BASIC PROTOCOL 12: EXAMINING THE GENOMIC CONTENT OF A CLASSICAL GENETIC INTERVAL

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Within a defined physical or genetic interval, what gene markers and SNPs are available for mapping a newly identified mutation? WormBase provides a page specifically for this problem.

Necessary Resources

Hardware

   A standard computer with a reasonably fast connection to the Internet (cable modem, DSL, or Ethernet recommended)

Software

   Web browser such as Internet Explorer (http://www.microsoft.com) or Mozilla (http://www.mozilla.org/firefox)

1. Click the Markers link at the right center top of the WormBase front page (Fig. 1.8.1) to begin a search for genetic markers and their strains (http://wormbase.org/db/searches/strains).

2. Choose the appropriate markers within an interval of 2 cM or less of a chosen target. Full instructions are given on the page; there are options to exclude subtle, male-sterile, or lethal phenotypes, to select SNPs (Swan et al., 2002) or snip-SNPs (Wicks et al., 2001), or to only show publicly available strains as sources of markers.

3. Click the Search link and examine the results. In Figure 1.8.19, an example is shown of gene markers in the vicinity of hid-3, an uncloned gene identified by screening for mutants defective in the control of dauer larval development during severe heat (Ailion and Thomas, 2003). A table (Fig. 1.8.20) as well as a graphical map is given.

Note that instructions for ordering strains are available from the CGC Strains link in the Worm Reagent section of the front page's Links directory (Fig. 1.8.1); presently, this link leads to the e-mail address of Theresa Stiernagle (stier@biosci.cbs.umn.edu) at the University of Minnesota.