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Functional and population genetic features of copy number variations in two dairy cattle populations
Young-Lim Lee
Wageningen Universiteit en Research
Corresponding Author
ORCiD: https://orcid.org/0000-0003-1182-0197
License:
This work is licensed under a CC BY 4.0 License. Read Full License
View the published version at BMC Genomics.
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 1,755 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 10kb distance) than the rest. Nevertheless, this LD is still lower than SNP-SNP LD ( r 2 =~0.5 at 10kb 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. Keywords : Copy number variations, Bos taurus , Linkage disequilibrium, population genetics
Keywords
Copy number variations, Bos taurus, Linkage disequilibrium, population genetics
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This preprint is under consideration at BMC Genomics. A preprint is a preliminary version of a manuscript that has not completed peer review at a journal. Research Square does not conduct peer review prior to posting preprints. The posting of a preprint on this server should not be interpreted as an endorsement of its validity or suitability for dissemination as established information or for guiding clinical practice.
Learn more about In Review
Research article
Functional and population genetic features of copy number variations in two dairy cattle populations
Young-Lim Lee
Wageningen Universiteit en Research
Corresponding Author
ORCiD: https://orcid.org/0000-0003-1182-0197
Badges
Prescreen
This manuscript passed our Prescreen assessment
Complete author information
Appropriate declaration statements
Potential risks to human health
Prescreen
Peer Review Timeline
CURRENT STATUS: Published
Version 5
Posted 15 Jan, 2020
Published
On 28 Jan, 2020
No community comments so far
Submission checks complete
On 14 Jan, 2020
Editorial decision: Accept
On 14 Jan, 2020
No comments provided
Submission checks complete
On 08 Jan, 2020
Editorial decision: Minor revision
On 08 Jan, 2020
No comments provided
Editorial decision: Minor revision
On 11 Dec, 2019
Editor assigned
On 10 Dec, 2019
Submission checks complete
On 09 Dec, 2019
Editor invited
On 09 Dec, 2019
No comments provided
Editorial decision: Minor revision
On 06 Dec, 2019
Editor assigned
On 21 Nov, 2019
Submission checks complete
On 20 Nov, 2019
Editor invited
On 20 Nov, 2019
No comments provided
Review #2 received
Received 22 Oct, 2019
Editorial decision: Major revision
On 22 Oct, 2019
Review #1 received
Received 11 Oct, 2019
Reviewer #2 agreed
On 30 Sep, 2019
Reviewer #1 agreed
On 23 Sep, 2019
Reviewers invited
Invitations sent on 22 Sep, 2019
Submission checks complete
On 03 Sep, 2019
Editor assigned
On 09 Aug, 2019
Editor invited
On 08 Aug, 2019
First submitted
On 07 Aug, 2019
Metrics
Comments: 0
PDF Downloads: ...
HTML Views: ...
Subject Areas
Epigenetics & Genomics
License:
This work is licensed under a CC BY 4.0 License. Read Full License
View the published version at BMC Genomics.
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 1,755 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 10kb distance) than the rest. Nevertheless, this LD is still lower than SNP-SNP LD ( r 2 =~0.5 at 10kb 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. Keywords : Copy number variations, Bos taurus , Linkage disequilibrium, population genetics
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Figure 5