ArticleGenes & genomics2019
Investigation of Hanwoo-specific structural variations using whole-genome sequencing data.
Article in Genes & genomics, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 4 papers.
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Who cites it
4 citing papers in PubMed.
- Digital PCR Methods for Discovering Molecular Markers for Hanwoo Cattle Breed Genotyping.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Taming transposable elements in livestock and poultry: a review of their roles and applications.Genetics, selection, evolution : GSE · 2023Review
- Comparison of digital PCR platforms using the molecular marker.Genomics & informatics · 2023Article
- Quantitative evaluation of the molecular marker using droplet digital PCR.Genomics & informatics · 2020Article
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10 authors.
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Abstract
backgroundThe 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.
objectiveTE-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.
resultsWe 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.
conclusionOur 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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