Summary of Study ST002272

This data is available at the NIH Common Fund's National Metabolomics Data Repository (NMDR) website, the Metabolomics Workbench, https://www.metabolomicsworkbench.org, where it has been assigned Project ID PR001453. The data can be accessed directly via it's Project DOI: 10.21228/M8X13R This work is supported by NIH grant, U2C- DK119886.

See: https://www.metabolomicsworkbench.org/about/howtocite.php

This study contains a large results data set and is not available in the mwTab file. It is only available for download via FTP as data file(s) here.

Study ID	ST002272
Study Title	Metabolic changes in seeds of malting barley produced under drought or elevated temperature
Study Type	Barley seed phenotyping and GC-MS based metabolomic analysis
Study Summary	Plants of a “Hana-type” landrace (B1) were taller, flowered earlier and produced heavier, larger and more vigorous seeds that resisted ageing longer compared to a semi-dwarf breeding line (B2). Drought significantly reduced seed yield in both genotypes, and elevated temperature reduced seed size. Genotype B2 showed partial thermodormancy that was alleviated by drought and elevated temperature, in line with lower abundance of the TF ABI5, a key regulator of seed dormancy and vigour. Metabolite profiling revealed clear differences between the embryos of B1 and B2. Drought, but not elevated temperature, affected the metabolism of amino acids, organic acids, osmolytes and nitrogen assimilation, in the seeds of both genotypes.
Institute	INRAE
Last Name	CLEMENT
First Name	Gilles
Address	Route de ST-Cyr, Versailles, Ile de France, 78026, France
Email	gilles.clement@inrae.fr
Phone	+33 (0) 1 30 83 31 67
Submit Date	2022-08-29
Num Groups	6
Total Subjects	18
Raw Data Available	Yes
Raw Data File Type(s)	cdf
Analysis Type Detail	GC-MS
Release Date	2023-03-01
Release Version	1

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Project:

Project ID:	PR001453
Project DOI:	doi: 10.21228/M8X13R
Project Title:	Germination physiology
Project Summary:	Seeds are the major component of feed and food and the majority of crops are produced from seeds. This means that as the world population increases so does the demand for seed. Sub-optimal seed performance can lead to major economic losses and food supply shortages and this is set to be aggravated by climate change as abiotic constraints negatively impact seed quality. Our aim is to decrypt the central mechanisms that mediate germination while exploring their potential in applications to enhance seed performance. In particular, we seek to understand how seeds interpret and respond to environmental variations pre- and post-harvest. We apply a multidisciplinary approach using molecular genetics, multi-omics, statistical learning, bioinformatics, biochemistry, histology and physiology to study seeds from a wide range of species such as oilseed crops (e.g. camelina, cabbage), legumes (e.g. bean, lentil), cereals (e.g barley, maize) and vegetable crops (e.g. tomato and lettuce). Nonetheless, the majority of our fundamental research focuses on the genetic model Arabidopsis.
Institute:	INRAE
Last Name:	Rajjou
First Name:	Loic
Address:	Route de ST-Cyr, Versailles, Ile de France, 78026, France
Email:	Loic.Rajjou@inrae.fr
Phone:	+33 (0) 130833891

Subject:

Subject ID:	SU002358
Subject Type:	Plant
Subject Species:	Hordeum vulgare
Taxonomy ID:	4513

Factors:

Subject type: Plant; Subject species: Hordeum vulgare (Factor headings shown in green)

mb_sample_id	local_sample_id	Genotype	Culture_condition
SA217797	2110-C-R3	HOR 2110 - B1	control temp_18/22°C
SA217798	2110-C-R2	HOR 2110 - B1	control temp_18/22°C
SA217799	2110-C-R1	HOR 2110 - B1	control temp_18/22°C
SA217794	2110-DR-R3	HOR 2110 - B1	DROUGHT
SA217795	2110-DR-R2	HOR 2110 - B1	DROUGHT
SA217796	2110-DR-R1	HOR 2110 - B1	DROUGHT
SA217800	2110-ET-R3	HOR 2110 - B1	elevated temp_25/31°C
SA217801	2110-ET-R2	HOR 2110 - B1	elevated temp_25/31°C
SA217802	2110-ET-R1	HOR 2110 - B1	elevated temp_25/31°C
SA217806	4710-C-R1	HOR 4710 - B2	control temp_18/22°C
SA217807	4710-C-R3	HOR 4710 - B2	control temp_18/22°C
SA217808	4710-C-R2	HOR 4710 - B2	control temp_18/22°C
SA217803	4710-DR-R3	HOR 4710 - B2	DROUGHT
SA217804	4710-DR-R1	HOR 4710 - B2	DROUGHT
SA217805	4710-DR-R2	HOR 4710 - B2	DROUGHT
SA217809	4710-ET-R3	HOR 4710 - B2	elevated temp_25/31°C
SA217810	4710-ET-R1	HOR 4710 - B2	elevated temp_25/31°C
SA217811	4710-ET-R2	HOR 4710 - B2	elevated temp_25/31°C

Showing results 1 to 18 of 18

Showing results 1 to 18 of 18

Collection:

Collection ID:	CO002351
Collection Summary:	Isolated embryos from barley seeds were harvested and inserted in a previously weighed eppendorf tubes, frozen in liquid nitrogen and weighed fastly again. They were grinded by shaking with a metal ball.
Sample Type:	Seeds
Storage Conditions:	-80℃

Treatment:

Treatment ID:	TR002370
Treatment Summary:	Two barley genotypes (Hordeum vulgare L.), the Austrian landrace HOR 2110 (termed “B1”) and the breeding line HOR 4710 (termed “B2”) were used. For each genotype, seedlings were grown in a greenhouse in pots (30 x 30 x 15 cm, 4 plants per pot) at a 23/15 °C day/night cycle until anthesis. After half of the spikes had flowered, plants were kept for another seven days under the same conditions, and then randomly selected and subjected either to control conditions (C, 22/18 °C and regular watering) or elevated temperature (ET, 28/25 °C and regular watering,) or drought (D, 22/18 °C and 15 % field capacity). After harvest, seeds were cleaned, dried at 20 °C and 20 % relative humidity (RH) for eight weeks (for after-ripening), and then stored at 18 °C.

Treatment ID:

TR002370

Treatment Summary:

Two barley genotypes (Hordeum vulgare L.), the Austrian landrace HOR 2110 (termed “B1”) and the breeding line HOR 4710 (termed “B2”) were used. For each genotype, seedlings were grown in a greenhouse in pots (30 x 30 x 15 cm, 4 plants per pot) at a 23/15 °C day/night cycle until anthesis. After half of the spikes had flowered, plants were kept for another seven days under the same conditions, and then randomly selected and subjected either to control conditions (C, 22/18 °C and regular watering) or elevated temperature (ET, 28/25 °C and regular watering,) or drought (D, 22/18 °C and 15 % field capacity). After harvest, seeds were cleaned, dried at 20 °C and 20 % relative humidity (RH) for eight weeks (for after-ripening), and then stored at 18 °C.

Sample Preparation:

Sampleprep ID:	SP002364
Sampleprep Summary:	For metabolite profiling, three biological replicates of 12 mg of barley embryos manually dissected from dry mature seeds were ground with mortar and pestle in liquid nitrogen and stored at -80 °C. All steps were performed in 2 ml Safelock Eppendorf tubes. The ground frozen samples (12 mg) were resuspended in 1 ml of frozen (-20°C) Water:Acetonitrile:Isopropanol (2:3:3 v/v/v/) containing Ribitol at 4 mg.L-1 and extracted for 10 min at 4°C with shaking at 1400 rpm in an Eppendorf Thermomixer. Insoluble material was removed by centrifugation at 20000g for 5 min. 25 µL were collected and dried for 150 min in a SpeedVac. Fiehn et al (the Plant Journal (2008) 53, 691-704).
Processing Storage Conditions:	-20℃
Extract Storage:	-80℃

Combined analysis:

Analysis ID	AN003714
Analysis type	MS
Chromatography type	GC
Chromatography system	Agilent 7890A
Column	Restek Rxi-5Sil (30m x 0.25mm,0.25m) with 10m precolumn
MS Type	EI
MS instrument type	Single quadrupole
MS instrument name	Agilent 5975C
Ion Mode	POSITIVE
Units	nmoles/mg DW and arbitrary/mg DW

Chromatography:

Chromatography ID:	CH002751
Chromatography Summary:	The instrument was an Agilent 7890A gas chromatograph coupled to an Agilent 5975C mass spectrometer. The column was an Rxi-5SilMS from Restek (30 m with 10 m integraguard column). The liner (Restek # 20994) was changed before each derivatization series. Oven temperature ramp was 70 °C for 7 min then 10 °C/min to 330 °C for 5 min (run length 38 min). Helium constant flow was 0.7 mL/min. Temperatures were the following: injector: 250°C, transfer line: 290°C, source: 250 °C and quadripole 150 °C. 5 scans per second were acquired spanning a 50 to 600 Da range. Instrument was tuned with PFTBA with the 69 m/z and 219 m/z of equal intensities. 5 scans per second were acquired. The split mode conditions were: 70°C for 2 min then 30°C per min to 330 °C for 5 min. Helium constant flow 1 mL/min.
Instrument Name:	Agilent 7890A
Column Name:	Restek Rxi-5Sil (30m x 0.25mm,0.25m) with 10m precolumn
Flow Rate:	0.7 ml/min
Injection Temperature:	250°C
Chromatography Type:	GC

MS:

MS ID:	MS003463
Analysis ID:	AN003714
Instrument Name:	Agilent 5975C
Instrument Type:	Single quadrupole
MS Type:	EI
MS Comments:	Temperatures were the following: injector: 250°C, transfer line: 290°C, source: 250 °C and quadripole 150 °C. 5 scans per second were acquired spanning a 50 to 600 Da range. Instrument was tuned with PFTBA with the 69 m/z and 219 m/z of equal intensities. 5 scans per second were acquired. The split mode conditions were: 70°C for 2 min then 30°C per min to 330 °C for 5 min. Helium constant flow 1 mL/min. Data processing: Raw Agilent datafiles were converted in NetCDF format and analyzed with AMDIS http://chemdata.nist.gov/mass-spc/amdis/. An home retention indices/ mass spectra library built from the NIST, Golm , http://gmd.mpimp-golm.mpg.de/ and Fiehn databases and standard compounds was used for metabolites identification. Peak areas were also determined with the Targetlynx software (Waters) after conversion of the NetCDF file in masslynx format as well as TargetSearch. AMDIS, Target Lynx and TargetSearch in splitless and split 30 modes data were compiled in one single Excel File for comparison. After blank mean substraction peak areas were normalized to Ribitol and Fresh Weight. Statistical analysis was made with TMEV http://www.tm4.org/mev.html : univariate analysis by permutation (1way-anova and 2-way anova) were firstly used to select the significant metabolites (P-value < 0.01). Multivariate analysis (hierarchical clustering and principal component analysis) were then made on them. Absolute quantification: A response coefficient was determined for 4 ng each of a set of 103 métabolites, respectively to the same amount of ribitol. This factor was used to give an estimation of the absolute concentration of the metabolite in what we may call a “one point calibration”. Metabolites rich in nitrogen (basic aminoacids and polyamines) gave several analytes (up to 5 for glutamine and asparagine). The peak area as TIC equivalent of these analytes were summed to express the contents of these metabolites. They are referred to “sum” in the tables.
Ion Mode:	POSITIVE