Summary of study ST000561

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 PR000412. The data can be accessed directly via it's Project DOI: 10.21228/M8SS33 This work is supported by NIH grant, U2C- DK119886.

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Study IDST000561
Study TitleExploring the link between genotype, phenotype and metabolome for tomato seed quality attributes
Study TypeTomato Seed Metabolites Profiling (dry seed and 6 hour imbibed seeds comparision)
Study SummaryIn this study the F8 population of 100 Recombinant Inbred Lines (RILs) obtained from a cross between Solanum lycopersicum X Solanum pimpinellifolium were intelligently allocated to two sub-populations optimized for the distribution of parental alleles using the R-procedure DesignGG (Li et al., 2009; Joosen et al., 2013); hence 50 RIL lines were used for dry seeds and 50 lines for 6h imbibed seeds
Institute
Wageningen University & Research
DepartmentPlant Physiology
LaboratoryWageningen Seed Lab, Lab
Last NameLigterink
First NameWilco
AddressDroevendaalsesteeg 1, NL-6708 PB Wageningen, The Netherlands
Emailwilco.ligterink@wur.nl
Phone31 317 48 28 09
Submit Date2017-02-07
Num Groups1
Total Subjects100
PublicationsMetabolomic analysis of tomato seed germination, Metabolomics DOI: 10.1007/s11306-017-1284-x
Analysis Type DetailGC-MS
Release Date2017-10-25
Release Version1
Wilco Ligterink Wilco Ligterink
https://dx.doi.org/10.21228/M8SS33
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

Select appropriate tab below to view additional metadata details:


Project:

Project ID:PR000412
Project DOI:doi: 10.21228/M8SS33
Project Title:Metabolomic analysis of tomato seed germination
Project Summary:Genomic approaches have accelerated the study of the quantitative genetics that underlie phenotypic variation. We have utilized gas chromatography-time-of-flight/mass spectrometry (GC-TOF-MS) metabolite profiling to characterize tomato seeds during dry and imbibed stages using a recombinant inbred line (RIL) population of Solanum lycopersicum x Solanum pimpinellifolium. In this article we describe, for the first time in tomato, the use of a generalized genetical genomics (GGG) model to study metabolite changes in tomato seeds incorporating genetics as well as environmental effects in a single QTL analysis. The GGG design was used to map genetic quantitative trait loci (G QTLs) and environmental changes by genetic-by-environment interactions (G x E QTLs). A significant canonical correlation was found between metabolites and seed quality traits, revealing a close link between seed quality phenotypes and a specific combination of metabolites. Densely connected metabolites were extracted using graph clustering from correlation networks, and the clusters were evaluated by biochemical-pathway enrichment analysis. The evidence from this study suggests that the number of significant correlations varied among individual metabolites and that the obtained clusters were significantly enriched for metabolites involved in specific biochemical pathways. Thus, the methods described here have the potential to reveal regulatory networks that contribute to our understanding of the complex nature of seed quality.
Institute:Wageningen University & Research
Laboratory:Lab. Of Plant Physiology
Last Name:Henk W.M. Hilhorst
First Name:Henk
Address:Wageningen, Droevendaalsesteeg 1, NL-6708 PB Wageningen, The Netherlands
Email:henk.hilhorst@wur.nl
Phone:31 317 48 28 09
Funding Source:Technology Foundation (STW) and Higher Education Commission, Pakistan

Subject:

Subject ID:SU000583
Subject Type:Plant
Subject Species:Solanum lycopersicum
Taxonomy ID:4081
Genotype Strain:S. lycopersicum X S. pimpinellifolium
Age Or Age Range:Dry Seeds - 6 hours Imbibed Seeds
Species Group:Plant

Factors:

Subject type: Plant; Subject species: Solanum lycopersicum (Factor headings shown in green)

mb_sample_id local_sample_id Treatment
SA0289272396hImbibedSeeds
SA0289282416hImbibedSeeds
SA0289292366hImbibedSeeds
SA0289302356hImbibedSeeds
SA0289312336hImbibedSeeds
SA0289322426hImbibedSeeds
SA0289332446hImbibedSeeds
SA0289342556hImbibedSeeds
SA0289352546hImbibedSeeds
SA0289362506hImbibedSeeds
SA0289372476hImbibedSeeds
SA0289382326hImbibedSeeds
SA0289392316hImbibedSeeds
SA0289402156hImbibedSeeds
SA0289412146hImbibedSeeds
SA0289422136hImbibedSeeds
SA0289432116hImbibedSeeds
SA0289442216hImbibedSeeds
SA0289452236hImbibedSeeds
SA0289462296hImbibedSeeds
SA0289472286hImbibedSeeds
SA0289482256hImbibedSeeds
SA0289492246hImbibedSeeds
SA0289502566hImbibedSeeds
SA0289512646hImbibedSeeds
SA0289522926hImbibedSeeds
SA0289532936hImbibedSeeds
SA0289542916hImbibedSeeds
SA0289552906hImbibedSeeds
SA0289562886hImbibedSeeds
SA0289572946hImbibedSeeds
SA0289582976hImbibedSeeds
SA0289593076hImbibedSeeds
SA0289603056hImbibedSeeds
SA0289613036hImbibedSeeds
SA0289623016hImbibedSeeds
SA0289632866hImbibedSeeds
SA0289642856hImbibedSeeds
SA0289652716hImbibedSeeds
SA0289662706hImbibedSeeds
SA0289672686hImbibedSeeds
SA0289682096hImbibedSeeds
SA0289692726hImbibedSeeds
SA0289702786hImbibedSeeds
SA0289712846hImbibedSeeds
SA0289722836hImbibedSeeds
SA0289732826hImbibedSeeds
SA0289742816hImbibedSeeds
SA0289752636hImbibedSeeds
SA0289762066hImbibedSeeds
SA028977243DrySeeds
SA028978245DrySeeds
SA028979240DrySeeds
SA028980238DrySeeds
SA028981237DrySeeds
SA028982246DrySeeds
SA028983248DrySeeds
SA028984257DrySeeds
SA028985253DrySeeds
SA028986252DrySeeds
SA028987249DrySeeds
SA028988234DrySeeds
SA028989230DrySeeds
SA028990212DrySeeds
SA028991216DrySeeds
SA028992210DrySeeds
SA028993208DrySeeds
SA028994207DrySeeds
SA028995217DrySeeds
SA028996218DrySeeds
SA028997227DrySeeds
SA028998226DrySeeds
SA028999222DrySeeds
SA029000219DrySeeds
SA029001258DrySeeds
SA029002259DrySeeds
SA029003289DrySeeds
SA029004295DrySeeds
SA029005287DrySeeds
SA029006280DrySeeds
SA029007279DrySeeds
SA029008298DrySeeds
SA029009299DrySeeds
SA029010306DrySeeds
SA029011304DrySeeds
SA029012302DrySeeds
SA029013300DrySeeds
SA029014277DrySeeds
SA029015276DrySeeds
SA029016265DrySeeds
SA029017262DrySeeds
SA029018261DrySeeds
SA029019260DrySeeds
SA029020266DrySeeds
SA029021267DrySeeds
SA029022275DrySeeds
SA029023274DrySeeds
SA029024273DrySeeds
SA029025269DrySeeds
SA029026205DrySeeds
Showing results 1 to 100 of 100

Collection:

Collection ID:CO000577
Collection Summary:None
Collection Protocol ID:SL_COL_PROT
Collection Protocol Filename:SL_COL_PROT.pdf
Sample Type:Seeds
Volumeoramount Collected:30 mg

Treatment:

Treatment ID:TR000597
Treatment Summary:In this study the F8 population of 100 Recombinant Inbred Lines (RILs) obtained from a cross between Solanum lycopersicum X Solanum pimpinellifolium were intelligently allocated to two sub-populations optimized for the distribution of parental alleles using the R-procedure DesignGG (Li et al., 2009; Joosen et al., 2013); hence 50 RIL lines were used for dry seeds and 50 lines for 6h imbibed seeds
Treatment:Metabolites were extracted from dry and 6 hour imbibed seeds
Treatment Route:Seed
Plant Growth Location:The S. lycopersicum × S. pimpinellifolium RIL population was grown twice under controlled conditions in the greenhouse facilities at Wageningen University, in the Netherlands.
Plant Plot Design:RCBD
Plant Light Period:16h light and 8h dark (long-day conditions)
Plant Humidity:30% RH
Plant Temp:The day and night temperatures were maintained at 25 °C and 15 °C, respectively
Plant Watering Regime:Watered Daily
Plant Nutritional Regime:All the RILs were uniformly supplied with the basic dose of fertilizer
Plant Growth Stage:Seeds were extracted from healthy fruits and treated with 1% hydrochloric acid (HCL) to remove the large pieces of the pulp that were sticking onto the seeds.
Plant Storage:The cleaned seeds were dried for 3d at 20 °C and were stored in a cool, dry storage room (13 °C and 30% RH) in paper bags

Sample Preparation:

Sampleprep ID:SP000590
Sampleprep Summary:The extraction method is modified from the method previously described by (Roessner et al., 2000). Approximately a bulk of approximately 70-100 seeds (30mg) seeds were homogenized in 2 ml tubes with 2 iron balls (2.5mm), pre-cooled in liquid nitrogen. For the homogenization the micro-dismembrator (Sartorius) is used at 1500 rpm. 700μl methanol/ chloroform (4:3) was added together with the standard (0.2mg/ml ribitol) and mixed thoroughly. After 10 minutes sonication, 200μl MQ was added to the mixture followed by vortexing and centrifuging (5 mins 13,500rpm). Methanol phase was collected in a glass vial. 500μl methanol/chloroform was added to the remaining organic phase and kept on ice for 10 minutes. 200μl MQ was added followed by vortexing and centrifuging (5 mins 13,500rpm). Again, the methanol phase was collected and mixed with the other collected phase. 100μl was dried overnight in a speedvac (35°C Savant SPD121). The GC-TOF-MS method was previously described by (Carreno-Quintero et al., 2012) with some minor modifications. Detector voltage was set at 1600V. Raw data was processed using the chromaTOF software 2.0 (leco instruments) and further processed using the Metalign software (Lommen, 2009), to extract and align the mass signals. A signal-to-noise ratio of 2 was used. The output was further processed by the Metalign Output Transformer (METOT; Plant Research International, Wageningen) and the mass signals that were present in less than 3 RILs were discarded. Out of all the mass signals, centrotypes are formed using the MSclust program (Tikunov et al., 2011). This resulted in 160 unique centrotypes (representative masses). The mass spectra of these centrotypes were used for identification by matching to an in-house constructed library, the NIST05 (National Institute of Standards and Technology, Gaithersburg, MD, USA; http://www.nist.gov/srd/mslist.htm) and Golm libraries (http://csbdb.mpimp-golm.mpg.de/csbdb/gmd/gmd.html)). This identification is based on spectra similarity and comparison with retention indices calculated by using a 3rd order polynomial function (Strehmel et al., 2008).
Sampleprep Protocol Filename:SL_COL_PROT.pdf
Processing Method:For the homogenization the micro-dismembrator (Sartorius) is used at 1500 rpm
Cell Type:Seeds

Combined analysis:

Analysis ID AN000862 AN000863
Analysis type MS MS
Chromatography type GC GC
Chromatography system Agilent 6890N Agilent 6890N
Column Zebron Z-guard guard column GC Cap 5m x 0.1mm Zebron Z-guard guard column GC Cap 5m x 0.1mm
MS Type EI EI
MS instrument type GC x GC-TOF GC x GC-TOF
MS instrument name Agilent Agilent
Ion Mode POSITIVE POSITIVE
Units Peak Area Peak Area

Chromatography:

Chromatography ID:CH000613
Chromatography Summary:Untargetted GC-TOF-MS
Methods Filename:SL_COL_PROT.pdf
Chromatography Comments:Detector voltage: 1600
Instrument Name:Agilent 6890N
Column Name:Zebron Z-guard guard column GC Cap 5m x 0.1mm
Column Temperature:300°C
Flow Rate:1ml/min
Injection Temperature:70°C
Internal Standard:Ribitol
Retention Index:1000-3100
Retention Time:300-1800 sec
Sample Injection:2µL
Solvent A:20mg 0-methylhydroxylamine hydrochloride/ml pyridine
Solvent B:MSTFA (derivatization agent)
Analytical Time:1800sec
Oven Temperature:70->300
Running Voltage:1600
Time Program:1800 sec
Transferline Temperature:270°C
Washing Buffer:CHCl3
Target Sample Temperature:40°C
Sample Syringe Size:25°C
Randomization Order:Yes
Chromatography Type:GC

MS:

MS ID:MS000763
Analysis ID:AN000862
Instrument Name:Agilent
Instrument Type:GC x GC-TOF
MS Type:EI
MS Comments:Dry Seed condition
Ion Mode:POSITIVE
  
MS ID:MS000764
Analysis ID:AN000863
Instrument Name:Agilent
Instrument Type:GC x GC-TOF
MS Type:EI
MS Comments:6 hours Imbibed Seeds
Ion Mode:POSITIVE
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