Abstract
Preserving genetic diversity is pivotal for enhancing genetic improvement and facilitating adaptive responses to selection. This study focuses on identifying key genetic variants, including single nucleotide polymorphisms (SNPs), insertion/deletion polymorphisms (INDELs), and copy number variants (CNVs), while exploring the genomic evolutionary connectedness among seven Iranian horses representing five indigenous breeds: Caspian, Turkemen, DareShuri, Kurdish, and Asil. Using whole-genome resequencing, we generated 2.7 Gb of sequence data, with raw reads ranging from 1.2 Gb for Caspian horses to 0.38 Gb for Turkoman horses. Post-filtering, approximately 1.9 Gb of reads remained, with ~ 1.5 Gb successfully mapped to the horse reference genome (EquCab3.0), achieving mapping rates between 76.4% (Caspian) and 98.35% (Turkoman). We identified 2,909,816 SNPs in Caspian horses, constituting around 0.1% of the genome. Notably, 71% of these SNPs were situated in intergenic regions, while 8.5 and 6.8% were located upstream and downstream, respectively. A comparative analysis of SNPs between Iranian and non-Iranian horse breeds showed that Caspian horses had the lowest number of shared SNPs with Turkoman horses. Instead, they showed a closer genetic relationship with DareShuri, Quarter, Arabian, Standardbred, and Asil breeds. Hierarchical clustering highlighted Caspian horses as a distinct cluster, underscoring their distinctive genomic signature. Caspian horses exhibit a unique genetic profile marked by an enrichment of private mutations in neurological genes, influencing sensory perception and awareness. This distinct genetic makeup shapes mating preferences and signifies a separate evolutionary trajectory. Additionally, significant non-synonymous single nucleotide polymorphisms (nsSNPs) in reproductive genes offer intervention opportunities for managing Caspian horses. These findings reveal the population genetic structure of Iranian horse breeds, contributing to the advancement of knowledge in areas such as conservation, performance traits, climate adaptation, reproduction, and resistance to diseases in equine science.
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Data availability
The datasets generated during and/or analyzed during the current study are not publicly available due to privacy policy of Agricultural Biotechnology Research Institute of Iran but are available from the corresponding author on reasonable request.
Change history
09 April 2024
The original online version of this article was revised: ORCID ID of the author Mehrshad Zeinalabedini has been corrected.
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Acknowledgements
The authors would like to acknowledge the initial support provided by Dr. Hamid Kohram, former professor at the Department of Animal Science, College of Agriculture and Natural Resources, University of Tehran, Iran. In February 2020, Dr. Kohram passed away due to complications from COVID-19.
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This work was supported by a PhD grant from “College of Agriculture and Natural Resources, University of Tehran, Iran” and “Agricultural Biotechnology Research Institute, Iran”.
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BA, MZ and GHS conceived and designed the study. BA and MZ performed the bioinformatics and analyzed the data. BA, MZ, RT, MRG, and MFV wrote the manuscript. MZ, RT, MM, MRG, MFV, MKN, and TS edited the manuscript. All authors approved the manuscript before submission.
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Arefnejad, B., Zeinalabedini, M., Talebi, R. et al. Unveiling the population genetic structure of Iranian horses breeds by whole-genome resequencing analysis. Mamm Genome (2024). https://doi.org/10.1007/s00335-024-10035-6
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DOI: https://doi.org/10.1007/s00335-024-10035-6