2011
DOI: 10.1186/1471-2164-12-103
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Whole-genome resequencing shows numerous genes with nonsynonymous SNPs in the Japanese native cattle Kuchinoshima-Ushi

Abstract: BackgroundBecause 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.ResultsIn 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 r… Show more

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Cited by 74 publications
(82 citation statements)
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“…However, it could also be related to differences between C. angulata and C. gigas genomes, that may reflect the finding that C. angulata is evolutionarily more distant from the reference genome (C. gigas) than is usually thought [37e39]. On the other hand, the average mapping depth presents lower values than those observed in the wild C. gigas oyster (50-fold) [3] and Korean cattle (45.6-fold) [40] but higher than those previously reported in whole-genome re-sequenced carried out in cattle of the Black Angus and Holstein breed (9.8-fold and 10.8-fold, respectively) [41] or Japanese native cattle (15.8-fold) [42]. So, in spite of the large number of scaffolds existing in the reference genome, ranging between 100 bp and 1.9 millions bp in size (Supplementary file 1), both the coverage of reads and the mapping depth obtained (83.36% and 29.34-fold respectively) are in the range of optimal values required for the analysis of the genome of C. angulata by a whole-genome re-sequencing approach.…”
Section: Sequencing Mapping and Snp/indel Detectioncontrasting
confidence: 71%
“…However, it could also be related to differences between C. angulata and C. gigas genomes, that may reflect the finding that C. angulata is evolutionarily more distant from the reference genome (C. gigas) than is usually thought [37e39]. On the other hand, the average mapping depth presents lower values than those observed in the wild C. gigas oyster (50-fold) [3] and Korean cattle (45.6-fold) [40] but higher than those previously reported in whole-genome re-sequenced carried out in cattle of the Black Angus and Holstein breed (9.8-fold and 10.8-fold, respectively) [41] or Japanese native cattle (15.8-fold) [42]. So, in spite of the large number of scaffolds existing in the reference genome, ranging between 100 bp and 1.9 millions bp in size (Supplementary file 1), both the coverage of reads and the mapping depth obtained (83.36% and 29.34-fold respectively) are in the range of optimal values required for the analysis of the genome of C. angulata by a whole-genome re-sequencing approach.…”
Section: Sequencing Mapping and Snp/indel Detectioncontrasting
confidence: 71%
“…The present authors examined whether the 75 genes containing non-synonymous mutations were reportedly associated with economically important traits such as milk production, meat production and growth rate in other breeds of cattle. The current results were compared with the list of genes containing nsSNPs associated with economically important traits obtained in the study by Kawahara-Miki et al (2011). Of the 75 genes containing nsSNPs, four (Supplementary Table S5) matched the genes that are potentially associated with economically important traits such as milk production and meat production.…”
Section: Discussionmentioning
confidence: 99%
“…The possibility of introgression of genetic material from populations or species not sampled in our analysis limits our ability to make inferences about Asian cattle, but they promise to be an interesting area for future research. Although Kawahara-Miki et al (51) suggested that Japanese cattle are sister to all other domesticated cattle, their omission of an indicine breed in their analyses makes this conclusion difficult to test. In addition, introgression among taurine and indicine lines would produce a similar result in a tree-based analysis.…”
Section: Taurine Indicinementioning
confidence: 98%