Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Transcription profiling of rice transgenics expressing rice full-length cDNAs vs wild-type Col-0

ABSTRACT: We generated more than 23,000 independent Arabidopsis transgenic lines that expressed rice fl-cDNAs (Rice FOX Arabidopsis lines). The short generation time and rapid and efficient transformation frequency of Arabidopsis enabled the functions of the rice genes to be analyzed rapidly. We screened rice FOX Arabidopsis lines for alterations in morphology, photosynthesis, element accumulation, pigment accumulation, hormone profiles, secondary metabolites, pathogen resistance, salt-tolerance, UV signaling, high light tolerance, and heat stress tolerance. Since we isolated 6 genes (AK069096, AK073112, AK073675, AK065297, AK102323 and AK073210) causing an increase in the abundance of metabolites or pigments detected by absorption data, we investigated the expression profiles in transgenic plants by using microarray analysis. Expression of the genes encoding chalcone synthase and dihydroflavonol-4-reductase was increased in all 6 cDNA transformants. These results indicate that an increase in expression of the genes encoding flavonoid biosynthesis enzymes caused an accumulation of pigments in these 6 transformants. Experiment Overall Design: Total RNA was isolated from aerial parts of re-transformants of some rice cDNAs and wild type using an RNAqueous Kit (Ambion, Inc, USA).

ORGANISM(S): Arabidopsis thaliana

SUBMITTER: Minami Matsui

PROVIDER: E-GEOD-13165 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Systematic approaches to using the FOX hunting system to identify useful rice genes.

Kondou Youichi Y Higuchi Mieko M Takahashi Shinya S Sakurai Tetsuya T Ichikawa Takanari T Kuroda Hirofumi H Yoshizumi Takeshi T Tsumoto Yuko Y Horii Yoko Y Kawashima Mika M Hasegawa Yukako Y Kuriyama Tomoko T Matsui Keiko K Kusano Miyako M Albinsky Doris D Takahashi Hideki H Nakamura Yukiko Y Suzuki Makoto M Sakakibara Hitoshi H Kojima Mikiko M Akiyama Kenji K Kurotani Atsushi A Seki Motoaki M Fujita Miki M Enju Akiko A Yokotani Naoki N Saitou Tsutomu T Ashidate Kozue K Fujimoto Naka N Ishikawa Yasuo Y Mori Yayoi Y Nanba Rie R Takata Kazumasa K Uno Kuniko K Sugano Shoji S Natsuki Jun J Dubouzet Joseph Gogo JG Maeda Satoru S Ohtake Miki M Mori Masaki M Oda Kenji K Takatsuji Hiroshi H Hirochika Hirohiko H Matsui Minami M

The Plant journal : for cell and molecular biology 20081029 5

Ectopic gene expression, or the gain-of-function approach, has the advantage that once the function of a gene is known the gene can be transferred to many different plants by transformation. We previously reported a method, called FOX hunting, that involves ectopic expression of Arabidopsis full-length cDNAs in Arabidopsis to systematically generate gain-of-function mutants. This technology is most beneficial for generating a heterologous gene resource for analysis of useful plant gene functions ...[more]

PMID: 18980645

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Project description:RNA from the aerial parts of 15-day-old eceriferum cer6-2 mutant and control plants were used in microarray experiments to screen for differentially expressed genes. Among those which were down regulated in the mutant, several were known to be involved in various plant defense mechanisms. The most remarkable difference was measured for the transcripts encoding the pathogenesis-related protein1 (PR-1), which is a marker of the systemic acquired resistance (SAR) pathway, with a 100-fold decrease in the cer6-2 mutant. Further Q-PCR experiments showed that the PR-1 transcript levels were low in two other eceriferum mutants, representing 1/200th and 1/25th of the normal values in the aerial part of 15-day-old cer2 and cer1-1 mutants, respectively. Interestingly, PR-1 mRNA levels were closed to the normal values in the cer3-1 and cer6-2R mutant, the latter being a plant where the synthesis of the very-long chain fatty acids, which is deficient in the cer6-2 plants, is partially restored. Altogether, these results strongly suggested that the amount of PR1-mRNA was not directly correlated to the amount of epicuticular wax on the leaves, but was rather correlated to the presence or absence of some particular lipid-constituents in the epicuticular wax layer. Related publication:; Garbay B, Tautu MT, Costaglioli P. Low level of pathogenesis-related protein 1 mRNA expression in 15-day-old Arabidopsis cer6-2 and cer2 eceriferum mutants. Plant Science 2007; Volume 172, Issue 2, Pages 299-305 Experiment Overall Design: Total RNA was purified from the aerial parts of 2-week-old plants (20 plants were pooled for each genotype). Arabidopsis plants were grown under long-day conditions (16 h light:8 h dark) at 22Â°C and 80% relative humidity. The control plants and the cer mutant were cultivated in the same phytotron, and the Petri dishes were placed randomly on the same shelf. This was done to avoid any difference in plant growth conditions between the mutants and the control plants. The microarrays used were Agilent Arabidopsis2. GSM87735 represents the direct experiment (cer6-2 Cy3, Ler-0 Cy5), and GSM88340 represents the dye-swap (Ler-0 Cy3, cer6-2 Cy5)

Dataset Information

Transcription profiling of rice transgenics expressing rice full-length cDNAs vs wild-type Col-0

Publications

Systematic approaches to using the FOX hunting system to identify useful rice genes.

Similar Datasets

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