1. Welcome to the Quantitative Trait Loci (QTL) Tutorial This tutorial will describe how to navigate the section of Gramene that provides information on Quantitative Trait Loci (QTL). QTL are a statistical creation that identifies a particular region of the genome as containing a gene (or genes) that is associated with the trait being assayed or measured. Gramene v. 20
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4. 1 1 2 3 Browse Traits Trait Name Trait Symbol TO Accession # of QTL Species Name Trait Name Trait Synonyms Linkage Group Trait Category Trait symbol Published Symbol QTL Accession Map set name Map Position QTL Accession Species Published Symbol Trait Symbol Trait Name TO Accession Trait Synonyms Trait Category Linkage Group Map Position Genome Position Comments DBX References QTL Search Maps DB Literature DB Ontology DB Genomes DB
6. QTL Home Page Click here for a simple search by trait or term Click here to do a comprehensive search for multiple traits or terms Click here for help files Click here for this tutorial For answers to FAQ , click here
7. 1. Simple Search: by Trait Click a trait to browse QTL in that trait category 2. Limit search by term field. Default searches all fields. 1. Search by trait name, symbol or category, chromosome #, QTL symbol or accession ID. Wildcard searches include the * (i.e. seed*) 3. Limit search by species if desired. 4. Click submit.
8. Simple Search: Browse by Trait Ontology A. Click on Trait Name to view all the QTL detected for this trait There were 17 traits found under the category “Development.” Number of QTL that are detected for this trait and listed in the QTL database B. Click to view trait summary from the Ontology Database See Ontology Tutorial Click on the column titles to view a sorted display list.
9. Results for simple search Click to go to Map Set Info (see Maps tutorial) Click to view position location on map ( slide 12 ) Click to download tab delimited results data Note: Results from all search options display this table format Click to go to QTL Detail Page ( slide 10 ) There were 4 QTL for “Basic Vegetative Phase.” Click on the active link column titles to sort list by that column
10. QTL Detail Click to view literature for citations ( See Literature Tutorial ) Click to view position on Map ( see Map Tutorial ) (see slide 12) Click to view all places this QTL has been mapped to on the genome. Linkage group (chromosome) QTL has been mapped to; Click to view all QTL on this chromosome Gramene-assigned standardized trait symbol; Click to view all QTL with this symbol QTL symbol as assigned in the publication cited Gramene-assigned QTL accession ID Ontology category (slide 8) and accession (slide 11) QTL belongs to. See Ontology Tutorial Click to view QTL on genome browser. (see genomes tutorial ) Map set name
11. Trait Ontology (TO) Accession See Ontology Tutorial for more information on ontology Number of associations this term has to the database. In this case, they are all QTL “ Basic Vegetative phase” is an example of “vegetative growth time”, which is a growth and development trait.
12. Map Position QTL map shows QTL trait symbols as features. Click on any feature to view more information about that feature. See Maps tutorial for more information.
13. 3. Power Search To construct a comprehensive query, s elect criteria to exclude in your search To construct a comprehensive query, s elect criteria to include in your search To select multiple trait names or species, hold "Control" (or "Command" on Mac) key while selecting multiple traits. Click to submit Note: Results from all search options display the same table format. See Slide 9 for results navigation.
14. QTL Help Tutorial link offers three tutorial formats – PowerPoint, PDF or HTML. QTL help file show database summary, description of terms, and search help. Click for Frequently Asked Questions (next slide.)
15. FAQ Select module for FAQ Search FAQ by keyword Submit a question to Gramene
16. Contact Gramene Use the feedback button, located at the top of every page, to provide feedback or to ask questions about Gramene. Email Gramene at gramene@gramene.org or
Editor's Notes
Search either by entering a term or browsing by trait category.
Option 2: Search You 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 you may choose to restrict the search to any one of the following: Trait name , Trait symbol, Trait category, Linkage group (chromosome), Published QTL symbol, QTL accession ID . Additionally, you may restrict the search to a single species by selecting it from the "Species" menu.
Option 1: Browse by Traits The user can browse the QTL by trait categories and the trait names. 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." Clicking on the hyperlinked trait name will perform a database search for all the QTL associated with that trait. 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.
Ontology is 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.
Goes to CMap database
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*".
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