TY - JOUR
T1 - Abundant sequence divergence in the native Japanese cattle Mishima-Ushi (Bos taurus) detected using whole-genome sequencing
AU - Tsuda, Kaoru
AU - Kawahara-Miki, Ryouka
AU - Sano, Satoshi
AU - Imai, Misaki
AU - Noguchi, Tatsuo
AU - Inayoshi, Yousuke
AU - Kono, Tomohiro
N1 - Funding Information:
We thank Kazuma Tada, Risuke Kawauchi, Masakatsu Hikichi, Yoshifumi Hironaga, and the Mishima-Cattle Conservation Association on Mishima Island for providing blood samples from Mishima-Ushi individuals; Koji Nomura, the mayor of Hagi-City, Yamaguchi Prefecture, for supporting this project; and Takashi Hirano for valuable discussions. This study was funded by a MEXT-Supported Program for the Strategic Research Foundation at Private Universities ( S0801025 ).
PY - 2013/10
Y1 - 2013/10
N2 - 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.
AB - 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.
KW - Bos taurus
KW - Economic trait
KW - Mishima-Ushi
KW - Next-generation sequencing
KW - Non-synonymous SNPs
KW - Whole-genome sequence analysis
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U2 - 10.1016/j.ygeno.2013.08.002
DO - 10.1016/j.ygeno.2013.08.002
M3 - Article
C2 - 23938316
AN - SCOPUS:84886296997
VL - 102
SP - 372
EP - 378
JO - Genomics
JF - Genomics
SN - 0888-7543
IS - 4
ER -