Liu, Yu ; Université de Liège - ULiège > TERRA Research Centre ; State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
LIU, Wen-wen; State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
LI, Li; State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
Francis, Frédéric ; Université de Liège - ULiège > TERRA Research Centre > Gestion durable des bio-agresseurs
WANG, Xi-feng; State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
Language :
English
Title :
Transcriptome analysis reveals different response of resistant and susceptible rice varieties to rice stripe virus infection
Publication date :
07 July 2020
Journal title :
Journal of Integrative Agriculture
ISSN :
2095-3119
eISSN :
2352-3425
Publisher :
Editorial Department of Scientia Agricultura Sinica
Abramovitch, R B, Anderson, J C, Martin, G B, Bacterial elicitation and evasion of plant innate immunity. Nature Reviews Molecular Cell Biology, 7, 2006, 601.
Agrawal, G K, Jwa, N S, Rakwal, R, A novel rice (Oryza sativa L.) acidic PR1 gene highly responsive to cut, phytohormones, and protein phosphatase inhibitors. Biochemical and Biophysical Research Communications 274 (2000), 157–165.
Bailey-Serres, J, Mittler, R, The roles of reactive oxygen species in plant cells. Plant Physiology, 141, 2006, 311.
Bari, R, Jones, J D G, Role of plant hormones in plant defence responses. Plant Molecular Biology 69 (2009), 473–488.
Chen, M Y, Ye, W Y, Xiao, H M, Li, M Z, Cao, Z H, Ye, X H, Zhao, X X, He, K, Li, F, LncRNAs are potentially involved in the immune interaction between small brown planthopper and rice stripe virus. Journal of Integrative Agriculture 18 (2019), 2814–2822.
Chisholm, S T, Coaker, G, Day, B, Staskawicz, B J, Host–microbe interactions: shaping the evolution of the plant immune response. Cell 124 (2006), 803–814.
Cho, W, Lian, S, Kim, S, Seo, B, Jung, J, Kim, K, Time-course RNA-Seq analysis reveals transcriptional changes in rice plants triggered by rice stripe virus infection. PLoS ONE, 10, 2015, e0136736.
Derrien, B, Baumberger, N, Schepetilnikov, M, Viotti, C, De Cillia, J, Ziegler-graff, V, Isono, E, Schumacher, K, Genschik, P, Degradation of the antiviral component ARGONAUTE1 by the autophagy pathway. Proceedings of the National Academy of Science of Sciences of the United States of America 109 (2012), 15942–15946.
Deslande, L, Oliver, J, Peeters, N, Feng, D X, Khounlotham, M, Boucher, C, Somssich, I, Genin, S, Marco, Y, Physical interaction between RRS1-R, a protein conferring resistance to bacterial wilt, and PopP2, a type III effector targeted to the plant nucleus. Proceedings of the National Academy of Sciences of Sciences of the United States of America 100 (2003), 8024–8029.
Ding, Y, Sun, T, Ao, K, Peng, Y, Zhang, Y, Li, X, Zhang, Y, Opposite roles of salicylic acid receptors NPR1 and NPR3/NPR4 in transcriptional regulation of plant immunity. Cell 173 (2018), 1454–1467.
Gadea, J, Mayda, M E, Conejero, V, Vera, P, Characterization of defence-related genes ectopically expressed in viroid-infection tomato plants. Molecular Plant–Microbe Interactions 9 (1996), 409–415.
Gaffney, T, Friedrich, L, Vernooij, B, Negrotto, D, Nye, G, Uknes, S, Ward, E, Kessmann, H, Ryals, J, Requirement of salicylic acid for the induction of systemic acquired resistance. Science 261 (1993), 754–756.
Garber, M, Grabherr, M G, Guttman, M, Trapnell, C, Computational methods for transcriptome annotation and quantification using RNA-seq. Nature Methods 8 (2011), 469–477.
Hwang, S H, Kwon, S I, Jang, J Y, Fang, I L, Lee, H, Choi, C, Park, S, Ahn, I, Bae, S C, Hwang, D J, OsWRKY51, a rice transcription factor, functions as a positive regulator in defense response against Xanthomonas oryzae pv. oryzae. Plant Cell Reports 35 (2016), 1975–1985.
He, P, Shan, L, Sheen, J, Elicitation and suppression of microbe-associated molecular pattern-triggered immunity in plant–microbe interactions. Cellular Microbiology 9 (2007), 1385–1396.
Jiang, C J, Shimono, M, Sugano, S, Kojima, M, Liu, X, Inoue, H, Sakakibara, H, Takatsuji, H, Cytokinins act synergistically with salicylic acid to activate defense gene expression in rice. Molecular Plant–Microbe Interactions 26 (2013), 287–296.
Khokon, M, Uraji, M, Munemasa, S, Okuma, E, Murata, Y, Chitosan-induced stomatal closure accompanied by peroxidase-mediated reactive oxygen species production in Arabidopsis. Bioscience Biotechnology and Biochemistry 74 (2010), 2313–2315.
Koornneef, A, Leon-Reyes, A, Ritsema, T, Verhage, A, Den Otter, F C, Van Loon, L C, Pieterse, C M, Kinetics of salicylate-mediated suppression of jasmonate signaling reveal a role for redox modulation. Plant Physiology 147 (2008), 1358–1368.
Li, L, Guo, C, Wang, B, Zhou, T, Lei, Y, Dai, Y H, He, W, Liang, C, Wang, X F, RNAi-mediated transgenic rice resistance to Rice stripe virus. Journal of Integrative Agriculture 15 (2016), 2539–2549.
Liu, Q, Luo, L, Zheng, L, Lignins: Biosynthesis and biological functions in plants. International Journal of Molecular Sciences, 19, 2018, 335.
Liu, Y, Liu, Y, Spetz, C, Li, L, Wang, X F, Comparative transcriptome analysis in Triticum aestivum infecting wheat dwarf virus reveals the effects of viral infection on phytohormone and photosynthesis metabolism pathways. Phytopathology Research, 2, 2020, 3.
Liu, Y, Schiff, M, Czymmek, K, Tallóczy, Z, Levine, B, Dinesh-kumar, S P, Autophagy regulates programmed cell death during the plant innate immune response. Cell 121 (2005), 567–577.
Moffat, C S, Ingle, R A, Wathugala, D L, Saunders, N J, Knight, H, Knight, M R, ERF5 and ERF6 play redundant roles as positive regulators of JA/ET-mediated defense against Botrytis cinerea in Arabidopsis. PLoS ONE, 7, 2012, e35995.
Mortazavi, A, Williams, B A, McCue, K, Schaeffer, L, Wold, B, Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nature Methods 5 (2008), 1–8.
Peng, Q, Wang, Z W, Liu, P F, Liang, Y P, Zhao, Z Z, Li, W H, LIU, X L, Xia, Y, Oxathiapiprolin, a novel chemical inducer activates the plant disease resistance. International Journal of Molecular Sciences, 21, 2020, 1223.
Qin, F L, Liu, W W, Wu, N, Zhang, L, Zhou, X P, Wang, X F, Invasion of midgut epithelial cells by a persistently transmitted virus is mediated by sugar transporter 6 in its insect vector. PLoS Pathogens, 14, 2018, e1007201.
Qiu, S, Chen, X, Zhai, Y, Cui, W, Ai, X, Rao, S, Chen, J, Yan, F, Downregulation of light-harvesting complex II induces ROS-mediated defense against turnip mosaic virus infection in Nicotiana benthamiana. Frontiers in Microbiology, 5, 2021, 690988.
Rao, M S, Van Vleet, T R, Ciurlionis, R, Buck, W R, Mittelstadt, S W, Blomme, E A G, Liguori, M J, Comparison of RNA-Seq and microarray gene expression platforms for the toxicogenomic evaluation of liver from short-term rat toxicity studies. Frontiers in Genetics, 9, 2019, 636.
Savary, S, Willocquet, L, Pethybridge, S J, Esker, P, McRoberts, N, Nelson, A, The global burden of pathogens and pests on major food crops. Nature Ecology & Evolution 3 (2019), 430–439.
Sun, F, Fang, P, Li, J, Du, L L, Lan, Y, Zhou, T, Fan, Y J, Shen, W B, Zhou, Y L, RNA-seq-based digital gene expression analysis reveals modification of host defense responses by rice stripe virus during disease symptom development in Arabidopsis. Virology Journal, 13, 2016, 202.
Sun, S S, Ren, Y X, Wang, D X, Farooq, T, He, Z F, Zhang, C, Li, S F, Yang, X L, Zhou, X P, A group I WRKY transcription factor regulates mulberry mosaic dwarf-associated virus-triggered cell death in Nicotiana benthamiana. Molecular Plant Pathology 23 (2022), 237–253.
Tao, Z, Liu, H, Qiu, D, Zhou, Y, Li, X, Xu, C, Wang, S, A pair of allelic WRKY genes play opposite roles in rice–bacteria interactions. Plant Physiology 151 (2009), 936–948.
Tripathy, B C, Oelmüller, R, Reactive oxygen species generation and signaling in plants. Plant Signaling & Behavior 7 (2012), 1621–1633.
Wang, B, Hajano, J U D, Ren, Y D, Lu, C, Wang, X F, iTRAQ-based quantitative proteomics analysis of rice leaves infected by rice stripe virus reveals several proteins involved in symptom formation. Virology Journal, 12, 2015, 99.
Wang, H D, Chen, J P, Zhang, H M, Sun, X L, Zhu, J L, Wang, A G, Sheng, W X, Adams, M J, Recent rice stripe virus epidemics in Zhejiang province, China, and experiments on sowing date, disease-yield loss relationships, and seedling susceptibility. Plant Disease 92 (2008), 78–81.
Wang, Z, Gerstein, M, Snyder, M, RNA-Seq: A revolutionary tool for transcriptomics. Nature Reviews Genetics 10 (2009), 57–63.
Wei, T Y, Yang, J G, Liao, F L, Gao, F L, Lu, L M, Zhang, X T, Li, F, Wu, Z J, Lin, Q Y, Xie, L H, Lin, H X, Genetic diversity and population structure of rice stripe virus in China. Journal of General Virology 90 (2009), 1025–1034.
Wu, G T, Zheng, G X, Hu, Q, Ma, M G, Li, M J, Sun, X C, Yan, F, Qing, L, NS3 protein from rice stripe virus affects the expression of endogenous genes in Nicotiana benthamiana. Virology Journal, 15, 2018, 105.
Xiong, R Y, Wu, J X, Zhou, Y J, Zhou, X P, Identification of a movement protein of the tenuivirus rice stripe virus. Journal of Virology 82 (2008), 12304–12311.
Xiong, R Y, Wu, J X, Zhou, Y J, Zhou, X P, Characterization and subcellular localization of an RNA silencing suppressor encoded by rice stripe tenuivirus. Virology 387 (2009), 29–40.
Yang, D L, Yang, Y N, He, Z H, Roles of plant hormones and their interplay in rice immunity. Molecular Plant 6 (2013), 675–685.
Yin, J J, Xiong, J, XU, L T, Chen, X W, Li, W T, Recent advances in plant immunity with cell death: A review. Journal of Integrative Agriculture 21 (2022), 610–620.
Yoda, H, Ogawa, M, Yamaguchi, Y, Koizumi, N, Kusano, T, Sano, H, Identification of early-responsive genesassociated with the hypersensitive response to tobacco mosaic virus and characterization of a WRKY-type transcription factor in tobacco plants. Molecular Genetics and Genomics 267 (2002), 154–161.
Zarei, A, Körbes, A P, Younessi, P, Montiel, G, Champion, A, Memelink, J, Two GCC boxes and AP2/ERF-domain transcription factor ORA59 in jasmonate/ethylene-mediated activation of the PDF1.2 promoter in Arabidopsis. Plant Molecular Biology 75 (2011), 321–331.
Zhang, H M, Sun, H R, Wang, H D, Chen, J P, Advances on molecular biology of rice stripe virus. Acta Phytophylacica Sinica 34 (2007), 436–440 (in Chinese).
Zhang, J, Li, W, Xiang, T T, Liu, Z X, Laluk, K, Ding, X J, Zou, Y, Gao, M, Zhang, X J, Chen, S, Mengiste, T, Zhang, Y L, Zhou, J M, Receptor-like cytoplasmic kinases integrate signaling from multiple plant immune receptors and are targeted by a Pseudomonas syringae effector. Cell Host & Microbe 7 (2010), 290–301.
Zhang, S T, Zhu, C, Lyu, Y M, Chen, Y, Zhang, Z H, Lai, Z X, Lin, Y L, Genome-wide identification, molecular evolution, and expression analysis provide new insights into the APETALA2/ethylene responsive factor (AP2/ERF) superfamily in Dimocarpus longan Lour. BMC Genomics, 21, 2020, 62.
Zhao, Y, Wei, T, Yin, K Q, Chen, Z, Gu, H, Qu, L J, Qin, G, Arabidopsis RAP2.2 plays an important role in plant resistance to Botrytis cinerea and ethylene responses. New Phytologist 195 (2012), 450–460.
Zhou, Y J, Li, S, Cheng, Z B, Zhou, T, Fan, Y J, Research advances in rice stripe disease in China. Jiangsu Journal of Agricultural Sciences 28 (2012), 1007–1015 (in Chinese).
