Abundant sequence divergence in the native Japanese cattle Mishima-Ushi (Bos taurus) detected using whole-genome sequencing

Kaoru Tsuda, Ryouka Kawahara-Miki, Satoshi Sano, Misaki Imai, Tatsuo Noguchi, Yousuke Inayoshi, Tomohiro Kono

Research output: Contribution to journalArticlepeer-review

10 Citations (Scopus)

Abstract

The native Japanese cattle Mishima-Ushi, a designated national natural treasure, are bred on a remote island, which has resulted in the conservation of their genealogy. We examined the genetic characteristics of 8 Mishima-Ushi individuals by using single nucleotide polymorphisms (SNPs), insertions, and deletions obtained by whole-genome sequencing. Mapping analysis with various criteria showed that predicted heterozygous SNPs were more prevalent than predicted homozygous SNPs in the exonic region, especially non-synonymous SNPs. From the identified 6.54. million polymorphisms, we found 400 non-synonymous SNPs in 313 genes specific to each of the 8 Mishima-Ushi individuals. Additionally, 3,170,833 polymorphisms were found between the 8 Mishima-Ushi individuals. Phylogenetic analysis confirmed that the Mishima-Ushi population diverged from another strain of Japanese cattle. This study provides a framework for further genetic studies of Mishima-Ushi and research on the function of SNP-containing genes as well as understanding the genetic relationship between the domestic and native Japanese cattle breeds.

Original languageEnglish
Pages (from-to)372-378
Number of pages7
JournalGenomics
Volume102
Issue number4
DOIs
Publication statusPublished - 2013 Oct

Keywords

  • Bos taurus
  • Economic trait
  • Mishima-Ushi
  • Next-generation sequencing
  • Non-synonymous SNPs
  • Whole-genome sequence analysis

ASJC Scopus subject areas

  • Genetics

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