Summary of Study ST003797

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 PR002372. The data can be accessed directly via it's Project DOI: 10.21228/M81G01 This work is supported by NIH grant, U2C- DK119886.

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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.

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Study IDST003797
Study TitleGenetic architecture for maize leaf and kernel metabolome in CUBIC population
Study SummaryMaize is one of the most important crops worldwide, and enhancements of yield and quality are primary breeding targets for its genetic improvement. Here, we explored the metabolome profiling for maize leaf and kernel from a synthetic population CUBIC (Complete-diallel plus Unbalanced Breeding-derived Inter-Cross) of 1404 maize progenies derived from 24 diverse founders. 67 metabolite from leaf and 68 from kernel confirmed by authentic standardswith gas chromatography-mass spectroscopy (GC-MS) for metabolic profiling were selected for further genetic exploration. Using single-locus and haplotype-based genome-wide association study (sGWAS and hGWAS, respectively), we investigated the genetic basis for primary metabolite accumulation in maize leaves and kernels at a genome-wide scale with 1373 mQTL identified. We identified three genes (ZmASN2, ZmMIPS1 and ZmMGL) to regulate kernel filling and a variety of metabolites, affecting the nutritional value of maize kernels and a novel gene, ZmAVT1A-1, which regulates amino acid levels and enhances maize NUE-related traits through the allocation of nitrogen from vegetative organs to kernels. Our study provided a valuable resource for understanding maize primary metabolism and offered novel insights into the metabolic organization at the genetic and molecular levels that can enable crop genetic improvement.
Institute
Huazhong Agricultural University
Last NameJin
First NameMin
AddressHainan Province Sanya City Yazhouwan lab
Email834245464@qq.com
Phone13098856456
Submit Date2025-03-10
Raw Data AvailableYes
Raw Data File Type(s)d
Analysis Type DetailGC-MS
Release Date2025-03-20
Release Version1
Min Jin Min Jin
https://dx.doi.org/10.21228/M81G01
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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Project:

Project ID:PR002372
Project DOI:doi: 10.21228/M81G01
Project Title:Genetic architecture for maize leaf and kernel metabolome in CUBIC population
Project Summary:Maize is one of the most important crops worldwide, and enhancements of yield and quality are primary breeding targets for its genetic improvement. Here, we explored the metabolome profiling for maize leaf and kernel from a synthetic population of 1404 maize progenies derived from 24 diverse founders. 67 metabolite from leaf and 68 from kernel confirmed by authentic standards were selected for further genetic exploration. Combined with genomic variations and transriptome data equipped for this population mGWAS (metabolite genome-wide association study) was performed 1373 mQTL (metabolite quantitative trait locus) identified. This study thus enhanced our genetic resources for understanding and manipulating the regulation of primary metabolites as well as metabolic-associated traits.
Institute:Huazhong Agricultural University
Last Name:Jin
First Name:Min
Address:Hainan Province Sanya City Yazhouwan lab
Email:834245464@qq.com
Phone:13098856456

Subject:

Subject ID:SU003931
Subject Type:Plant
Subject Species:Zea mays
Taxonomy ID:4577

Factors:

Subject type: Plant; Subject species: Zea mays (Factor headings shown in green)

mb_sample_id local_sample_id Genotype Sample source
SA413087L_217MG_1000 Leaf
SA413088S_1010MG_1000 Seed
SA413089L_1025MG_1001 Leaf
SA413090S_1011MG_1001 Seed
SA413091L_1026MG_1002 Leaf
SA413092S_1012MG_1002 Seed
SA413093S_1013MG_1003 Seed
SA413094L_1027MG_1004 Leaf
SA413095S_1014MG_1004 Seed
SA413096L_1028MG_1005 Leaf
SA413097S_1015MG_1005 Seed
SA413098L_1029MG_1006 Leaf
SA413099S_1016MG_1006 Seed
SA413100L_1030MG_1007 Leaf
SA413101S_1017MG_1007 Seed
SA413102L_1031MG_1008 Leaf
SA413103S_1018MG_1008 Seed
SA413104L_1032MG_1009 Leaf
SA413105S_1019MG_1009 Seed
SA413106L_295MG_100 Leaf
SA413107S_100MG_100 Seed
SA413108L_1033MG_1010 Leaf
SA413109S_1020MG_1010 Seed
SA413110L_1034MG_1011 Leaf
SA413111S_1021MG_1011 Seed
SA413112L_1035MG_1012 Leaf
SA413113S_1022MG_1012 Seed
SA413114L_1036MG_1013 Leaf
SA413115S_1023MG_1013 Seed
SA413116L_1037MG_1014 Leaf
SA413117L_1038MG_1015 Leaf
SA413118S_1025MG_1015 Seed
SA413119L_1039MG_1016 Leaf
SA413120S_1026MG_1016 Seed
SA413121L_1040MG_1017 Leaf
SA413122S_1027MG_1017 Seed
SA413123L_1041MG_1018 Leaf
SA413124S_1028MG_1018 Seed
SA413125L_1459MG_1019 Leaf
SA413126L_296MG_101 Leaf
SA413127S_101MG_101 Seed
SA413128L_1042MG_1020 Leaf
SA413129S_1030MG_1020 Seed
SA413130L_218MG_1021 Leaf
SA413131S_1031MG_1021 Seed
SA413132L_1451MG_1022 Leaf
SA413133S_1032MG_1022 Seed
SA413134S_1033MG_1023 Seed
SA413135L_1043MG_1024 Leaf
SA413136S_1034MG_1024 Seed
SA413137L_1044MG_1025 Leaf
SA413138S_1035MG_1025 Seed
SA413139L_1045MG_1026 Leaf
SA413140S_1036MG_1026 Seed
SA413141L_1046MG_1027 Leaf
SA413142S_1037MG_1027 Seed
SA413143L_1047MG_1028 Leaf
SA413144S_1038MG_1028 Seed
SA413145L_1048MG_1029 Leaf
SA413146S_1039MG_1029 Seed
SA413147L_297MG_102 Leaf
SA413148S_102MG_102 Seed
SA413149L_1049MG_1030 Leaf
SA413150S_1040MG_1030 Seed
SA413151L_1050MG_1031 Leaf
SA413152S_1041MG_1031 Seed
SA413153L_1051MG_1032 Leaf
SA413154S_1042MG_1032 Seed
SA413155L_1052MG_1033 Leaf
SA413156S_1043MG_1033 Seed
SA413157L_1053MG_1034 Leaf
SA413158S_1044MG_1034 Seed
SA413159L_1054MG_1035 Leaf
SA413160S_1045MG_1035 Seed
SA413161L_1055MG_1036 Leaf
SA413162S_1046MG_1036 Seed
SA413163L_1056MG_1037 Leaf
SA413164S_1047MG_1037 Seed
SA413165L_1057MG_1038 Leaf
SA413166S_1048MG_1038 Seed
SA413167L_1058MG_1039 Leaf
SA413168S_1049MG_1039 Seed
SA413169L_298MG_103 Leaf
SA413170S_103MG_103 Seed
SA413171L_1059MG_1040 Leaf
SA413172S_1050MG_1040 Seed
SA413173L_1060MG_1041 Leaf
SA413174S_1051MG_1041 Seed
SA413175L_1061MG_1042 Leaf
SA413176S_1052MG_1042 Seed
SA413177L_1062MG_1043 Leaf
SA413178S_1053MG_1043 Seed
SA413179L_1063MG_1044 Leaf
SA413180S_1054MG_1044 Seed
SA413181L_1064MG_1045 Leaf
SA413182S_1055MG_1045 Seed
SA413183L_1065MG_1046 Leaf
SA413184S_1056MG_1046 Seed
SA413185L_1066MG_1047 Leaf
SA413186S_1057MG_1047 Seed
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Collection:

Collection ID:CO003924
Collection Summary:Each maize individual were sampled with two tissues: Kernel and leaf.The sampled tissues were mixed between three replicates and immediately snap-frozen in liquid nitrogen, and stored at -80℃ before metabolite extraction.
Sample Type:Seeds, Leaves

Treatment:

Treatment ID:TR003940
Treatment Summary:Each maize individual with different genotypes was sampled with leaf and kernel.

Sample Preparation:

Sampleprep ID:SP003937
Sampleprep Summary:50 mg powder grind from each sample was extracted with 1 ml methanol:methyl-tert-butyl-ether (MTBE) solution (1:3, v/v). A 300-µl aliquot was obtained from the lower polar phase and dried in a SpeedVac concentrator without heating. The dried residue was derivatized with N-methyl-N-(trimethylsilyl) trifluoroacetamide (MSTFA) and then analyzed by GC-MS.

Combined analysis:

Analysis ID AN006242
Analysis type MS
Chromatography type GC
Chromatography system Agilent 7890A
Column Agilent DB5-MS (30m x 0.25mm, 0.25um)
MS Type EI
MS instrument type Single quadrupole
MS instrument name Agilent 5975C
Ion Mode POSITIVE
Units Relative peak area to 13C-ribitol

Chromatography:

Chromatography ID:CH004733
Chromatography Summary:One µl was taken from each sample and injected into GC-MS at 270°C in a split mode (50: 1) with helium carrier gas (> 99.999% purity) flow set to 1 ml/min, and separated by a DB-35MS UI (30 m × 0.25 mm, 0.25 µm) capillary column.The temperature of leaf sample was isothermal for 4 min at 90°C, followed by an 8°C per min ramp up to 205°C, then held for 2 min, and finally ramped up at a rate of 15°C per min to 310°C, held for 2 min. The temperature of kernel sample was isothermal for 5 min at 90°C, followed by an 8°C per min ramp up to 205°C, then held for 5 min, and finally ramped up at a rate of 12°C per min to 310°C, held for 5 min.
Instrument Name:Agilent 7890A
Column Name:Agilent DB5-MS (30m x 0.25mm, 0.25um)
Column Temperature:90℃-205℃-310℃
Flow Gradient:none
Flow Rate:1 mL/min
Injection Temperature:270°C
Internal Standard:13CRibitol
Retention Time:14.725min(leaf); 16.240min(kernel)
Sample Injection:1μL
Solvent A:none
Solvent B:none
Analytical Time:29min(leaf); 38min(kernel)
Transferline Temperature:300℃
Washing Buffer:Hexane and Methanol
Weak Wash Solvent Name:Hexane
Weak Wash Volume:8μL
Strong Wash Solvent Name:Methanol
Strong Wash Volume:8μL
Sample Syringe Size:10μL
Randomization Order:Yes
Chromatography Type:GC

MS:

MS ID:MS005945
Analysis ID:AN006242
Instrument Name:Agilent 5975C
Instrument Type:Single quadrupole
MS Type:EI
MS Comments:The ion source temperature was set to 230°C. The mass range analyzed was from m/z 85 to 700. Agilent MassHunter Qualitative Analysis (version B06.00) and Agilent MassHunter Quantitative Analysis (version B.07.01) were used to analyze GC-MS data. The NIST library and an in-house database produced using authentic standards were used for metabolite identification.
Ion Mode:POSITIVE
Helium Flow:1mL/min
Ion Source Temperature:230℃
Ion Spray Voltage:1411V
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