Characterization of a Minimal Microsatellite Set for Whole Genome Scans Informative in Warmblood and Coldblood Horse Breeds

The availability of a high-quality draft sequence of the horse makes known the physical location of microsatellites. The aim of the present study was to establish a highly polymorphic minimal screening set of microsatellite markers for horses (MSSH) annotated on the horse genome assembly EquCab2.0. We have used the previously reported linkage and radiation hybrid maps and have extended these marker sets by filling in gaps as noted from annotation on the horse sequence. This MSSH covers all autosomes and the X chromosome with 322 evenly spaced microsatellites whose positions were determined on the horse genome assembly (EquCab2.0). The average chromosomal distance among markers amounts to 7.44 Mb. The characteristics established for this microsatellite set were the number of alleles, the observed heterozygosity (HET), and the polymorphism information content (PIC) for Hanoverian warmblood (HW) and several German coldblood horse breeds (CB). The average number of alleles was 7.3 and 8.0 in HW and CB, respectively. HET was at 71% for HW and CB, PIC at 65% (HW) and 67% (CB). This MSSH allows scanning of the whole horse genome at close to 7- to 10-Mb resolution.