Characterization of a minimal microsatellite set for whole genome scans informative in warmblood and coldblood horse breeds.

The research study aimed to develop a highly polymorphic minimal screening set of microsatellite markers that is equally informative in both warmblood and coldblood horse breeds, by using the high-quality draft sequence of the horse genome.

Overview of The Study

• The research project was started to produce a high-quality, minimal screening set of microsatellite markers for horses, known as the MSSH.
• This set was developed using the EquCab2.0 horse genome assembly, along with existing linkage and radiation hybrid maps.
• The researchers worked to fill in gaps from the horse sequence, expanding upon the available marker sets.

MSSH Composition and Distribution

• This study resulted in the MSSH covering all autosomes and the X chromosome with 322 evenly distributed microsatellites.
• The average distance between these markers is approximately 7.44 Megabases (Mb), allowing for a near 7- to 10-Mb resolution when scanning the whole horse genome.
• The developed markers set was highly polymorphic with the number of alleles averaging 7.3 and 8.0 in Hanoveria Warmbloodn (HW) and German Coldblood (CB) horse breeds, respectively.

Microsatellite Set Characteristics

• Characteristics of these microsatellite markers were determined by assessing their number of alleles, the observed heterozygosity (HET), and the polymorphism information content (PIC).
• The observed heterozygosity, which measures the genetic variation within the population, was about 71% in both HW and CB horse breeds.
• Similarly, the PIC which is frequently used in linkage analysis and a measure of a marker’s informativeness, was at 65% for HW and 67% for CB horse breeds.

Implication for Genomic Studies

• The availability of such a polymorphic minimal screening set of microsatellite markers plays an important role in genomic studies. It allows for comprehensive scanning of the whole genome enabling identification of genetic variations associated with different traits in horse breeds.
• It’s an important tool in the research and application of equine genetics, particularly in exploring genetic diversity, linkage mapping, and population genetics.