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. 2011 Feb 10:12:103.
doi: 10.1186/1471-2164-12-103.

Whole-genome resequencing shows numerous genes with nonsynonymous SNPs in the Japanese native cattle Kuchinoshima-Ushi

Ryouka Kawahara-Miki  1 , Kaoru Tsuda, Yuh Shiwa, Yuko Arai-Kichise, Takashi Matsumoto, Yu Kanesaki, Sen-ichi Oda, Shizufumi Ebihara, Shunsuke Yajima, Hirofumi Yoshikawa, Tomohiro Kono
Affiliations

Whole-genome resequencing shows numerous genes with nonsynonymous SNPs in the Japanese native cattle Kuchinoshima-Ushi

Ryouka Kawahara-Miki et al. BMC Genomics. .

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.

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Figures

Figure 1
Figure 1
Habitat and morphological characteristics of Kuchinoshima-Ushi. A: Kuchinoshima Island located in the Tokara Archipelago, Japan. B: Picture of Kuchinoshima-Ushi used in this study, which kept at Shitara Field, Nagoya University. C: Picture of ancient Japanese cattle pulling a traditional Japanese cart in the Heian Age. This picture scroll, entitled "Heiji-Monogatari-Emaki" and drawn in the 13th century, is a national treasure stored at the Tokyo National Museum. Image: TNM Image Archives http://TnmArchives.jp/.
Figure 2
Figure 2
Mapped and unmapped reads to the bovine reference genome. Mapped reads were 790,926,088 (86%) of all the reads (916,449,194). Among the mapped reads, 239,789,699 reads (26% of the total reads) were mapped to multiple chromosomal positions and 551,136,389 reads (60% of the total reads) were uniquely mapped. The number of unmapped reads was 125,523,106 (14%).
Figure 3
Figure 3
Identified SNPs and small indels. Identified SNPs (A) and small indels (B). We used the RefSeq and GenBank gene sets (16,635 genes) to annotate the detected variants. We found 1,003,695 intron SNPs, 17,684 untranslated regions (UTRs), 801 splice-site SNPs, 8,719 synonymous SNPs, and 11,713 nonsynonymous substitutions. Among the identified indels, 104,389 were found in intron regions, 2,942 in exon regions, and 138 in splice-sites.
Figure 4
Figure 4
Functional annotation of the genes containing nsSNPs. A. Gene ontology (GO) terms enriched in the 100 genes containing the highest number of nsSNPs. Blue columns show the percentage of genes among these nsSNP-containing genes, and red columns show the percentage of genes within the whole genome. In this chart, the secondary level terms are used as GO terms. B. Identified nsSNPs reportedly associated with phenotypes in the other breed of cattle. Six SNP sites exactly matched mutations reported in previous studies to be associated with economically important traits [25,26,29,30,35]. "-" implies the absence of record in the dbSNP database. EBV: estimated breeding values; SCS: somatic cell score.
Figure 5
Figure 5
Maximum likelihood tree of bovine-related species. Breeds of the species "Bos Taurus" (Hereford, Holstein, Tuli, and Kuchinoshima-Ushi) were boxed in pink. Numbers beside internal branches indicate bootstrap (BS) values (> 50%) from 1,000 replicates (left) and Bayesian posterior probabilities (right), respectively (shown as percentages). "-" indicates a node not recovered in the Bayesian analysis or <50% of BS values. "Mithan", also called "gayal", is a domesticated gaur.
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