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

Abstract

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.

The domestic horse harbours Y‐chromosomal microsatellite polymorphism only on two widely distributed male lineages

“…In contrast, the average number of alleles is about seven to eight per microsatellite when screening randomly chosen autosomal microsatellites in modern horses. 7 We note that all three Y-chromosomal microsatellite mutations occurred on the backbone of the two major lines HT1 and HT2. This suggests that the derived haplotypes found in Northern horses (HT4, HT5, HT6) 3 originated relatively recently compared to the common haplotypes HT1 and HT2.…”

“…Our data reinforce previous findings of a severe reduction of the genetic variability on the horse Y chromosome and provide further evidence for a very recent origin of modern horse paternal lineages. In contrast, the average number of alleles is about seven to eight per microsatellite when screening randomly chosen autosomal microsatellites in modern horses . We note that all three Y‐chromosomal microsatellite mutations occurred on the backbone of the two major lines HT1 and HT2.…”

Assessment of 17 microsatellite loci for their use in parentage verification and individual identification in the Balkan donkey breed

“…Short tandem repeats (STR) or microsatellites are genetic markers commonly used for genetic variability studies and paternity testing in different animal species and breeds (ARANGURES-MENDEZ et al, 2001;JORDANA et al, 2001;VAN DE GOOR et al, 2010;DIMITRIJEVIC et al, 2013;DA SILVA et al, 2014). They are used both as in-house assembled and optimized microsatellite panels (REIS et al, 2008;MITTMANN et al, 2010) or as kits originally developed for paternity testing and forensic applications (FORNAL et al, 2013). Genotyping of donkeys is most commonly based upon using equine STR loci (BLASI et al, 2005;CIAMPOLINI et al, 2007;BORDONARO et al, 2012;ZHU et al, 2013;MATASSINO et al, 2014).…”

Stallion semen quality depends on major histocompatibility complex matching to teaser mare

“…Overall genetic similarity between stallions and mares was estimated from 20 polymorphic microsatellite loci located on 20 different chromosomes (Table ) (Mittmann, Lampe, Mömke, Zeitz, & Distl, ). Genomic DNA was extracted from blood with the BioSprint robotic workstation (Qiagen) using conditions specified by the DNeasy blood and tissue kit (Qiagen).…”