{
"METABOLOMICS WORKBENCH":{"STUDY_ID":"ST000561","ANALYSIS_ID":"AN000863","VERSION":"1","CREATED_ON":"February 21, 2017, 2:47 pm"},

"PROJECT":{"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","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"},

"STUDY":{"STUDY_TITLE":"Exploring the link between genotype, phenotype and metabolome for tomato seed quality attributes","STUDY_TYPE":"Tomato Seed Metabolites Profiling (dry seed and 6 hour imbibed seeds comparision)","STUDY_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","INSTITUTE":"Wageningen UR","DEPARTMENT":"Plant Physiology","LABORATORY":"Wageningen Seed Lab, Lab","LAST_NAME":"Ligterink","FIRST_NAME":"Wilco","ADDRESS":"Droevendaalsesteeg 1, NL-6708 PB Wageningen, The Netherlands","EMAIL":"wilco.ligterink@wur.nl","PHONE":"31 317 48 28 09","NUM_GROUPS":"1","TOTAL_SUBJECTS":"100"},

"SUBJECT":{"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"},
"SUBJECT_SAMPLE_FACTORS":[
{
"Subject ID":"F8_Tomato",
"Sample ID":"205",
"Factors":{"Treatment":"DrySeeds"}
},
{
"Subject ID":"F8_Tomato",
"Sample ID":"207",
"Factors":{"Treatment":"DrySeeds"}
},
{
"Subject ID":"F8_Tomato",
"Sample ID":"208",
"Factors":{"Treatment":"DrySeeds"}
},
{
"Subject ID":"F8_Tomato",
"Sample ID":"210",
"Factors":{"Treatment":"DrySeeds"}
},
{
"Subject ID":"F8_Tomato",
"Sample ID":"212",
"Factors":{"Treatment":"DrySeeds"}
},
{
"Subject ID":"F8_Tomato",
"Sample ID":"216",
"Factors":{"Treatment":"DrySeeds"}
},
{
"Subject ID":"F8_Tomato",
"Sample ID":"217",
"Factors":{"Treatment":"DrySeeds"}
},
{
"Subject ID":"F8_Tomato",
"Sample ID":"218",
"Factors":{"Treatment":"DrySeeds"}
},
{
"Subject ID":"F8_Tomato",
"Sample ID":"219",
"Factors":{"Treatment":"DrySeeds"}
},
{
"Subject ID":"F8_Tomato",
"Sample ID":"222",
"Factors":{"Treatment":"DrySeeds"}
},
{
"Subject ID":"F8_Tomato",
"Sample ID":"226",
"Factors":{"Treatment":"DrySeeds"}
},
{
"Subject ID":"F8_Tomato",
"Sample ID":"227",
"Factors":{"Treatment":"DrySeeds"}
},
{
"Subject ID":"F8_Tomato",
"Sample ID":"230",
"Factors":{"Treatment":"DrySeeds"}
},
{
"Subject ID":"F8_Tomato",
"Sample ID":"234",
"Factors":{"Treatment":"DrySeeds"}
},
{
"Subject ID":"F8_Tomato",
"Sample ID":"237",
"Factors":{"Treatment":"DrySeeds"}
},
{
"Subject ID":"F8_Tomato",
"Sample ID":"238",
"Factors":{"Treatment":"DrySeeds"}
},
{
"Subject ID":"F8_Tomato",
"Sample ID":"240",
"Factors":{"Treatment":"DrySeeds"}
},
{
"Subject ID":"F8_Tomato",
"Sample ID":"243",
"Factors":{"Treatment":"DrySeeds"}
},
{
"Subject ID":"F8_Tomato",
"Sample ID":"245",
"Factors":{"Treatment":"DrySeeds"}
},
{
"Subject ID":"F8_Tomato",
"Sample ID":"246",
"Factors":{"Treatment":"DrySeeds"}
},
{
"Subject ID":"F8_Tomato",
"Sample ID":"248",
"Factors":{"Treatment":"DrySeeds"}
},
{
"Subject ID":"F8_Tomato",
"Sample ID":"249",
"Factors":{"Treatment":"DrySeeds"}
},
{
"Subject ID":"F8_Tomato",
"Sample ID":"252",
"Factors":{"Treatment":"DrySeeds"}
},
{
"Subject ID":"F8_Tomato",
"Sample ID":"253",
"Factors":{"Treatment":"DrySeeds"}
},
{
"Subject ID":"F8_Tomato",
"Sample ID":"257",
"Factors":{"Treatment":"DrySeeds"}
},
{
"Subject ID":"F8_Tomato",
"Sample ID":"258",
"Factors":{"Treatment":"DrySeeds"}
},
{
"Subject ID":"F8_Tomato",
"Sample ID":"259",
"Factors":{"Treatment":"DrySeeds"}
},
{
"Subject ID":"F8_Tomato",
"Sample ID":"260",
"Factors":{"Treatment":"DrySeeds"}
},
{
"Subject ID":"F8_Tomato",
"Sample ID":"261",
"Factors":{"Treatment":"DrySeeds"}
},
{
"Subject ID":"F8_Tomato",
"Sample ID":"262",
"Factors":{"Treatment":"DrySeeds"}
},
{
"Subject ID":"F8_Tomato",
"Sample ID":"265",
"Factors":{"Treatment":"DrySeeds"}
},
{
"Subject ID":"F8_Tomato",
"Sample ID":"266",
"Factors":{"Treatment":"DrySeeds"}
},
{
"Subject ID":"F8_Tomato",
"Sample ID":"267",
"Factors":{"Treatment":"DrySeeds"}
},
{
"Subject ID":"F8_Tomato",
"Sample ID":"269",
"Factors":{"Treatment":"DrySeeds"}
},
{
"Subject ID":"F8_Tomato",
"Sample ID":"273",
"Factors":{"Treatment":"DrySeeds"}
},
{
"Subject ID":"F8_Tomato",
"Sample ID":"274",
"Factors":{"Treatment":"DrySeeds"}
},
{
"Subject ID":"F8_Tomato",
"Sample ID":"275",
"Factors":{"Treatment":"DrySeeds"}
},
{
"Subject ID":"F8_Tomato",
"Sample ID":"276",
"Factors":{"Treatment":"DrySeeds"}
},
{
"Subject ID":"F8_Tomato",
"Sample ID":"277",
"Factors":{"Treatment":"DrySeeds"}
},
{
"Subject ID":"F8_Tomato",
"Sample ID":"279",
"Factors":{"Treatment":"DrySeeds"}
},
{
"Subject ID":"F8_Tomato",
"Sample ID":"280",
"Factors":{"Treatment":"DrySeeds"}
},
{
"Subject ID":"F8_Tomato",
"Sample ID":"287",
"Factors":{"Treatment":"DrySeeds"}
},
{
"Subject ID":"F8_Tomato",
"Sample ID":"289",
"Factors":{"Treatment":"DrySeeds"}
},
{
"Subject ID":"F8_Tomato",
"Sample ID":"295",
"Factors":{"Treatment":"DrySeeds"}
},
{
"Subject ID":"F8_Tomato",
"Sample ID":"298",
"Factors":{"Treatment":"DrySeeds"}
},
{
"Subject ID":"F8_Tomato",
"Sample ID":"299",
"Factors":{"Treatment":"DrySeeds"}
},
{
"Subject ID":"F8_Tomato",
"Sample ID":"300",
"Factors":{"Treatment":"DrySeeds"}
},
{
"Subject ID":"F8_Tomato",
"Sample ID":"302",
"Factors":{"Treatment":"DrySeeds"}
},
{
"Subject ID":"F8_Tomato",
"Sample ID":"304",
"Factors":{"Treatment":"DrySeeds"}
},
{
"Subject ID":"F8_Tomato",
"Sample ID":"306",
"Factors":{"Treatment":"DrySeeds"}
},
{
"Subject ID":"F8_Tomato",
"Sample ID":"206",
"Factors":{"Treatment":"6hImbibedSeeds"}
},
{
"Subject ID":"F8_Tomato",
"Sample ID":"209",
"Factors":{"Treatment":"6hImbibedSeeds"}
},
{
"Subject ID":"F8_Tomato",
"Sample ID":"211",
"Factors":{"Treatment":"6hImbibedSeeds"}
},
{
"Subject ID":"F8_Tomato",
"Sample ID":"213",
"Factors":{"Treatment":"6hImbibedSeeds"}
},
{
"Subject ID":"F8_Tomato",
"Sample ID":"214",
"Factors":{"Treatment":"6hImbibedSeeds"}
},
{
"Subject ID":"F8_Tomato",
"Sample ID":"215",
"Factors":{"Treatment":"6hImbibedSeeds"}
},
{
"Subject ID":"F8_Tomato",
"Sample ID":"221",
"Factors":{"Treatment":"6hImbibedSeeds"}
},
{
"Subject ID":"F8_Tomato",
"Sample ID":"223",
"Factors":{"Treatment":"6hImbibedSeeds"}
},
{
"Subject ID":"F8_Tomato",
"Sample ID":"224",
"Factors":{"Treatment":"6hImbibedSeeds"}
},
{
"Subject ID":"F8_Tomato",
"Sample ID":"225",
"Factors":{"Treatment":"6hImbibedSeeds"}
},
{
"Subject ID":"F8_Tomato",
"Sample ID":"228",
"Factors":{"Treatment":"6hImbibedSeeds"}
},
{
"Subject ID":"F8_Tomato",
"Sample ID":"229",
"Factors":{"Treatment":"6hImbibedSeeds"}
},
{
"Subject ID":"F8_Tomato",
"Sample ID":"231",
"Factors":{"Treatment":"6hImbibedSeeds"}
},
{
"Subject ID":"F8_Tomato",
"Sample ID":"232",
"Factors":{"Treatment":"6hImbibedSeeds"}
},
{
"Subject ID":"F8_Tomato",
"Sample ID":"233",
"Factors":{"Treatment":"6hImbibedSeeds"}
},
{
"Subject ID":"F8_Tomato",
"Sample ID":"235",
"Factors":{"Treatment":"6hImbibedSeeds"}
},
{
"Subject ID":"F8_Tomato",
"Sample ID":"236",
"Factors":{"Treatment":"6hImbibedSeeds"}
},
{
"Subject ID":"F8_Tomato",
"Sample ID":"239",
"Factors":{"Treatment":"6hImbibedSeeds"}
},
{
"Subject ID":"F8_Tomato",
"Sample ID":"241",
"Factors":{"Treatment":"6hImbibedSeeds"}
},
{
"Subject ID":"F8_Tomato",
"Sample ID":"242",
"Factors":{"Treatment":"6hImbibedSeeds"}
},
{
"Subject ID":"F8_Tomato",
"Sample ID":"244",
"Factors":{"Treatment":"6hImbibedSeeds"}
},
{
"Subject ID":"F8_Tomato",
"Sample ID":"247",
"Factors":{"Treatment":"6hImbibedSeeds"}
},
{
"Subject ID":"F8_Tomato",
"Sample ID":"250",
"Factors":{"Treatment":"6hImbibedSeeds"}
},
{
"Subject ID":"F8_Tomato",
"Sample ID":"254",
"Factors":{"Treatment":"6hImbibedSeeds"}
},
{
"Subject ID":"F8_Tomato",
"Sample ID":"255",
"Factors":{"Treatment":"6hImbibedSeeds"}
},
{
"Subject ID":"F8_Tomato",
"Sample ID":"256",
"Factors":{"Treatment":"6hImbibedSeeds"}
},
{
"Subject ID":"F8_Tomato",
"Sample ID":"263",
"Factors":{"Treatment":"6hImbibedSeeds"}
},
{
"Subject ID":"F8_Tomato",
"Sample ID":"264",
"Factors":{"Treatment":"6hImbibedSeeds"}
},
{
"Subject ID":"F8_Tomato",
"Sample ID":"268",
"Factors":{"Treatment":"6hImbibedSeeds"}
},
{
"Subject ID":"F8_Tomato",
"Sample ID":"270",
"Factors":{"Treatment":"6hImbibedSeeds"}
},
{
"Subject ID":"F8_Tomato",
"Sample ID":"271",
"Factors":{"Treatment":"6hImbibedSeeds"}
},
{
"Subject ID":"F8_Tomato",
"Sample ID":"272",
"Factors":{"Treatment":"6hImbibedSeeds"}
},
{
"Subject ID":"F8_Tomato",
"Sample ID":"278",
"Factors":{"Treatment":"6hImbibedSeeds"}
},
{
"Subject ID":"F8_Tomato",
"Sample ID":"281",
"Factors":{"Treatment":"6hImbibedSeeds"}
},
{
"Subject ID":"F8_Tomato",
"Sample ID":"282",
"Factors":{"Treatment":"6hImbibedSeeds"}
},
{
"Subject ID":"F8_Tomato",
"Sample ID":"283",
"Factors":{"Treatment":"6hImbibedSeeds"}
},
{
"Subject ID":"F8_Tomato",
"Sample ID":"284",
"Factors":{"Treatment":"6hImbibedSeeds"}
},
{
"Subject ID":"F8_Tomato",
"Sample ID":"285",
"Factors":{"Treatment":"6hImbibedSeeds"}
},
{
"Subject ID":"F8_Tomato",
"Sample ID":"286",
"Factors":{"Treatment":"6hImbibedSeeds"}
},
{
"Subject ID":"F8_Tomato",
"Sample ID":"288",
"Factors":{"Treatment":"6hImbibedSeeds"}
},
{
"Subject ID":"F8_Tomato",
"Sample ID":"290",
"Factors":{"Treatment":"6hImbibedSeeds"}
},
{
"Subject ID":"F8_Tomato",
"Sample ID":"291",
"Factors":{"Treatment":"6hImbibedSeeds"}
},
{
"Subject ID":"F8_Tomato",
"Sample ID":"292",
"Factors":{"Treatment":"6hImbibedSeeds"}
},
{
"Subject ID":"F8_Tomato",
"Sample ID":"293",
"Factors":{"Treatment":"6hImbibedSeeds"}
},
{
"Subject ID":"F8_Tomato",
"Sample ID":"294",
"Factors":{"Treatment":"6hImbibedSeeds"}
},
{
"Subject ID":"F8_Tomato",
"Sample ID":"297",
"Factors":{"Treatment":"6hImbibedSeeds"}
},
{
"Subject ID":"F8_Tomato",
"Sample ID":"301",
"Factors":{"Treatment":"6hImbibedSeeds"}
},
{
"Subject ID":"F8_Tomato",
"Sample ID":"303",
"Factors":{"Treatment":"6hImbibedSeeds"}
},
{
"Subject ID":"F8_Tomato",
"Sample ID":"305",
"Factors":{"Treatment":"6hImbibedSeeds"}
},
{
"Subject ID":"F8_Tomato",
"Sample ID":"307",
"Factors":{"Treatment":"6hImbibedSeeds"}
}
],
"COLLECTION":{"COLLECTION_SUMMARY":"None","COLLECTION_PROTOCOL_ID":"SL_COL_PROT","COLLECTION_PROTOCOL_FILENAME":"SL_COL_PROT.pdf","VOLUMEORAMOUNT_COLLECTED":"30 mg"},

"TREATMENT":{"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"},

"SAMPLEPREP":{"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"},

"CHROMATOGRAPHY":{"CHROMATOGRAPHY_SUMMARY":"Untargetted GC-TOF-MS","CHROMATOGRAPHY_TYPE":"GC","INSTRUMENT_NAME":"Agilent 6890N","COLUMN_NAME":"Zebron Z-guard guard column GC Cap 5m x 0.1mm","FLOW_RATE":"1ml/min","COLUMN_TEMPERATURE":"300°C","METHODS_FILENAME":"SL_COL_PROT.pdf","SOLVENT_A":"20mg 0-methylhydroxylamine hydrochloride/ml pyridine","SOLVENT_B":"MSTFA (derivatization agent)","INJECTION_TEMPERATURE":"70°C","INTERNAL_STANDARD":"Ribitol","RETENTION_INDEX":"1000-3100","RETENTION_TIME":"300-1800 sec","SAMPLE_INJECTION":"2µL","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_COMMENTS":"Detector voltage: 1600"},

"ANALYSIS":{"ANALYSIS_TYPE":"MS"},

"MS":{"INSTRUMENT_NAME":"Agilent","INSTRUMENT_TYPE":"GC x GC-TOF","MS_TYPE":"EI","ION_MODE":"POSITIVE","MS_COMMENTS":"6 hours Imbibed Seeds"},

"MS_METABOLITE_DATA":{
"Units":"Peak Area",

"Data":[{"Metabolite":"Citrate","206":"10928.02256","209":"7932.912588","211":"11531.38203","213":"18936.63444","214":"9120.162057","215":"7958.648135","221":"9626.162075","223":"5751.906204","224":"7866.021177","225":"7071.238276","228":"7498.823743","229":"15688.86634","231":"4510.294363","232":"13996.52478","233":"10454.01153","235":"6825.021775","236":"8288.432558","239":"10367.31434","241":"6563.273444","242":"8314.007862","244":"10278.22575","247":"11309.40354","250":"10127.65275","254":"15616.82348","255":"9946.687178","256":"18823.95793","263":"5568.488758","264":"8285.810483","268":"4511.819466","270":"6526.695709","271":"7056.10659","272":"9120.864627","278":"14872.21151","281":"8894.401675","282":"9794.256755","283":"7992.249479","284":"6361.470827","285":"9711.062273","286":"7763.195153","288":"8570.144622","290":"9718.110334","291":"10294.4723","292":"9906.815567","293":"8556.819691","294":"5688.296804","297":"7787.91539","301":"8702.55097","303":"7169.875572","305":"8400.455279","307":"9279.88369"},{"Metabolite":"Monomethyl 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