Abundant sequence divergence in the native Japanese cattle Mishima-Ushi (Bos taurus) detected using whole-genome sequencing.
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.
Genome Research Center, NODAI Research Institute, Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya-ku, Tokyo 156-8502, Japan.
Kaoru
K
Tsuda
Ryouka
R
Kawahara-Miki
Satoshi
S
Sano
Misaki
M
Imai
Tatsuo
T
Noguchi
Yousuke
Y
Inayoshi
Tomohiro
T
Kono
D000818:Animals; D001947:Breeding; D002417:Cattle / Q000145:classification* / Q000235:genetics*; D019143:Evolution, Molecular; D005091:Exons; D014644:Genetic Variation; D016678:Genome; D006579:Heterozygote; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D006720:Homozygote; D054643:INDEL Mutation; D007564:Japan; D010802:Phylogeny; D020641:Polymorphism, Single Nucleotide
BACs; Bos taurus; CAST; CFTR; Economic trait; GAA; GO; MEGA; Mishima-Ushi; Molecular Evolutionary Genetics Analysis; NCAPG; NJ; Next-generation sequencing; Non-synonymous SNPs; PCR; QTL; SNPs; UTRs; Whole-genome sequence analysis; bacterial artificial chromosomes; calpastatin; cystic fibrosis transmembrane conductance regulator; gene ontology; glucosidase, and alpha acid; indels; insertions and deletions; mitochondrial DNA; mtDNA; neighbor-joining; non-SMC condensing I complex, subunit G; non-synonymous SNPs; nsSNPs; polymerase chain reaction; quantitative trait locus; single-nucleotide polymorphisms; untranslated regions