Louisiana Marsh Dieback Genetic Marker Data for Amplified Fragment Length Polymorphism Data (Brown Marsh Fingerprint Data)

• Identification_Information
• Data_Quality_Information
• Entity_and_Attribute_Information
• Distribution_Information
• Metadata_Reference_Information

Identification_Information:

Citation:

Citation_Information:

Originator:

Louisiana State University, Department of Agronomy and Environmental Management

Publication_Date: 2005

Title:

Louisiana Marsh Dieback Genetic Marker Data for Amplified Fragment Length Polymorphism Data (Brown Marsh Fingerprint Data)

Geospatial_Data_Presentation_Form: Digital tabular data

Larger_Work_Citation:

Citation_Information:

Originator:

Barataria-Terrebonne National Estuary Program Scientific-Technical Committee

Publication_Date: 20010207

Title:

Requests for submission of Scope of Services for Marsh Dieback and Nutria Control Emergency Response

Geospatial_Data_Presentation_Form: document

Publication_Information:

Publication_Place: Thibodaux, LA

Publisher:

Barataria-Terrebonne National Estuary Program Scientific-Technical Committee

Online_Linkage: <http://www.brownmarsh.net/reports/brown_marsh_rfp.pdf>

Description:

Abstract:

This data set consists of the data for 693 AFLP markers generated by a technique knows as amplified fragment length polymorphism on 44 brown marsh accessions. The data were used to measure genetic diversity among the brown marsh accessions.

Purpose:

The bands in different brown marsh accession were scored and then these were analyzed using software known as NTSYS-PC to measure the genetic diversity among them. Those accessions with the presence of a particular band or marker can be judged similar in their genetic make up.

Time_Period_of_Content:

Time_Period_Information:

Range_of_Dates/Times:

Beginning_Date: 2001

Ending_Date: 2003

Currentness_Reference: ground condition

Status:

Progress: Complete

Maintenance_and_Update_Frequency: None planned

Spatial_Domain:

Description_of_Geographic_Extent: Coastal Louisiana

Bounding_Coordinates:

West_Bounding_Coordinate: -93.910681

East_Bounding_Coordinate: -88.777417

North_Bounding_Coordinate: 30.509791

South_Bounding_Coordinate: 28.892107

Keywords:

Theme:

Theme_Keyword_Thesaurus: None

Theme_Keyword: emergent vegetation

Theme_Keyword: brown marsh

Theme_Keyword: dead zone

Theme_Keyword: transition zone

Theme_Keyword: dieback

Theme_Keyword: genetic diversity

Theme_Keyword: accession

Theme_Keyword: saltmarsh

Theme_Keyword: amplified fragment length polymorphism

Theme_Keyword: AFLP

Place:

Place_Keyword_Thesaurus: None

Place_Keyword: Louisiana

Place_Keyword: Coastal Louisiana

Place_Keyword: LA

Place_Keyword: Southern Louisiana

Place_Keyword: Terrebonne Basin

Place_Keyword: Barataria Basin

Taxonomy:

Keywords/Taxon:

Taxonomic_Keyword_Thesaurus: None

Taxonomic_Keywords: Spartina alterniflora

Taxonomic_Keywords: species

Taxonomic_Classification:

Taxon_Rank_Name: Kingdom

Taxon_Rank_Value: Plantae

Taxonomic_Classification:

Taxon_Rank_Name: Division

Taxon_Rank_Value: Magnoliophyta

Taxonomic_Classification:

Taxon_Rank_Name: Class

Taxon_Rank_Value: Liliopsida

Taxonomic_Classification:

Taxon_Rank_Name: Subclass

Taxon_Rank_Value: Commelinidae

Taxonomic_Classification:

Taxon_Rank_Name: Order

Taxon_Rank_Value: Cyperales

Taxonomic_Classification:

Taxon_Rank_Name: Family

Taxon_Rank_Value: Poaceae

Taxonomic_Classification:

Taxon_Rank_Name: Genus

Taxon_Rank_Value: Spartina

Taxonomic_Classification:

Taxon_Rank_Name: Species

Taxon_Rank_Value: alterniflora

Applicable_Common_Name: smooth cordgrass

Access_Constraints:

Data generated by the Brown Marsh principal investigators will be available only to the project’s other principal investigators, following the established QA/QC review, for a period of two years. After two years from the finalization of the data, it shall be made available to the public. Please contact the principal investigator for exact date of availability. It is strongly recommended that these data be directly acquired from the Brown Marsh Database Information Management System server and not indirectly through other sources which may have changed the data in some way.

Use_Constraints:

Acknowledgement of the principal investigator as a data source would be appreciated in products developed from these data, and such acknowledgement as is standard for citation and legal practices for data source is expected by users of these data. Users should be aware that comparison with other data sets for the same area from other time periods may be inaccurate due to inconsistencies resulting from changes in mapping conventions, methodologies, data collections and computer processes over time. The principal investigator and the distributor shall not be liable for improper or incorrect use of these data, based on the description of appropriate/inappropriate uses described in this metadata document. The principal investigator and distributor make no claims as to the data’s suitability for other purposes. These data are not legal documents and are not to be used as such.

Point_of_Contact:

Contact_Information:

Contact_Organization_Primary:

Contact_Organization:

Louisiana State University, Department of Agronomy and Environmental Management

Contact_Person: Prasanta K. Subudhi

Contact_Position: Assistant Professor

Contact_Address:

Address_Type: Physical

Address: 215 Sturgis Hall

City: Baton Rouge

State_or_Province: LA

Postal_Code: 70803

Country: USA

Contact_Voice_Telephone: 225 578-1303

Contact_Facsimile_Telephone: 225 578-1403

Contact_Electronic_Mail_Address: psubudhi@agcrt.lsu.edu

Native_Data_Set_Environment: Microsoft Excel 2000

Cross_Reference:

Citation_Information:

Originator:

Vos, P., R. Hogers, M. Bleeker, M. Reijans, T. van de Lee, M. Hornes, A. Frijters, J. Pot, J. Peleman, M. Kuiper, and M. Zabeau

Publication_Date: 199511

Title: AFLP: a new technique for DNA fingerprinting

Geospatial_Data_Presentation_Form: journal article

Publication_Information:

Publication_Place: Oxford, UK

Publisher: Oxford University Press

Series_Information:

Series_Name: Nucleic Acids Research

Issue_Identification: Vol. 23, Issue 21 4407-4414

Analytical_Tool:

Analytical_Tool_Description: PTC-100 Thermocycler - thermal cycler

Tool_Access_Information:

Online_Linkage: <http://www.mjr.com>

Tool_Access_Instructions: See website for information

Tool_Contact:

Contact_Information:

Contact_Organization_Primary:

Contact_Organization: Bio-Rad Laboratories, INC

Contact_Address:

Address_Type: Mailing

Address: 590 Lincoln Street

City: Waltham

State_or_Province: MA

Postal_Code: 02451

Country: USA

Contact_Voice_Telephone: 888 735-8437

Contact_Facsimile_Telephone: 617 923-8080

Data_Quality_Information:

Attribute_Accuracy:

Attribute_Accuracy_Report:

The accuracy of the attributes is determined by the accuracy of the DNA processing and analysis. Only good quality genomic DNA was used for analyses; quality of the DNA was determined by running a 1% agarose gel and an adjustment of the final concentration to 50ng/µl. The AFLP protocol (Vos, et al. 1995) was followed.

Logical_Consistency_Report:

Sites were chosen according to the dieback zones, and distances of two sampling sites varied from 10 to 15 meters. All samples were labeled according to the zones where collected occur. Six additional sampling sites (outside of the dieback region in coastal Louisiana) were chosen for normal healthy marsh environment. All equipment were calibrated according to the manual or standard operating procedure.

Completeness_Report: There are no known omissions in the data.

Lineage:

Methodology:

Methodology_Type: Field/Lab

Methodology_Identifier:

Methodology_Keyword_Thesaurus: None

Methodology_Keyword: sites

Methodology_Keyword: dieback zones

Methodology_Keyword: samples

Methodology_Keyword: greenhouse

Methodology_Keyword: container

Methodology_Keyword: reestablished

Methodology_Keyword: ramets

Methodology_Keyword: S. alterniflora

Methodology_Keyword: young green tissue

Methodology_Keyword: labeled

Methodology_Description:

Sample collection - From nineteen dieback sites across the Terrebonne and Barataria basins, surviving ramets of S. alterniflora were collected from the interior dead zone (where dieback impact was severe) and from transition zones on the periphery of the dead zones (where dieback impact was less severe). Samples were also collected from six normal and healthy marsh sites in coastal Louisiana (four in the south-west part of the state and two in close promixity of the dieback area.) Individual samples were labeled and brought back to the Golden Meadows Plant Materials Center in Galliano. The samples were reestablished in containers. From each of these 40 samples, young green leaf tissue (approximately 5-10gm) were collected and stored at -80 degrees C until DNA extraction.

Methodology:

Methodology_Type: Lab

Methodology_Identifier:

Methodology_Keyword_Thesaurus: None

Methodology_Keyword: liquid nitrogen

Methodology_Keyword: microcentrifuge tube

Methodology_Keyword: agarose gel

Methodology_Keyword: concentration

Methodology_Keyword: genomic DNA

Methodology_Keyword: incubation

Methodology_Keyword: AFLP protocol

Methodology_Keyword: AFLP bands

Methodology_Keyword: thermocycler

Methodology_Keyword: intervals

Methodology_Description:

DNA isolation and AFLP protocol - Leaf tissues from each individual were ground into a fine powder in liquid nitrogen using a mortar and pestle, and approximately 100mg of the powder were transferred to a microcentrifuge tube. Good quality genomic DNA was extracted using the GenElute Plant Genomic DNA kit. AFLP protocol was followed as described by Vos et al. (1995). Five hundred nanograms of genomic DNA of each S. alterniflora individual was digested with 5U of EcoRI (Invitrogen, Carlsbad, CA) and 5U of MseI (New England Biolabs, Inc., Beverly, MA) in a reaction volume of 30 µl at 370 C for 2 hours in a restriction ligation buffer (10mM Tris-HAc, pH 7.5, 10 mM MgAc2, 50 mM KAc, 5mM DTT, and 0.005% BSA), followed by incubation at 700 C for 15 minutes to inactivate the restriction enzymes. Twenty microliters of the digested DNA was then mixed with 10 µl of ligation mix containing 1 µl of EcoRI adapter (5 pMol), 1 µl MseI adapter (50 pMol), 1 U T4 DNA ligase, 6 µl of 5X ligation buffer with ATP, and incubated again at 200 C in a PTC-100 Thermocycler (MJ Research, Inc., Waltham, Mass.) for 3 hours. Ligated DNA products were diluted 10 times, and diluted ligated DNA was preamplified using EcoRI-Pre and MseI-Pre primers following 30 cycles (940 C 30 Sec, 560 C 60 Sec, 720 C 60 Sec) of amplification. The adapter and pre-amplification primers were synthesized according to Vos et al. (1995). The preamplified PCR products were run on a 1.5% agarose gel in which a low-molecular weight smear was visible, indicating the presence of abundant PCR products. Then the preamplified PCR products were diluted 20 times with sterile water for selective amplification. Selective amplification PCR was performed in 12-µl reaction volumes containing 25 ng each of EcoRI+3 and MseI+3 primers, 3 µl of template DNA, 0.3 mM of all four dNTP, 2.5 mM MgCl2, 0.25 U Taq polymerase (Promega Corporation, Madison, WI) and 1x PCR buffer supplied with the Taq polymerase. Twelve EcoRI+MseI primer combinations (Table 2) were used for selective amplification using the PTC-100 thermal cycler. The thermocycler was programmed as follows: cycle 1 for 30 seconds at 940 C, 1 minute at 650 C, 1 minute at 720 C; cycles 2-13: annealing temperature was reduced by 0.70 C in every successive cycle; cycles 14-36: annealing at 560 C; final extension for 5 minutes at 720 C and hold at 40 C. AFLP reaction products (12 µl) were added to an equal volume of loading dye (0.025% each of Xylene Cyanol and Bromophenol blue, deionised formamide, 10 mM EDTA). Denaturing of the samples was done for 4 minutes at 950 C immediately before loading and then placed on ice while loading into the gel. Three microliters of the AFLP reaction products were analyzed on 6% denaturing polyacrylamide gels and electrophoresed in 0.5x TBE at 500 C, 110 W for 2 hours. A Bio-Rad Sequi-Gen® (38 x 50 cm) unit was used to run the gels. Silver staining of the gels was done manually following the procedure of Fritz et al. (1999). After the gels were developed, a sheet of 3 mm Whatman white paper was placed under the developed gel to visualize the AFLP bands and then scanned directly using a scanner.

Process_Step:

Process_Description: See methodology

Process_Date: 2000-2005

Entity_and_Attribute_Information:

Overview_Description:

Entity_and_Attribute_Overview:

The tabular data for the brown marsh fingerprinting is organized according to the number of genotypes analyzed (44) and the number of markers generated (693). The corresponding markers and its genotype were assigned either "1", "2", or "999" to indicate the presence (1) or absence (2) of the AFLP band (999 indicates no data). Markers were assigned ascending numbers for identification purposed, while the genotypes were assigned an alpha-numerical identification tag. The alpha codes designate if the sample was collected from "D" (dead zone), "T" (transition zone), "AD" (adjacent to a dead zone), or "AT" (adjacent to a transition zone.) Other genotype identification tags were assigned for those samples outside the brown marsh area, those of normal healthy coastal Louisiana marshes. Tags 44, 49, 75, and 90 were from sites in south-west Louisiana and tags 10 and Vermiliion were taken from sites closer to the brown marsh area.

Entity_and_Attribute_Detail_Citation: Prasanta K. Subudhi, written comm. 5-27-05

Distribution_Information:

Distributor:

Contact_Information:

Contact_Organization_Primary:

Contact_Organization: U.S. Geological Survey, National Wetlands Research Center

Contact_Person: Scott Wilson

Contact_Position: Electrical Engineer

Contact_Address:

Address_Type: Mailing and Physical

Address: 700 Cajundome Blvd

City: Lafayette

State_or_Province: LA

Postal_Code: 70506

Country: USA

Contact_Voice_Telephone: 337 266-8664

Contact_Facsimile_Telephone: 337 266-8513

Contact_Electronic_Mail_Address: scott_wilson@usgs.gov

Distribution_Liability:

Although these data have been processed successfully on a computer system at the designated principal investigator’s facility, no warranty expressed or implied is made regarding the accuracy or utility of the data on any other system or for general or scientific purposes, nor shall the act of distribution constitute any such warranty. This disclaimer applies both to individual use of the data and aggregate use with other data. It is strongly recommended that these data are directly acquired from the official Brown Marsh Database Information Management System server or from the principal investigator, and not indirectly through other sources which may have changed the data in some way. It is also strongly recommended that careful attention be given to the contents of the metadata file associated with these data. The Brown Marsh committee shall not be held liable for improper or incorrect use of the data described and/or contained herein. So, these data are provided as is and without any express or implied warranties. Also, use of trade names or commercial products in the metadata file is solely for the purpose of providing specific information, and does not imply recommendation or endorsement. Any downloading and use of these data signifies a user’s agreement to comprehension and compliance of the disclaimer. Insure all portions of metadata are read and clearly understood before using these data in order to protect both user and principal investigators interests.

Standard_Order_Process:

Digital_Form:

Digital_Transfer_Information:

Format_Name: Microsoft Excel

Format_Version_Number: 2000+

File_Decompression_Technique: none

Digital_Transfer_Option:

Online_Option:

Computer_Contact_Information:

Network_Address:

Network_Resource_Name: <http://www.brownmarsh.net>

Fees: None, if available online

Custom_Order_Process: None

Metadata_Reference_Information:

Metadata_Date: 20050531

Metadata_Contact:

Contact_Information:

Contact_Organization_Primary:

Contact_Organization: U.S. Geological Survey/NWRC

Contact_Position: Metadata specialist

Contact_Address:

Address_Type: Mailing and Physical

Address: 700 Cajundome Blvd

City: Lafayette

State_or_Province: LA

Postal_Code: 70506

Country: USA

Contact_Voice_Telephone: 337 266-8500

Contact_Facsimile_Telephone: 337 266-8513

Metadata_Standard_Name: Content Standard for Digital Geospatial Metadata

Metadata_Standard_Version: FGDC-STD-001-1998

Metadata_Extensions:

Profile_Name:

Biological Data Profile of Content Standard for Digital Geospatial Metadata

Online_Linkage: <http://www.fgdc.gov/standards/status/sub5_2.html>

Metadata_Access_Constraints: None

Metadata_Use_Constraints:

Acknowledgement of the National Wetlands Research Center as the metadata source would be appreciated. Please cite the original metadata when using portions to create another record for slightly altered data, such as reprojection.