The Western Ecotype of the Kazakh Horse: Current Status and Genomic Characterisation

Background/Objectives: The Kazakh horse comprises several locally adapted types and ecotypes of the Eurasian Steppe. The Adai is its western ecotype, kept year-round on desert pasture in Mangystau, Western Kazakhstan, and recognised as a separate breed in 2024 without genetic evaluation. We asked whether that label corresponds to a genetic unit and whether the population has remained closed. Methods: We genotyped 533 horses recorded as Adai, 500 traced to five farms in Mangystau, against 988 reference horses of 45 breeds on 36,193 shared autosomal SNPs. Structure was assessed by principal component analysis, pairwise FST with block-jackknife intervals, neighbour-joining trees and cross-validated individual assignment; introgression per animal by an f4 statistic against an empirical null of 223 reference-steppe horses, with the ancestry scale calibrated on 1800 simulated crosses built from real genotypes; and eight body measurements were modelled within farms. Results: The Adai was not separable from the Central Asian steppe complex as a population: pairwise FST was 0.004–0.008 against Tuva, Yili, Sanhe and Mongolian horses, and two Adai farms differed from each other as much as an Adai farm differed from a reference-steppe breed. Individual assignment was nonetheless accurate against those breeds (86–100% pairwise), but the same classifier separated two herds of Adai at 69–85%, so assignment accuracy on thousands of markers tracks marker number rather than breed identity. Against the empirical null, 15.6% of Adai exceeded the 95th percentile and twelve exceeded the maximum. The estimator carries a floor of 3.7 percentage points on an unadmixed Adai; on the calibrated scale, 9.6% of animals reached the ancestry expected from one Thoroughbred great-grandparent and 4.2% that expected from one grandparent (15.8% and 4.6% uncalibrated). Introgression was concentrated: one farm carried 42% of its horses at a great-grandparent equivalent or more against 0–9% at the other four, a difference that survived every analysis accounting for family structure. Ancestry showed no within-farm association with any of eight body measurements, with or without age in the model. Conclusions: The Adai is not a differentiated population but part of a continuous steppe complex, and carries undocumented ancestry of Thoroughbred affinity concentrated in particular holdings. As managed, it cannot be certified from a document or a phenotype. Genomic verification at registration is a plausible instrument, but the marker panel it would require was not developed or validated here.