Survey of population structure and linkage disequilibrium pattern of Iranian native horse breeds by SNP markers

Articles in Press

Document Type : Research Paper

Authors

Department of Animal Science, Faculty of Agriculture, University of Zanjan, Zanjan, Iran.

Abstract

The aim of this study was to investigate the structure and genetic distances, inbreeding, and linkage disequilibrium (LD) in Iranian native horse breeds. Samples on 167 horses including Arabian Asil (24), Caspian (22), Dareshouri (15), Kurdish (66), and Turkmen (40) breeds were used. The samples were genotyped using Illumina 70k SNP equine bead chip. Data quality control was applied and loci with MAF < 2%, Mind < 5%, HWE (<10-6), and genotype call rate < 1% were removed. Finally, 159 horses with 45,270 SNP loci were reminded for the genetic structure analyse. Clustering analyse showed that in K=5 Caspian and Kurdish breeds were placed in a common cluster, and Turkmen, Dareshouri, and Arabian Asil breeds were also located in distinct clusters. The LD decay among all breeds showed a significant decrease below 400 bp. Caspian and Dareshouri breeds experienced the lowest and highest LD and the highest and lowest effective population size, respectively. The inbreeding value based on the runs of homozygosity (ROH) were highest and lowest for Arabian Asil and Caspian breeds, respectively. The results showed that the Iranian native horse breeds were well identified by SNP markers, which can be used for stud base foundations of breeds with more accuracy.

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Main Subjects

Iranian Journal of animal Science

Articles in Press, Accepted Manuscript
Available Online from 10 July 2024

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History

  • Receive Date: 07 November 2023
  • Revise Date: 11 April 2024
  • Accept Date: 28 May 2024

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