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BioMed Research International
Volume 2016, Article ID 9739505, 9 pages
http://dx.doi.org/10.1155/2016/9739505
Research Article

Genome-Wide Transcriptome Analysis of Cadmium Stress in Rice

Agrogenomics Research Center, National Institute of Agrobiological Sciences, Tsukuba, Ibaraki 305-8602, Japan

Received 26 November 2015; Revised 26 January 2016; Accepted 28 January 2016

Academic Editor: Yan-Bo Hu

Copyright © 2016 Youko Oono et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Linked References

  1. CODEX, “Report of the 38th session of the CODEX Committee on Food Additives and Contaminants,” ALINORM 06/29/12, Codex Alimentarius Commission, 2006. View at Google Scholar
  2. B. Halliwell and J. M. C. Gutteridge, “Oxygen-toxicity, oxygen radicals, transition-metals and disease,” Biochemical Journal, vol. 219, no. 1, pp. 1–14, 1984. View at Publisher · View at Google Scholar · View at Scopus
  3. Z. Wang, M. Gerstein, and M. Snyder, “RNA-Seq: a revolutionary tool for transcriptomics,” Nature Reviews Genetics, vol. 10, no. 1, pp. 57–63, 2009. View at Publisher · View at Google Scholar · View at Scopus
  4. Y. Oono, T. Yazawa, Y. Kawahara et al., “Genome-wide transcriptome analysis reveals that cadmium stress signaling controls the expression of genes in drought stress signal pathways in rice,” PLoS ONE, vol. 9, no. 5, Article ID e96946, 2014. View at Publisher · View at Google Scholar · View at Scopus
  5. S. Yoshida, D. A. Forno, J. H. Cock, and K. A. Gomez, Laboratory Manual for Physiological Studies of Rice, International Rice Research Institute, Manila, Philippines, 3rd edition, 1976.
  6. S. Sauve, W. A. Norvell, M. McBride, and W. Hendershot, “Speciation and complexation of cadmium in extracted soil solutions,” Environmental Science & Technology, vol. 34, no. 2, pp. 291–296, 2000. View at Publisher · View at Google Scholar · View at Scopus
  7. Y. Kawahara, Y. Oono, H. Wakimoto et al., “TENOR: database for comprehensive mRNA-Seq experiments in rice,” Plant and Cell Physiology, vol. 57, no. 1, article e7, 2016. View at Publisher · View at Google Scholar
  8. M. Martin, “Cutadapt removes adapter sequences from high-throughput sequencing reads,” EMBnet Journal, vol. 17, no. 1, pp. 10–12, 2011. View at Publisher · View at Google Scholar
  9. Y. Oono, Y. Kawahara, H. Kanamori et al., “mRNA-seq reveals a comprehensive transcriptome profile of rice under phosphate stress,” Rice, vol. 4, no. 2, pp. 50–65, 2011. View at Publisher · View at Google Scholar · View at Scopus
  10. H. Li and R. Durbin, “Fast and accurate short read alignment with Burrows-Wheeler transform,” Bioinformatics, vol. 25, no. 14, pp. 1754–1760, 2009. View at Publisher · View at Google Scholar · View at Scopus
  11. A. Mortazavi, B. A. Williams, K. McCue, L. Schaeffer, and B. Wold, “Mapping and quantifying mammalian transcriptomes by RNA-Seq,” Nature Methods, vol. 5, no. 7, pp. 621–628, 2008. View at Publisher · View at Google Scholar · View at Scopus
  12. M. Zhang, X. Liu, L. Yuan et al., “Transcriptional profiling in cadmium-treated rice seedling roots using suppressive subtractive hybridization,” Plant Physiology and Biochemistry, vol. 50, no. 1, pp. 79–86, 2012. View at Publisher · View at Google Scholar · View at Scopus
  13. K. Lee, D. W. Bae, S. H. Kim et al., “Comparative proteomic analysis of the short-term responses of rice roots and leaves to cadmium,” The Journal of Plant Physiology, vol. 167, no. 3, pp. 161–168, 2010. View at Publisher · View at Google Scholar · View at Scopus
  14. K. Shah, R. G. Kumar, S. Verma, and R. S. Dubey, “Effect of cadmium on lipid peroxidation, superoxide anion generation and activities of antioxidant enzymes in growing rice seedlings,” Plant Science, vol. 161, no. 6, pp. 1135–1144, 2001. View at Publisher · View at Google Scholar · View at Scopus
  15. L. Perfus-Barbeoch, N. Leonhardt, A. Vavasseur, and C. Forestier, “Heavy metal toxicity: cadmium permeates through calcium channels and disturbs the plant water status,” Plant Journal, vol. 32, no. 4, pp. 539–548, 2002. View at Publisher · View at Google Scholar · View at Scopus
  16. R. Mittler, S. Vanderauwera, N. Suzuki et al., “ROS signaling: the new wave?” Trends in Plant Science, vol. 16, no. 6, pp. 300–309, 2011. View at Publisher · View at Google Scholar · View at Scopus
  17. C. Frova, “The plant glutathione transferase gene family: genomic structure, functions, expression and evolution,” Physiologia Plantarum, vol. 119, no. 4, pp. 469–479, 2003. View at Publisher · View at Google Scholar · View at Scopus
  18. C. Cosio and C. Dunand, “Specific functions of individual class III peroxidase genes,” Journal of Experimental Botany, vol. 60, no. 2, pp. 391–408, 2009. View at Publisher · View at Google Scholar · View at Scopus
  19. C. Cobbett and P. Goldsbrough, “Phytochelatins and metallothioneins: roles in heavy metal detoxification and homeostasis,” Annual Review of Plant Biology, vol. 53, pp. 159–182, 2002. View at Publisher · View at Google Scholar · View at Scopus
  20. K. Yamaguchi-Shinozaki and K. Shinozaki, “Transcriptional regulatory networks in cellular responses and tolerance to dehydration and cold stresses,” Annual Review of Plant Biology, vol. 57, pp. 781–803, 2006. View at Publisher · View at Google Scholar · View at Scopus
  21. R. Cailliatte, A. Schikora, J.-F. Briat, S. Mari, and C. Curie, “High-affinity manganese uptake by the metal transporter NRAMP1 is essential for Arabidopsis growth in low manganese conditions,” Plant Cell, vol. 22, no. 3, pp. 904–917, 2010. View at Publisher · View at Google Scholar · View at Scopus
  22. A. Sasaki, N. Yamaji, K. Yokosho, and J. F. Ma, “Nramp5 is a major transporter responsible for manganese and cadmium uptake in rice,” Plant Cell, vol. 24, no. 5, pp. 2155–2167, 2012. View at Publisher · View at Google Scholar · View at Scopus
  23. N. Satoh-Nagasawa, M. Mori, N. Nakazawa et al., “Mutations in rice (Oryza sativa) heavy metal ATPase 2 (OsHMA2) restrict the translocation of zinc and cadmium,” Plant and Cell Physiology, vol. 53, no. 1, pp. 213–224, 2012. View at Publisher · View at Google Scholar · View at Scopus
  24. Y. O. Korshunova, D. Eide, W. G. Clark, M. L. Guerinot, and H. B. Pakrasi, “The IRT1 protein from Arabidopsis thaliana is a metal transporter with a broad substrate range,” Plant Molecular Biology, vol. 40, no. 1, pp. 37–44, 1999. View at Publisher · View at Google Scholar · View at Scopus
  25. N. E. Grossoehme, S. Akilesh, M. L. Guerinot, and D. E. Wilcox, “Metal-binding thermodynamics of the histidine-rich sequence from the metal-transport protein IRT1 of Arabidopsis thaliana,” Inorganic Chemistry, vol. 45, no. 21, pp. 8500–8508, 2006. View at Publisher · View at Google Scholar · View at Scopus
  26. S. Lee and G. An, “Over-expression of OsIRT1 leads to increased iron and zinc accumulations in rice,” Plant, Cell and Environment, vol. 32, no. 4, pp. 408–416, 2009. View at Publisher · View at Google Scholar · View at Scopus
  27. L. Wang, W. Xie, Y. Chen et al., “A dynamic gene expression atlas covering the entire life cycle of rice,” Plant Journal, vol. 61, no. 5, pp. 752–766, 2010. View at Publisher · View at Google Scholar · View at Scopus
  28. G. M. He, X. P. Zhu, A. A. Elling et al., “Global epigenetic and transcriptional trends among two rice subspecies and their reciprocal hybrids,” Plant Cell, vol. 22, no. 1, pp. 17–33, 2010. View at Publisher · View at Google Scholar · View at Scopus
  29. T. T. Lu, G. J. Lu, D. L. Fan et al., “Function annotation of the rice transcriptome at single-nucleotide resolution by RNA-seq,” Genome Research, vol. 20, no. 9, pp. 1238–1249, 2010. View at Publisher · View at Google Scholar · View at Scopus
  30. P. Pedas, C. K. Ytting, A. T. Fuglsang, T. P. Jahn, J. K. Schjoerring, and S. Husted, “Manganese efficiency in Barley: identification and characterization of the metal ion transporter HvIRT1,” Plant Physiology, vol. 148, no. 1, pp. 455–466, 2008. View at Publisher · View at Google Scholar · View at Scopus