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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\u2010chromosome sequence illustrates how long\u2010read and Hi\u2010C\/T2T data improve genome completeness and the representation of complex regions. On this foundation, high\u2010coverage resequencing of ancient and modern horses has clarified the geographical core of domestication in the Volga\u2013Don region, the Bronze Age replacement of earlier domestic lineages and the long\u2010term impact of human management on behaviour, conformation and mobility. Comparative analyses of mitochondrial DNA, Y\u2010chromosomal haplotypes and autosomal runs of homozygosity further reveal a combination of diverse maternal lineages, highly constrained paternal lineages and breed\u2010specific 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\n                    <jats:italic>MSTN<\/jats:italic>\n                    \u2010guided performance profiling,\n                    <jats:italic>EPAS1<\/jats:italic>\n                    \u2010based altitude adaptation and molecular tests for\n                    <jats:italic>GYS1<\/jats:italic>\n                    ,\n                    <jats:italic>SCN4A<\/jats:italic>\n                    ,\n                    <jats:italic>PPIB<\/jats:italic>\n                    and\n                    <jats:italic>MYH1<\/jats:italic>\n                    . We conclude by considering how telomere\u2010to\u2010telomere assemblies, pangenome resources, improved structural\u2010variant detection and closer integration between population genomics and functional studies may support conservation, health surveillance and molecular breeding in diverse horse populations.\n                  <\/jats:p>","DOI":"10.1111\/eva.70283","type":"journal-article","created":{"date-parts":[[2026,6,18]],"date-time":"2026-06-18T06:08:50Z","timestamp":1781762930000},"update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":1,"title":["Integrative Advances in Equine Genomics From Reference Assemblies to Evolutionary History and Key Traits"],"prefix":"10.1111","volume":"19","author":[{"ORCID":"https:\/\/orcid.org\/0009-0002-6056-3246","authenticated-orcid":false,"given":"Ying","family":"Lu","sequence":"first","affiliation":[{"name":"Faculty of Animal Science and Technology Yunnan Agricultural University  Kunming 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