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KMID : 0381120190410020233
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Genes and Genomics
2019 Volume.41 No. 2 p.233 ~ p.240
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Investigation of Hanwoo-specific structural variations using whole-genome sequencing data
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Park Jang-Ho
Shin Won-Seok
Mun Se-Young
Oh Man-Hwan
Lim Da-Jeong
Oh Dong-Yep
Bhak Young-June
Bhak Jong
Park Yong-Soo
Han Kyu-Dong
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Abstract
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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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KEYWORD
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Structural variation, Transposable element, TE-mediated deletion, Molecular marker
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