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• Differences in level of LD were found between breeds representing different horse types. • Breeds representing the same horse type showed similar trends of historical N e. • Longer haplotype block structure was found in Arabian breed than in native horse breeds. • Population history and breeding schemes may influence patterns of LD. This study was conducted to investigate linkage disequilibrium (LD), historical effective population size (N e) and haplotype block structures in genomes of highly selected Polish Arabian (AR; n=124) horses and conserved horse breeds derived from Polish native breeds, in particular, Malopolski (MLP; n=56), Sokolski (SOK; n=107), Sztumski (SZTUM; n=69), Hucul (HC; n=116) and Polish Konik (KN; n=99) horses, based on single nucleotide polymorphisms (SNPs) from the Neogen Equine Community BeadChip assay (Illumina, San Diego, CA). LD analysis was performed based on the pairwise r2 statistic of SNPs at a distance up to 5Mb. At a short distance, up to 100kb, the lower average r2 was observed in SOK (0.09) and SZTUM (0.10) breeds, representing draft horse type, and the highest average r2 was observed in AR (0.19) and MLP (0.17) breeds, representing light horse type. At a distance of 4-5Mb, the average values of r2 were 0.03 for HC and KN, 0.02 for AR and MLP and 0.01 for SOK and SZTUM. About 100 generations ago, effective population size (N e) ranged from 518 (SOK) to 310 (AR) and five generations ago from 85 (SOK) to 40 (HC). A total of 6,162 (AR), 5,792 (MLP), 5,744 (HC), 5,429 (KN), 5,542 (SOK) and 4,848 (SZTUM) haplotype block structures, spanning 656.2Mb (AR), 439.4Mb (MLP), 381.2Mb (HC), 344.3 (KN), 206.7 (SOK) and 171.0Mb (SZTUM) of the genome were detected. Mean block lengths were estimated as 106.5±138kb, 75.9±120kb, 66.4±109kb, 63.4±109kb, 37.3±80kb and 35.3±81kb for AR, MLP, HC, KN, SOK and SZTUM, respectively. A visible similarity in the decay of LD across the genome, as well as in trends of historical N e, were found for breeds representing the same horse type. Differences in the span of haplotype block structures were found between AR and Polish native horse breeds, which may reflect different demographic population histories and differences in intensity of selection. [ABSTRACT FROM AUTHOR]