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Mogens Agerbo Krogh

Fine resolution CNV catalogue from deeply sequenced cattle genomes

Research output: Contribution to book/anthology/report/proceedingConference abstract in proceedingsResearchpeer-review

  • Y.L. Lee, Wageningen University & Reserch, Animal Breeding and Genomics, P.O. Box 338, 6700 AH, Wageningen, the Netherlands, Netherlands
  • H. Takada, Unit of Animal Genomics, GIGA-R & Faculty of Veterinary Medicine, University of Liège, Belgium
  • G.C.M. Moreira, Unit of Animal Genomics, GIGA-R & Faculty of Veterinary Medicine, University of Liège, Belgium
  • L. Karim, GIGA Institute, GIGA Genomics Platform, Liège, Liège, Belgium, Belgium
  • GplusE Consortium, Genotype Plus Environment Consortium (www.gpluse.eu)
  • ,
  • M. Bosse, Wageningen University & Reserch, Animal Breeding and Genomics, P.O. Box 338, 6700 AH, Wageningen, the Netherlands, Netherlands
  • A. Bouwman, Wageningen University & Reserch, Animal Breeding and Genomics, P.O. Box 338, 6700 AH, Wageningen, the Netherlands, Netherlands
  • E. Mullaart, CRV B.V., P.O. Box 454, 6800 AL, Arnhem, the Netherlands, Netherlands
  • W. Coppieters, GIGA Institute, GIGA Genomics Platform, Liège, Liège, Belgium, Belgium
  • M. Georges, Unit of Animal Genomics, GIGA-R & Faculty of Veterinary Medicine, University of Liège, Belgium
  • T. Druet, Unit of Animal Genomics, GIGA-R & Faculty of Veterinary Medicine, University of Liège, Belgium
  • C. Charlier, Unit of Animal Genomics, GIGA-R & Faculty of Veterinary Medicine, University of Liège, Belgium
Genomes consist of various forms of variations that ultimately contribute to shaping phenotypes. Copy number variations (CNVs) are a form of genetic variation, and arise from gain or loss of DNA. CNV discovery depends on the quality of both sequencing data and reference genome, but in livestock an accurate CNV catalogue and an investigation of the functional impact of CNVs are lacking. We used deeply sequenced cattle genomes from 131 Dutch Friesian Holstein trios (mean coverage: 26x), mapped to the reference genome ARS1.2, to study CNVs. Harnessing the unique pedigree structure in livestock populations, we eliminated spurious CNVs, based on the Mendelian inheritance pattern. Offspring of the 131 probands (~5 animals/proband) enabled us to trace the inheritance of interesting CNVs.
observed in the probands. Among ~10,000 high quality CNVs, which were ascertained at base pair resolution, ~3,000
overlapped with the coding sequence. Subsequently, we used histone and chromatin modification assay data to
investigate whether CNVs are overlapping with gene regulatory elements. Among the ~7,000 CNVs in non-coding
regions, ~200 overlapped with putative regulatory elements such as enhancers, promoters, and open chromatin
regions. These overlaps imply that CNVs can alter gene expression, either by directly affecting coding sequences
or by interrupting gene regulatory elements. A highly interesting CNV in our catalogue is GC gene duplication,
overlapping with the last exon of the GC gene. This duplication is located at ~36 kb distance from several known
clinical mastitis QTLs. Using RNA seq data generated from liver tissues of Holstein cows (n=178), we confirmed
that the duplication is associated with increased expression of GC. This valuable CNV catalogue warrants follow-up
research on the functional impact of CNVs.
Original languageEnglish
Title of host publicationBook of Abstracts of the 71st Annual Meeting of the European Federation of Animal Science
Volume26
Place of publicationWageningen, The Netherlands
PublisherWageningen Academic Publishers
Publication yearDec 2020
Pages188
ISBN (print)978-90-8686-349-5
ISBN (Electronic)978-90-8686-900-8
DOIs
Publication statusPublished - Dec 2020
Event71st Annual Meeting of European Federation of Animal Science - Virtual
Duration: 1 Dec 20204 Dec 2020

Conference

Conference71st Annual Meeting of European Federation of Animal Science
LocationVirtual
Periode01/12/202004/12/2020

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