Comparative analysis of genomic diversity and genetic architecture amongst 14 horse breeds using ultra high-density SNP arrays: Implications for conservation and breeding

Articles in Press

Document Type : Research Article (Regular Paper)

Authors

1 Department of Animal Science, Faculty of Agriculture, Shahid Bahonar University of Kerman, Kerman, Iran

2 Department of Animal Science, Faculty of Agriculture, university of Jiroft, Jiroft, Iran

Abstract

Genetic variability is fundamental for the adaptability, health, and long-term sustainability of horse populations. This study sought to provide a comprehensive assessment of genomic diversity, population structure, and selection signatures across 14 horse breeds, encompassing five indigenous Iranian breeds (Iranian Arabian-Asil, Turkmen, Caspian, Kurdish, Dareshuri) as well as nine international breeds (Thoroughbred, Quarter Horse, Belgian, Arabian, Welsh Pony, Standardbred, Icelandic, Lusitano, Morgan), based on ultra-high-density SNP array data. Following quality control and imputation, we analyzed the combined dataset of 1.57 million SNPs across 438 individuals to assess within- and between-breed genetic diversity, population structure, and signatures of selection. Observed heterozygosity (Hₒ) ranged from 0.1727 (Thoroughbred) to 0.2068 (Welsh), with Iranian breeds generally demonstrating lower allelic richness and effective number of alleles. Pairwise FST and private allele analyses revealed moderate genetic differentiation, with Thoroughbred and Icelandic being the most divergent, while Iranian breeds revealed high shared ancestry. Population history assessments via Tajima’s D and Garza–Williamson M-ratio highlighted varying degrees of past bottlenecks, most evident in Dareshuri and Kurdish populations. Population structure analyses (PCA and PCoA) showed well-defined breed clusters, highlighting both geographic origin and selective breeding history. HapFLK analysis detected 83 candidate genes under selection, associated with neural development, immune response, coat color and traits related to performance or reproduction. These findings emphasize the combined effects of historical selection, demographic events, and breed management on the genomic architecture of horse populations. The results provide applicable information for conservation strategies and breeding programs aimed at maintaining genetic diversity while preserving breed-specific traits, particularly in endangered Iranian and intensively selected international breeds.

Keywords

Main Subjects

References

Almarzook, S., Reissmann, M., Arends, D., Brockmann, G.A., 2017. Genetic diversity of Syrian Arabian horses. Animal Genetics 48(4), 486-489.
Amirinia, C., Seyedabadi, H., Banabazi, M.H., Kamali, M.A., 2007. Bottleneck study and genetic structure of Iranian Caspian horse population using microsatellites. Pakistan Journal of Biological Sciences 10(9), 1540-1543.
Amjadi, M.A., Yeganeh, H.M., Sadeghi, M., Abbas Raza, S.H., Yang, J., Najafabadi, H.A., Batool, U., Shoorei, H., Abdelnour, S.A., Ahmed, J.Z., 2021. Microsatellite analysis of genetic diversity and population structure of the Iranian Kurdish horse. Journal of Equine Veterinary Science 98, 103358.
Arefnejad, B., Zeinalabedini, M., Talebi, R., Mardi, M., Ghaffari, M.R., Vahidi, M.F., Nekouei, M.K., Szmatoła T, Salekdeh, G.H., 2024. Unveiling the population genetic structure of Iranian horse breeds by whole-genome resequencing analysis. Mammalian Genome 35, 201-227.
Atroshchenko, M., Dementieva, N., Shcherbakov, Y., Nikolaeva, O., Azovtseva, A., Ryabova, A., Nikitkina, E., Makhmutova, O., Datsyshin, A., Zakharov, V., Zaitsev, A., 2023. The genetic diversity of horse native breeds in Russia. Genes 14(12), 2148.
Bazvand, B., Rashidi, A., Zandi, M.B., Moradi, M.H., Rostamzadeh, J., Mahmoudi, P., 2025. Population structure and signature of selection for body size in some Iranian and exotic horse breeds. Journal of Equine Veterinary Science 152, 105658.
Bazvand, B., Rashidi, A., Zandi, M.B., Moradi, M.H., Rostamzadeh, J., 2024. Genome-wide analysis of population structure, effective population size and inbreeding in Iranian and exotic horses. PLoS One 19(3), e0299109.
Browning, B.L., Zhou, Y., Browning, S.R., 2018. A one-penny imputed genome from next-generation reference panels. American Journal of Human Genetics 103(3), 338-348.
Chang, C.C., Chow, C.C., Tellier, L.C., Vattikuti, S., Purcell, S.M., Lee, J.J., 2015. Second-generation PLINK: rising to the challenge of larger and richer datasets. Gigascience 4, 7.
Chang, L.Y., Toghiani, S., Hay, E.H., Aggrey, S.E., Rekaya, R., 2019. A weighted genomic relationship matrix based on fixation index (FST) prioritized SNPs for genomic selection. Genes 10(11), 922.
Charlesworth, B., 2009. Fundamental concepts in genetics: effective population size and patterns of molecular evolution and variation. Nature Reviews Genetics 10(3), 195-205.
Cortes-Rodriguez, N., Campana, M.G., Berry, L., Faegre, S., Derrickson, S.R., Ha, R.R., Dikow, R.B., Rutz, C., Fleischer, R.C., 2019. Population genomics and structure of the critically endangered Mariana Crow (Corvus kubaryi). Genes 10(3), 187.
Cosgrove, E.J., Sadeghi, R., Schlamp, F., Holl, H.M., Moradi-Shahrbabak, M., Miraei-Ashtiani, S.R., Abdalla, S., Shykind, B., Troedsson, M., Stefaniuk-Szmukier, M., Prabhu, A., Bucca, S., Bugno-Poniewierska, M., Wallner, B., Malek, J., Miller, D.C., Clark, A.G., Antczak, D.F., Brooks, S.A., 2020. Genome diversity and the origin of the Arabian horse. Scientific Reports 10, 9702.
Cozzi, M.C., Strillacci, M.G., Valiati, P., Rogliano, E., Bagnato, A., Longeri, M., 2018. Genetic variability of Akhal-Teke horses bred in Italy. PeerJ 6, e4889.
Danecek, P., Auton, A., Abecasis, G., Albers, C.A., Banks, E., DePristo, M.A., Handsaker, R.E., Lunter, G., Marth, G.T., Sherry, S.T., McVean, G., Durbin, R., 1000 genomes project analysis group, 2011. The variant call format and VCFtools. Bioinformatics 27(15), 2156-2158.
Durward-Akhurst, S.A., Schaefer, R.J., Grantham, B., Carey, W.K., Mickelson, J.R., McCue, M.E., 2021. Genetic variation and the distribution of variant types in the horse. Frontiers in Genetics 12, 758366.
Esdaile, E., Avila, F., Bellone, R.R., 2022. Analysis of genetic diversity in the American Standardbred horse utilizing short tandem repeats and single nucleotide polymorphisms. Journal of Heredity 113(3), 238-247.
Fages, A., Hanghøj, K., Khan, N., Gaunitz, C., Seguin-Orlando, A., Leonardi, M., McCrory Constantz, C., Gamba, C., Al-Rasheid, K.A.S., Albizuri, S., Alfarhan, A.H., Allentoft, M., Alquraishi, S., Anthony, D., Baimukhanov, N., Barrett, J.H., Bayarsaikhan, J., Benecke, N., Bernáldez-Sánchez, E., Berrocal-Rangel, L., Biglari, F., Boessenkool, S., Boldgiv, B., Brem, G., Brown, D., Burger, J., Crubézy, E., Daugnora, L., Davoudi, H., de Barros Damgaard, P., de Los Ángeles de Chorro Y de Villa-Ceballos. M., Deschler-Erb. S., Detry. C., Dill. N., do Mar Oom. M., Dohr. A., Ellingvåg. S., Erdenebaatar. D., Fathi. H., Felkel. S., Fernández-Rodríguez. C., García-Viñas. E., Germonpré. M., Granado. J.D., Hallsson. J.H., Hemmer. H., Hofreiter. M., Kasparov. A., Khasanov. M., Khazaeli. R., Kosintsev. P., Kristiansen. K., Kubatbek. T., Kuderna. L., Kuznetsov. P., Laleh. H., Leonard. J.A., Lhuillier. J., Liesau von Lettow-Vorbeck. C., Logvin. A., Lõugas. L., Ludwig. A., Luis. C., Arruda. A.M., Marques-Bonet. T., Matoso Silva. R., Merz. V., Mijiddorj. E., Miller. B.K., Monchalov. O., Mohaseb. F.A., Morales. A., Nieto-Espinet. A., Nistelberger. H., Onar. V., Pálsdóttir. A.H., Pitulko. V., Pitskhelauri. K., Pruvost. M., Rajic Sikanjic. P., Rapan Papeša. A., Roslyakova. N., Sardari. A., Sauer. E., Schafberg. R., Scheu. A., Schibler. J., Schlumbaum. A., Serrand. N., Serres-Armero. A., Shapiro. B., Sheikhi Seno. S., Shevnina. I., Shidrang. S., Southon. J., Star. B., Sykes. N., Taheri. K., Taylor. W., Teegen. W.R., Trbojević Vukičević. T., Trixl. S., Tumen. D., Undrakhbold. S., Usmanova. E., Vahdati. A., Valenzuela-Lamas. S., Viegas. C., Wallner. B., Weinstock. J., Zaibert. V., Clavel. B., Lepetz. S., Mashkour. M., Helgason. A., Stefánsson. K., Barrey. E., Willerslev. E., Outram. A.K., Librado. P., Orlando, L., 2019. Tracking five millennia of horse management with extensive ancient genome time series. Cell 177(6), 1419-1435.e31.
Fariello, M.I., Boitard, S., Naya, H., SanCristobal, M., Servin, B., 2013. Detecting signatures of selection through haplotype differentiation among hierarchically structured populations. Genetics 193(3), 929-941.
Gabriel, S.B., Schaffner, S.F., Nguyen, H., Moore, J.M., Roy, J., Blumenstiel, B., Higgins, J., DeFelice, M., Lochner, A., Faggart, M., Liu-Cordero, S.N., Rotimi, C., Adeyemo, A., Cooper, R., Ward, R., Lander, E.S., Daly, M.J., Altshuler, D., 2002. The structure of haplotype blocks in the human genome. Science 296(5576), 2225-2229.
Garza, J.C., Williamson, E.G., 2001. Detection of reduction in population size using data from microsatellite loci. Molecular Ecology 10(2), 305-318.
Greenbaum, G., Templeton, A.R., Zarmi, Y., Bar-David, S., 2014. Allelic richness following population founding events: a stochastic modeling framework incorporating gene flow and genetic drift. PLoS One 9(12), e115203.
Hedayat Evrigh, N., Omri, M., Boustan, A., Seyedsharifi, R., Vahedi, V., 2018. Genetic diversity and structure of Iranian horses’ population based on mitochondrial markers. Journal of Equine Veterinary Science 64, 107-111.
Hou, L., Sulayman, A., Zeng, Y., Zhou, L., Aimaier, A., Kader, A., Shi, L., 2025. Analysis of genetic diversity and race genetic structure of major horse breeds in Xinjiang, China. Animals 15(18), 2690.
Hu, M., Jiang, H., Lai, W., Shi, L., Yi, W., Sun, H., Chen, C., Yuan, B., Yan, S., Zhang, J., 2023. Assessing genomic diversity and signatures of selection in Chinese Red Steppe cattle using high-density SNP array. Animals 13(10), 1717.
Khanshour, A., Conant, E., Juras, R., Cothran, E.G., 2013. Microsatellite analysis of genetic diversity and population structure of Arabian horse populations. Journal of Heredity 104(3), 386-398.
Leroy, G., Callède, L., Verrier, E., Mériaux, J.C., Ricard, A., Danchin-Burge, C., Rognon, X., 2009. Genetic diversity of a large set of horse breeds raised in France assessed by microsatellite polymorphism. Genetics Selection Evolution 41(1), 31.
Luikart, G., Sherwin, W.B., Steele, B.M., Allendorf, F.W., 1998. Usefulness of molecular markers for detecting population bottlenecks via monitoring genetic change. Molecular Ecology 7(8), 963-974.
Machmoum, M., Boujenane, I., Azelhak, R., Badaoui, B., Petit, D., Piro, M., 2020. Genetic diversity and population structure of Arabian horse populations using microsatellite markers. Journal of Equine Veterinary Science 93, 103200.
Momen, M., Brauer, K., Patterson, M.M., Sample, S.J., Binversie, E.E., Davis, B.W., Cothran, E.G., Rosa, G.J.M., Brounts, S.H., Muir, P., 2023. Genetic architecture and polygenic risk score prediction of degenerative suspensory ligament desmitis (DSLD) in the Peruvian horse. Frontiers in Genetics 14, 1201628. https://doi.org/10.5061/dryad.cnp5hqc9p.
Momen, M., Brounts, S.H., Binversie, E.E., Sample, S.J., Rosa, G.J.M., Davis, B.W., Muir, P., 2022. Selection signature analyses and genome-wide association reveal genomic hotspot regions that reflect differences between breeds of horse with contrasting risk of degenerative suspensory ligament desmitis. G3 12(10), jkac179.
Moradi, M.H., Khalt-Abadi Farahani, A.H., 2018. Estimation of inbreeding values using genomic run of homozygosity and study of evolutionary trend for effective population size in some Asian horse breeds. Iranian Journal of Animal Science 49(3), 381-392.
Moravčíková, N., Kasarda, R., Vostra Vydrova, H., Vostry, L., Karásková, B., Candrák, J., Halo, M., 2024. Genomic variability of the MHC region: empirical evidence from five horse breeds. Livestock Science 284, 105480.
Mousavi, S.F., Razmkabir, M., Rostamzadeh, J., Seyedabadi, H.R., Naboulsi, R., Petersen, J.L., Lindgren, G., 2023. Genetic diversity and signatures of selection in four indigenous horse breeds of Iran. Heredity 131(2), 96-108.
Nei, M., Li, W.H., 1979. Mathematical model for studying genetic variation in terms of restriction endonucleases. Proceedings of the National Academy of Sciences of the United States of America 76, 5269-5273.
Ospina, J.A., Lopez-Alvarez, D., Gimode, W., Wenzl, P., Carvajal-Yepes, M., 2024. Genome-wide association study of cassava brown streak disease resistance in cassava germplasm conserved in South America. Scientific Reports 14(1), 23141.
Petersen, J.L., Mickelson, J.R., Cothran, E.G., Andersson, L.S., Axelsson, J., Bailey, E., Bannasch, D., Binns, M.M., Borges, A.S., Brama, P., da Câmara Machado, A., Distl, O., Felicetti, M., Fox-Clipsham, L., Graves, K.T., Guérin, G., Haase, B., Hasegawa, T., Hemmann, K., Hill, E.W., Leeb, T., Lindgren, G., Lohi, H., Lopes, M.S., McGivney, B.A., Mikko, S., Orr, N., Penedo, M.C.T., Piercy, R.J., Raekallio, M., Rieder, S., Røed, K.H., Silvestrelli, M., Swinburne, J., Tozaki, T., Vaudin, M., Wade, C.M., McCue, M.E., 2013. Genetic diversity in the modern horse illustrated from genome-wide SNP data. PLoS One 8(1), e54997.
Pjontek, J., Kadlečík, O., Kasarda, R., Horný, M., 2012. Pedigree analysis in four Slovak endangered horse breeds. Czech Journal of Animal Science 57(2), 54-64.
R Core Team, 2023. R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. URL https://www.R-project.org/
Sadeghi, R., Moradi-Shahrbabak, M., Miraei Ashtiani, S.R., Schlamp, F., Cosgrove, E.J., Antczak, D.F., 2019. Genetic diversity of Persian Arabian horses and their relationship to other native Iranian horse breeds. Journal of Heredity 110(2), 173-182. https://datadryad.org/dataset/doi:10.5061/dryad.54vb7f2.
Santos, W.B., Schettini, G.P., Maiorano, A.M., Bussiman, F.O., Balieiro, J.C.C., Ferraz, G.C., Pereira, G.L., Baldassini, W.A., Neto, O.R.M., Oliveira, H.N., Curi, R.A., 2021. Genome-wide scans for signatures of selection in Mangalarga Marchador horses using high-throughput SNP genotyping. BMC Genomics 22(1), 737.
Schaefer, R.J., Schubert, M., Bailey, E., Bannasch, D.L., Barrey, E., Bar-Gal, G.K., Brem, G., Brooks, S.A., Distl, O., Fries, R., Finno, C.J., Gerber, V., Haase, B., Jagannathan, V., Kalbfleisch, T., Leeb, T., Lindgren, G., Lopes, M.S., Mach, N., da Câmara Machado, A., MacLeod, J.N., McCoy, A., Metzger, J., Penedo, C., Polani, S., Rieder, S., Tammen, I., Tetens, J., Thaller, G., Verini-Supplizi, A., Wade, C.M., Wallner, B., Orlando, L., Mickelson, J.R., McCue, M.E., 2017. Developing a 670k genotyping array to tag ~2M SNPs across 24 horse breeds. BMC Genomics 18(1), 565.
Tajima, F., 1989. Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 123(3), 585-595.
Temple, S.D., Waples, R.K., Browning, S.R., 2024. Modeling recent positive selection using identity-by-descent segments. American Journal of Human Genetics 111(11), 2510-2529.
Vázquez-Armijo, J.F., Parra-Bracamonte, G.M., Velazquez, M.A., Sifuentes-Rincón, A.M., Tinoco-Jaramillo, J.L., Ambriz-Morales, P., Arellano-Vera, W., Moreno-Medina, V.R., 2017. Diversity and effective population size of four horse breeds from microsatellite DNA markers in South-Central Mexico. Archives Animal Breeding 60(2), 137-143.
Ventura, R.V., Brito, L.F., Oliveira, G.A. Jr, Daetwyler, H.D., Schenkel, F.S., Sargolzaei, M., Vandervoort, G., Silva, F.F., Miller, S.P., Carvalho, M.E., Santana. M.H.A., Mattos, E.C., Fonseca, P., Eler, J.P., Sterman, J.B., 2020. A comprehensive comparison of high-density SNP panels and an alternative ultra-high-density panel for genomic analyses in Nellore cattle. Animal Production Science 60(3), 333-346.
Vitti, J.J., Grossman, S.R., Sabeti, P.C., 2013. Detecting natural selection in genomic data. Annual Review of Genetics 47, 97-120.
Weir, B.S., Cockerham, C.C., 1984. Estimating F-statistics for the analysis of population structure. Evolution 38(6), 1358-1370.
Weir, B.S., Goudet, J., 2017. Understanding population structure: FST measures and their interpretation in an evolutionary context. G3 7(4), 1495-1501.
Xuereb, A., Nahuelpi, R.M., Normandeau, E., Babin, C., Laporte, M., Mallet, A., Yáñez, J.M., Mallet, M., Bernatchez, L., 2023. Design and validation of a high-density single nucleotide polymorphism array for the Eastern oyster (Crassostrea virginica). G3 13(6), jkad071.
Yordanov, G., Yordanov, T., Mehandjyiski, I., Radoslavov, G., Salkova, D., Hristov, P., 2025. Population structure and genetic diversity among Shagya Arabian horse genealogical lineages in Bulgaria based on microsatellite genotyping. Veterinary Sciences 12(8), 776.
Yu, N., Jensen-Seaman, M.I., Chemnick, L., Ryder, O., Li, W.H., 2004. Nucleotide diversity in gorillas. Genetics 166, 1375-1383.
Zheng, X., Levine, D., Shen, J., Gogarten, S.M., Laurie, C., Weir, B.S., 2012. A high-performance computing toolset for relatedness and principal component analysis of SNP data. Bioinformatics 28(24), 3326-3328.
Journal of Livestock Science and Technologies

Articles in Press, Accepted Manuscript
Available Online from 03 February 2026

Files

Share

How to cite

Statistics