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Detection of selective sweep in European wild sheep breeds

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Abstract

In wild animal populations, there is a differentiation between populations due to natural selection. The direction and pressure of natural selection in the wild sheep are different in the various geographic areas. Linkage disequilibrium studies showed that regions of the genome in whole wild sheep are under natural selection and that natural selection can affect immune or reproductive or metabolic traits. The study aimed to identify genomic regions under natural selection in wild sheep. For this purpose, the genetic information of 24 European wild sheep and 24 Sardinian wild sheep was used. The genotypes were determined using Illumina 50 K SNPChip arrays based on Oar_4.0 version of the sheep genome. After quality control steps, finally, 31,560 SNP markers were analyzed. The value of LD was calculated by calculating the r2 statistic between all pairs of locations through PLINK software. To identify signs of selection based on linkage disequilibrium methods, an extended haplotype homozygosity test of XP-EHH crossing population and iHS intrapopulation was used. The results of iHS studies showed that in European and Sardinian wild sheep, the highest iHS coefficient under natural selection was observed on 3 and 2 chromosome numbers, respectively. Also, the results of XP-EHH studies showed that the largest XP-EHH coefficients under natural selection in European wild sheep compared to Sardinian and vice versa in Sardinian wild sheep compared to European wild sheep were observed on 3 and 16 chromosome numbers, respectively. In addition, the results of gene cycle studies showed that COPB1, SEC24D, ZDHHC17, BBS4, RFX3, SLC26A8, CAMK2D, GRIA1, GRM1, GRID2, PPP2R1A, CPEB4, PLEKHA5 and KIF13A, VPS39, VPS53, DTNBP1, DYNC1I1, FAM91A genes are under natural selection in Sardinian and European wild sheeps, respectively. The direction and selection pressure of natural selection in the two breeds of wild sheep is different due to different geographic conditions.

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Funding

This work was supported by the University of Torbat Heydarieh [Grant Numbers 141, 09/07/2022].

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Authors and Affiliations

  1. Department of Plant Production, University of Torbat Heydarieh, Torbat Heydarieh, 9516168595, Iran

    Masoud Alipanah & Faezeh Gharari

  2. Department of Animal Science, Ferdowsi University of Mashhad, Mashhad, 9177948974, Iran

    Seyed Mostafa Mazloom & Faezeh Gharari

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  1. Masoud Alipanah
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No Animal Care Committee approval was necessary for the purposes of this study, as all information required was obtained from pre-existing databases. (http://widde.toulouse.inra.fr).

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Alipanah, M., Mazloom, S.M. & Gharari, F. Detection of selective sweep in European wild sheep breeds. 3 Biotech 14, 122 (2024). https://doi.org/10.1007/s13205-024-03964-1

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