Microarray Data Analysis of as-induced Rice Roots by using Easygo and Mapman Softwares
Authors: Thi Thuy Quynh Nguyen , Le Ngoc Han Pham , Khanh Tam Vo , Thi Kim Hue Phung , -Lien Huang Tsai 
Published: September 2019

Rice is one of the most important crops in Asian countries such as China, Vietnam... Many recent reports indicate that the arsenic content in rice exceeds the threshold and affects human health. Studying of molecular mechanisms and finding the arsenic resistance genes in rice which is extremely important and urgent. In this study, we analyzed the transcriptional changes of arsenic-treated rice root cells during 24 hours by microarray technique. Results showed that a large number of the differentially expressed genes (720 genes). EasyGO and Mapman softwares are powerful tools in analyzing microarray data and classifying functional groups as well as the important metabolic pathways in the cell. Results of microarray analysis using EasyGO showed that 74 down-regulated genes related to cellular component, 200 up-regulated genes involved in catalytic activity, 93 up-regulated genes involved in biological processes as responding to environmental stress, and 64 detoxification-realted genes are increased expression such as cytochrome P450, Glutathione-S-transferase and UDP-Glycosyltransferase. Mapman's microarray analysis reaults also indicate that numerous of arsenic-tolerance genes of rice roots. These results support for searching indicated genes in the selection of As-tolerance rice varieties.

Keywords

Asen, EasyGO, Mapman, microarray, Oryza sativa L.

References

[1] S.K. Panda, R.K. Upadhyay, S. Nath, Arsenic stress in plants. Journal of Agronomy and Crop Science 196 (2010) 161-174. https://doi.org/10. 1111/j.1439-037X.2009. 00407.x.[2] M.A. Rahman, H. Hasengawa, M.M. Rahman, M.A Miah, A. Tasmin. Arsenic accumulation in rice (Oryza sativa L.): Human exposure through food chain. Ecotoxicology and Environmental Safety 69 (2008): 317-324. https://doi.org/10. 1016/j.ecoenv.2007.01.005.[3] K.A. Marrs, The function and regulation of Glutathione S-transferase in plants. Plant Mol Biol 47 (1996) 127-58. https://doi.org/10.1146/ annurev.arplant.47.1.127.[4] L.M. DelRazo, B. Quintanilla-Vega, E. Brambila-Colombres, E.S. Caldero ́n-Aranda, M. Manno, A. Albores, Stress proteins induced by Arsenic. Toxicology and Applied Pharmacology 177 (2001)132-148. https://doi.org/10.1006/taap. 2001.9291.[5] T.L. Huang, Q.T.T. Nguyen, S.F. Fu, C.Y. Lin, Y.C. Chen, H.J. Huang, Transcriptomic changes and signalling pathways induced by arsenic stress in rice roots. Plant Molecular Biology 80 (2012) 587-608. https://link.springer.com/article/10.10 07/s11103-012-9969-z.[6] O. Thimm, O. Bläsing, Y. Gibon, A. Nagel, S. Meyer, P. Krüger, J. Selbig, L.A. Müller, S.Y Rhee, M. Stitt, Mapman: a user-driven tool to display genomics data sets onto diagrams of metabolic pathways and other biological processes. The Plant Journal 37 (2004) 914-939. https://doi.org/10.1111/j.1365-313X.2004. 02016.x.[7] J. Hartley-Whitker, G. Ainsworth, A.A. Meharg, Copper- and arsenate-induced oxidative stress in Holcus lanatus L. clones with differential sensitivity. Plant, Cell and Environment 24 (2001) 713-722. https://doi.org/10.1046/j.0016-8025.2001.00721.x.[8] S. Mishara, A.B. Jha, R.S. Dubey, Arsenite treatment induces oxidative stress, upregulates antioxidant system, and causes phytochelatin synthesis in rice seedlings. Protoplasma 248 (2011) 565-577. https://doi.org/10.1007/s00709-010-0210-0.[9] M. Chabannes, A. Barakate, C. Lapierre, J.M. Marita, Strong decrease in lignin content without significant alteration of plant development is induced by simultaneous down-regulation of cinnamoyl CoA reductase (CCR) and cinnamyl alcohol dehydrogenase (CAD) in tobacco plants, The Plant 28 (2001): 257-270. https://doi.org/10. 1046/j.1365-313X.2001.01140.x.[10] T. Goujon, V. Ferret, I. Mila, B. Pollet, Down-regulation of the AtCCR1 gene in Arabidopsis thaliana: effects on phenotype, lignins and cell wall degradability. Planta 217 (2003) 218-228. https://doi.org/10.1007/s00425-003-0987-6.[11] C. Li, S. Feng, Y. Shoa, L. Jiang, X. Lu, X. Hou, Effects of arsenic on seed germination and physiological activities of wheat seedlings. Journal of Environmental Sciences. 19 (2007) 725-732. https://doi.org/10.1016/S1001-0742(07) 60121-1.[12] A.A. Meharg, J. Harley-Whitaker, Arsenic uptake and metabolism in arsenic resistant and nonresistant plant species. New Phytologist 154 (2002) 29-43. https://doi.org/10.1046/j.1469-8137.2002.00363.x.