20
views
0
recommends
+1 Recommend
0 collections
    0
    shares
      • Record: found
      • Abstract: found
      • Article: found
      Is Open Access

      Transcriptomic analysis of rice in response to iron deficiency and excess

      research-article

      Read this article at

      Bookmark
          There is no author summary for this article yet. Authors can add summaries to their articles on ScienceOpen to make them more accessible to a non-specialist audience.

          Background

          Iron (Fe) is essential micronutrient for plants and its deficiency as well as toxicity is a serious agricultural problem. The mechanisms of Fe deficiency are reasonably understood, however our knowledge about plants response to excess Fe is limited. Moreover, the regulation of small open reading frames (sORFs) in response to abiotic stress has not been reported in rice. Understanding the regulation of rice transcriptome in response to Fe deficiency and excess could provide bases for developing strategies to breed plants tolerant to Fe deficiency as well as excess Fe.

          Results

          We used a novel rice 110 K microarray harbouring ~48,620 sORFs to understand the transcriptomic changes that occur in response to Fe deficiency and excess. In roots, 36 genes were upregulated by excess Fe, of which three were sORFs. In contrast, 1509 genes were upregulated by Fe deficiency, of which 90 (6%) were sORFs. Co-expression analysis revealed that the expression of some sORFs was positively correlated with the genes upregulated by Fe deficiency. In shoots, 50 (19%) of the genes upregulated by Fe deficiency and 1076 out of 2480 (43%) genes upregulated by excess Fe were sORFs. These results suggest that excess Fe may significantly alter metabolism, particularly in shoots.

          Conclusion

          These data not only reveal the genes regulated by excess Fe, but also suggest that sORFs might play an important role in the response of plants to Fe deficiency and excess.

          Electronic supplementary material

          The online version of this article (doi:10.1186/s12284-014-0018-1) contains supplementary material, which is available to authorized users.

          Related collections

          Most cited references77

          • Record: found
          • Abstract: found
          • Article: found
          Is Open Access

          Improvement of the Oryza sativa Nipponbare reference genome using next generation sequence and optical map data

          Background Rice research has been enabled by access to the high quality reference genome sequence generated in 2005 by the International Rice Genome Sequencing Project (IRGSP). To further facilitate genomic-enabled research, we have updated and validated the genome assembly and sequence for the Nipponbare cultivar of Oryza sativa (japonica group). Results The Nipponbare genome assembly was updated by revising and validating the minimal tiling path of clones with the optical map for rice. Sequencing errors in the revised genome assembly were identified by re-sequencing the genome of two different Nipponbare individuals using the Illumina Genome Analyzer II/IIx platform. A total of 4,886 sequencing errors were identified in 321 Mb of the assembled genome indicating an error rate in the original IRGSP assembly of only 0.15 per 10,000 nucleotides. A small number (five) of insertions/deletions were identified using longer reads generated using the Roche 454 pyrosequencing platform. As the re-sequencing data were generated from two different individuals, we were able to identify a number of allelic differences between the original individual used in the IRGSP effort and the two individuals used in the re-sequencing effort. The revised assembly, termed Os-Nipponbare-Reference-IRGSP-1.0, is now being used in updated releases of the Rice Annotation Project and the Michigan State University Rice Genome Annotation Project, thereby providing a unified set of pseudomolecules for the rice community. Conclusions A revised, error-corrected, and validated assembly of the Nipponbare cultivar of rice was generated using optical map data, re-sequencing data, and manual curation that will facilitate on-going and future research in rice. Detection of polymorphisms between three different Nipponbare individuals highlights that allelic differences between individuals should be considered in diversity studies. Electronic supplementary material The online version of this article (doi:10.1186/1939-8433-6-4) contains supplementary material, which is available to authorized users.
            Bookmark
            • Record: found
            • Abstract: not found
            • Book: not found

            Mineral nutrition of higher plant

              Bookmark
              • Record: found
              • Abstract: found
              • Article: not found

              Direct control of shoot meristem activity by a cytokinin-activating enzyme.

              The growth of plants depends on continuous function of the meristems. Shoot meristems are responsible for all the post-embryonic aerial organs, such as leaves, stems and flowers. It has been assumed that the phytohormone cytokinin has a positive role in shoot meristem function. A severe reduction in the size of meristems in a mutant that is defective in all of its cytokinin receptors has provided compelling evidence that cytokinin is required for meristem activity. Here, we report a novel regulation of meristem activity, which is executed by the meristem-specific activation of cytokinins. The LONELY GUY (LOG) gene of rice is required to maintain meristem activity and its loss of function causes premature termination of the shoot meristem. LOG encodes a novel cytokinin-activating enzyme that works in the final step of bioactive cytokinin synthesis. Revising the long-held idea of multistep reactions, LOG directly converts inactive cytokinin nucleotides to the free-base forms, which are biologically active, by its cytokinin-specific phosphoribohydrolase activity. LOG messenger RNA is specifically localized in shoot meristem tips, indicating the activation of cytokinins in a specific developmental domain. We propose the fine-tuning of concentrations and the spatial distribution of bioactive cytokinins by a cytokinin-activating enzyme as a mechanism that regulates meristem activity.
                Bookmark

                Author and article information

                Contributors
                khurram.bashir@riken.jp
                kohanada@psc.riken.jp
                minami.shimizu@riken.jp
                motoaki.seki@riken.jp
                ahnaka@mail.ecc.u-tokyo.ac.jp
                annaoko@mail.ecc.u-tokyo.ac.jp
                Journal
                Rice (N Y)
                Rice (N Y)
                Rice
                Springer New York (New York )
                1939-8425
                1939-8433
                12 September 2014
                12 September 2014
                2014
                : 7
                : 18
                Affiliations
                [ ]Laboratory of Plant Biotechnology, Department of Global Agricultural Sciences, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657 Japan
                [ ]Plant Genomics Network Research Team, Center for Sustainable Resource Science, RIKEN Yokohama Campus, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama City, 230-0045 Kanagawa, Japan
                [ ]Gene Discovery Research Group, Center for Sustainable Resource Science, RIKEN Yokohama Campus, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama City, 230-0045 Kanagawa, Japan
                [ ]Frontier Research Academy for Young Researchers, Department of Bioscience and Bioinformatics, Kyusyu Institute of Technology, Iizuka, 820-8502 Fukuoka, Japan
                [ ]Kihara Institute for Biological Research, Yokohama City University, 22-2 Seto, Kanazawa-ku, Yokohama, 236-0027 Japan
                [ ]Research Institute for Bioresources and Biotechnology, Ishikawa Prefectural University, 1-308 Suematsu, Nonoichi-shi, 921-8836 Ishikawa, Japan
                Article
                18
                10.1186/s12284-014-0018-1
                4884027
                26224551
                11e658e0-1a91-4fa8-bbee-dd58ce625bc6
                © Bashir et al.; licensee Springer. 2014

                This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited.

                History
                : 10 April 2014
                : 23 July 2014
                Categories
                Research
                Custom metadata
                © The Author(s) 2014

                Agriculture
                excess fe,fe deficiency,iron,peptides,rice,small open reading frames
                Agriculture
                excess fe, fe deficiency, iron, peptides, rice, small open reading frames

                Comments

                Comment on this article