Investigation of Hanwoo-specific structural variations using whole-genome sequencing data
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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.
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.
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.
Our study showed that one of the SVs, TE-mediated deletion, could be utilized as a molecular maker to distinguish between Hanwoo and Holstein.
KeywordsStructural variation Transposable element TE-mediated deletion Molecular marker
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).
Compliance with ethical standards
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.
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).
- Heo EJ, Ko EK, Seo KH, Chon JW, Kim YJ, Park HJ, Wee SH, Moon JS (2014) Comparison of the microsatellite and single nucleotide polymorphism methods for discriminating among Hanwoo (Korean Native Cattle), imported, and crossbred beef in Korea. Korean J Food Sci Anim Resour 34:763–768CrossRefPubMedPubMedCentralGoogle Scholar