SE128:/S1/M1/D2

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"

PubMed

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

PubMed

Data Analysis Information

ID	D2
Title	Metabolome analysis
Data Analysis Details ID	DS2
Recommended decimal places of m/z
Comment

Data Analysis Details Information

ID	DS2
Title	Metabolome analysis
Description	Missing values of these data, which appeared when a metabolite was not detected in a sample, were replaced with the number 20 because the average noise level of our in-house LC-MS-based metabolome system is approximately 20. We performed three biologically independent measurements and used the average values of the replication. Peaks of metabolites that showed a signal-to-noise (S/N) ratio (S, average value of three biologically independent replicates; N, average value of three buffer-only injections) of more than 10 in at least one sample were selected. The resulting data matrix was subjected to hierarchical clustering analysis following transformation to binary logarithm (log2) values. A Venn diagram of the metabolites that showed S/N ratios of more than 10 was also generated using the same metabolic profile data. These analyses were performed using R v. 2.15.0 statistical software with the ‘heatmap2’ and ‘venn.diagram’ functions, respectively.
Comment_of_details	Data on metabolome analysis are available at Data Resources of Plant Metabolomics (DROP Met) accessible via the Platform for RIKEN Metabolomics (PRIMe) website at http://prime.psc.riken.jp.

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