Legend to Primer Tables

Owned by barbara
Last updated: May 29, 2009Version comment
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Table legend for 2000 marker map

Marker Number

This is the name of the marker, which is called "assay number" by Research Genetics.

LG

Linkage group or chromosome number, according to Knapik, et al.(1998), A microsatellite genetic linkage map for zebrafish (Danio rerio). Nature Genetics 18, 338-343 and Johnson SL, et al. (1996), Centromere-linkage analysis and consolidation of the zebrafish genetic map. Genetics 142(4):1277-1288. This nomenclature has now been standardized throughout the zebrafish community.

Forward Sequence +

primer sequence of forward primer

# of bases

number of bases in the primer

Reverse Sequence -

primer sequence of reverse primer

Allele sizes

AB1, AB2, IN1, IN2 - these are the allele sizes in base pairs for the reference cross AB and India progeny (Knapik et al. (1996), A reference cross panel for zebrafish (Danio rerio) anchored with simple sequence length polymorphisms. Development 123, 451-460) unless otherwise indicated. Allele sizes followed by an asterisk are the published expected allele sizes in strain AB, and the size followed by a pound (#) is the published expected allele size for the strain C32. Other crosses (either with other AB and India, or with other strains) may have different allele sizes.

Comments
  1. "use at your own risk" - these are markers that were described in Knapik, et al. (1998) Nature Genetics that have since proved to be unreliable in PCRs with some of our reference cross DNA samples. We include them because they have map positions and they may be useful in either different strains of fish or as STS-markers, but cannot vouch for their quality.
  2. Markers developed by other researchers, but mapped on our map by us, are cited in this column.
Additional info

PCR and gel separation conditions for these markers are as in Knapik, et al.(1998). We have found that markers with allele size differences of greater than 10-15 bp can often be scored on agarose gels (NuSieve or MetaPhor) without radioactivity, so we encourage that you try this with markers on your own cross (again, allele sizes may vary depending on the strains and/or individuals you use).

In addition to the markers in this table, all other non-polymorphic, unmapped primer pairs are available from Research Genetics as well, on a "use at your own risk" basis (i.e. we have not used them extensively for genotyping, so we cannot vouch for their quality).

Citation info

If you refer to any of the as of yet unpublished markers described here (those that were not released in either of our two previous publications), we ask that you please cite "N. Shimoda et al., A genetic linkage map of the zebrafish with 2000 SSLP (microsatellite) markers (manuscript in preparation)." [updated reference] Thanks for your support!