Summary of Study ST003350

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 PR002084. The data can be accessed directly via it's Project DOI: 10.21228/M87K0X 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.

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Study IDST003350
Study TitleDissecting the Genetic Basis of UV-B Responsive Metabolites in Rice
Study SummaryUV-B, an important environmental factor, has been shown to affect the yield and quality of rice (Oryza sativa) worldwide. However, the biochemical and genetic basis of the metabolome underlying the response to UV-B stress remain elusive in rice. In this study, we performed comprehensive metabolic profiling of leaves from 160 diverse rice accessions under UV-B and normal-light conditions using a widely targeted metabolomics approach. Our results revealed substantial differences in the accumulation of metabolites between the two major rice subspecies indica and japonica, especially after UV-B treatment, shedding light on the possible role and mechanism of metabolome changes in subspecies differentiation and the stress response.
Institute
Industrial Crops Institute of Hubei Academy of Agricultural Sciences
Last NameZhang
First NameFeng
Address43 nanhu road, hongshan district, wuhan city, hubei province, Wuhan, Hubei,430064,China
Emailzhangfeng2023@hbaas.ac.cn
Phone027-15926268746
Submit Date2024-06-18
Raw Data AvailableYes
Raw Data File Type(s)mzML
Analysis Type DetailLC-MS
Release Date2024-08-12
Release Version1
Feng Zhang Feng Zhang
https://dx.doi.org/10.21228/M87K0X
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

Select appropriate tab below to view additional metadata details:

Project:

Project ID:PR002084
Project DOI:doi: 10.21228/M87K0X
Project Title:Metabolics studies under UV-B conditions in rice leaf
Project Summary:We performed comprehensive metabolic profiling of leaves from 160 diverse rice accessions under UV-B and normal-light conditions using a widely targeted metabolomics approach
Institute:Industrial Crops Institute of Hubei Academy of Agricultural Sciences
Last Name:Zhang
First Name:Feng
Address:43 Nanhu road, Hongshan district, wuhan city, Hubei province, Wuhan, Hubei, 430064, China
Email:zhangfeng2023@hbaas.ac.cn
Phone:027-15926268746

Subject:

Subject ID:SU003471
Subject Type:Plant
Subject Species:Oryza sativa
Taxonomy ID:4530

Factors:

Subject type: Plant; Subject species: Oryza sativa (Factor headings shown in green)

mb_sample_id local_sample_id Sample source Theatment
SA365356ma249-305-p-1Rice CK
SA365357ma249-276-p-1Rice CK
SA365358ma249-279-p-1Rice CK
SA365359ma249-281-p-1Rice CK
SA365360ma249-283-p-1Rice CK
SA365361ma249-284-p-1Rice CK
SA365362ma249-287-p-1Rice CK
SA365363ma249-294-p-1Rice CK
SA365364ma249-307-p-1Rice CK
SA365365ma249-271-p-1Rice CK
SA365366ma249-308-p-1Rice CK
SA365367ma249-311-p-1Rice CK
SA365368ma249-312-p-1Rice CK
SA365369ma249-313-p-1Rice CK
SA365370ma249-314-p-1Rice CK
SA365371ma249-318-p-1Rice CK
SA365372ma249-321-p-1Rice CK
SA365373ma249-275-p-1Rice CK
SA365374ma249-269-p-1Rice CK
SA365375ma249-324-p-1Rice CK
SA365376ma249-237-p-1Rice CK
SA365377ma249-213-p-1Rice CK
SA365378ma249-222-p-1Rice CK
SA365379ma249-224-p-1Rice CK
SA365380ma249-227-p-1Rice CK
SA365381ma249-230-p-1Rice CK
SA365382ma249-231-p-1Rice CK
SA365383ma249-233-p-1Rice CK
SA365384ma249-239-p-1Rice CK
SA365385ma249-267-p-1Rice CK
SA365386ma249-243-p-1Rice CK
SA365387ma249-244-p-1Rice CK
SA365388ma249-250-p-1Rice CK
SA365389ma249-255-p-1Rice CK
SA365390ma249-258-p-1Rice CK
SA365391ma249-259-p-1Rice CK
SA365392ma249-266-p-1Rice CK
SA365393ma249-322-p-1Rice CK
SA365394ma249-325-p-1Rice CK
SA365395ma249-206-p-1Rice CK
SA365396ma249-489-p-1Rice CK
SA365397ma249-463-p-1Rice CK
SA365398ma249-466-p-1Rice CK
SA365399ma249-468-p-1Rice CK
SA365400ma249-469-p-1Rice CK
SA365401ma249-471-p-1Rice CK
SA365402ma249-481-p-1Rice CK
SA365403ma249-484-p-1Rice CK
SA365404ma249-490-p-1Rice CK
SA365405ma249-459-p-1Rice CK
SA365406ma249-494-p-1Rice CK
SA365407ma249-498-p-1Rice CK
SA365408ma249-499-p-1Rice CK
SA365409ma249-503-p-1Rice CK
SA365410ma249-506-p-1Rice CK
SA365411ma249-517-p-1Rice CK
SA365412ma249-006-p-1Rice CK
SA365413ma249-461-p-1Rice CK
SA365414ma249-455-p-1Rice CK
SA365415ma249-332-p-1Rice CK
SA365416ma249-376-p-1Rice CK
SA365417ma249-338-p-1Rice CK
SA365418ma249-345-p-1Rice CK
SA365419ma249-347-p-1Rice CK
SA365420ma249-348-p-1Rice CK
SA365421ma249-349-p-1Rice CK
SA365422ma249-356-p-1Rice CK
SA365423ma249-361-p-1Rice CK
SA365424ma249-383-p-1Rice CK
SA365425ma249-452-p-1Rice CK
SA365426ma249-396-p-1Rice CK
SA365427ma249-397-p-1Rice CK
SA365428ma249-419-p-1Rice CK
SA365429ma249-422-p-1Rice CK
SA365430ma249-425-p-1Rice CK
SA365431ma249-429-p-1Rice CK
SA365432ma249-441-p-1Rice CK
SA365433ma249-442-p-1Rice CK
SA365434ma249-211-p-1Rice CK
SA365435ma249-001-p-1Rice CK
SA365436ma249-205-p-1Rice CK
SA365437ma249-073-p-1Rice CK
SA365438ma249-057-p-1Rice CK
SA365439ma249-062-p-1Rice CK
SA365440ma249-063-p-1Rice CK
SA365441ma249-066-p-1Rice CK
SA365442ma249-067-p-1Rice CK
SA365443ma249-068-p-1Rice CK
SA365444ma249-072-p-1Rice CK
SA365445ma249-074-p-1Rice CK
SA365446ma249-048-p-1Rice CK
SA365447ma249-075-p-1Rice CK
SA365448ma249-076-p-1Rice CK
SA365449ma249-078-p-1Rice CK
SA365450ma249-079-p-1Rice CK
SA365451ma249-080-p-1Rice CK
SA365452ma249-082-p-1Rice CK
SA365453ma249-083-p-1Rice CK
SA365454ma249-054-p-1Rice CK
SA365455ma249-047-p-1Rice CK
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Collection:

Collection ID:CO003464
Collection Summary:The fully expanded leaves of at least three lines from each variety in UV-B and normal conditions were harvested and snap-frozen in liquid nitrogen and stored at −80 °C for a metabolite sample and every sample was repeated two times.
Sample Type:Leaves

Treatment:

Treatment ID:TR003480
Treatment Summary:160 rice accessions were selected for UV-B stress, which included 76 Indica, 58 Japonica, 3 Admix, 17 Aus and 6 VI based on the proportion of rice different subgroups in the 533 rice varieties from all over the world. Information about these accessions, including variety name and place of origin are listed in Supplementary_Table3.xlsx. The 160 rice accessions were sown and grown in a growth pool in Huazhong Agricultural University, Wuhan. After one week, each variety was divided into two groups respectively and grown in two areas with equal condition. Four weeks later, rice seedlings in one area were moved to a UV-B chamber (TL40W/302 nm narrowband UV-B tube, Philips, Netherlands) with 30 μW cm−2 UV-B intensity. UV-B intensity was detected by a UV radiometer with the UV-295 detector from the photoelectric instrument factory (Beijing Normal University, China). The CK samples were not treated with UV-B.

Sample Preparation:

Sampleprep ID:SP003478
Sampleprep Summary:100 mg powder was weighed and extracted overnight at 4°C with 1.0 ml of 70% aqueous methanol (methanol: H2O, 70:30, v/v)

Combined analysis:

Analysis ID AN005491
Analysis type MS
Chromatography type Reversed phase
Chromatography system SHIMADZU LC-20A
Column Shimadzu Shim-pack VP-ODS C18 (150 x 2mm, 5um)
MS Type ESI
MS instrument type QTRAP
MS instrument name Applied Biosystems 4000 Q TRAP
Ion Mode POSITIVE
Units Relative intensity

Chromatography:

Chromatography ID:CH004174
Chromatography Summary:HPLC, Shim-pack UFLC SHIMADZU CBM20A system; shim-pack VP-ODS C18 (particle size 5.0μm, length 2×150mm)
Instrument Name:SHIMADZU LC-20A
Column Name:Shimadzu Shim-pack VP-ODS C18 (150 x 2mm, 5um)
Column Temperature:40
Flow Gradient:100:0 (A:B) V/V at 0 min, 5:95 (A:B) V/V at 20.0 min, 5:95 (A:B) V/V at 22.0 min, 95:5 (A:B) V/V at 22.1 min, 95:5 (A:B) V/V at 25.0 min
Flow Rate:0.25mL/min
Solvent A:100% water; 0.04% acetic acid
Solvent B:100% acetonitrile; 0.04% acetic acid
Chromatography Type:Reversed phase

MS:

MS ID:MS005217
Analysis ID:AN005491
Instrument Name:Applied Biosystems 4000 Q TRAP
Instrument Type:QTRAP
MS Type:ESI
MS Comments:-
Ion Mode:POSITIVE
Analysis Protocol File:ZF_MS_method.pdf
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