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Version: 2.0
Template Description: Verrsion 2.0 of the emplate for QTL DataVerrsion 2.0 of the emplate for QTL Data
Instructions
This template is for both summaried QTL data in whch only the signifant regions above a defined threshold are recorded and detailed QTL data in which data cna be provided for all positions with each chromosome analysised. Use the 'QTL' section for summarized data and the 'QTL Scores' section for the detailed data. You should provide one or both of these sections, even though both are marked as optional.
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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| QTL Study | General experiment details about the QTL Study | Mandatory
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| QTL | QTL data | Optional
Multiple sheets allowed
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| QTL Scores | QTL data | Optional
Multiple sheets allowed
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| Populations | | Mandatory
Multiple sheets allowed
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| Trial Sites | | Optional
Multiple sheets allowed
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| Trials | Information about the locaation, data and conditions of the trial | Mandatory
Multiple sheets allowed
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| Trait Measurements | Information on the traits measured in the study | Mandatory
Multiple sheets allowed
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| Markers | Markers used in the study | Optional
Multiple sheets allowed
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| Maps | | Optional
Multiple sheets allowed
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| Accessions | | Optional
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
QTL Study
Section Description: General experiment details about the QTL Study
| Field Name | Description | Conditions |
| Study Name | The name of the study
Example: Drought tolerence | Mandatory
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| QTL Analysis Method | Statistical method used for measure the QTL
Example: Composite interval mapping (CIM) | Mandatory
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| Statistics | Any additional statistics that the data contributors wishes to provide
Example: Population mean 0.97
.V. = 22.6
(0.05) = 0.61
error mean square = 0.1448 | Optional
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| Heritability | The genetic component of total trait variance in the specified environment. Reported as the
and environment
Example: 0.75 "Bozeman 2000" | Optional
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| Type I Error Rate Per Locus | Probability of calling the locus significant by chance
Example: 0.05 | Optional
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| R2 Definition | Exact definition of the "R-squared" used
Example: "R-squared is the proportin of the total phenotype or
variance explained by a multiple regression model
the significant QTL and their interactions." | Optional
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| Comments | Any additional information supporting the data that the authors want to add. Multiple comments can be separated with a semi-colon | Optional
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QTL
Section Description: QTL data
| Field Name | Description | Conditions |
| QTL Name | The proposed name for the QTL, usually specific for the species and/or lab. For example the proposed barley name consists of a "Q", a 2-4 letter acronym for the trait, a ".", a four letter string of the first two letters of the parents, a "-", and the chromosome.
Example: QHD.StMo-2H | Mandatory
Unique
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| Synonym | Alternate name for this QTL
Example: QHD.umn.2H.1 | Optional
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| Trait Measurement ID | Denotes the trait measured for this QTL. Trait Measurement ID <b>must</b> relate to Trait Measurement ID in the Trait Measurements sheet or file
Example: ABA
Example: ASI | Mandatory
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| Trial ID | A unique identier for the trial which is usually a combination of the location name, year of experiment and conditions. The Trial ID <b>must</b> relate to Trial ID in the Trials sheet or file.
Example: C1F3TL92AWW | Mandatory
Unique
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| Map ID | The Map on which the QTL data can be projected. The Map ID <b>must</b> relate to Map ID in the Maps sheet or file.
Example: Hordeum-Pillen-4H
Example: C1:Ch1 | Optional
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| Map Position | Point or span of the QTL position on the map
Example: 45-55 cM | Optional
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| Chromosome | Chromosome where the QTL was mapped. A S (short) or L (long) is appended if the position on the chromosome arm is known. If the map is defined this field need not be provided.
Example: 2H | Optional
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| Associated Gene | Gene assigned to the trait measured. Can either be a gene name or more appropreately a Gene Ontology Term ID. Multiple genes can be separate with a semi-colon
Example: Bmy1 (Hordeum) | Optional
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| Nearest Marker | The closest molecular marker mapped to the LOD peak within this QTL. If provided the marker <b>must</b> relate to a marker in marker sheet or file if this is present.
Example: ABC465 | Optional
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| Significant Marker | The molecular markers and/or genes mapped within this QTL. Multiple markers are separated with a semi-colon. If provided the marker <b>must</b> relate to a marker in marker sheet or file if this is present.
Example: ABC465 | Optional
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| Likelihood Ratio | The Likelihood Ratio for the QTL
Example: 12.32 | Optional
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| LOD Peak Height | Highest LOD value of the QTL
Example: 9.5 | Mandatory
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| LOD Threshold | Threshold value for the significant LOD interval
Example: 2.5 | Mandatory
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| Phenotypic R2 | Phenotypic variance explained by the QTL (expressed as a fraction)
Example: 0.42 | Optional
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| Genetic R2 | Genetic variance explained by the QTL (expressed as a fraction)
Example: 0.45 | Optional
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| Allele effect (effect of allele sub.) | Effect of allele substitution, if additive and dominance effects are unknown.
Example: -0.47 | Optional
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| Additive effect | Additive effect of allele substitution. (e.g. for Heading Date, value + units)
Example: 2 days | Optional
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| Dominance effect | Dominance effect of allele substitution, i.e deviation from the additive effect (e.g. Kernel weight
lys3)
Example: 25 mg | Optional
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| Epistasis | The interaction between two or more genes to control a single phenotype
Example: No epistasis was detected between markers assiciated with this QTL | Optional
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| Parent With Higher Scoring Allele | Parent with the higher value of whatever is being measured. This does not imply more favorable, (ex. Higher DON toxin levels). Must relate to the value for Parent A or Parent B
Example: Apex (barley) | Optional
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| Interactions | Text field to explain epistasis or interaction with the environment
Example: "The portion of the phenotypic variance explained by the
of the Marker x Environment = 0.4 %" | Optional
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| Significance x Environment | Genotype x environment
Example: 0.001 | Optional
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| Image | Link to any image a contributing author would like to include with the data
Example: http://www.graingenes.org/cgi-bin/ace/tree/graingenes?name=Sprout%20scoring%20scale&class=Image | Optional
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| References | Link to reference(s). Multiple references should be separated with a space
Example: http://wheat.pw.usda.gov/cgi-bin/graingenes/report.cgi?class=reference&name=GNM-38-1098 | Optional
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| Comments | Any additional information supporting the data that the authors / curators want to add. Multiple references should be separated with a semi-colon
Example: "Higher scores in the 'higher scoring allele' class indicate a
higher accumulation of DON, and therefore not desirable" | Optional
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QTL Scores
Section Description: QTL data
| Field Name | Description | Conditions |
| Trait Measurement ID | Denotes the trait measured for this QTL. Trait Measurement ID <b>must</b> relate to Trait Measurement ID in the Trait Measurements sheet or file
Example: ABA
Example: ASI | Mandatory
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| Trial ID | A unique identier for the trial which is usually a combination of the location name, year of experiment and conditions. The Trial ID <b>must</b> relate to Trial ID in the Trials sheet or file.
Example: C1F3TL92AWW | Mandatory
Unique
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| Chromosome | Chromosome where the QTL was mapped.
Example: 2H | Optional
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| Position | The position in cM
Example: 9.5 | Mandatory
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| LOD Score | LOD score at this position
Example: 9.5 | Mandatory
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Populations
Section Description: none
| Field Name | Description | Conditions |
| Population ID | An identifier of the population, usually consisting of a identifier for the cross and population type
Example: C1F3 | Mandatory
Unique
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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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| Parental Mean SD | Mean and standard deviation for each parent
Example: Clark's Cream 0.38 0.21 | Optional
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| Map Study Name | Denotes the map study for this cross. It must relate to the Map Study Name in the maps sheet or file if this is provided.
Example: Barley, AxHs/QTL | Optional
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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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| Number of Markers Tested | Number of molecular markers used
Example: 130 | Optional
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| Type of Markers Tested | Type of molecular markers used
Example: SSR | Optional
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Trial Sites
Section Description: none
see section: experimentalSites in GCPPhenotypingTemplate2.0
for the following fields
siteID, country, primaryAdminSubdivision, secondaryAdminSubdivision, locality, nameExperimentalSite, latitudeString, longitudeString, latitudeDecimal, longitudeDecimal, elevation, coordinateErrorDistance, institution, remark
Trials
Section Description: Information about the locaation, data and conditions of the trial
| Field Name | Description | Conditions |
| Trial ID | A unique identier for the trial which is usually a combination of the location name, year of experiment and conditions.
Example: C1F3TL92AWW | Mandatory
Unique
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| Population ID | Denotes the population in which this QTL was found. The Population ID <b>must</b> relate to Population ID in the Populations sheet or file. | Mandatory
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| Site ID | Unique site identifier where the trial was executed. <b>Must</b> must relate to Site ID in the Trial Sites sheet or fle, if provided, | Mandatory
Unique
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| Soil Texture | Soil type at the location of the experiment
Example: Brown clay loam soils of pH 7.5 | Optional
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| Conditions | General conditions of the trial. More details can be given under moisture and irrigation
Example: Well Watered
Example: Intermediate Stress
Example: Severe Stress | Optional
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| Moisture | Crop available moisture, the amount of water available to the crop during the growing season
Example: 200 mM | Optional
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| Irrigation | Type, number of days, total amount or just yes/no
Example: yes | Optional
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| Season | The season or cycle in which the trail was carried out. Required if there are more than one planting season at this location
Example: Winter | Optional
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| Planting Date | Month and year the experimental plants were put into the ground. Must be in ISO 8601 format. This format is written in the form YYYY-MM-DD, where YYYY is the year in the usual Gregorian calendar, MM is the month of the year between 01 (January) and 12 (December), and DD is the day of the month between 01 and 31. The hyphens can be omitted if compactness of the representation is more important than human readability, for example as in 19950204. If only the month or even only the year is known: 1995-02 or 1995.
Example: 200103-- | Optional
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| Harvest Date | Month and year the experimental plants were harvested. Must be in ISO 8601 format. This format is written in the form YYYY-MM-DD, where YYYY is the year in the usual Gregorian calendar, MM is the month of the year between 01 (January) and 12 (December), and DD is the day of the month between 01 and 31. The hyphens can be omitted if compactness of the representation is more important than human readability, for example as in 19950204. If only the month or even only the year is known: 1995-02 or 1995.
Example: 200106-- | Optional
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| Testing Date | Month and year the experimental plants were tested for the QTL. Must be in ISO 8601 format. This format is written in the form YYYY-MM-DD, where YYYY is the year in the usual Gregorian calendar, MM is the month of the year between 01 (January) and 12 (December), and DD is the day of the month between 01 and 31. The hyphens can be omitted if compactness of the representation is more important than human readability, for example as in 19950204. If only the month or even only the year is known: 1995-02 or 1995.
Example: 200108-- | Optional
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| Experimental Design | Test describing the design of the experiment
Example: Randomized complete block | Mandatory
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| Replications | Number of experimental replicates
Example: 3 | Mandatory
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| Remarks | Any additional information supporting the data that the authors / curators want to add. Multiple references should be separated with a semi-colon | Optional
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Trait Measurements
Section Description: Information on the traits measured in the study
| Field Name | Description | Conditions |
| Trait Measurement ID | Unique value within the dataset that denotes the trait measurement. Usually an abreviation of the trait name and the timing of the measurement
Example: ABA
Example: ASI | Mandatory
Unique
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| Trait Measurement Name | The name of the trait measured. It should describe a specific trait and when it was measured relative to specific point in the plant's development
Example: ABA response at germination
Example: Anthesis-silking interval | Mandatory
Unique
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| Trait Ontology ID | An identifier of the phenotypic trait affected by the QTL. The Trait ID <b>must</b> be a valid Trait Onology Term ID
Example: TO:0000615
Example: TO:0000463 | Mandatory
Unique
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| Measurement Timing | The point at which the measurement relative to specific point in the plant's development | Optional
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| Trait Measurement Description | A description of the trait, provides information about the trait measurement in addition
Example: ABA response at germination | Optional
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| Pathology | Optional Information about any disease to which the trait is related. For example the common name of the disease.
Example: Barley Yellow Dwarf | Optional
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| Protocol | Experimental protocol for the trait study.
Example: "DON levels were measured by gas chromatography" | Optional
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| Remarks | Any additional information supporting the data that the authors / curators want to add. Multiple references should be separated with a semi-colon | Optional
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Markers
Section Description: Markers used in the study
see section: markers in GCPMappingTemplate2.0
for the following fields
marker, forwardPrimer, reversePrimer, annealingTm, minAllele, maxAllele, genBankAccessionNumber, references
Maps
Section Description: none
see section: maps in GCPMappingTemplate2.0
for the following fields
studyName, mapID, mapName, chromosome, marker, position
| Field Name | Description | Conditions |
| Study Name | Descriptive name of the map study | Mandatory
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Accessions
Section Description: none
see section: generalPassportData in GCPPassportTemplate2.0
for the following fields
germplasmID, holdingInstitute, collectionName, localUniqueID, genus, species, countryOfOrigin, accessionName
| 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. | Optional
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| Accession name | Either a registered or other formal designation given to the accession. First letter uppercase. Multiple names separated with semicolon without space.
Example: CIMMYTWHEAT | Mandatory
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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, U.S. Department of Agriculture, University of Missouri
Developed by Guy Davenport (CIMMYT), Miguel Anducho (CIMMYT), Xunbi Xu (IITA-Nairobi), David Matthrews (Cornell), Victoria Carollo (U.S. Department of Agriculture), 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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