Summary of Study ST003541
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 PR002177. The data can be accessed directly via it's Project DOI: 10.21228/M8723W This work is supported by NIH grant, U2C- DK119886.
See: https://www.metabolomicsworkbench.org/about/howtocite.php
| Study ID | ST003541 |
| Study Title | Metabolomic analysis of fluorescent hairy roots overexpressing the Gretchen Hagen 3_62 genes enhancing soybean resistance to cyst nematodes |
| Study Summary | The Gretchen Hagen 3 genes maintain endogenous hormone homeostasis by conjugating excess hormones with amino acids. Herein, we identified the members of the GH3 family in soybeans and analyzed their phylogeny, gene duplication, structure, domains, conserved motifs, cis-elements in promoter regions for stress responses, and functional characteristics. We found that GH3 genes are induced by pathogens in Group-II. Furthermore, 8 out of 16 Group-II genes responded to cyst nematode infection. Through functional analysis of eight GmGH3 genes via overexpression, they play a negative role in soybean resistance to cyst nematode. In addition, our metabolomic analysis showed that overexpression of Glyma.02G125600, Glyma.17G165500, and Glyma.13G284600 affected the content of salicylic acid and jasmonic acid. Our findings clarify the functional features of GH3 genes and reveal their involvement in plant hormone signaling pathways. This provides valuable insights into the complex molecular mechanisms underlying the interaction between soybeans and cyst nematode. |
| Institute | Shenyang Agricultural University |
| Last Name | Yang |
| First Name | Xiaowen |
| Address | College of Plant Protection |
| 2020200130@stu.syau.edu.cn | |
| Phone | 15702428682 |
| Submit Date | 2024-09-29 |
| Analysis Type Detail | GC-MS |
| Release Date | 2024-11-15 |
| Release Version | 1 |
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Project:
| Project ID: | PR002177 |
| Project DOI: | doi: 10.21228/M8723W |
| Project Title: | Metabolomic analysis of fluorescent hairy roots overexpressing the Gretchen Hagen 3 genes enhancing soybean resistance to cyst nematodes |
| Project Summary: | Soybean root samples were collected, target metabolites were extracted, standard curves were established, methodology verification was performed, LC-MS/MS metabolites were detected, and data were analyzed.Metabolome analysis was conducted on FHRs overexpressing these genes to investigate how plant hormones play a role in soybean resistance to SCN. These results provide a new framework for understanding the interaction between soybean and SCN. |
| Institute: | Shenyang Agricultural University |
| Last Name: | Yang |
| First Name: | Xiaowen |
| Address: | College of Plant Protection |
| Email: | 2020200130@stu.syau.edu.cn |
| Phone: | 15702428682 |
Subject:
| Subject ID: | SU003670 |
| Subject Type: | Plant |
| Subject Species: | Glycine max |
| Taxonomy ID: | 3847 |
Factors:
Subject type: Plant; Subject species: Glycine max (Factor headings shown in green)
| mb_sample_id | local_sample_id | Sample source | Phenotype |
|---|---|---|---|
| SA387601 | CK-1 | Plant root | control |
| SA387602 | CK-2 | Plant root | control |
| SA387603 | CK-3 | Plant root | control |
| SA387604 | CK-4 | Plant root | control |
| SA387605 | CK-5 | Plant root | control |
| SA387606 | CK-6 | Plant root | control |
| SA387607 | GH3_62-1 | Plant root | transgene |
| SA387608 | GH3_62-2 | Plant root | transgene |
| SA387609 | GH3_62-3 | Plant root | transgene |
| SA387610 | GH3_62-4 | Plant root | transgene |
| SA387611 | GH3_62-5 | Plant root | transgene |
| SA387612 | GH3_62-6 | Plant root | transgene |
| Showing results 1 to 12 of 12 |
Collection:
| Collection ID: | CO003663 |
| Collection Summary: | Liquid nitrogen grinding samples, weighing a certain amount of samples into mass spectrometry water, vortex mixing, as diluted samples; Take a dilution sample of 100 μL and add 400 μL precipitator (acetonitrile: Water = 1:1), vortex mixing, extraction at 4°C for 30 min, centrifugation at 12000 rpm and 4°C for 10 min, taking 300 μL supernatant slowly through the extraction column, adding 500 μL eluent (30% acetonitrile), slowly through the extraction column, mixing the two times of flow solution, LC-MS analysis. |
| Sample Type: | Plant roots |
Treatment:
| Treatment ID: | TR003679 |
| Treatment Summary: | Take a dilution sample of 100 μL and add 400 μL precipitator (acetonitrile: Water = 1:1), vortex mixing, extraction at 4°C for 30 min, centrifugation at 12000 rpm and 4°C for 10 min, taking 300 μL supernatant slowly through the extraction column, adding 500 μL eluent (30% acetonitrile), slowly through the extraction column, mixing the two times of flow solution, LC-MS analysis. |
Sample Preparation:
| Sampleprep ID: | SP003677 |
| Sampleprep Summary: | Take a dilution sample of 100 μL and add 400 μL precipitator (acetonitrile: Water = 1:1), vortex mixing, extraction at 4°C for 30 min, centrifugation at 12000 rpm and 4°C for 10 min, taking 300 μL supernatant slowly through the extraction column, adding 500 μL eluent (30% acetonitrile), slowly through the extraction column, mixing the two times of flow solution, LC-MS analysis. |
Combined analysis:
| Analysis ID | AN005813 |
|---|---|
| Analysis type | MS |
| Chromatography type | HILIC |
| Chromatography system | AB Sciex QTRAP 6500+ |
| Column | Agilent ZORBAX Eclipse Plus C18 (100 x 2.1mm,1.8um) |
| MS Type | EI |
| MS instrument type | QTRAP |
| MS instrument name | AB Sciex QTRAP 6500+ |
| Ion Mode | POSITIVE |
| Units | Peak area |
Chromatography:
| Chromatography ID: | CH004416 |
| Instrument Name: | AB Sciex QTRAP 6500+ |
| Column Name: | Agilent ZORBAX Eclipse Plus C18 (100 x 2.1mm,1.8um) |
| Column Temperature: | 35°C |
| Flow Gradient: | The initial proportion of mobile phase B is set at 15%, which then linearly increases at a rate of 0.8% per minute until it reaches 45%, where it is held for 5 minutes to adequately elute moderately polar metabolites. Afterward, it increases at a rate of 2% per minute up to 90%, and finally remains at this composition for an additional 5 minutes to clean the chromatographic column and collect less polar metabolites. |
| Flow Rate: | 0.35 mL/min |
| Solvent A: | 100% Water; 5mM Ammonium Acetate (Adjusted to pH 4.5 with Acetic Acid) |
| Solvent B: | 100% Acetonitrile |
| Chromatography Type: | HILIC |
MS:
| MS ID: | MS005533 |
| Analysis ID: | AN005813 |
| Instrument Name: | AB Sciex QTRAP 6500+ |
| Instrument Type: | QTRAP |
| MS Type: | EI |
| MS Comments: | The concentration series of the standard solution were detected by LC-MS, and the ratio of the concentration of the standard product to the internal standard was taken as the horizontal coordinate and the ratio of the peak area of the standard product to the internal standard was taken as the vertical coordinate to investigate the linearity of the standard solution. QC samples were tested by inserting a number of needles at intervals in each batch of samples. The RSD of all QC samples was calculated with the concentration of the standard substance to evaluate stability. According to the established sample pretreatment and instrumental analysis methods, all samples were quantitatively analyzed. |
| Ion Mode: | POSITIVE |
