Zebrafish Map 2K

Information

This is the latest version of the map, totalling 2000 markers and presented by Nobuyoshi Shimoda at the 1998 Cold Spring Harbor Zebrafish meeting, is available as follows:

• Primer sequences and linkage groups are available in tabular format with a table legend.
• The genomic sequences (from which primers were designed) for most of the markers have been deposited in the dbSTS database at NCBI. We are preparing the remaining sequences for submission and adding them as they are ready. Individual accession numbers for each marker have been added to the 'Primer Sequences and Linkage Groups' tables for each linkage group
• Map locations for all markers are available in graphic form.
• PCR conditions including cycle profiles and reagent concentrations are available here.
• We recommended a specific set of markers for "first-pass mapping". These markers can be resolved on metaphor-agarose gels.

61 markers from the previous map (Knapik et al., 1998) were excluded from this version of the map; a list is available


Good luck mapping!

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Primer Sequences and Linkage Groups

A complete table for all of the primer sequences is rather cumbersome for viewing as a single document in a web browser. For that reason, you may either view them in tabular format for each of the linkage groups, or you may download a file containing all of the data (an Excel spreadsheet [483K], you might want to get a copy of the legend too).

Legend

Linkage Group Figures

The figures for linkage groups 1, 2, 8, 9, 10, 11, 12, 15, 16, 17, 18, 19 and 21have been 'flipped' to match the orientation used by Postlethwait et al. (Nature Gentics 18 p. 345, 1998).  Linkage group 4 has more serious differences between our data and Postlethwait's, but the discrepancy has not been resolved so the figure has not been altered.

PCR Conditions for SSR Markers

PROFILE:

Presoak: 94 degrees C for 5.0 minutes
Denaturation: 94 degrees C for 1.0 minute
Annealing: 58 degrees C for 1.0 minute
Polymerization: 72 degrees C for 1.5 minute
PCR Cycles: 27
Thermal Cycler: MJ Research PTC-100

BUFFER:

MgCL2: 1.5 mM
KCl: 50 mM
Tris-HCl: 10 mM, pH: 8.3

REAGENTS:

Template: 10 ng
Primer: 375 nM each
dNTPs: 200 uM each
Taq Polymerase: 0.034 units/ul
Total Vol: 10 ul