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Gramene QTL Database

Help Document:

The database provides the following types of information on a QTL:

• QTL: A quantitative trait locus.
• QTL accession ID: The Gramene QTL accession ID is unique for each QTL.
• Species: The species in which the QTL was detected.
• Trait symbol: A standardized abbreviation for the trait assigned by Gramene curators. The symbol is displayed as a QTL feature name in maps.
• Trait name: The name of the trait for which the QTL was detected.
• Published QTL symbol: QTL symbol assigned by the author in the source paper.
• Trait synonym(s): Other names for the trait.
• Trait category: Each trait belongs to a parent trait category. These are assigned by agronomic importance.
  • Abiotic stress: Traits related to stresses from abiotic environment, e.g., water, light, temperature, or chemical.
  • Anatomy: Traits directly measuring plant parts such as root, stem or leaf.
  • Biochemical: Biochemical and physiological traits, e.g., enzyme activity.
  • Biotic stress: Traits related to stresses from pests and pathogens.
  • Development: Traits related to plant and plant part development. Also includes maturity related traits.
  • Quality: Traits of economic importance that may affect product quality.
  • Sterility or fertility: Traits related to male and female flower sterility or fertility, including incompatibility.
  • Vigor: Traits related to growth and dormancy.
  • Yield: Traits contributing directly to yield based on economic value.
• Chromosome: The linkage group or the chromosome number on which the QTL was mapped.
• Mappings: Links to the Gramene Markers, Maps and Genomes databases and displays the QTL feature and position there. For rice QTL with genome positions, in addition to the original "experimental" QTL positions, we currently also provide the inferred positions on the Gramene Annotated Nipponbare Sequence map.
• Associations to the molecular markers: QTL associated markers are critically important to fine mapping, map-based positional cloning, and marker-assisted selection (MAS). Currently, two types of markers have been provided to a particular QTL:
  • QTL colocalized markers: Molecular markers are colocalized or overlapped with a QTL region on the original QTL map.
  • QTL neighboring markers: Molecular markers are not colocalized, but adjacent to a QTL region on the original QTL map.
• Ontology association: One or multiple composite associated terms are used to define the associated feature for the particular QTL. The composite associated term consists of:
  • Trait Ontology(TO (Trait ontology))
  • Plant Structure(PO (Plant structure ontology))
  • Growth Growth and Development Stage (PO (Growth stage ontology))
  • Species Ontology (Taxonomy ontology)
• Comments: Any comments by the Gramene curators.
• DBXRefs: Links to the Gramene citation record where the information on the QTL was published.

QTL search/browse options:

A. Simple Search

Using the "Simple Search", the user can browse through the QTL database by trait categories and traits or search for a term in one or all the fields.

Option 1: Browse by Traits

The user can browse the QTL by trait categories and the trait names.

1. Click on the name of a trait category from the list under section "Search by Trait Category." This opens a list of traits belonging to this category and tells you how many traits are in this category.
• This list displays a maximum of 25 trait names per page. In order to view the next 25 trait names, please click on "Next" or type the page number you want to view and hit the button "Page."
• The number associated with each trait tells you the number of QTL that are detected for this trait and are listed in the QTL database.
• You can sort the trait names in alphabetical order or by number of associated QTL by clicking on the column headers "Trait name" or "Number of QTL."
2. Clicking on the hyperlinked trait name will perform a database search for all the QTL associated with that trait.
3. Clicking on the hyperlinked TO accession number brings you to the appropriate entry in the Trait Ontology database where you can find the trait definition as well as its synonyms. For more information on the Trait Ontology and its use, please visit the Ontology Tutorial and Help pages.

Option 2: Search

The user can search the QTL database for a term, using the symbol "*" for wild card searches (e.g., "seed*"). The default behavior is to search all fields in the database for the supplied term, though the user may choose to restrict the search to any one of the following:

• Trait name
• Trait symbol
• Trait synonyms
• Trait category
• Linkage group
• Chromosome
• Published QTL symbol
• TO accession
• QTL accession ID

Additionally, the user may restrict the search to a single species by selecting it from the "Species" menu.

B. Power Search

Using the "Power Search," the user can construct a comprehensive query of the database.

• The user can select one or multiple trait terms in the "Include" field of "Trait Names". The user should hold "Control" (or "Command" on Mac) key while selecting multiple traits.
• The user can select one or multiple species in the "Include" field of "Species."
• The user can type one or multiple linkage group names in the "Include" field of "Linkage Groups." Separate multiple terms with spaces or commas. Indicate wildcards with the "*" character.
• The user can also use the "Exclude" feature to modify his query.

For example, if the user wants to get all QTL associated with traits, "Seed dormancy" and "Seed Longevity", on chromosome 1 from the "Rice" and "Wild Rice" species, he could do it as follows:

• Select "Seed dormancy" and "Seed Longevity" in the "Include" field of "Trait Names".
• Select "Rice" and "Wild Rice" in the "Include" field of "Species".
• Type "1*" in the "Include" field of "Linkage Groups". With the wild card "*", the user could include the linkage groups with the names of "1a", "1b", etc.
• Type "10*", "11*" and "12*" in the "Exclude" field of "Linkage Groups". In this way, the user can exclude them while using "1*".

QTL Search Results

The search from Options 1 and 2 above returns a table with search results. This page displays a maximum of 25 QTL entries per page. To view next 25 QTL entries, click on "Next" or type the page number you want to view and hit the button "Page". In order to set the priority for displays, you can sort the search results by clicking on any one of the column headings. The search results tells you about the following information:

• QTL accession ID
• Species name
• Trait symbol
• Trait name
• Published symbol
• Linkage group
• Trait synonyms
• Trait category
• Linkage group
• Map (Original QTL map)
• Map position on the original QTL map

Click on a hyperlinked QTL accession ID to view a more detailed information page for the selected QTL.

QTL Detail Page Display:

The QTL detail page displays more information on the selected QTL. These are:

• QTL accession ID
• Species
• Trait symbol
• Trait name
• Published symbol
• Trait synonym(s)
• Trait category
• Chromosome
• Mappings
• Related ontologies
• Comments
• DBXRefs

User Feedback

• We are in the process of developing a new user interface. Please suggest additional fields you'd like to search for by either using the "Feedback" link at the top of the Gramene pages or by going to the following URL: /db/feedback/send_feedback?refer_to_url=/db/qtl/qtl_display
• If you find any inconsistencies or mistakes, please communicate them to us by clicking on the "feedback" link. Your suggestions and feedback are highly appreciated by the Gramene staff.