society B: Biological Sciences 368:20120426.
     連結：
190. Haq, M., Mia, M. T., Rabbi, M., and Ali, M. 2010. Incidence and severity of rice diseases and insect pests in relation to climate change. Pages 445-457 in: Climate Change and Food Security in South Asia. Springer.
     連結：
191. Hedden, P. 2003. The genes of the Green Revolution. TRENDS in Genetics 19:5-9.
     連結：
192. Heitz, T., Widemann, E., Lugan, R., Miesch, L., Ullmann, P., Désaubry, L., Holder, E., Grausem, B., Kandel, S., and Miesch, M. 2012. Cytochromes P450 CYP94C1 and CYP94B3 catalyze two successive oxidation steps of plant hormone jasmonoyl-isoleucine for catabolic turnover. Journal of Biological Chemistry 287:6296-6306.
     連結：
193. Helliwell, E. E., Wang, Q., and Yang, Y. 2013. Transgenic rice with inducible ethylene production exhibits broad‐spectrum disease resistance to the fungal pathogens Magnaporthe oryzae and Rhizoctonia solani. Plant Biotechnology Journal 11:33-42.
     連結：
194. Hilaire, E., Young, S. A., Willard, L. H., McGee, J. D., Sweat, T., Chittoor, J., Guikema, J. A., and Leach, J. E. 2001. Vascular defense responses in rice: peroxidase accumulation in xylem parenchyma cells and xylem wall thickening. Molecular Plant-Microbe Interactions 14:1411-1419.
     連結：
195. Hsieh, W., Smith, S., and Snyder, W. 1977. Mating groups in Fusarium moniliforme. Phytopathology 67:1041-1043.
     連結：
196. Hsu, C. C., Huang, J. W., and Chen, C. Y. 2013. The cause of rice bakanae disease in Taiwan. Plant Pathology Bulletin 22:279-289.
     連結：
197. Ikeda, A., Ueguchi-Tanaka, M., Sonoda, Y., Kitano, H., Koshioka, M., Futsuhara, Y., Matsuoka, M., and Yamaguchi, J. 2001. slender rice, a constitutive gibberellin response mutant, is caused by a null mutation of the SLR1 gene, an ortholog of the height-regulating gene GAI/RGA/RHT/D8. The Plant Cell 13:999-1010.
     連結：
198. Inoue, H., Hayashi, N., Matsushita, A., Xinqiong, L., Nakayama, A., Sugano, S., Jiang, C.-J., and Takatsuji, H. 2013. Blast resistance of CC-NB-LRR protein Pb1 is mediated by WRKY45 through protein–protein interaction. Proceedings of the National Academy of Sciences 110:9577-9582.
     連結：
199. Itoh, H., Ueguchi-Tanaka, M., Sato, Y., Ashikari, M., and Matsuoka, M. 2002. The gibberellin signaling pathway is regulated by the appearance and disappearance of SLENDER RICE1 in nuclei. The Plant Cell 14:57-70.
     連結：
200. Izzati Mohd Zainudin, N., Razak, A., and Salleh, B. 2008. Bakanae disease of rice in Malaysia and Indonesia: etiology of the causal agent based on morphological, physiological and pathogenicity characteristics. Journal of Plant Protection Research 48:475-485.
     連結：
201. Ji, Z., Zeng, Y., Liang, Y., Qian, Q., and Yang, C. 2016. Transcriptomic dissection of the rice–Fusarium fujikuroi interaction by RNA-Seq. Euphytica 211:123-137.
     連結：
202. Jinek, M., Chylinski, K., Fonfara, I., Hauer, M., Doudna, J. A., and Charpentier, E. 2012. A programmable dual-RNA–guided DNA endonuclease in adaptive bacterial immunity. Science 337:816-821.
     連結：
203. Kanehisa, M., and Goto, S. 2000. KEGG: kyoto encyclopedia of genes and genomes. Nucleic Acids Research 28:27-30.
     連結：
204. Kanehisa, M., Sato, Y., Kawashima, M., Furumichi, M., and Tanabe, M. 2016. KEGG as a reference resource for gene and protein annotation. Nucleic Acids Research 44:D457-D462.
     連結：
205. Kanehisa, M., Furumichi, M., Tanabe, M., Sato, Y., and Morishima, K. 2017. KEGG: new perspectives on genomes, pathways, diseases and drugs. Nucleic Acids Research 45:D353-D361.
     連結：
206. Khush, G. S. 1999. Green revolution: preparing for the 21st century. Genome 42:646-655.
     連結：
207. Konishi, H., Ishiguro, K., and Komatsu, S. 2001. A proteomics approach towards understanding blast fungus infection of rice grown under different levels of nitrogen fertilization. Proteomics 1:1162-1171.
     連結：
208. Kurosawa, E. 1926. Experimental studies on the nature of the substance secreted by the" bakanae" fungus. Natural History Society of Formosa 16:213-227.
     連結：
209. Kyozuka, J. 2007. Control of shoot and root meristem function by cytokinin. Current Opinion in Plant Biology 10:442-446.
     連結：
210. La Camera, S., Gouzerh, G., Dhondt, S., Hoffmann, L., Fritig, B., Legrand, M., and Heitz, T. 2004. Metabolic reprogramming in plant innate immunity: the contributions of phenylpropanoid and oxylipin pathways. Immunological Reviews 198:267-284.
     連結：
211. Langmead, B., and Salzberg, S. L. 2012. Fast gapped-read alignment with Bowtie 2. Nature Methods 9:357-359.
     連結：
212. Leslie, J. F. 1995. Gibberella fujikuroi: available populations and variable traits. Canadian Journal of Botany 73:282-291.
     連結：
213. Li, T., Liu, B., Spalding, M. H., Weeks, D. P., and Yang, B. 2012. High-efficiency TALEN-based gene editing produces disease-resistant rice. Nature Biotechnology 30:390-392.
     連結：
214. Lin, S., Staahl, B., Alla, R. K., and Doudna, J. A. 2014. Enhanced homology-directed human genome engineering by controlled timing of CRISPR/Cas9 delivery. Elife 3:e04766.
     連結：
215. Liu, L.-Y. D., Tseng, H.-I., Lin, C.-P., Lin, Y.-Y., Huang, Y.-H., Huang, C.-K., Chang, T.-H., and Lin, S.-S. 2014. High-throughput transcriptome analysis of the leafy flower transition of Catharanthus roseus induced by peanut witches’-broom phytoplasma infection. Plant and Cell Physiology 55:942-957.
     連結：
216. Liu, X., Bai, X., Wang, X., and Chu, C. 2007. OsWRKY71, a rice transcription factor, is involved in rice defense response. Journal of Plant Physiology 164:969-979.
     連結：
217. Liu, X., Li, F., Tang, J., Wang, W., Zhang, F., Wang, G., Chu, J., Yan, C., Wang, T., and Chu, C. 2012. Activation of the jasmonic acid pathway by depletion of the hydroperoxide lyase OsHPL3 reveals crosstalk between the HPL and AOS branches of the oxylipin pathway in rice. PLoS ONE 7:e50089.
     連結：
218. Lyons, R., Manners, J. M., and Kazan, K. 2013. Jasmonate biosynthesis and signaling in monocots: a comparative overview. Plant Cell Reports 32:815-827.
     連結：
219. Mahmood, T., Jan, A., Kakishima, M., and Komatsu, S. 2006. Proteomic analysis of bacterial‐blight defense‐responsive proteins in rice leaf blades. Proteomics 6:6053-6065.
     連結：
220. Malamy, J., and Klessig, D. F. 1992. Salicylic acid and plant disease resistance. The Plant Journal 2:643-654.
     連結：
221. Manandhar, H., Mathur, S., Smedegaard-Petersen, V., and Thordal-Christensen, H. 1999. Accumulation of transcripts for pathogenesis–related proteins and peroxidase in rice plants triggered by Pyricularia oryzae, Bipolaris sorokiniana and uv light. Physiological and Molecular Plant Pathology 55:289-295.
     連結：
222. Manosalva, P. M., Davidson, R. M., Liu, B., Zhu, X., Hulbert, S. H., Leung, H., and Leach, J. E. 2009. A germin-like protein gene family functions as a complex quantitative trait locus conferring broad-spectrum disease resistance in rice. Plant Physiology 149:286-296.
     連結：
223. Mao, Y., Zhang, H., Xu, N., Zhang, B., Gou, F., and Zhu, J.-K. 2013. Application of the CRISPR–Cas system for efficient genome engineering in plants. Molecular Plant 6:2008.
     連結：
224. Matić, S., Bagnaresi, P., Biselli, C., Carneiro, G. A., Siciliano, I., Valé, G., Gullino, M. L., and Spadaro, D. 2016. Comparative transcriptome profiling of resistant and susceptible rice genotypes in response to the seedborne pathogen Fusarium fujikuroi. BMC Genomics 17:608.
     連結：
225. Matsushita, A., Inoue, H., Goto, S., Nakayama, A., Sugano, S., Hayashi, N., and Takatsuji, H. 2013. Nuclear ubiquitin proteasome degradation affects WRKY45 function in the rice defense program. The Plant Journal 73:302-313.
     連結：
226. Mei, C., Qi, M., Sheng, G., and Yang, Y. 2006. Inducible overexpression of a rice allene oxide synthase gene increases the endogenous jasmonic acid level, PR gene expression, and host resistance to fungal infection. Molecular Plant-Microbe Interactions 19:1127-1137.
     連結：
227. Miller, J. C., Holmes, M. C., Wang, J., Guschin, D. Y., Lee, Y.-L., Rupniewski, I., Beausejour, C. M., Waite, A. J., Wang, N. S., and Kim, K. A. 2007. An improved zinc-finger nuclease architecture for highly specific genome editing. Nature Biotechnology 25:778-785.
     連結：
228. Monaghan, J., and Zipfel, C. 2012. Plant pattern recognition receptor complexes at the plasma membrane. Current Opinion in Plant Biology 15:349-357.
     連結：
229. Mur, L. A., Kenton, P., Atzorn, R., Miersch, O., and Wasternack, C. 2006. The outcomes of concentration-specific interactions between salicylate and jasmonate signaling include synergy, antagonism, and oxidative stress leading to cell death. Plant Physiology 140:249-262.
     連結：
230. Nahar, K., Kyndt, T., De Vleesschauwer, D., Höfte, M., and Gheysen, G. 2011. The jasmonate pathway is a key player in systemically induced defense against root knot nematodes in rice. Plant Physiology 157:305-316.
     連結：
231. Navarro, L., Bari, R., Achard, P., Lisón, P., Nemri, A., Harberd, N. P., and Jones, J. D. 2008. DELLAs control plant immune responses by modulating the balance of jasmonic acid and salicylic acid signaling. Current Biology 18:650-655.
     連結：
232. Niewoehner, O., Jinek, M., and Doudna, J. A. 2013. Evolution of CRISPR RNA recognition and processing by Cas6 endonucleases. Nucleic Acids Research 42:1341-1353.
     連結：
233. Norman-Setterblad, C., Vidal, S., and Palva, E. T. 2000. Interacting signal pathways control defense gene expression in Arabidopsis in response to cell wall-degrading enzymes from Erwinia carotovora. Molecular Plant-Microbe Interactions 13:430-438.
     連結：
234. Ohira, K., Ojima, K., and Fujiwara, A. 1973. Studies on the nutrition of rice cell culture I. A simple, defined medium for rapid growth in suspension culture. Plant and Cell Physiology 14:1113-1121.
     連結：
235. Ou, S. 1984. Exploring tropical rice diseases: a reminiscence. Annual Review of Phytopathology 22:1-11.
     連結：
236. Pan, C., Ye, L., Qin, L., Liu, X., He, Y., Wang, J., Chen, L., and Lu, G. 2016. CRISPR/Cas9-mediated efficient and heritable targeted mutagenesis in tomato plants in the first and later generations. Scientific Reports 6:24765.
     連結：
237. Park, W.-S., Choi, H.-W., Han, S.-S., Shin, D.-B., Shim, H.-K., Jung, E.-S., Lee, S.-W., Lim, C.-K., and Lee, Y.-H. 2009. Control of bakanae disease of rice by seed soaking into the mixed solution of procholraz and fludioxnil. Research in Plant Disease 15:94-100.
     連結：
238. Passardi, F., Cosio, C., Penel, C., and Dunand, C. 2005. Peroxidases have more functions than a Swiss army knife. Plant Cell Reports 24:255-265.
     連結：
239. Peng, J., Carol, P., Richards, D. E., King, K. E., Cowling, R. J., Murphy, G. P., and Harberd, N. P. 1997. The Arabidopsis GAI gene defines a signaling pathway that negatively regulates gibberellin responses. Genes & Development 11:3194-3205.
     連結：
240. Pieterse, C. M., Leon-Reyes, A., Van der Ent, S., and Van Wees, S. C. 2009. Networking by small-molecule hormones in plant immunity. Nature Chemical Biology 5:308-316.
     連結：
241. Pinot, F., and Beisson, F. 2011. Cytochrome P450 metabolizing fatty acids in plants: characterization and physiological roles. The Federation of European Biochemical Societies Journal 278:195-205.
     連結：
242. Qin, X., Liu, J. H., Zhao, W. S., Chen, X. J., Guo, Z. J., and Peng, Y. L. 2013. Gibberellin 20-oxidase gene OsGA20ox3 regulates plant stature and disease development in rice. Molecular Plant-Microbe Interactions 26:227-239.
     連結：
243. Qiu, D., Xiao, J., Xie, W., Cheng, H., Li, X., and Wang, S. 2009. Exploring transcriptional signalling mediated by OsWRKY13, a potential regulator of multiple physiological processes in rice. BMC Plant Biology 9:74.
     連結：
244. Qiu, D., Xiao, J., Xie, W., Liu, H., Li, X., Xiong, L., and Wang, S. 2008. Rice gene network inferred from expression profiling of plants overexpressing OsWRKY13, a positive regulator of disease resistance. Molecular Plant 1:538-551.
     連結：
245. Qiu, D., Xiao, J., Ding, X., Xiong, M., Cai, M., Cao, Y., Li, X., Xu, C., and Wang, S. 2007. OsWRKY13 mediates rice disease resistance by regulating defense-related genes in salicylate-and jasmonate-dependent signaling. Molecular Plant-Microbe Interactions 20:492-499.
     連結：
246. Ray, A., and Langer, M. 2002. Homologous recombination: ends as the means. Trends in Plant Science 7:435-440.
     連結：
247. Reuber, T. L., Plotnikova, J. M., Dewdney, J., Rogers, E. E., Wood, W., and Ausubel, F. M. 1998. Correlation of defense gene induction defects with powdery mildew susceptibility in Arabidopsis enhanced disease susceptibility mutants. The Plant Journal 16:473-485.
     連結：
248. Riemann, M., Riemann, M., and Takano, M. 2008. Rice JASMONATE RESISTANT 1 is involved in phytochrome and jasmonate signalling. Plant, Cell & Environment 31:783-792.
     連結：
249. Riemann, M., Haga, K., Shimizu, T., Okada, K., Ando, S., Mochizuki, S., Nishizawa, Y., Yamanouchi, U., Nick, P., and Yano, M. 2013. Identification of rice Allene Oxide Cyclase mutants and the function of jasmonate for defence against Magnaporthe oryzae. The Plant Journal 74:226-238.
     連結：
250. Robert-Seilaniantz, A., Grant, M., and Jones, J. D. 2011. Hormone crosstalk in plant disease and defense: more than just jasmonate-salicylate antagonism. Annual Review of Phytopathology 49:317-343.
     連結：
251. Roberts, W. K., and Selitrennikoff, C. P. 1990. Zeamatin, an antifungal protein from maize with membrane-permeabilizing activity. Microbiology 136:1771-1778.
     連結：
252. Ross, C. A., Liu, Y., and Shen, Q. J. 2007. The WRKY gene family in rice (Oryza sativa). Journal of Integrative Plant Biology 49:827-842.
     連結：
253. Sakamoto, T., Miura, K., Itoh, H., Tatsumi, T., Ueguchi-Tanaka, M., Ishiyama, K., Kobayashi, M., Agrawal, G. K., Takeda, S., and Abe, K. 2004. An overview of gibberellin metabolism enzyme genes and their related mutants in rice. Plant Physiology 134:1642-1653.
     連結：
254. Sallaud, C., Meynard, D., Van Boxtel, J., Gay, C., Bes, M., Brizard, J.-P., Larmande, P., Ortega, D., Raynal, M., and Portefaix, M. 2003. Highly efficient production and characterization of T-DNA plants for rice (Oryza sativa L.) functional genomics. Theoretical and Applied Genetics 106:1396-1408.
     連結：
255. Sampson, T. R., Saroj, S. D., Llewellyn, A. C., Tzeng, Y.-L., and Weiss, D. S. 2013. A CRISPR/Cas system mediates bacterial innate immune evasion and virulence. Nature 497:254-257.
     連結：
256. Santiago-Sotelo, P., and Ramirez-Prado, J. 2012. prfectBLAST: a platform-independent portable front end for the command terminal BLAST+ stand-alone suite. BioTechniques 53:299.
     連結：
257. Sapranauskas, R., Gasiunas, G., Fremaux, C., Barrangou, R., Horvath, P., and Siksnys, V. 2011. The Streptococcus thermophilus CRISPR/Cas system provides immunity in Escherichia coli. Nucleic Acids Research 39:9275-9282.
     連結：
258. Schneider, C. A., Rasband, W. S., and Eliceiri, K. W. 2012. NIH Image to ImageJ: 25 years of image analysis. Nature Methods 9:671-675.
     連結：
259. Shan, Q., Wang, Y., Li, J., and Gao, C. 2014. Genome editing in rice and wheat using the CRISPR/Cas system. Nature Protocols 9:2395-2410.
     連結：
260. Shan, Q., Wang, Y., Chen, K., Liang, Z., Li, J., Zhang, Y., Zhang, K., Liu, J., Voytas, D. F., and Zheng, X. 2013a. Rapid and efficient gene modification in rice and Brachypodium using TALENs. Molecular Plant 6:1365-1368.
     連結：
261. Shan, Q., Wang, Y., Li, J., Zhang, Y., Chen, K., Liang, Z., Zhang, K., Liu, J., Xi, J. J., and Qiu, J.-L. 2013b. Targeted genome modification of crop plants using a CRISPR-Cas system. Nature Biotechnology 31:686-688.
     連結：
262. Sharma, R., Cao, P., Jung, K.-H., Sharma, M. K., and Ronald, P. C. 2013. Construction of a rice glycoside hydrolase phylogenomic database and identification of targets for biofuel research. Frontiers in Plant Science 4.
     連結：
263. Shen, X., Liu, H., Yuan, B., Li, X., Xu, C., and Wang, S. 2011. OsEDR1 negatively regulates rice bacterial resistance via activation of ethylene biosynthesis. Plant, Cell & Environment 34:179-191.
     連結：
264. Shimono, M., Sugano, S., Nakayama, A., Jiang, C.-J., Ono, K., Toki, S., and Takatsuji, H. 2007. Rice WRKY45 plays a crucial role in benzothiadiazole-inducible blast resistance. The Plant Cell 19:2064-2076.
     連結：
265. Shimono, M., Koga, H., Akagi, A., Hayashi, N., Goto, S., Sawada, M., Kurihara, T., Matsushita, A., Sugano, S., and JIANG, C. J. 2012. Rice WRKY45 plays important roles in fungal and bacterial disease resistance. Molecular Plant Pathology 13:83-94.
     連結：
266. Shukla, V. K., Doyon, Y., Miller, J. C., DeKelver, R. C., Moehle, E. A., Worden, S. E., Mitchell, J. C., Arnold, N. L., Gopalan, S., and Meng, X. 2009. Precise genome modification in the crop species Zea mays using zinc-finger nucleases. Nature 459:437-441.
     連結：
267. Siciliano, I., Amaral Carneiro, G., Spadaro, D., Garibaldi, A., and Gullino, M. L. 2015. Jasmonic acid, abscisic acid, and salicylic acid are involved in the phytoalexin responses of rice to Fusarium fujikuroi, a high gibberellin producer pathogen. Journal of Agricultural and Food Chemistry 63:8134-8142.
     連結：
268. Silverman, P., Seskar, M., Kanter, D., Schweizer, P., Metraux, J.-P., and Raskin, I. 1995. Salicylic acid in rice (biosynthesis, conjugation, and possible role). Plant Physiology 108:633-639.
     連結：
269. Silverstone, A. L., Jung, H.-S., Dill, A., Kawaide, H., Kamiya, Y., and Sun, T.-p. 2001. Repressing a repressor gibberellin-induced rapid reduction of the RGA protein in Arabidopsis. The Plant Cell 13:1555-1566.
     連結：
270. Sinkunas, T., Gasiunas, G., Waghmare, S. P., Dickman, M. J., Barrangou, R., Horvath, P., and Siksnys, V. 2013. In vitro reconstitution of Cascade‐mediated CRISPR immunity in Streptococcus thermophilus. The EMBO Journal 32:385-394.
     連結：
271. Sorek, R., Lawrence, C. M., and Wiedenheft, B. 2013. CRISPR-mediated adaptive immune systems in bacteria and archaea. Annual Review of Biochemistry 82:237-266.
     連結：
272. Sugano, S., Jiang, C.-J., Miyazawa, S.-I., Masumoto, C., Yazawa, K., Hayashi, N., Shimono, M., Nakayama, A., Miyao, M., and Takatsuji, H. 2010. Role of OsNPR1 in rice defense program as revealed by genome-wide expression analysis. Plant Molecular Biology 74:549-562.
     連結：
273. Sun, T.-p. 2011. The molecular mechanism and evolution of the GA–GID1–DELLA signaling module in plants. Current Biology 21:R338-R345.
     連結：
274. Symington, L. S., and Gautier, J. 2011. Double-strand break end resection and repair pathway choice. Annual Review of Genetics 45:247-271.
     連結：
275. Taheri, P., and Tarighi, S. 2010. Riboflavin induces resistance in rice against Rhizoctonia solani via jasmonate-mediated priming of phenylpropanoid pathway. Journal of Plant Physiology 167:201-208.
     連結：
276. Takatsuji, H., Jiang, C.-J., and Sugano, S. 2010. Salicylic acid signaling pathway in rice and the potential applications of its regulators. Japan Agricultural Research Quarterly: JARQ 44:217-223.
     連結：
277. Takeuchi, K., Gyohda, A., Tominaga, M., Kawakatsu, M., Hatakeyama, A., Ishii, N., Shimaya, K., Nishimura, T., Riemann, M., and Nick, P. 2011. RSOsPR10 expression in response to environmental stresses is regulated antagonistically by jasmonate/ethylene and salicylic acid signaling pathways in rice roots. Plant and Cell Physiology 52:1686-1696.
     連結：
278. Tamaoki, D., Seo, S., Yamada, S., Kano, A., Miyamoto, A., Shishido, H., Miyoshi, S., Taniguchi, S., Akimitsu, K., and Gomi, K. 2013. Jasmonic acid and salicylic acid activate a common defense system in rice. Plant Signaling & Behavior 8:e24260.
     連結：
279. Tanaka, N., Matsuoka, M., Kitano, H., Asano, T., Kaku, H., and Komatsu, S. 2006. gid1, a gibberellin‐insensitive dwarf mutant, shows altered regulation of probenazole‐inducible protein (PBZ1) in response to cold stress and pathogen attack. Plant, Cell & Environment 29:619-631.
     連結：
280. Taniguchi, S., HOSOKAWA‐SHINONAGA, Y., Tamaoki, D., Yamada, S., Akimitsu, K., and Gomi, K. 2014. Jasmonate induction of the monoterpene linalool confers resistance to rice bacterial blight and its biosynthesis is regulated by JAZ protein in rice. Plant, Cell & Environment 37:451-461.
     連結：
281. Tao, Z., Liu, H., Qiu, D., Zhou, Y., Li, X., Xu, C., and Wang, S. 2009. A pair of allelic WRKY genes play opposite roles in rice-bacteria interactions. Plant Physiology 151:936-948.
     連結：
282. Terns, M. P., and Terns, R. M. 2011. CRISPR-based adaptive immune systems. Current Opinion in Microbiology 14:321-327.
     連結：
283. Thaler, J. S., Humphrey, P. T., and Whiteman, N. K. 2012. Evolution of jasmonate and salicylate signal crosstalk. Trends in Plant Science 17:260-270.
     連結：
284. Thomma, B. P., Penninckx, I. A., Cammue, B. P., and Broekaert, W. F. 2001. The complexity of disease signaling in Arabidopsis. Current Opinion in Immunology 13:63-68.
     連結：
285. Tian, T., Liu, Y., Yan, H., You, Q., Yi, X., Du, Z., Xu, W., and Su, Z. 2017. agriGO v2. 0: a GO analysis toolkit for the agricultural community, 2017 update. Nucleic Acids Research.
     連結：
286. Tong, X., Qi, J., Zhu, X., Mao, B., Zeng, L., Wang, B., Li, Q., Zhou, G., Xu, X., and Lou, Y. 2012. The rice hydroperoxide lyase OsHPL3 functions in defense responses by modulating the oxylipin pathway. The Plant Journal 71:763-775.
     連結：
287. Townsend, J. A., Wright, D. A., Winfrey, R. J., Fu, F., Maeder, M. L., Joung, J. K., and Voytas, D. F. 2009. High-frequency modification of plant genes using engineered zinc-finger nucleases. Nature 459:442-445.
     連結：
288. Untergasser, A., Cutcutache, I., Koressaar, T., Ye, J., Faircloth, B. C., Remm, M., and Rozen, S. G. 2012. Primer3—new capabilities and interfaces. Nucleic Acids Research 40:e115-e115.
     連結：
289. Vigers, A. J., Roberts, W. K., and Selitrennikoff, C. P. 1991. A new family of plant antifungal proteins. Molecular Plant-Microbe Interactions 4:315-323.
     連結：
290. Vlot, A. C., Dempsey, D. M. A., and Klessig, D. F. 2009. Salicylic acid, a multifaceted hormone to combat disease. Annual Review of Phytopathology 47:177-206.
     連結：
291. Vogt, T. 2010. Phenylpropanoid biosynthesis. Molecular Plant 3:2-20.
     連結：
292. Voigt, K., Schleier, S., and Brückner, B. 1995. Genetic variability in Gibberella fujikuroi and some related species of the genus Fusarium based on random amplification of polymorphic DNA (RAPD). Current Genetics 27:528-535.
     連結：
293. Vouillot, L., Thélie, A., and Pollet, N. 2015. Comparison of T7E1 and surveyor mismatch cleavage assays to detect mutations triggered by engineered nucleases. G3: Genes, Genomes, Genetics 5:407-415.
     連結：
294. Wang, L., Shen, R., Chen, L. T., and Liu, Y. G. 2014. Characterization of a novel DUF1618 gene family in rice. Journal of Integrative Plant Biology 56:151-158.
     連結：
295. Wiedenheft, B., Sternberg, S. H., and Doudna, J. A. 2012. RNA-guided genetic silencing systems in bacteria and archaea. Nature 482:331-338.
     連結：
296. Wollenweber, H. W. 1931. Fusarium-Monographie. Parasitology Research 3:269-516.
     連結：
297. Woo, J. W., Kim, J., Kwon, S. I., Corvalán, C., Cho, S. W., Kim, H., Kim, S.-G., Kim, S.-T., Choe, S., and Kim, J.-S. 2015. DNA-free genome editing in plants with preassembled CRISPR-Cas9 ribonucleoproteins. Nature Biotechnology 33:1162-1164.
     連結：
298. Xie, K., and Yang, Y. 2013. RNA-guided genome editing in plants using a CRISPR–Cas system. Molecular Plant 6:1975-1983.
     連結：
299. Yamada, S., Kano, A., Tamaoki, D., Miyamoto, A., Shishido, H., Miyoshi, S., Taniguchi, S., Akimitsu, K., and Gomi, K. 2012. Involvement of OsJAZ8 in jasmonate-induced resistance to bacterial blight in rice. Plant and Cell Physiology 53:2060-2072.
     連結：
300. Yan, H., Saika, H., Maekawa, M., Takamure, I., Tsutsumi, N., Kyozuka, J., and Nakazono, M. 2007. Rice tillering dwarf mutant dwarf3 has increased leaf longevity during darkness-induced senescence or hydrogen peroxide-induced cell death. Genes & Genetic Systems 82:361-366.
     連結：
301. Yang, D.-L., Li, Q., Deng, Y.-W., Lou, Y.-G., Wang, M.-Y., Zhou, G.-X., Zhang, Y.-Y., and He, Z.-H. 2008. Altered disease development in the eui mutants and Eui overexpressors indicates that gibberellins negatively regulate rice basal disease resistance. Molecular Plant 1:528-537.
     連結：
302. Ye, M., Luo, S. M., Xie, J. F., Li, Y. F., Xu, T., Liu, Y., Song, Y. Y., Zhu-Salzman, K., and Zeng, R. S. 2012. Silencing COI1 in rice increases susceptibility to chewing insects and impairs inducible defense. PLoS ONE 7:e36214.
     連結：
303. Ying, J., Zhao, J., Hou, Y., Wang, Y., Qiu, J., Li, Z., Tong, X., Shi, Z., Zhu, J., and Zhang, J. 2017. Mapping the N-linked glycosites of rice (Oryza sativa L.) germinating embryos. PLoS ONE 12:e0173853.
     連結：
304. Yuan, Y., Zhong, S., Li, Q., Zhu, Z., Lou, Y., Wang, L., Wang, J., Wang, M., Li, Q., and Yang, D. 2007. Functional analysis of rice NPR1‐like genes reveals that OsNPR1/NH1 is the rice orthologue conferring disease resistance with enhanced herbivore susceptibility. Plant Botechnology Journal 5:313-324.
     連結：
305. Zhou, G., Qi, J., Ren, N., Cheng, J., Erb, M., Mao, B., and Lou, Y. 2009. Silencing OsHI‐LOX makes rice more susceptible to chewing herbivores, but enhances resistance to a phloem feeder. The Plant Journal 60:638-648.
     連結：
306. Zipfel, C. 2008. Pattern-recognition receptors in plant innate immunity. Current Opinion in Immunology 20:10-16.
     連結：
307. Zipfel, C. 2014. Plant pattern-recognition receptors. Trends in Immunology 35:345-351.
     連結：
308. Zulfugarov, I. S., Tovuu, A., Kim, C.-Y., Vo, K. T. X., Ko, S. Y., Hall, M., Seok, H.-Y., Kim, Y.-K., Skogstrom, O., and Moon, Y.-H. 2016. Enhanced resistance of PsbS-deficient rice (Oryza sativa L.) to fungal and bacterial pathogens. Journal of Plant Biology 59:616-626.
     連結：
309. Alché, J., Castro, A., Jiménez-López, J., Morales, S., Zafra, A., Hamman-Khalifa, A., and Rodríguez-García, M. 2007. Differential characteristics of olive pollen from different cultivars: biological and clinical implications. Journal of Investigational Allergology and Clinical Immunology 17:17-23.
310. Almagro, L., Gómez Ros, L., Belchi-Navarro, S., Bru, R., Ros Barceló, A., and Pedreno, M. 2008. Class III peroxidases in plant defence reactions. Journal of Experimental Botany 60:377-390.
311. Cong, L., Ran, F. A., Cox, D., Lin, S., Barretto, R., Habib, N., Hsu, P. D., Wu, X., Jiang, W., and Marraffini, L. A. 2013. Multiplex genome engineering using CRISPR/Cas systems. Science 339:819-823.
312. Desjardins, A. E., Plattner, R. D., and Nelson, P. E. 1997. Production of Fumonisin B (inf1) and Moniliformin by Gibberella fujikuroi from Rice from Various Geographic Areas. Applied and Environmental Microbiology 63:1838-1842.
313. Dong, J., Chen, C., and Chen, Z. 2003. Expression profiles of the Arabidopsis WRKY gene superfamily during plant defense response. Plant Molecular Biology 51:21-37.
314. Huang, T.-C., and Chu, S.-C. 2009. The occurrence and control of rice bakanae disease in Taiwan. Proceeding of Symposium on Achievement and Perpectives of Rice Protection in Taiwan:29-43.
315. Iqbal, M., Javed, N., Sahi, S. T., and Cheema, N. M. 2011. Genetic management of bakanae disease of rice and evaluation of various fungicides against Fusarium moniliforme in vitro. Pakistan Journal of Phytopathology 23:103-107.
316. Leubner-Metzger, G., and Meins Jr, F. 1999. Functions and regulation of plant ß-1, 3-glucanases (PR-2). Pages 49-76 in: Pathogenesis-Related Proteins in Plants. S. K. Datta and S. Muthukrishnan, eds. CRC Press LLC, Boca Raton, Florida.
317. Ma, L.-J., Geiser, D. M., Proctor, R. H., Rooney, A. P., O'Donnell, K., Trail, F., Gardiner, D. M., Manners, J. M., and Kazan, K. 2013. Fusarium pathogenomics. Annual Review of Microbiology 67:399-416.
318. Makarova, K. S., Grishin, N. V., Shabalina, S. A., Wolf, Y. I., and Koonin, E. V. 2006. A putative RNA-interference-based immune system in prokaryotes: computational analysis of the predicted enzymatic machinery, functional analogies with eukaryotic RNAi, and hypothetical mechanisms of action. Biology Direct 1:7.
319. Makarova, K. S., Haft, D. H., Barrangou, R., Brouns, S. J., Charpentier, E., Horvath, P., Moineau, S., Mojica, F. J., Wolf, Y. I., and Yakunin, A. F. 2011. Evolution and classification of the CRISPR–Cas systems. Nature Reviews Microbiology 9:467-477.
320. Mali, P., Yang, L., Esvelt, K. M., Aach, J., Guell, M., DiCarlo, J. E., Norville, J. E., and Church, G. M. 2013. RNA-guided human genome engineering via Cas9. Science 339:823-826.
321. Manandhar, J. 1999. Fusarium moniliforme in rice seeds: its infection, isolation, and longevity. Journal of Plant Diseases and Protection:598-607.
322. McHale, L., Tan, X., Koehl, P., and Michelmore, R. W. 2006. Plant NBS-LRR proteins: adaptable guards. Genome Biology 7:212.
323. Mew, T.-W., and Gonzales, P. 2002. A handbook of rice seedborne fungi. International Rice Research Institute.
324. Pieterse, C. M., Van der Does, D., Zamioudis, C., Leon-Reyes, A., and Van Wees, S. C. 2012. Hormonal modulation of plant immunity. Annual Review of Cell and Developmental Biology 28:489-521.
325. Sasaki, A., Ashikari, M., Ueguchi-Tanaka, M., Ito, H., Kobayashi, M., Kitano, H., and Matsuoka, M. 2001. Screening of rice Gibberellin-insensitive dwarf 1 mutants (GID1). in: 17th International Conference on Plant Growth Substances.
326. Schaffrath, U., Mauch, F., Freydl, E., Schweizer, P., and Dudler, R. 2000. Constitutive expression of the defense-related Rir1b gene in transgenic rice plants confers enhanced resistance to the rice blast fungus Magnaporthe grisea. Plant Molecular Biology 43:59-66.
327. Takahashi, N., Phinney, B. O., and MacMillan, J. 2012. Gibberellins. Springer Science & Business Media.
328. Van Loon, L. 1997. Induced resistance in plants and the role of pathogenesis-related proteins. European Journal of Plant Pathology 103:753-765.
329. Velazhahan, R., Datta, S. K., and Muthukrishnan, S. 1999. The PR-5 family: thaumatin-like proteins. Pathogenesis-Related Proteins in Plants:107-129.
330. Vijayan, P., Shockey, J., Lévesque, C. A., and Cook, R. J. 1998. A role for jasmonate in pathogen defense of Arabidopsis. Proceedings of the National Academy of Sciences 95:7209-7214.
331. Alché, J., Castro, A., Jiménez-López, J., Morales, S., Zafra, A., Hamman-Khalifa, A., and Rodríguez-García, M. 2007. Differential characteristics of olive pollen from different cultivars: biological and clinical implications. Journal of Investigational Allergology and Clinical Immunology 17:17-23.
332. Almagro, L., Gómez Ros, L., Belchi-Navarro, S., Bru, R., Ros Barceló, A., and Pedreno, M. 2008. Class III peroxidases in plant defence reactions. Journal of Experimental Botany 60:377-390.
333. Cong, L., Ran, F. A., Cox, D., Lin, S., Barretto, R., Habib, N., Hsu, P. D., Wu, X., Jiang, W., and Marraffini, L. A. 2013. Multiplex genome engineering using CRISPR/Cas systems. Science 339:819-823.
334. Desjardins, A. E., Plattner, R. D., and Nelson, P. E. 1997. Production of Fumonisin B (inf1) and Moniliformin by Gibberella fujikuroi from Rice from Various Geographic Areas. Applied and Environmental Microbiology 63:1838-1842.
335. Dong, J., Chen, C., and Chen, Z. 2003. Expression profiles of the Arabidopsis WRKY gene superfamily during plant defense response. Plant Molecular Biology 51:21-37.
336. Huang, T.-C., and Chu, S.-C. 2009. The occurrence and control of rice bakanae disease in Taiwan. Proceeding of Symposium on Achievement and Perpectives of Rice Protection in Taiwan:29-43.
337. Iqbal, M., Javed, N., Sahi, S. T., and Cheema, N. M. 2011. Genetic management of bakanae disease of rice and evaluation of various fungicides against Fusarium moniliforme in vitro. Pakistan Journal of Phytopathology 23:103-107.
338. Leubner-Metzger, G., and Meins Jr, F. 1999. Functions and regulation of plant ß-1, 3-glucanases (PR-2). Pages 49-76 in: Pathogenesis-Related Proteins in Plants. S. K. Datta and S. Muthukrishnan, eds. CRC Press LLC, Boca Raton, Florida.
339. Ma, L.-J., Geiser, D. M., Proctor, R. H., Rooney, A. P., O'Donnell, K., Trail, F., Gardiner, D. M., Manners, J. M., and Kazan, K. 2013. Fusarium pathogenomics. Annual Review of Microbiology 67:399-416.
340. Makarova, K. S., Grishin, N. V., Shabalina, S. A., Wolf, Y. I., and Koonin, E. V. 2006. A putative RNA-interference-based immune system in prokaryotes: computational analysis of the predicted enzymatic machinery, functional analogies with eukaryotic RNAi, and hypothetical mechanisms of action. Biology Direct 1:7.
341. Makarova, K. S., Haft, D. H., Barrangou, R., Brouns, S. J., Charpentier, E., Horvath, P., Moineau, S., Mojica, F. J., Wolf, Y. I., and Yakunin, A. F. 2011. Evolution and classification of the CRISPR–Cas systems. Nature Reviews Microbiology 9:467-477.
342. Mali, P., Yang, L., Esvelt, K. M., Aach, J., Guell, M., DiCarlo, J. E., Norville, J. E., and Church, G. M. 2013. RNA-guided human genome engineering via Cas9. Science 339:823-826.
343. Manandhar, J. 1999. Fusarium moniliforme in rice seeds: its infection, isolation, and longevity. Journal of Plant Diseases and Protection:598-607.
344. McHale, L., Tan, X., Koehl, P., and Michelmore, R. W. 2006. Plant NBS-LRR proteins: adaptable guards. Genome Biology 7:212.
345. Mew, T.-W., and Gonzales, P. 2002. A handbook of rice seedborne fungi. International Rice Research Institute.
346. Pieterse, C. M., Van der Does, D., Zamioudis, C., Leon-Reyes, A., and Van Wees, S. C. 2012. Hormonal modulation of plant immunity. Annual Review of Cell and Developmental Biology 28:489-521.
347. Sasaki, A., Ashikari, M., Ueguchi-Tanaka, M., Ito, H., Kobayashi, M., Kitano, H., and Matsuoka, M. 2001. Screening of rice Gibberellin-insensitive dwarf 1 mutants (GID1). in: 17th International Conference on Plant Growth Substances.
348. Schaffrath, U., Mauch, F., Freydl, E., Schweizer, P., and Dudler, R. 2000. Constitutive expression of the defense-related Rir1b gene in transgenic rice plants confers enhanced resistance to the rice blast fungus Magnaporthe grisea. Plant Molecular Biology 43:59-66.
349. Takahashi, N., Phinney, B. O., and MacMillan, J. 2012. Gibberellins. Springer Science & Business Media.
350. Van Loon, L. 1997. Induced resistance in plants and the role of pathogenesis-related proteins. European Journal of Plant Pathology 103:753-765.
351. Velazhahan, R., Datta, S. K., and Muthukrishnan, S. 1999. The PR-5 family: thaumatin-like proteins. Pathogenesis-Related Proteins in Plants:107-129.
352. Vijayan, P., Shockey, J., Lévesque, C. A., and Cook, R. J. 1998. A role for jasmonate in pathogen defense of Arabidopsis. Proceedings of the National Academy of Sciences 95:7209-7214.