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Evolutionary applications2026; 19(6); e70283; doi: 10.1111/eva.70283

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

Abstract: Horses are major domestic animals and cultural symbols that have accompanied humans for millennia. They underpin transport, agriculture, warfare and sport, and also provide a model for studying domestication, complex traits and adaptive evolution. Recent work in equine genomics has now generated a much richer picture of how these roles are grounded in the genome. This review brings together advances in several connected areas: the construction and refinement of reference assemblies; genomic reconstructions of origin, domestication and dispersal; global and regional patterns of genetic diversity; and the molecular basis of key traits such as athletic performance, coat colour, body size, environmental adaptation and inherited myopathies. The transition from EquCab1.0/2.0 to EquCab3.0 and a complete Y-chromosome sequence illustrates how long-read and Hi-C/T2T data improve genome completeness and the representation of complex regions. On this foundation, high-coverage resequencing of ancient and modern horses has clarified the geographical core of domestication in the Volga-Don region, the Bronze Age replacement of earlier domestic lineages and the long-term impact of human management on behaviour, conformation and mobility. Comparative analyses of mitochondrial DNA, Y-chromosomal haplotypes and autosomal runs of homozygosity further reveal a combination of diverse maternal lineages, highly constrained paternal lineages and breed-specific inbreeding histories. Against this background, studies of representative traits show how association signals, functional experiments and clinical evidence can be linked to practical tools for breeding and health management, for example through -guided performance profiling, -based altitude adaptation and molecular tests for , , and . We conclude by considering how telomere-to-telomere assemblies, pangenome resources, improved structural-variant detection and closer integration between population genomics and functional studies may support conservation, health surveillance and molecular breeding in diverse horse populations.
© 2026 The Author(s). Evolutionary Applications published by John Wiley & Sons Ltd.
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Publication Date: 2026-06-17 PubMed ID: 42328694PubMed Central: PMC13276278DOI: 10.1111/eva.70283Google Scholar: Lookup
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Summary

This research summary has been generated with artificial intelligence and may contain errors and omissions. Refer to the original study to confirm details provided. Submit correction.

Overview

  • This research article reviews recent advances in horse genomics, emphasizing how improved genome assemblies and genetic analyses have enhanced our understanding of horse domestication, evolution, genetic diversity, and key traits.
  • The insights gained have practical applications in breeding, health management, and conservation of horses.

Advances in Reference Genome Assemblies

  • Transition from EquCab1.0 and EquCab2.0 to EquCab3.0 has provided a more complete and accurate horse genome reference.
  • Technologies such as long-read sequencing and Hi-C/ T2T (telomere-to-telomere) scaffolding have improved the assembly, particularly in complex regions like the Y chromosome.
  • A complete sequence of the Y chromosome is now available, facilitating studies on paternal lineage and breeding history.

Genomic Reconstructions of Origin, Domestication, and Dispersal

  • High-coverage resequencing of ancient and modern horses helped pinpoint the domestication center to the Volga-Don region in western Eurasia.
  • Bronze Age horses replaced earlier domestic lineages, showing dynamic shifts in populations linked to human activity.
  • Human management over millennia has shaped horses’ behavior, physical conformation, and mobility patterns, as evidenced by genomic data.

Patterns of Genetic Diversity

  • Comparative analysis of mitochondrial DNA, Y chromosome haplotypes, and runs of homozygosity reveal:
    • Multiple, diverse maternal lineages indicating broad female genetic input.
    • Highly constrained or limited paternal lineages indicating selective breeding or bottlenecks.
    • Breed-specific histories of inbreeding and genetic diversity.

Molecular Basis of Key Traits

  • Studies on important traits include:
    • Athletic performance — identifying genetic markers associated with endurance, speed, and strength.
    • Coat color — connecting genomic loci with different pigmentation patterns.
    • Body size — understanding the genetic determinants of size variation across breeds.
    • Environmental adaptation — uncovering genomic variants linked to adaptation to high altitudes and different climates.
    • Inherited myopathies — pinpointing mutations responsible for muscle diseases affecting health and performance.
  • These genetic insights enable development of molecular tools that help guide breeding decisions, health screening, and performance profiling.

Applications and Future Directions

  • Integration of genome assemblies, population genomics, and functional studies are improving horse conservation strategies and veterinary health.
  • Emerging technologies and improved structural variant detection support the creation of a horse pangenome, capturing more genomic diversity.
  • Functional genomics combined with evolutionary history aids development of molecular tests for traits and diseases, enhancing precision breeding.
  • These advances promise better management of diverse horse populations worldwide, safeguarding both genetic health and desired performance traits.

Cite This Article

APA
Lu Y, Ma R, Wang B, Wu J, Chong Y, Gao Z, Deng W. (2026). Integrative Advances in Equine Genomics From Reference Assemblies to Evolutionary History and Key Traits. Evol Appl, 19(6), e70283. https://doi.org/10.1111/eva.70283

Publication

Evolutionary applications
ISSN: 1752-4571
NlmUniqueID: 101461828
Country: England
Language: English
Volume: 19
Issue: 6
Pages: e70283
PII: e70283

Researcher Affiliations

Lu, Ying
  • Faculty of Animal Science and Technology Yunnan Agricultural University Kunming China.
  • State Key Laboratory for Conservation and Utilization of Bio-Resource in Yunnan Kunming China.
Ma, Ruoshan
  • Faculty of Animal Science and Technology Yunnan Agricultural University Kunming China.
  • State Key Laboratory for Conservation and Utilization of Bio-Resource in Yunnan Kunming China.
Wang, Bo
  • Faculty of Animal Science and Technology Yunnan Agricultural University Kunming China.
  • State Key Laboratory for Conservation and Utilization of Bio-Resource in Yunnan Kunming China.
Wu, Jiao
  • Faculty of Animal Science and Technology Yunnan Agricultural University Kunming China.
  • State Key Laboratory for Conservation and Utilization of Bio-Resource in Yunnan Kunming China.
Chong, Yuqing
  • Faculty of Animal Science and Technology Yunnan Agricultural University Kunming China.
  • State Key Laboratory for Conservation and Utilization of Bio-Resource in Yunnan Kunming China.
Gao, Zhendong
  • Faculty of Animal Science and Technology Yunnan Agricultural University Kunming China.
  • State Key Laboratory for Conservation and Utilization of Bio-Resource in Yunnan Kunming China.
Deng, Weidong
  • Faculty of Animal Science and Technology Yunnan Agricultural University Kunming China.
  • State Key Laboratory for Conservation and Utilization of Bio-Resource in Yunnan Kunming China.

Conflict of Interest Statement

The authors declare no conflicts of interest.

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