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SSR Data In MaizeGDB

SSR Research Tools | SSR Browser | Discussion of SSR Data for the General Public


SSR Research Tools

Simple SSR Search: A popup window providing assistance with SSR searches This search form allows you to just enter basic name or repeat info to quickly retrieve the desired SSR. Use % as a wild card. If you are having difficulties, click on the green question-mark box. A sample search is provided to help you.

(see a sample SSR query)

This search can be executed on every page on the site by utilizing the form in the upper right corner. Choose "SSR" from the drop-down menu, enter your search term in the field, and hit return to find the SSR you're looking for.

Mapped SSRs: This utility displays the map locations of the SSRs in MaizeGDB. You can obtain this information by chromosome (1-10, below).
1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10

Mapped SSRs: (Detail) This utility displays the map locations of the SSRs in MaizeGDB. This table is sorted by Map and Map Coordinate. New! Includes Amplicon Length and Sequence Preview columns. You can obtain this information by chromosome (1-10, below).
1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10

Mapped & Anchored SSRs: This utility lists SSRs that are both genetically mapped (on IBM2) and also detect a BAC. New! Includes Amplicon Length and Sequence Preview columns. You can obtain this information by chromosome (1-10, below).
1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10

Complete List of SSR Repeats: Provides a complete list of SSR repeats available in MaizeGDB, linked to their respective full SSR records.
SSRs Derived From Genes: An up-to-date listing of SSRs and the genes from which they are derived, formatted in an easily-downloadable table.

You might also be interested in visually browsing our gel patterns.


SSR Browser

This tool allows you to specify detailed search criteria, much like the other advanced searches, but the output looks slightly different; it is intended to allow you to dig more directly into the data rather than just visiting individual records.

Set Up Criteria

Check the boxes next to the fields you want to search; if you just want to find records that have any value for that attribute, check the box and leave the criteria alone. You can use % or * as a wildcard in the text fields.

only SSRs with this string in (for example, you can filter for just the UMC SSRs)
only SSRs that are found in this bin ..
only SSRs that repeat (for example, you might want a repeat of ACT)
only SSRs that contain (for example, you might want only SSRs with primers containing GACTCT)

Sample Queries

Here are some example queries that you might want to try.

Show me UMC SSRs that repeat the unit AGG
Show me SSRs in bin 3.04 that repeat the unit ACT
Show me the Brookhaven National Lab SSRs in bin 1.01
Show me the UMC SSRs in bin 9.03

You may also be interested in SSR protocols from the Maize Mapping Project.


Discussion of SSR Data for the General Public

What is a SSR?

A SSR (or simple sequence repeat) is a repetition of a particular tiny genetic element found randomly in genetic data. For example, CACACACACA is a SSR, as it is a repetition of CA 5 times; this is often noted as (CA)5.

What value does storing and studying SSR data have?

SSRs are a very simple way of locating particular places on the chromosomes of an individual given their distinctive and easy to find form. Thus, SSRs are often used for the creation of maps, which show the relative location of particular specific element (or loci) in a given region of the genome.

What is the connection between corn and SSR data?

We can use SSR data to determine locations of more important elements, such as genes, using maps.

SSRs are quite polymorphic in maize (and other organisms). This is because the simple sequence is repeated a different number of times in different varieties of maize. This length difference can be used as an easily detected codominant marker.


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Last updated 1:45 pm, Dec 03, 2014.

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