Summary of Study ST003563

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 PR002197. The data can be accessed directly via it's Project DOI: 10.21228/M8N53N 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	ST003563
Study Title	Metabolic changes in imbibed 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
Department	IJPB, Institut Jean-Pierre Bourgin for Plant Sciences (INRAE / AgroParisTech / Université Paris-Sacaly)
Laboratory	Germination Physiology (PHYGERM)
Last Name	CLEMENT
First Name	Gilles
Address	Route de st-Cyr, Versailles, Ile-de-France, 78026, France
Email	loic.rajjou@inrae.fr
Phone	+33 (0) 1 30 83 38 91
Submit Date	2024-10-02
Num Groups	6
Total Subjects	18
Raw Data Available	Yes
Raw Data File Type(s)	cdf
Analysis Type Detail	GC-MS
Release Date	2024-12-31
Release Version	1

Select appropriate tab below to view additional metadata details:

Project:

Project ID:	PR002197
Project DOI:	doi: 10.21228/M8N53N
Project Title:	Metabolic changes in germinating seeds of malting barley produced under drought or elevated temperature (as a part of ECOSEED Project)
Project Type:	Research
Project Summary:	As a primary source of food and feed, seeds are essential for crop production, with demand rising alongside global population growth. However, climate change poses significant challenges to seed quality due to abiotic stressors, such as drought and elevated temperatures. These stresses affect not only the seeds themselves but also the environmental conditions in which mother plants develop, leading to broader impacts on seed quality and crop resilience. In this study, we examine metabolic changes in the seeds of malting barley, where mother plants were exposed to drought or elevated temperature conditions. By analyzing seeds from these stressed plants, we aim to reveal how environmental conditions experienced by the mother plant influence seed metabolism and performance. Our comprehensive approach provides a solid foundation for understanding how seeds respond to environmental variations passed down through their progeny.
Institute:	INRAE
Department:	IJPB, Institut Jean-Pierre Bourgin for Plant Sciences (INRAE / AgroParisTech / Université Paris-Sacaly)
Laboratory:	Germination Physiology (PHYGERM)
Last Name:	RAJJOU
First Name:	Loïc
Address:	Route de st-Cyr, Versailles, Ile-de-France, 78026, France
Email:	loic.rajjou@inrae.fr
Phone:	+33 (0) 1 30 83 38 91
Funding Source:	EU - KBBE-FP7

Subject:

Subject ID:	SU003692
Subject Type:	Plant
Subject Species:	Hordeum vulgare
Taxonomy ID:	4513
Species Group:	Plants

Factors:

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

mb_sample_id	local_sample_id	Sample source	Culture_condition
SA389382	4710-I5H-C-R1	Embryo	Control temp_18/22°C
SA389383	4710-I12H-C-R3	Embryo	Control temp_18/22°C
SA389384	4710-I12H-C-R2	Embryo	Control temp_18/22°C
SA389385	4710-I12H-C-R1	Embryo	Control temp_18/22°C
SA389386	4710-C-R2	Embryo	Control temp_18/22°C
SA389387	4710-I5H-C-R2	Embryo	Control temp_18/22°C
SA389388	4710-C-R1	Embryo	Control temp_18/22°C
SA389389	4710-I5H-C-R3	Embryo	Control temp_18/22°C
SA389390	4710-C-R3	Embryo	Control temp_18/22°C
SA389391	4710-I5H-DR-R1	Embryo	DROUGHT_18/22°C
SA389392	4710-DR-R1	Embryo	DROUGHT_18/22°C
SA389393	4710-DR-R2	Embryo	DROUGHT_18/22°C
SA389394	4710-I12H-DR-R3	Embryo	DROUGHT_18/22°C
SA389395	4710-I12H-DR-R2	Embryo	DROUGHT_18/22°C
SA389396	4710-I12H-DR-R1	Embryo	DROUGHT_18/22°C
SA389397	4710-I5H-DR-R3	Embryo	DROUGHT_18/22°C
SA389398	4710-DR-R3	Embryo	DROUGHT_18/22°C
SA389399	4710-I5H-DR-R2	Embryo	DROUGHT_18/22°C
SA389400	4710-I5H-ET-R2	Embryo	Elevated temp_25/28°C
SA389401	4710-I5H-ET-R3	Embryo	Elevated temp_25/28°C
SA389402	4710-I5H-ET-R1	Embryo	Elevated temp_25/28°C
SA389403	4710-ET-R1	Embryo	Elevated temp_25/28°C
SA389404	4710-ET-R2	Embryo	Elevated temp_25/28°C
SA389405	4710-I12H-ET-R1	Embryo	Elevated temp_25/28°C
SA389406	4710-I12H-ET-R2	Embryo	Elevated temp_25/28°C
SA389407	4710-I12H-ET-R3	Embryo	Elevated temp_25/28°C
SA389408	4710-ET-R3	Embryo	Elevated temp_25/28°C

Showing results 1 to 27 of 27

Showing results 1 to 27 of 27

Collection:

Collection ID:	CO003685
Collection Summary:	Isolated embryos from barley seeds were harvested and inserted in previously weighed eppendorf tubes, frozen in liquid nitrogen and weighed again. They were ground by shaking with a metal ball.
Sample Type:	Seeds

Treatment:

Treatment ID:	TR003701
Treatment Summary:	The barley genotype (Hordeum vulgare L.) of the breeding line HOR 4710 (termed “B2”) was used. 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 16 % 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:

TR003701

Treatment Summary:

The barley genotype (Hordeum vulgare L.) of the breeding line HOR 4710 (termed “B2”) was used. 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 16 % 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:	SP003699
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	AN005854
Analysis type	MS
Chromatography type	GC
Chromatography system	Agilent 7890A
Column	Restek Rxi-5Sil (30m x 0.25mm,0.25um)
MS Type	EI
MS instrument type	Single quadrupole
MS instrument name	Agilent 5975C
Ion Mode	POSITIVE
Units	nmoles/mg Dry Weight

Chromatography:

Chromatography ID:	CH004446
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,0.25um)
Column Temperature:	Oven temperature ramp was 70 °C for 7 min then 10 °C/min to 330 °C for 5 min (run length 38 min)
Flow Gradient:	NA
Flow Rate:	0.7 mL/min
Solvent A:	NA
Solvent B:	NA
Chromatography Type:	GC

MS:

MS ID:	MS005574
Analysis ID:	AN005854
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