Microsatellite marker panels for use in high-throughput genotyping of mouse crosses

Abstract

Iakoubova, Olga A., Christine L. Olsson, Katherine M. Dains, Jim Choi, Ivetta Kalcheva, L. Gordon Bentley, Madalyne Cunanan, David Hillman, Judi Louie, Migdad Machrus, and David B. West. Microsatellite marker panels for use in high-throughput genotyping of mouse crosses. Physiol Genomics 3: 145–148, 2000.—Several microsatellite genotyping panel sets have been developed that are polymorphic between C57BL/6J and CAST/Ei mice, or C57BL/6J and DBA/2J. One set of markers for each strain pair has an intermarker distance of ∼20 cM, and a second set has an intermarker distance of 5 cM. The 20-cM set contains 105 markers for C57BL/6J × DBA/2J and 108 for C57BL/6J × CAST/Ei, divided into 13 panels. Each 5-cM set includes 350 markers arranged into 45 panels. A panel contains a number of primer pairs whose fluorescently labeled PCR products can be pooled together and separated on one lane of a polyacrylamide gel. The sets are arranged by the size of the PCR product and by the type of fluorescent dye; 5-cM sets are also arranged by chromosomal region. The 20-cM sets are most useful for full-genome scans, the 5-cM sets are useful for full-genome and/or for region-specific chromosome screens. Both sets were proven as useful tools for speed congenic development, quantitative trait loci (QTL) analysis and physical mapping. These panel sets provide a throughput of 1,536–2,304 mouse genotypes daily per one gel-based system. Whole genome scans of one animal require 13 or 48 gel lanes, with 20 cM or 5 cM density, respectively.