Fine resolution CNV catalogue from deeply sequenced cattle genomes

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Fine resolution CNV catalogue from deeply sequenced cattle genomes. / Lee, Y.L.; Takada, H.; Moreira, G.C.M.; Karim, L.; GplusE Consortium; Bosse, M.; Bouwman, A.; Mullaart, E.; Coppieters, W.; Georges, M.; Druet, T.; Charlier, C.

Book of Abstracts of the 71st Annual Meeting of the European Federation of Animal Science. Bind 26 Wageningen, The Netherlands : Wageningen Academic Publishers, 2020. s. 188.

Publikation: Bidrag til bog/antologi/rapport/proceedingKonferenceabstrakt i proceedingsForskningpeer review

Harvard

Lee, YL, Takada, H, Moreira, GCM, Karim, L, GplusE Consortium, Bosse, M, Bouwman, A, Mullaart, E, Coppieters, W, Georges, M, Druet, T & Charlier, C 2020, Fine resolution CNV catalogue from deeply sequenced cattle genomes. i Book of Abstracts of the 71st Annual Meeting of the European Federation of Animal Science. bind 26, Wageningen Academic Publishers, Wageningen, The Netherlands, s. 188, 71st Annual Meeting of European Federation of Animal Science, 01/12/2020. https://doi.org/10.3920/978-90-8686-900-8

APA

Lee, Y. L., Takada, H., Moreira, G. C. M., Karim, L., GplusE Consortium, Bosse, M., Bouwman, A., Mullaart, E., Coppieters, W., Georges, M., Druet, T., & Charlier, C. (2020). Fine resolution CNV catalogue from deeply sequenced cattle genomes. I Book of Abstracts of the 71st Annual Meeting of the European Federation of Animal Science (Bind 26, s. 188). Wageningen Academic Publishers. https://doi.org/10.3920/978-90-8686-900-8

CBE

Lee YL, Takada H, Moreira GCM, Karim L, GplusE Consortium, Bosse M, Bouwman A, Mullaart E, Coppieters W, Georges M, Druet T, Charlier C. 2020. Fine resolution CNV catalogue from deeply sequenced cattle genomes. I Book of Abstracts of the 71st Annual Meeting of the European Federation of Animal Science. Wageningen, The Netherlands: Wageningen Academic Publishers. s. 188. https://doi.org/10.3920/978-90-8686-900-8

MLA

Lee, Y.L. o.a.. "Fine resolution CNV catalogue from deeply sequenced cattle genomes". Book of Abstracts of the 71st Annual Meeting of the European Federation of Animal Science. Wageningen, The Netherlands: Wageningen Academic Publishers. 2020, 188. https://doi.org/10.3920/978-90-8686-900-8

Vancouver

Lee YL, Takada H, Moreira GCM, Karim L, GplusE Consortium, Bosse M o.a. Fine resolution CNV catalogue from deeply sequenced cattle genomes. I Book of Abstracts of the 71st Annual Meeting of the European Federation of Animal Science. Bind 26. Wageningen, The Netherlands: Wageningen Academic Publishers. 2020. s. 188 https://doi.org/10.3920/978-90-8686-900-8

Author

Lee, Y.L. ; Takada, H. ; Moreira, G.C.M. ; Karim, L. ; GplusE Consortium ; Bosse, M. ; Bouwman, A. ; Mullaart, E. ; Coppieters, W. ; Georges, M. ; Druet, T. ; Charlier, C. / Fine resolution CNV catalogue from deeply sequenced cattle genomes. Book of Abstracts of the 71st Annual Meeting of the European Federation of Animal Science. Bind 26 Wageningen, The Netherlands : Wageningen Academic Publishers, 2020. s. 188

Bibtex

@inbook{23b36c06a97044a0a199f6446ddab6d3,
title = "Fine resolution CNV catalogue from deeply sequenced cattle genomes",
abstract = "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, ~3,000overlapped with the coding sequence. Subsequently, we used histone and chromatin modification assay data toinvestigate whether CNVs are overlapping with gene regulatory elements. Among the ~7,000 CNVs in non-codingregions, ~200 overlapped with putative regulatory elements such as enhancers, promoters, and open chromatinregions. These overlaps imply that CNVs can alter gene expression, either by directly affecting coding sequencesor 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 knownclinical mastitis QTLs. Using RNA seq data generated from liver tissues of Holstein cows (n=178), we confirmedthat the duplication is associated with increased expression of GC. This valuable CNV catalogue warrants follow-upresearch on the functional impact of CNVs.",
author = "Y.L. Lee and H. Takada and G.C.M. Moreira and L. Karim and {GplusE Consortium} and M. Bosse and A. Bouwman and E. Mullaart and W. Coppieters and M. Georges and T. Druet and C. Charlier and Leslie Foldager and Torben Larsen and Tine Rousing and Krogh, {Mogens Agerbo} and Jehan Ettema and S{\o}ren {\O}stergaard and S{\o}rensen, {Martin Tang} and Ingvartsen, {Klaus L{\o}nne}",
year = "2020",
month = dec,
doi = "10.3920/978-90-8686-900-8",
language = "English",
isbn = "978-90-8686-349-5",
volume = "26",
pages = "188",
booktitle = "Book of Abstracts of the 71st Annual Meeting of the European Federation of Animal Science",
publisher = "Wageningen Academic Publishers",
note = "71st Annual Meeting of European Federation of Animal Science, EAAP ; Conference date: 01-12-2020 Through 04-12-2020",

}

RIS

TY - ABST

T1 - Fine resolution CNV catalogue from deeply sequenced cattle genomes

AU - Lee, Y.L.

AU - Takada, H.

AU - Moreira, G.C.M.

AU - Karim, L.

AU - GplusE Consortium

AU - Bosse, M.

AU - Bouwman, A.

AU - Mullaart, E.

AU - Coppieters, W.

AU - Georges, M.

AU - Druet, T.

AU - Charlier, C.

AU - Foldager, Leslie

AU - Larsen, Torben

AU - Rousing, Tine

AU - Krogh, Mogens Agerbo

AU - Ettema, Jehan

AU - Østergaard, Søren

AU - Sørensen, Martin Tang

AU - Ingvartsen, Klaus Lønne

PY - 2020/12

Y1 - 2020/12

N2 - 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, ~3,000overlapped with the coding sequence. Subsequently, we used histone and chromatin modification assay data toinvestigate whether CNVs are overlapping with gene regulatory elements. Among the ~7,000 CNVs in non-codingregions, ~200 overlapped with putative regulatory elements such as enhancers, promoters, and open chromatinregions. These overlaps imply that CNVs can alter gene expression, either by directly affecting coding sequencesor 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 knownclinical mastitis QTLs. Using RNA seq data generated from liver tissues of Holstein cows (n=178), we confirmedthat the duplication is associated with increased expression of GC. This valuable CNV catalogue warrants follow-upresearch on the functional impact of CNVs.

AB - 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, ~3,000overlapped with the coding sequence. Subsequently, we used histone and chromatin modification assay data toinvestigate whether CNVs are overlapping with gene regulatory elements. Among the ~7,000 CNVs in non-codingregions, ~200 overlapped with putative regulatory elements such as enhancers, promoters, and open chromatinregions. These overlaps imply that CNVs can alter gene expression, either by directly affecting coding sequencesor 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 knownclinical mastitis QTLs. Using RNA seq data generated from liver tissues of Holstein cows (n=178), we confirmedthat the duplication is associated with increased expression of GC. This valuable CNV catalogue warrants follow-upresearch on the functional impact of CNVs.

U2 - 10.3920/978-90-8686-900-8

DO - 10.3920/978-90-8686-900-8

M3 - Conference abstract in proceedings

SN - 978-90-8686-349-5

VL - 26

SP - 188

BT - Book of Abstracts of the 71st Annual Meeting of the European Federation of Animal Science

PB - Wageningen Academic Publishers

CY - Wageningen, The Netherlands

T2 - 71st Annual Meeting of European Federation of Animal Science

Y2 - 1 December 2020 through 4 December 2020

ER -