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Population differentiated copy number variation of Bos taurus, Bos indicus and their African hybrids.

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  • Additional Information
    • Source:
      Publisher: BioMed Central Country of Publication: England NLM ID: 100965258 Publication Model: Electronic Cited Medium: Internet ISSN: 1471-2164 (Electronic) Linking ISSN: 14712164 NLM ISO Abbreviation: BMC Genomics Subsets: MEDLINE
    • Publication Information:
      Original Publication: London : BioMed Central, [2000-
    • Subject Terms:
    • Abstract:
      Background: CNV comprises a large proportion in cattle genome and is associated with various traits. However, there were few population-scale comparison studies on cattle CNV.
      Results: Here, autosome-wide CNVs were called by read depth of NGS alignment result and copy number variation regions (CNVRs) defined from 102 Eurasian taurine (EAT) of 14 breeds, 28 Asian indicine (ASI) of 6 breeds, 22 African taurine (AFT) of 2 breeds, and 184 African humped cattle (AFH) of 17 breeds. The copy number of every CNVRs were compared between populations and CNVRs with population differentiated copy numbers were sorted out using the pairwise statistics V ST and Kruskal-Wallis test. Three hundred sixty-two of CNVRs were significantly differentiated in both statistics and 313 genes were located on the population differentiated CNVRs.
      Conclusion: For some of these genes, the averages of copy numbers were also different between populations and these may be candidate genes under selection. These include olfactory receptors, pathogen-resistance, parasite-resistance, heat tolerance and productivity related genes. Furthermore, breed- and individual-level comparison was performed using the presence or copy number of the autosomal CNVRs. Our findings were based on identification of CNVs from short Illumina reads of 336 individuals and 39 breeds, which to our knowledge is the largest dataset for this type of analysis and revealed important CNVs that may play a role in cattle adaption to various environments.
      (© 2021. The Author(s).)
    • Comments:
      Erratum in: BMC Genomics. 2022 Mar 15;23(1):207. (PMID: 35291938)
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    • Contributed Indexing:
      Keywords: African indigenous cattle; Copy number variation (CNV); Indicine; Population differentiated CNV; Taurine
    • Publication Date:
      Date Created: 20210713 Date Completed: 20210714 Latest Revision: 20220716
    • Publication Date:
      20220716
    • Accession Number:
      PMC8276479
    • Accession Number:
      10.1186/s12864-021-07808-7
    • Accession Number:
      34253178