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Home / Equine Research Bank / Heredity (Edinb) / Genetic diversity and signatures of selection in four indige...
Heredity2023; 131(2); 96-108; doi: 10.1038/s41437-023-00624-7

Genetic diversity and signatures of selection in four indigenous horse breeds of Iran.

Abstract: Indigenous Iranian horse breeds were evolutionarily affected by natural and artificial selection in distinct phylogeographic clades, which shaped their genomes in several unique ways. The aims of this study were to evaluate the genetic diversity and genomewide selection signatures in four indigenous Iranian horse breeds. We evaluated 169 horses from Caspian (n = 21), Turkmen (n = 29), Kurdish (n = 67), and Persian Arabian (n = 52) populations, using genomewide genotyping data. The contemporary effective population sizes were 59, 98, 102, and 113 for Turkmen, Caspian, Persian Arabian, and Kurdish breeds, respectively. By analysis of the population genetic structure, we classified the north breeds (Caspian and Turkmen) and west/southwest breeds (Persian Arabian and Kurdish) into two phylogeographic clades reflecting their geographic origin. Using the de-correlated composite of multiple selection signal statistics based on pairwise comparisons, we detected a different number of significant SNPs under putative selection from 13 to 28 for the six pairwise comparisons (FDR < 0.05). The identified SNPs under putative selection coincided with genes previously associated with known QTLs for morphological, adaptation, and fitness traits. Our results showed HMGA2 and LLPH as strong candidate genes for height variation between Caspian horses with a small size and the other studied breeds with a medium size. Using the results of studies on human height retrieved from the GWAS catalog, we suggested 38 new putative candidate genes under selection. These results provide a genomewide map of selection signatures in the studied breeds, which represent valuable information for formulating genetic conservation and improved breeding strategies for the breeds.
© 2023. The Author(s).
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Publication Date: 2023-06-12 PubMed ID: 37308718PubMed Central: PMC10382556DOI: 10.1038/s41437-023-00624-7Google Scholar: Lookup
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  • Journal Article

Summary

This research summary has been generated with artificial intelligence and may contain errors and omissions. Refer to the original study to confirm details provided. Submit correction.

The research focuses on studying the genetic diversity in four indigenous horse breeds from Iran and identifying signatures of selection in their genomes which might provide insights into traits associated with adaptation and fitness.

Research Methods and Sample Composition

  • The research team collected genotyping data from 169 horses in total, spread across four indigenous breeds of Iran: Caspian (21), Turkmen (29), Kurdish (67), and Persian Arabian (52).

Identification and Evaluation of Genetic Diversity

  • The contemporary effective population sizes of the studied breeds were determined as Turkmen (59), Caspian (98), Persian Arabian (102), and Kurdish (113).
  • A population genetic structure analysis was carried out to classify the horse breeds based on their geographic origin.
  • Two phylogeographic clades were formed: North breeds (Caspian and Turkmen) and West/Southwest breeds (Persian Arabian and Kurdish), reflecting their distinct phylogeographic origins.

Analyzing Selection Signatures

  • The researchers performed pairwise comparison analysis using de-correlated composite of multiple selection signal statistics to identify selection signatures within the genomes of the studied breeds.
  • Between 13 to 28 significant Single Nucleotide Polymorphisms (SNPs) were detected as putative selection markers. These SNPs were associated with traits related to morphology, adaptation, and fitness in each of the six pairwise comparisons conducted.

Genomic Map of Selection Signatures and Result Analysis

  • Several genes, including HMGA2 and LLPH, were identified as strong candidate genes associated with height variation between the relatively smaller-sized Caspian horses and the medium-sized Turkmen, Kurdish, and Persian Arabian breeds.
  • Upon analyzing results of human height studies from the Genome-Wide Association Studies (GWAS) catalog, the researchers suggested 38 new putative candidate genes under selection.
  • Collectively, these results were used to develop a genomic map detailing the selection signatures in the studied Iranian horse breeds.
  • This map provides valuable data that can be used to devise genetic conservation strategies and improve breeding approaches for these animals.

Cite This Article

APA
Mousavi SF, Razmkabir M, Rostamzadeh J, Seyedabadi HR, Naboulsi R, Petersen JL, Lindgren G. (2023). Genetic diversity and signatures of selection in four indigenous horse breeds of Iran. Heredity (Edinb), 131(2), 96-108. https://doi.org/10.1038/s41437-023-00624-7

Publication

Heredity
ISSN: 1365-2540
NlmUniqueID: 0373007
Country: England
Language: English
Volume: 131
Issue: 2
Pages: 96-108

Researcher Affiliations

Mousavi, Seyedeh Fatemeh
  • Department of Animal Science, Faculty of Agriculture, University of Kurdistan, Sanandaj, Iran.
  • Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden.
Razmkabir, Mohammad
  • Department of Animal Science, Faculty of Agriculture, University of Kurdistan, Sanandaj, Iran. m.razmkabir@uok.ac.ir.
Rostamzadeh, Jalal
  • Department of Animal Science, Faculty of Agriculture, University of Kurdistan, Sanandaj, Iran. j.rostamzadeh@uok.ac.ir.
Seyedabadi, Hamid-Reza
  • Animal Science Research Institute of Iran, Agricultural Research Education and Extension Organization (AREEO), Karaj, Iran.
Naboulsi, Rakan
  • Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden.
  • Childhood Cancer Research Unit, Department of Women's and Children's Health, Karolinska Institute, Tomtebodavägen 18A, 17177, Stockholm, Sweden.
Petersen, Jessica L
  • Department of Animal Science, University of Nebraska, Lincoln, NE, USA.
Lindgren, Gabriella
  • Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden. gabriella.lindgren@slu.se.
  • Center for Animal Breeding and Genetics, Department of Biosystems, KU Leuven, 3001, Leuven, Belgium. gabriella.lindgren@slu.se.

MeSH Terms

  • Humans
  • Animals
  • Horses / genetics
  • Iran
  • Genome
  • Phenotype
  • Phylogeography
  • Genetic Variation
  • Polymorphism, Single Nucleotide
  • Selection, Genetic

Conflict of Interest Statement

The authors declare no competing interests.

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