title: Whole-genome resequencing shows numerous genes with nonsynonymous SNPs in the Japanese native cattle Kuchinoshima-Ushi.
abstract: BACKGROUND
  Because the Japanese native cattle Kuchinoshima-Ushi have been isolated in a small island and their lineage has been intensely protected, it has been assumed to date that numerous and valuable genomic variations are conserved in this cattle breed.
  
  
  RESULTS
  In this study, we evaluated genetic features of this breed, including single nucleotide polymorphism (SNP) information, by whole-genome sequencing using a Genome Analyzer II. A total of 64.2 Gb of sequence was generated, of which 86% of the obtained reads were successfully mapped to the reference sequence (Btau 4.0) with BWA. On an average, 93% of the genome was covered by the reads and the number of mapped reads corresponded to 15.8-fold coverage across the covered region. From these data, we identified 6.3 million SNPs, of which more than 5.5 million (87%) were found to be new. Out of the SNPs annotated in the bovine sequence assembly, 20,432 were found in protein-coding regions containing 11,713 nonsynonymous SNPs in 4,643 genes. Furthermore, phylogenetic analysis using sequence data from 10 genes (more than 10 kbp) showed that Kuchinoshima-Ushi is clearly distinct from European domestic breeds of cattle.
  
  
  CONCLUSIONS
  These results provide a framework for further genetic studies in the Kuchinoshima-Ushi population and research on functions of SNP-containing genes, which would aid in understanding the molecular basis underlying phenotypic variation of economically important traits in cattle and in improving intrinsic defects in domestic cattle breeds.
authors.affiliation: Genome Research Center, NODAI Research Institute, Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya-ku, Tokyo, Japan.
authors.forename: Ryouka
authors.initials: R
authors.lastname: Kawahara-Miki
authors.forename: Kaoru
authors.initials: K
authors.lastname: Tsuda
authors.forename: Yuh
authors.initials: Y
authors.lastname: Shiwa
authors.forename: Yuko
authors.initials: Y
authors.lastname: Arai-Kichise
authors.forename: Takashi
authors.initials: T
authors.lastname: Matsumoto
authors.forename: Yu
authors.initials: Y
authors.lastname: Kanesaki
authors.forename: Sen-ichi
authors.initials: S
authors.lastname: Oda
authors.forename: Shizufumi
authors.initials: S
authors.lastname: Ebihara
authors.forename: Shunsuke
authors.initials: S
authors.lastname: Yajima
authors.forename: Hirofumi
authors.initials: H
authors.lastname: Yoshikawa
authors.forename: Tomohiro
authors.initials: T
authors.lastname: Kono
mesh_terms: D000818:Animals; D001947:Breeding; D002417:Cattle / Q000235:genetics*; D002874:Chromosome Mapping; D005260:Female; D015723:Gene Library; D016678:Genome; D054643:INDEL Mutation; D007564:Japan; D008297:Male; D058977:Molecular Sequence Annotation; D010802:Phylogeny; D020641:Polymorphism, Single Nucleotide; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA; D012984:Software