Rat gene mapping using PCR-analyzed microsatellites.

TLDR

The study focuses on mapping rat genes by exploiting PCR‑analyzed microsatellites, which are frequently linked to coding sequences in public databases. The authors extracted 174 rat loci containing short tandem repeats, designed PCR primers to generate sequence‑tagged microsatellite sites, and mapped them to chromosomes using hybrid clones and segregation data from backcrosses and F2 crosses. They identified 134 polymorphic STMSs across 118 loci, observed length variation at 85 of 107 loci in eight inbred strains, constructed a 24‑linkage‑group map that aligns with a gene map, and provided corresponding mouse and human homolog locations.

Abstract

Abstract One hundred and seventy-four rat loci which contain short tandem repeat sequences were extracted from the GenBank or EMBL data bases and used to define primers for amplification by the polymerase chain reaction (PCR) of the microsatellite regions, creating PCR-formatted sequence-tagged microsatellite sites (STMSs). One hundred and thirty-four STMSs for 118 loci, including 6 randomly cloned STMSs, were characterized: (i) PCR-analyzed loci were assigned to specific chromosomes using a panel of rat x mouse somatic cell hybrid clones. (ii) Length variation of the STMSs among 8 inbred rat strains could be visualized at 85 of 107 loci examined (79.4%). (iii) A genetic map, integrating biochemical, coat color, mutant and restriction fragment length polymorphism loci, was constructed based on the segregation of 125 polymorphic markers in seven rat backcrosses and in two F2 crosses. Twenty four linkage groups were identified, all of which were assigned to a defined chromosome. As a reflection of the bias for coding sequences in the public data bases, the STMSs described herein are often associated with genes. Hence, the genetic map we report coincides with a gene map. The corresponding map locations of the homologous mouse and human genes are also listed for comparative mapping purposes.