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Detection of whole genome selection signatures of Pakistani Teddy goat

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Abstract

Background

Natural and artificial selection tend to cause variability that contributes to shape the genome of livestock in a way that differentiates them among the animal kingdom. The particular aim here is to identify positive selection signatures with whole genome pooled-sequence data of Pakistani Teddy goat.

Methods and results

Paired-end alignment of 635,357,043 reads of Teddy goat with (ARS1) reference genome assembly was carried out. Pooled-Heterozygosity (Hp) and Tajima’s D (TD) are applied for validation and getting better hits of selection signals, while pairwise FST statistics is conducted on Teddy vs. Bezoar (wild goat ancestor) for genomic differentiation, moreover annotation of regions under positive selection was also performed. Hp score with − ZHp > 5 detected six windows having highest hits on Chr. 29, 9, 25, 15 and 14 that harbor HRASLS5, LACE1 and AXIN1 genes which are candidate for embryonic development, lactation and body height. Secondly, − ZTD value of > 3.3 showed 4 windows with very strong hits on Chr.5 & 9 which harbor STIM1 and ADM genes related to body mass and weight. Lastly, − ZFST < − 5 generated four strong signals on Chr.5 & 12 harbor LOC102183233 gene. Other significant selection signatures encompass genes associated with wool production, prolificacy and coat colors traits in this breed.

Conclusions

In brief, this study identified the genes under selection in Pakistani Teddy goat that will be helpful to refining the marker-assisted breeding policies and converging required production traits within and across other goat breeds and to explore full genetic potential of this valued species of livestock.

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Data availability

Relevant data is available in the manuscript including supplementary files and supporting information. This article has already been submitted to a preprint platform distributed under a Creative Commons CC BY license having DOI number https://doi.org/10.20944/preprints202012.0421.v1.

Code availability

FST, TD scripts are available publicly, while \(Hp\) statistics was in-house written ruby script. Manhattan and other supplementary plots were plotted using Bioconductor qqMan package using R.

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Acknowledgements

Authors are obliged to Prof. Dr. Tosso Leeb & Dr. Vidhya Jagannathan for their continuous support and valued time for accomplishing this work. Thanks to Dr. Mushtaq Ahmad Gondal and Mr. Muhammad Sidique for helping in sample collection.

Funding

Sequencing of Pakistani goats were funded by Swiss National Science Foundation (31003A_172964), when RS was postdoc fellow at University of Bern under Swiss Government Excellence Scholarship/Hans Sigrist Foundation and now further analyzing this already generated publicly available data.

Author information

Authors and Affiliations

  1. Decode Genomics, Punjab University Employees Housing Scheme, Lahore, Pakistan

    Rashid Saif, Tania Mahmood, Aniqa Ejaz & Fraz Ahmad

  2. Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern, Switzerland

    Jan Henkel

  3. Department of Sciences and Humanities, National University of Computer and Emerging Sciences, Lahore, Pakistan

    Saeeda Zia

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  1. Rashid Saif
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Contributions

RS envisaged the idea, involved in critical thinking, analysis of data, editing, proofread and correspondence with journal. JH was involved in understandings the software and Linux features, analysis of data and provision of in-house \(Hp\) script. TM, AE and FA helped in data analysis and initial write-up. SZ helped in understanding the statistical methods and proof reading of the manuscript.

Corresponding author

Correspondence to Rashid Saif.

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Conflict of interest

There are no competing interests among the authors.

Ethical approval

All Pakistani animals were sampled with the consent of their owners by obeying the local regulations laid down by “Ethical Review Committee” UVAS-Pakistan, while sampling of Swiss animals was permitted by the “Cantonal Committee for Animal Experiments” (Canton of Bern; permit 75/16).

Consent to participation

Authors informed to the farmers and took their consent before collecting samples of their animals.

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Saif, R., Henkel, J., Mahmood, T. et al. Detection of whole genome selection signatures of Pakistani Teddy goat. Mol Biol Rep 48, 7273–7280 (2021). https://doi.org/10.1007/s11033-021-06726-x

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  • DOI: https://doi.org/10.1007/s11033-021-06726-x

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