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Functional and population genetic features of copy number variations in two dairy cattle populations
BACKGROUND: Copy Number Variations (CNVs) are gain or loss of DNA segments that are known to play a role in shaping a wide range of phenotypes. In this study, we used two dairy cattle populations, Holstein Friesian and Jersey, to discover CNVs using the Illumina BovineHD Genotyping BeadChip aligned...
Autores principales: | , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2020
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6988284/ https://www.ncbi.nlm.nih.gov/pubmed/31992181 http://dx.doi.org/10.1186/s12864-020-6496-1 |
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author | Lee, Young-Lim Bosse, Mirte Mullaart, Erik Groenen, Martien A. M. Veerkamp, Roel F. Bouwman, Aniek C. |
author_facet | Lee, Young-Lim Bosse, Mirte Mullaart, Erik Groenen, Martien A. M. Veerkamp, Roel F. Bouwman, Aniek C. |
author_sort | Lee, Young-Lim |
collection | PubMed |
description | BACKGROUND: Copy Number Variations (CNVs) are gain or loss of DNA segments that are known to play a role in shaping a wide range of phenotypes. In this study, we used two dairy cattle populations, Holstein Friesian and Jersey, to discover CNVs using the Illumina BovineHD Genotyping BeadChip aligned to the ARS-UCD1.2 assembly. The discovered CNVs were investigated for their functional impact and their population genetics features. RESULTS: We discovered 14,272 autosomal CNVs, which were aggregated into 1755 CNV regions (CNVR) from 451 animals. These CNVRs together cover 2.8% of the bovine autosomes. The assessment of the functional impact of CNVRs showed that rare CNVRs (MAF < 0.01) are more likely to overlap with genes, than common CNVRs (MAF ≥ 0.05). The Population differentiation index (Fst) based on CNVRs revealed multiple highly diverged CNVRs between the two breeds. Some of these CNVRs overlapped with candidate genes such as MGAM and ADAMTS17 genes, which are related to starch digestion and body size, respectively. Lastly, linkage disequilibrium (LD) between CNVRs and BovineHD BeadChip SNPs was generally low, close to 0, although common deletions (MAF ≥ 0.05) showed slightly higher LD (r(2) = ~ 0.1 at 10 kb distance) than the rest. Nevertheless, this LD is still lower than SNP-SNP LD (r(2) = ~ 0.5 at 10 kb distance). CONCLUSIONS: Our analyses showed that CNVRs detected using BovineHD BeadChip arrays are likely to be functional. This finding indicates that CNVs can potentially disrupt the function of genes and thus might alter phenotypes. Also, the population differentiation index revealed two candidate genes, MGAM and ADAMTS17, which hint at adaptive evolution between the two populations. Lastly, low CNVR-SNP LD implies that genetic variation from CNVs might not be fully captured in routine animal genetic evaluation, which relies solely on SNP markers. |
format | Online Article Text |
id | pubmed-6988284 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2020 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-69882842020-01-31 Functional and population genetic features of copy number variations in two dairy cattle populations Lee, Young-Lim Bosse, Mirte Mullaart, Erik Groenen, Martien A. M. Veerkamp, Roel F. Bouwman, Aniek C. BMC Genomics Research Article BACKGROUND: Copy Number Variations (CNVs) are gain or loss of DNA segments that are known to play a role in shaping a wide range of phenotypes. In this study, we used two dairy cattle populations, Holstein Friesian and Jersey, to discover CNVs using the Illumina BovineHD Genotyping BeadChip aligned to the ARS-UCD1.2 assembly. The discovered CNVs were investigated for their functional impact and their population genetics features. RESULTS: We discovered 14,272 autosomal CNVs, which were aggregated into 1755 CNV regions (CNVR) from 451 animals. These CNVRs together cover 2.8% of the bovine autosomes. The assessment of the functional impact of CNVRs showed that rare CNVRs (MAF < 0.01) are more likely to overlap with genes, than common CNVRs (MAF ≥ 0.05). The Population differentiation index (Fst) based on CNVRs revealed multiple highly diverged CNVRs between the two breeds. Some of these CNVRs overlapped with candidate genes such as MGAM and ADAMTS17 genes, which are related to starch digestion and body size, respectively. Lastly, linkage disequilibrium (LD) between CNVRs and BovineHD BeadChip SNPs was generally low, close to 0, although common deletions (MAF ≥ 0.05) showed slightly higher LD (r(2) = ~ 0.1 at 10 kb distance) than the rest. Nevertheless, this LD is still lower than SNP-SNP LD (r(2) = ~ 0.5 at 10 kb distance). CONCLUSIONS: Our analyses showed that CNVRs detected using BovineHD BeadChip arrays are likely to be functional. This finding indicates that CNVs can potentially disrupt the function of genes and thus might alter phenotypes. Also, the population differentiation index revealed two candidate genes, MGAM and ADAMTS17, which hint at adaptive evolution between the two populations. Lastly, low CNVR-SNP LD implies that genetic variation from CNVs might not be fully captured in routine animal genetic evaluation, which relies solely on SNP markers. BioMed Central 2020-01-28 /pmc/articles/PMC6988284/ /pubmed/31992181 http://dx.doi.org/10.1186/s12864-020-6496-1 Text en © The Author(s). 2020 Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. |
spellingShingle | Research Article Lee, Young-Lim Bosse, Mirte Mullaart, Erik Groenen, Martien A. M. Veerkamp, Roel F. Bouwman, Aniek C. Functional and population genetic features of copy number variations in two dairy cattle populations |
title | Functional and population genetic features of copy number variations in two dairy cattle populations |
title_full | Functional and population genetic features of copy number variations in two dairy cattle populations |
title_fullStr | Functional and population genetic features of copy number variations in two dairy cattle populations |
title_full_unstemmed | Functional and population genetic features of copy number variations in two dairy cattle populations |
title_short | Functional and population genetic features of copy number variations in two dairy cattle populations |
title_sort | functional and population genetic features of copy number variations in two dairy cattle populations |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6988284/ https://www.ncbi.nlm.nih.gov/pubmed/31992181 http://dx.doi.org/10.1186/s12864-020-6496-1 |
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