Summary of Study ST000353

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 PR000282. The data can be accessed directly via it's Project DOI: 10.21228/M8G308 This work is supported by NIH grant, U2C- DK119886.

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Study IDST000353
Study TitleThe Development of Metabolomic Markers in African Bermudagrass (C. transvaalensis) for Sting Nematode (Belonolaimus longicaudatus) Response
Study TypeDisease response in terms of nematode reproduction and root weight
Study SummaryThe objective of the proposed pilot study is to identify metabolites up- and down-regulated in African bermudagrass that are tolerant and sensitive to the sting nematode and develop metabolomic markers for the highest expressed metabolites associated with tolerance. Future work will include additional accessions and species of bermudagrass, and testing under field conditions. Bermudagrass accessions identified as tolerant or sensitive by Pang et al. (2011) will be assessed under controlled greenhouse conditions to identify metabolites linked to sting nematode tolerance. Nematode response will be quantified through determination of root length and weight and the number of nematodes present 136 days after inoculation. Higher root length and weight indicate tolerance or resistance. Higher nematode counts indicate greater reproduction (i.e. a susceptible plant), while lower counts indicate that the accession may have some resistance. Metabolites from root tissue of these accessions will be compared to identify those associated with tolerance/resistance, and those that are associated with nematode infestation by comparing inoculated plants to uninoculated controls. Metabolomic markers will then be developed for the metabolites associated with tolerance/resistance. These markers will be used to guide future screening of bermudagrass accessions for breeding nematode-tolerant or -resistant varieties.
Institute
University of Florida
DepartmentSECIM
LaboratoryTurfgrass Breeding
Last NameBenda
First NameNicole
Address2005 SW 23rd St
Emailnbenda@ufl.edu
Phone352-792-4561
Submit Date2015-11-13
Num Groups3
Total Subjects42
Raw Data AvailableYes
Raw Data File Type(s)mzML
Analysis Type DetailLC-MS
Release Date2017-07-10
Release Version1
Nicole Benda Nicole Benda
https://dx.doi.org/10.21228/M8G308
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

Select appropriate tab below to view additional metadata details:

Project:

Project ID:PR000282
Project DOI:doi: 10.21228/M8G308
Project Title:The Development of Metabolomic Markers in Bermudagrass (Cynodon spp.) for Sting Nematode (Belonolaimus longicaudatus) Response
Project Summary:The majority of golf courses in Florida experience damage from plant-parasitic nematodes and more than 80% of golf courses in Florida are at risk for nematode-related damage (Crow, 2005). With limited availability of nematicides and lack of tolerant cultivars, turf managers need new genetically resistant cultivars. Use of resistant or tolerant grasses is the most efficient, environmentally friendly and, in the long run, least costly component of IPM. Current screening of new genotypes for nematode resistance is labor- and time-intensive, with three months required soley for nematode development on test plants. We intend to develop metabolomic markers or a signature pattern associated with nematode resistance or tolerance. Screening plants for these markers or a signature pattern of would greatly speed up the screening process and development of resistant cultivars.
Institute:University of Florida
Department:Agronomy
Laboratory:Turfgrass Breeding
Last Name:Kenworthy
First Name:Kevin
Address:2005 SW 23rd Street, Gainesville FL 32611
Email:nbenda@ufl.edu
Phone:352-792-4561

Subject:

Subject ID:SU000373
Subject Type:Plant
Subject Species:Cynodon transvaalensis
Taxonomy ID:75728
Genotype Strain:AB03, AB33, and AB39
Age Or Age Range:4 month old plant clones
Subject Comments:(African Bermudagrass,C. transvaalensis)
Species Group:Plant

Factors:

Subject type: Plant; Subject species: Cynodon transvaalensis (Factor headings shown in green)

mb_sample_id local_sample_id Plant genotype Nematode inoculation
SA015451AB03_I_13AB03 inoc
SA015452AB03_I_1AB03 inoc
SA015453AB03_I_10AB03 inoc
SA015454AB03_I_7AB03 inoc
SA015455AB03_I_2AB03 inoc
SA015456AB03_I_4AB03 inoc
SA015457AB03_I_5AB03 inoc
SA015458AB03_U_14AB03 uninoc
SA015459AB03_U_8AB03 uninoc
SA015460AB03_U_11AB03 uninoc
SA015461AB03_U_7AB03 uninoc
SA015462AB03_U_6AB03 uninoc
SA015463AB03_U_4AB03 uninoc
SA015464AB03_U_3AB03 uninoc
SA015465AB33_I_10AB33 inoc
SA015466AB33_I_11AB33 inoc
SA015467AB33_I_8AB33 inoc
SA015468AB33_I_5AB33 inoc
SA015469AB33_I_3AB33 inoc
SA015470AB33_I_1AB33 inoc
SA015471AB33_I_2AB33 inoc
SA015472AB33_U_11AB33 uninoc
SA015473AB33_U_9AB33 uninoc
SA015474AB33_U_13AB33 uninoc
SA015475AB33_U_2AB33 uninoc
SA015476AB33_U_8AB33 uninoc
SA015477AB33_U_4AB33 uninoc
SA015478AB33_U_7AB33 uninoc
SA015479AB39_I_11AB39 inoc
SA015480AB39_I_9AB39 inoc
SA015481AB39_I_12AB39 inoc
SA015482AB39_I_8AB39 inoc
SA015483AB39_I_3AB39 inoc
SA015484AB39_I_1AB39 inoc
SA015485AB39_I_4AB39 inoc
SA015486AB39_U_9AB39 uninoc
SA015487AB39_U_10AB39 uninoc
SA015488AB39_U_7AB39 uninoc
SA015489AB39_U_5AB39 uninoc
SA015490AB39_U_2AB39 uninoc
SA015491AB39_U_3AB39 uninoc
SA015492AB39_U_6AB39 uninoc
Showing results 1 to 42 of 42

Collection:

Collection ID:CO000367
Collection Summary:Rinsed roots were cut off the plant, placed into paper envelopes, and immediately placed into liquid nitrogen. Roots were stored at -80°C until freeze-drying. Freeze-dried roots were held at room temperature in ziploc bags with silica gel packets. They were then frozen in liquid nitrogen and ground to a powder in a tissue homogenizer with ball bearings (Geno/Grinder 2010), and then stored in 2 ml snap-cap plastic tubes at room temperature.
Sample Type:plant root tissue
Collection Method:whole plant destruction
Collection Location:greenhouse
Collection Frequency:once
Collection Duration:1-2 minutes to cut off and rinse the roots prior to placement into liquid nitrogen
Collection Time:136 days after inoculation
Volumeoramount Collected:0.2-0.5 grams of root tissue, dry weight
Storage Conditions:1)-80C until freeze-drying. 2) Held at room temperature in ziploc bags with silica packets. 3) Frozen in liquid nitrogen and ground using a Geno/Grinder 2010. 4) Transferred to 2 mL tubes and held at room temperature.
Collection Vials:Paper coin envelopes
Storage Vials:2 ml snap-cap plastic tubes
Collection Tube Temp:liquid nitrogen (-196°C)
Additives:none

Treatment:

Treatment ID:TR000387
Treatment Summary:Plants clones propagated by stolons were allowed to establish for 30 days in 4 cm diameter conetainers filled with sand. Fifty sting nematodes (mixed age and gender) were added to each conetainer and allowed to grow and reproduce for 90 days. Nematodes were then rinsed off of roots for quantification, and plant roots were frozen in liquid nitrogen and stored at -80C until they were freeze-dried.Freeze-dried roots were ground to a powder and then submitted for global metabolomic analysis.
Treatment:Biotic
Treatment Compound:Sting nematode, Belonolaimus longicaudatus
Plant Growth Support:sand in conetainers- 4 cm wide, 30 cm deep
Plant Growth Location:temperature controlled greenhouse
Plant Plot Design:complete randomized design
Plant Light Period:Natural lighting, ca. 11:13 Light:Dark
Plant Humidity:ca.50%RH
Plant Temp:25°C
Plant Watering Regime:Twice daily for 5 min
Plant Nutritional Regime:Weekly liquid fertilizer of 24-8-16 (N-P-K)
Plant Estab Date:2015-09-24
Plant Harvest Date:2016-04-02
Plant Growth Stage:non-reproductive
Plant Metab Quench Method:liquid nitrogen, followed by storage at -80°C
Plant Harvest Method:rinsed roots were cut off the plant and placed into paper envelopes
Plant Storage:1)-80C until freeze-drying. 2) Held at room temperature in ziploc bags with silica packets. 3) Frozen in liquid nitrogen and ground using a Geno/Grinder 2010. 4) Transferred to 2 mL tubes and held at room temperature.

Sample Preparation:

Sampleprep ID:SP000380
Sampleprep Summary:none
Sampleprep Protocol Filename:Maize_Tissue_sample_prep.pdf

Combined analysis:

Analysis ID AN000575 AN000576
Analysis type MS MS
Chromatography type Reversed phase Reversed phase
Chromatography system Thermo Scientific-Dionex Ultimate 3000 Thermo Scientific-Dionex Ultimate 3000
Column ACE Excel 2 C18-PFP (100 x 2.1mm, 2um) ACE Excel 2 C18-PFP (100 x 2.1mm, 2um)
MS Type ESI ESI
MS instrument type Orbitrap Orbitrap
MS instrument name Thermo Q Exactive Orbitrap Thermo Q Exactive Orbitrap
Ion Mode POSITIVE NEGATIVE
Units peak area peak area

Chromatography:

Chromatography ID:CH000411
Chromatography Summary:See document
Methods Filename:Metabolomics_LCMSProtocol.pdf
Appendix_A_-_Internal_Standard_Prep_GLCMS.pdf
Instrument Name:Thermo Scientific-Dionex Ultimate 3000
Column Name:ACE Excel 2 C18-PFP (100 x 2.1mm, 2um)
Flow Rate:0.350mL/min-0.600mL/min
Internal Standard:Appendix A - Internal Standard Prep GLCMS.pdf
Solvent A:100% water; 0.1% formic acid
Solvent B:100% acetonitrile
Chromatography Type:Reversed phase

MS:

MS ID:MS000511
Analysis ID:AN000575
Instrument Name:Thermo Q Exactive Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:HESI
Ion Mode:POSITIVE
Analysis Protocol File:Metabolomics_LCMSProtocol.pdf
  
MS ID:MS000512
Analysis ID:AN000576
Instrument Name:Thermo Q Exactive Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:HESI
Ion Mode:NEGATIVE
Analysis Protocol File:Metabolomics_LCMSProtocol.pdf
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