SE128:/S1/M1/D1

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Sample Set Information

ID TSE8
Title Determination of growth stages and metabolic profiles in Brachypodium distachyon for comparison of developmental context with Triticeae crops
Description Brachypodium distachyon is an emerging model plant for studying biological phenomena in temperate grasses. Study of the growth scale is essential to analyse spatio-temporal changes in molecular factors throughout the life cycle. For sensitive and robust staging based on morphology in B. distachyon, we demonstrated the utility of the BBCH (Biologische Bundesanstalt, Bundessortenamt and CHemical industry) scale, which is comparable to the Zadoks scale conventionally used for Triticeae crops. We compared the chronological progression of B. distachyon accessions Bd21 and Bd3-1, in addition to the progression of Chinese Spring wheat. The comparison of growth stages illustrates the morphological similarities and differences in the timing of life cycle events. Furthermore, we compared metabolite accumulation patterns across different growth stages and across different stress conditions using a widely targeted metabolome analysis. Metabolic profiling determined commonalities and specificities in chemical properties that were dependent on organisms, growth stages and/or stress conditions. Most metabolites accumulated equivalently in B. distachyon and wheat. This qualitative similarity indicated the superiority of B. distachyon as a model for Triticeae crops. The growth scale of B. distachyon should provide a conceptual framework for comparative analysis and for knowledge integration between this model grass and crops in the Pooideae subfamily.
Authors Yoshihiko Onda, Kei Hashimoto, Takuhiro Yoshida, Tetsuya Sakurai, Yuji Sawada, Masami Yokota Hirai, Kiminori Toyooka, Keiichi Mochida, and Kazuo Shinozaki
Reference Onda et al. (2015) Proceedings Biological Sciences,Jul 22;282(1811). pii: 20150964. doi: 10.1098/rspb.2015.0964.
Comment Data on metabolome analysis are available at Data Resources of Plant Metabolomics (DROP Met) as "Metabolome data across different growth stages and across under different stress conditions in Brachypodium distachyon and wheat"


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The raw data files are available at DROP Met web site in PRIMe database of RIKEN.

Sample Information

ID S1
Title Dry seeds of diploid accessions of Brachypodium distachyon Bd21 and Bd3-1
Organism - Scientific Name Brachypodium distachyon
Organism - ID NCBI taxonomy 15368
Compound - ID
Compound - Source
Preparation Dry seeds of diploid accessions of B. distachyon Bd21 and Bd3-1 were provided by the National Plant Germplasm System of USDA-ARS. The dry seeds were sown on damp filter paper in a plastic Petri dish, incubated at 4℃ in the dark for 3 days to synchronize germination, and then germinated in a growth chamber (MLR-350HT, Sanyo, Osaka, Japan) at 25℃ under a day length of 16 h at approximately 100µmol/s/m.The germinated shoots were transplanted to pots filled with autoclaved Pro-Mix Mycorryzae (Premier Tech, Quebec, Canada). Plants were grown under controlled conditions of 22°C with a day length of 20 h at approximately 100 µmol m−2 s−1. Relative humidity was maintained at 40–60%. Plants were irrigated and fertilized every 3–4 days with 5000-fold-diluted Professional HYPONeX 10-30-20 (Hyponex Japan, Osaka, Japan). The developmental stages observed during the life cycle of B. distachyon (electronic supplementary material, table S1 and figure S1) were adapted to the BBCH decimal coding system based on morphology according to a previous report.
Sample Preparation Details ID SS1
Comment

Sample Preparation Details Information

ID SS1
Title Detail of samples
Description Brachypodium distachyon (Bd21 and Bd3-1) and wheat (Chinese Spring) were grown at the same time under a day length of 20 h as described above. Plants were grown in plastic Petri dishes until the BBCH11 stage, and then transplanted to the pots and grown until BBCH15 as described above. For temperature stress treatments, plants at BBCH15 were subjected to 2, 12, 32 or 42°C for 24 h under a day length of 20 h. For salt stress treatments, plants at BBCH15 were subjected to 24 h of 100 or 500 mM NaCl treatment by bottom watering under a day length of 20 h. Seeds or the first leaves were collected from six to 15 individuals, lyophilized, and disrupted by TissueLyser (Qiagen, Tokyo, Japan).
Comment_of_details

Analytical Method Information

ID M1
Title UPLC-MS/MS(triple quadrupole)
Method Details ID MS1
Sample Amount
Comment

Analytical Method Details Information

ID MS1
Title UPLC-MS/MS (triple quadrupole)
Instrument UPLC-TQS (Waters)
Instrument Type
Ionization ESI
Ion Mode Positive
Description Quantitative data for metabolite accumulation were obtained by UPLC-TQS (Waters, Tokyo, Japan) as described previously.
Comment_of_details Sawada et al. Plant Cell Physiol. 2009 Jan;50(1):37-47


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Data Analysis Information

ID D1
Title Statistical analysis
Data Analysis Details ID DS1
Recommended decimal places of m/z
Comment


Data Analysis Details Information

ID DS1
Title Statistical analysis
Description Statistical differences in the days from imbibition to reach each BBCH growth stage were analysed between accessions of B. distachyon by t-test (p < 0.05). These analyses were performed using R v. 2.15.0 statistical software.
Comment_of_details
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