ArticleBMC genomics2011
Whole-genome resequencing shows numerous genes with nonsynonymous SNPs in the Japanese native cattle Kuchinoshima-Ushi.
Article in BMC genomics, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 45 papers.
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45 citing papers in PubMed.
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- Four Target Resequencing for the Bovine Major Histocompatibility Complex Region. Proof of Concept.HLA · 2025Article
- Genetic variation analysis of Guanling cattle based on whole-genome resequencing.Animal bioscience · 2024Article
- Whole genome sequencing identified genomic diversity and candidated genes associated with economic traits in Northeasern Merino in China.Frontiers in genetics · 2024Article
- Whole-genome sequencing and genomic analysis of Norduz goat (Capra hircus).Mammalian genome : official journal of the International Mammalian Genome Society · 2023Article
- Assessing Genomic Diversity and Selective Pressures in Bohai Black Cattle Using Whole-Genome Sequencing Data.Animals : an open access journal from MDPI · 2022Article
- Genomic Diversity and Selection Signatures for Weining Cattle on the Border of Yunnan-Guizhou.Frontiers in genetics · 2022Article
- Genomics of Adaptations in Ungulates.Animals : an open access journal from MDPI · 2021Review
- Insights into adaption and growth evolution: a comparative genomics study on two distinct cattle breeds from Northern and Southern China.Molecular therapy. Nucleic acids · 2021Article
- Assessing genomic diversity and signatures of selection in Jiaxian Red cattle using whole-genome sequencing data.BMC genomics · 2021Review
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- BGVD: An Integrated Database for Bovine Sequencing Variations and Selective Signatures.Genomics, proteomics & bioinformatics · 2020Article
- Genomic analyses suggest adaptive differentiation of northern European native cattle breeds.Evolutionary applications · 2019Article
- Genomic variants identified from whole-genome resequencing of indicine cattle breeds from Pakistan.PloS one · 2019Article
- Article
- Genome-Wide SNP Discovery in Indigenous Cattle Breeds of South Africa.Frontiers in genetics · 2019Article
- Whole-Genome Sequencing of Three Native Cattle Breeds Originating From the Northernmost Cattle Farming Regions.Frontiers in genetics · 2018Article
- The evolution of the natural killer complex; a comparison between mammals using new high-quality genome assemblies and targeted annotation.Immunogenetics · 2017Article
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11 authors.
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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.
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