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Investigation of Hanwoo-specific structural variations using whole-genome sequencing data

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Abstract

Background

The total length of the cattle genome is approximately ~ 3 billion base pairs. About half of the bovine genome (46.5%) is composed of transposable elements (TEs). The TEs could be a major source of genomic structural variations (SVs) between cattle breeds. These SVs have led to genomic fluidity and rearrangements between interspecies.

Objective

TE-mediated insertion and deletion events could have a strong influence on the bovine genome. This study aimed to investigate TE-mediated deletion events that are common to 12 Hanwoo genome resequencing data.

Results

We compared 12 Hanwoo genome resequencing data with the cattle reference genome (Bos taurus_UMD_3.1.1) and six other open source data (2 Jersey, 2 Holstein, 2 Angus). By using BreakDancer program, the common SVs to the 12 Hanwoo genomes were detected. A total of 299 Hanwoo-specific SV candidates were detected. Among them, 56 Hanwoo-specific TE-mediated deletion candidate loci were validated by PCR and Sanger sequencing. Finally, we identified one locus, DEL_96, which is an authentic Hanwoo-specific deletion. The DEL_96 event occurred by nonallelic homologous end-joining between LINE (BovB) and unique sequence with 1 bp microhomology. The 370 bp deletion event appeared to be only in the Hanwoo individuals after the divergence of Hanwoo and Holstein lineages.

Conclusion

Our study showed that one of the SVs, TE-mediated deletion, could be utilized as a molecular maker to distinguish between Hanwoo and Holstein.

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Acknowledgements

This work was supported by Korea Institute of Planning and Evaluation for Technology in Food, Agriculture and Forestry (IPET) through Advanced Production Technology Development Program, funded by Ministry of Agriculture, Food and Rural Affairs (MAFRA) (116065).

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Authors and Affiliations

  1. Department of Nanobiomedical Science and BK21 PLUS NBM Global Research Center for Regenerative Medicine, Dankook University, Cheonan, 31116, Republic of Korea

    Jangho Park, Wonseok Shin, Seyoung Mun, Man Hwan Oh & Kyudong Han

  2. Animal Genomics and Bioinformatics Division, 1500, Kongjwipatjwi-ro, Iseo-myeon, Wanju-gun, Jeollabuk-do, 55365, Republic of Korea

    Dajeong Lim

  3. Livestock Research Institute, Yeongju, Gyeongbuk, 36052, Republic of Korea

    Dong-Yep Oh

  4. Department of Biomedical Engineering, School of Life sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, Republic of Korea

    Youngjune Bhak & Jong Bhak

  5. Department of Equine Industry, Korea National College of Agriculture and Fisheries, Jeonju, 54874, Republic of Korea

    Yong-Soo Park

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  1. Jangho Park
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  2. Wonseok Shin
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  3. Seyoung Mun
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  4. Man Hwan Oh
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  5. Dajeong Lim
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  7. Youngjune Bhak
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  8. Jong Bhak
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  9. Yong-Soo Park
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  10. Kyudong Han
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Correspondence to Yong-Soo Park or Kyudong Han.

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Conflict of interest

Jangho Park, Wonseok Shin, Seyoung Mun, Man Hwan Oh, Dajung Im, Dong-Yep Oh, Youngjune Bhak, Jong Bhak, Yong-Soo Park, and Kyudong Han declare that we have no conflict of interest.

Ethical approval

All research protocols and animal experiments in this study were reviewed and approved by the Institutional Animal Care and Use Committee (IACUC) in Gyeongsangbuk-do, Republic of Korea (Gyeongbuk IACUC-81).

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Park, J., Shin, W., Mun, S. et al. Investigation of Hanwoo-specific structural variations using whole-genome sequencing data. Genes Genom 41, 233–240 (2019). https://doi.org/10.1007/s13258-018-0772-3

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