Integrative Advances in Equine Genomics From Reference Assemblies to Evolutionary History and Key Traits

Area of Science:

• Equine genomics
• Animal genetics
• Domestication studies

Background:

• Horses are significant domestic animals with deep historical ties to human civilization.
• Equine genomics offers insights into domestication, evolution, and trait development.
• Previous genome assemblies had limitations in representing complex genomic regions.

Purpose of the Study:

• To review recent advances in equine genomics.
• To synthesize findings on horse domestication, genetic diversity, and trait genetics.
• To highlight the application of genomic data in horse breeding and health.

Main Methods:

• Refinement of reference genome assemblies using long-read and Hi-C/T2T data.
• High-coverage resequencing of ancient and modern horses.
• Comparative analyses of mitochondrial DNA, Y-chromosomal haplotypes, and autosomal runs of homozygosity.
• Association studies and functional experiments for trait-related genes.

Main Results:

• Clarified the domestication core in the Volga-Don region and Bronze Age lineage shifts.
• Revealed diverse maternal and constrained paternal lineages, with breed-specific inbreeding.
• Identified genetic underpinnings for traits like athletic performance (e.g., MSTN), altitude adaptation (e.g., EPAS1), and inherited myopathies (e.g., GYS1, SCN4A, PPIB, MYH1).

Conclusions:

• Improved genome assemblies enhance understanding of complex genomic regions.
• Genomic insights are crucial for understanding horse history and adaptation.
• Genomic tools are increasingly valuable for practical applications in horse conservation, health, and breeding.