A genome-wide scan for diversifying selection signatures in selected horse breeds.
Authors: Gurgul Artur, Jasielczuk Igor, Semik-Gurgul Ewelina, Pawlina-Tyszko Klaudia, Stefaniuk-Szmukier Monika, Szmatoła Tomasz, Polak Grażyna, Tomczyk-Wrona Iwona, Bugno-Poniewierska Monika
Journal: PloS one
Summary
# Editorial Summary Selective breeding has fundamentally shaped the genomes of different horse breeds, but identifying the specific genetic regions responsible for breed-defining traits requires systematic analysis across large DNA datasets. Researchers used FST analysis—a population genetics method that measures allele frequency differences between groups—to scan the genomes of six Polish horse breeds (representing light horses, draft types, and primitive ponies) and identify regions under diversifying selection. The study revealed multiple genomic signatures associated with functionally important processes including body size regulation, energy metabolism during exercise, cardiac function, reproductive traits, and disease resistance; notably, they confirmed previously identified associations between LCORL/NCAPG genes on equine chromosome 3 and larger frame size in draft horses, whilst smaller primitive breeds showed selection signals in the opposite direction at the same loci, and pinpointed the TBX3 gene as responsible for blue dun coat colour in Polish Koniks. For equine professionals involved in breeding decisions, performance assessment, or explaining phenotypic variation to clients, these findings provide molecular-level evidence that breed characteristics aren't arbitrary—they reflect genuine genomic divergence shaped by historical selection pressures—though the authors appropriately note that functional validation studies are needed before linking specific genes to specific traits in practice. The FST-based approach demonstrated here offers a replicable framework for identifying selection signatures in other horse populations and breeds, potentially guiding breeding strategies or helping predict metabolic, reproductive, and performance traits from genetic profiles.
Read the full abstract on PubMed
Practical Takeaways
- •Understanding breed-specific genetic selection signatures can inform breeding decisions and help predict phenotypic traits and performance capabilities across different horse types
- •The genomic regions identified provide markers for coat color, body size, and health-related traits that breeders may use to maintain breed standards and genetic diversity
- •Further functional studies are needed to translate these genetic findings into practical breeding and selection protocols for equine practitioners
Key Findings
- •FST-based genome-wide analysis identified selection signatures in six Polish horse breeds classified as light, draft, and primitive types
- •Confirmed association of ECA3 loci (LCORL and NCAPG genes) with body size regulation in draft and primitive horses
- •Identified robust selection signal at TBX3 gene locus responsible for dun coat color dilution in Polish Konik horses
- •Candidate genes under selection were associated with energy homeostasis, cardiac function, fertility, disease resistance, and motor coordination