Version: 2.0

Template Description: The DArT Genotyping Template. DArT (Diversity Array technology) is a generic and cost-effective genotyping technology. It was invented by Dr Andrzej Kilian , to overcome some of the limitations of other molecular marker technologies such as RFLP, AFLP and SSRThe DArT Genotyping Template. DArT (Diversity Array technology) is a generic and cost-effective genotyping technology. It was invented by Dr Andrzej Kilian , to overcome some of the limitations of other molecular marker technologies such as RFLP, AFLP and SSR

Mappings for this template

Sections available in this template

Source

Section Description: Information on the source of the dataset, the species it concerns and the name and version of the dataset

see section: source in GCPDataSubmissionTemplate2.0

for the following fields institute, principalInvestigator, projectCode, projectName, emailContact, species, ploidy, datasetName, version, creationDate, remark

Experiment

Section Description: General experiment data

see section: experiment in GCPGenotypingTemplate2.0

for the following fields operationalTaxonomicUnit, purposeOfStudy, missingData, remark

Quality Assessment

Section Description: Information about the quality measures used

see section: qualityAssessment in GCPDataSubmissionTemplate2.0

for the following fields qualityMeasure, standard, control, errorEstimator

Conditions

Section Description: Experimental conditions

see section: conditions in GCPGenotypingTemplate2.0

for the following fields samplingStrategy, controlGenotypes, sizeStandard, dnaExtraction, dnaAmplificationDetection, diversityArrayLibrary, genotypingSoftware, imageAnalysisSoftware, reference

Data Matrix (Markers)

Section Description: Matrix of data with markers as the first column

Data Matrix (Samples)

Section Description: Matrix of data with sample IDs as the first column

Markers

Section Description: Information about markers used in the experiment

Markers (optional)

The spreadsheet consists of ten columns, which each row representing a SSR marker.

see section: markers in GCPMappingTemplate2.0

for the following fields marker, sNPDetected, restrictionEnzymes, adapterSequence, forwardPrimer, reversePrimer, annealingTm, dye, genBankAccessionNumber, references

Maps

Section Description: none

see section: maps in GCPMappingTemplate2.0

for the following fields mapID, mapName, chromosome, marker, position

Samples

Section Description: Information about accessions used in the experiment

Sample (optional)

The first field in the sample is the SampleID, which relates directly to the SampleID field in the data spreadsheet or file. This SampleID is a unique identifier of a DNA sample, which can be a sample in a well on a gel or a LIMS entry. It could even by a unique identifier developed specifically for this dataset. In the case of multiple extractions from the same material then each same would have a unique SampleID. Please refer to the section on Multiple Data Points for more details.

The GermplasmID field is an optional field for collections where a new GermplasmID is assigned each time an accession is regenerated or for some other reason a new seed or germplasm sample is taken. For this reason an accession in this case is a collection of samples with different GermplasmIDs. GermplasmID are often unique within a specific database for this reason they should be prefixed by the data name or abbreviation. For example, an entry with GermplasmID 2341 in IWIS, would be IWIS:2341.

The remaining accession data should be either in multi-crop passport descriptors (MCPD) or EURISCO descriptors format. These descriptors are MCPD defines a total of 28 descriptors for passport data, each of which equates to a column in the template. EURISCO defines an additional 6 descriptors for a total of 33 descriptors. Only a few MCPD or EURISCO descriptors are mandatory and for the sake of brevity only the mandatory and some recommended optional fields are described here. However, the mandatory descriptor provides sufficient information to allow the accession to be found in the appropriate National Inventory or genebank. For a full description of all MCPD and EURISCO descriptors please refer to the EURISCO_Descriptors.doc file, which is available fro the EPGRIS website (http://www.ecpgr.cgiar.org/epgris/) and or can be downloaded with the passport template.

see section: generalPassportData in GCPPassportTemplate2.0

for the following fields germplasmID, sampleID, localUniqueID, holdingInstitute, collectionName, genus, species, countryOfOrigin

Institutions

Section Description: List of institute codes used in passport data sections and their corresponding decoded name and addresses.

see section: institutions in GCPDataSubmissionTemplate2.0

for the following fields faoInstituteCode, organizationName, street, cityState, zipCode, country, institutionalEmail, institutionalTelephone, fax, url, primaryContactName