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Version: 2.0
Template Description: Version 2.0 of the GCP Mapping template updated with recommendations from Data Quality Workshop. Template for Genetic Mapping DataVersion 2.0 of the GCP Mapping template updated with recommendations from Data Quality Workshop. Template for Genetic Mapping Data
Mappings for this template
Sections available in this template
| Section Name | Description | Conditions |
| Source | Information on the source of the dataset, the species it concerns and the name and version of the dataset | Mandatory
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| Quality Assessment | Information about the quality measures used | Mandatory
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| Map Study | General experiment details about the Map Study | Mandatory
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| Maps | Information about the maps provided by this study | Mandatory
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| Markers | Information about markers used in the experiment | Optional
Multiple sheets allowed
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| Map Data | Mapping data. | Optional
Multiple sheets allowed
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| Accessions | Information about accessions used in the experiment | Mandatory
Multiple sheets allowed
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| Institutions | List of institute codes used in passport data sections and their corresponding decoded name and addresses. | Optional
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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
Quality Assessment
Section Description: Information about the quality measures used
see section: qualityAssessment in GCPDataSubmissionTemplate2.0
for the following fields
qualityMeasure, standard, control, errorEstimator
Map Study
Section Description: General experiment details about the Map Study
| Field Name | Description | Conditions |
| Study Name | Descriptive name of the study | Mandatory
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| Parent A | Germplasm name for a parent in the population. Male and Female can be noted. This can either be a name or Germplasm ID to values in the If the accession data is provide it must relate to SampleID in the accession sheet or file if this is provided.
Example: P43C9-1-1-1-1-1-BBBBB
Example: Apex (barley) | Mandatory
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| Parent B | Germplasm name for another parent in the population. Male and Female can be noted. This can either be a name or Germplasm ID to values in the If the accession data is provide it must relate to SampleID in the accession sheet or file if this is provided.
Example: SC-Malawi | Mandatory
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| Population Size | Number of individuals in the mapping population.
Example: 130 | Mandatory
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| Population Type | Type of population used for mapping.
Example: BC2F2 | Mandatory
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| Purpose of the Study | Description of the reason for the study. | Mandatory
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| Mapping Software | The name and version of the genotyping software used. | Mandatory
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| Mapping Function | The name of the mapping function used to convert recombinant frequency to genetic distance.
Example: Kosambi | Mandatory
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| Scoring Scheme | The name of the scoring scheme used
Example: ABH-
Example: 123 | Mandatory
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| Remark | none | Optional
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Maps
Section Description: Information about the maps provided by this study
| Field Name | Description | Conditions |
| Map ID | An identifier of the map. Can be a combination of the cross name and chromosome map.
Example: C1:Ch1 | Mandatory
Unique
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| Map Name | The name of the map, which like the Map ID, can be a combination of the cross name and chromosome map, except it should be in a easily understandable form. | Optional
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| Chromosome | The name of the chromosome to which this map relates
Example: C1Ch1 | Optional
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| Marker | The name of the marker used. If the marker data is provide it must relate to Marker name in the marker sheet or file. | Mandatory
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| Position | The position in cM of the marker of the map | Optional
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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.
| Field Name | Description | Conditions |
| Marker | A unique name of the marker used | Mandatory
Unique
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| Motif | The motif, if the marker is an SSR. Please provide the di- nucleotide, tri-nucleotide or complex motif noting the repeating unit and number of copies in the motif. For example (CT)15, (GTC)7 or
(AT)4A(AT)7. Providing the motif of the SSR will allow researchers to determine expected allele sizes more actually and to provide some level of quality control. Furthermore, different types of SSR may not evolve at the same rate and the motif is required to separate them in the analyses. | Optional
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| Forward Primer | The sequence of forward primer used in the PCR to detect the allele | Optional
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| Reverse Primer | The sequence of reverse primer used in the PCR to detect the allele | Optional
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| Annealing Tm | The annealing temperature of the PCR used to detect the allele | Optional
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| Min Allele | The size in bp of smallest allele product expected in the PCR | Optional
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| Max Allele | The size in bp of largest allele product expected in the PCR | Optional
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| GenBank Accession Number | A NCBI GenBank accession number for the marker reference sequence | Optional
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| References | A semi-colon separated list references to the marker published in an article or database. | Optional
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Map Data
Section Description: Mapping data.
| Field Name | Description | Conditions |
| Marker | The name of the marker used, which must relate to the Marker name in the data sheet or file. | Mandatory
Unique
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| Score | The scoring data for this marker against each individual in the population. | Optional
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Accessions
Section Description: Information about accessions used in the experiment
see section: generalPassportData in GCPPassportTemplate2.0
for the following fields
germplasmID, localUniqueID, holdingInstitute, collectionName, genus, species, countryOfOrigin
| Field Name | Description | Conditions |
| Country of Origin | Code of the country in which the sample was originally collected. Use 3-letter ISO 3166-1 extended country codes. ORGCTY in the Bioversity Multicrop Passport Descriptors. | Optional
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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
Copyright (c) 2004-2006 CIMMYT, CIMMYT, Cornell, IITA-Nairobi, IRRI, IRRI, University of Missouri
Developed by Guy Davenport (CIMMYT), Miguel Anducho (CIMMYT), Xunbi Xu (IITA-Nairobi), David Matthrews (Cornell), Victoria Carollo (IRRI), Mary Schaeffer (University of Missouri), Genevieve Aquino (IRRI)
This work is licensed under a Creative Commons Attribution-ShareAlike 2.5 License.
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