Detection of copy number variants in African goats using whole genome sequence data.

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  • Additional Information
    • Corporate Authors:
      VarGoats Consortium
    • 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:
      DNA Copy Number Variations* ; Goats*/genetics; Africa ; Animals ; Genome
    • Abstract:
      Background: Copy number variations (CNV) are a significant source of variation in the genome and are therefore essential to the understanding of genetic characterization. The aim of this study was to develop a fine-scaled copy number variation map for African goats. We used sequence data from multiple breeds and from multiple African countries.
      Results: A total of 253,553 CNV (244,876 deletions and 8677 duplications) were identified, corresponding to an overall average of 1393 CNV per animal. The mean CNV length was 3.3 kb, with a median of 1.3 kb. There was substantial differentiation between the populations for some CNV, suggestive of the effect of population-specific selective pressures. A total of 6231 global CNV regions (CNVR) were found across all animals, representing 59.2 Mb (2.4%) of the goat genome. About 1.6% of the CNVR were present in all 34 breeds and 28.7% were present in all 5 geographical areas across Africa, where animals had been sampled. The CNVR had genes that were highly enriched in important biological functions, molecular functions, and cellular components including retrograde endocannabinoid signaling, glutamatergic synapse and circadian entrainment.
      Conclusions: This study presents the first fine CNV map of African goat based on WGS data and adds to the growing body of knowledge on the genetic characterization of goats.
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    • Grant Information:
      8042-31000-001-02S Agricultural Research Service; 0500-00093-001-00-D Agricultural Research Service
    • Contributed Indexing:
      Keywords: African goats; Copy number variations; Whole genome sequence
    • Publication Date:
      Date Created: 20210530 Date Completed: 20210601 Latest Revision: 20210604
    • Publication Date:
      20231215
    • Accession Number:
      PMC8164248
    • Accession Number:
      10.1186/s12864-021-07703-1
    • Accession Number:
      34051743