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 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.ConclusionsThese 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.
Highlights
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
Sequencing, mapping, and single nucleotide polymorphism (SNP)/indel detection Whole-genome sequencing was performed on a Genome Analyzer II (GAII) using the genomic DNA from a Kuchinoshima-Ushi male and generated 64.2 Gb of high quality sequence on 34 paired-end lanes (75-bp reads in 28 lanes and 36-bp reads in 6 lanes)
We performed mapping analysis using repeat-masking sequences ftp://hgdownload.cse.ucsc. edu/goldenPath/bosTau4/bigZips/, which showed that high number of reads mapped to BTA13 disappeared (Additional file 1)
Summary
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. Kuchinoshima-Ushi, which have been used mainly as pack animals, are characterized genetically as being lean with a small body size (approximately 500-kg adult males and 300-kg females), wide breast, narrow waist, and horns. They have variable coat colours, including black, black with white spots, and brown. The four major Japanese domestic cattle breeds, namely, Japanese Black, Japanese Brown, Japanese Shorthorn, and Japanese Polled, are bred mainly for meat in Japan. These breeds were established by crossing Japanese native cattle with several European cattle breeds during the mid-19th century to improve the native stock. The specific characteristics inherited by modern Japanese domestic cattle are unknown
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