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Research article
Marina Solé
Sveriges lantbruksuniversitet
Corresponding Author
ORCiD: https://orcid.org/0000-0001-7884-1051
License:
This work is licensed under a CC BY 4.0 License. Read Full License
Background Copy Number Variation (CNV) is a common form of genetic variation underlying animal evolution and phenotypic diversity across a wide range of species. In the mammalian genome, high frequency of CNV differentiation between breeds may be candidates for population-specific selection. However, CNV differentiation, selection and its population genetics have been poorly explored in horses.
Results We investigated the patterns, population variation and gene annotation of CNV using the Axiom ® Equine Genotyping Array (670,796 SNPs) from a large cohort of individuals (N=1,755) belonging to eight European horse breeds, varying from draught horses to several warmblood populations. After quality control, 152,64 0 SNP CNVs (individual markers), 18,800 segment CNVs (consecutive SNP CNVs of same gain/loss state or both) and 939 CNV regions (CNVRs; overlapping segment CNVs by at least 1bp) compared to the average signal of the reference (Belgian draught horse) were identified. Our analyses showed that Equus caballus chromosome 12 (ECA12) was the most enriched in segment CNV gains and losses (~3% average proportion of the genome covered), but the highest number of segment CNVs were detected on ECA1 and ECA20 (regardless of size). The Friesian horses showed private SNP CNV gains (>20% of the samples) on ECA1 and Exmoor ponies displayed private SNP CNV losses on ECA25 (>20% of the samples). The Warmblood cluster showed private SNP CNV gains located in ECA9 and Draught cluster showed private SNP CNV losses located in ECA7. The length of the CNVRs ranged from 1 kb to 21.3 Mb. A total of 10,612 genes were annotated within the CNVRs. The PANTHER annotation of these genes showed significantly under- and overrepresented gene ontology biological terms related to cellular processes and immunity (Bonferroni P-value < 0.05). We identified 80 CNVRs overlapping with known QTL for fertility, coat colour, conformation and temperament. We also report 67 novel CNVRs.
Conclusions This work revealed that CNV patterns, in the genome of some European horse breeds, occurred in specific genomic regions. The results provide support to the hypothesis that high frequency private CNVs residing in genes may potentially be responsible for the diverse phenotypes seen between horse breeds.
Keywords
Copy number variation, Horse, Structural variation, SNP genotyping array
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CURRENT STATUS: Published
View the published article at BMC Genomics.
No community comments so far
Submission checks complete
On 06 Nov, 2019
Editorial decision: Accept
On 25 Sep, 2019
Version 2
Posted 26 Sep, 2019
No comments provided
Editorial decision: Minor revision
On 23 Sep, 2019
Reviewer #1 agreed
On 12 Sep, 2019
Review #1 received
Received 12 Sep, 2019
Editor assigned
On 10 Sep, 2019
Reviewers invited
Invitations sent on 10 Sep, 2019
Submission checks complete
On 09 Sep, 2019
Editor invited
On 09 Sep, 2019
No comments provided
Editorial decision: Minor revision
On 25 Aug, 2019
Review #1 received
Received 04 Aug, 2019
Reviewer #1 agreed
On 02 Jul, 2019
Reviewer #2 agreed
On 02 Jul, 2019
Reviewers invited
Invitations sent on 30 Jun, 2019
Submission checks complete
On 19 Jun, 2019
Editor invited
On 30 May, 2019
Editor assigned
On 30 May, 2019
First submitted
On 29 May, 2019
Metrics
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Subject Areas
Epigenetics & Genomics
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A new preprint design is coming!
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See the published version of this preprint at BMC Genomics.
This is a preprint, 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
Marina Solé
Sveriges lantbruksuniversitet
Corresponding Author
ORCiD: https://orcid.org/0000-0001-7884-1051
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
View the published article at BMC Genomics.
No community comments so far
Submission checks complete
On 06 Nov, 2019
Editorial decision: Accept
On 25 Sep, 2019
Version 2
Posted 26 Sep, 2019
No comments provided
Editorial decision: Minor revision
On 23 Sep, 2019
Reviewer #1 agreed
On 12 Sep, 2019
Review #1 received
Received 12 Sep, 2019
Editor assigned
On 10 Sep, 2019
Reviewers invited
Invitations sent on 10 Sep, 2019
Submission checks complete
On 09 Sep, 2019
Editor invited
On 09 Sep, 2019
No comments provided
Editorial decision: Minor revision
On 25 Aug, 2019
Review #1 received
Received 04 Aug, 2019
Reviewer #1 agreed
On 02 Jul, 2019
Reviewer #2 agreed
On 02 Jul, 2019
Reviewers invited
Invitations sent on 30 Jun, 2019
Submission checks complete
On 19 Jun, 2019
Editor invited
On 30 May, 2019
Editor assigned
On 30 May, 2019
First submitted
On 29 May, 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 article at BMC Genomics.
Background Copy Number Variation (CNV) is a common form of genetic variation underlying animal evolution and phenotypic diversity across a wide range of species. In the mammalian genome, high frequency of CNV differentiation between breeds may be candidates for population-specific selection. However, CNV differentiation, selection and its population genetics have been poorly explored in horses.
Results We investigated the patterns, population variation and gene annotation of CNV using the Axiom ® Equine Genotyping Array (670,796 SNPs) from a large cohort of individuals (N=1,755) belonging to eight European horse breeds, varying from draught horses to several warmblood populations. After quality control, 152,64 0 SNP CNVs (individual markers), 18,800 segment CNVs (consecutive SNP CNVs of same gain/loss state or both) and 939 CNV regions (CNVRs; overlapping segment CNVs by at least 1bp) compared to the average signal of the reference (Belgian draught horse) were identified. Our analyses showed that Equus caballus chromosome 12 (ECA12) was the most enriched in segment CNV gains and losses (~3% average proportion of the genome covered), but the highest number of segment CNVs were detected on ECA1 and ECA20 (regardless of size). The Friesian horses showed private SNP CNV gains (>20% of the samples) on ECA1 and Exmoor ponies displayed private SNP CNV losses on ECA25 (>20% of the samples). The Warmblood cluster showed private SNP CNV gains located in ECA9 and Draught cluster showed private SNP CNV losses located in ECA7. The length of the CNVRs ranged from 1 kb to 21.3 Mb. A total of 10,612 genes were annotated within the CNVRs. The PANTHER annotation of these genes showed significantly under- and overrepresented gene ontology biological terms related to cellular processes and immunity (Bonferroni P-value < 0.05). We identified 80 CNVRs overlapping with known QTL for fertility, coat colour, conformation and temperament. We also report 67 novel CNVRs.
Conclusions This work revealed that CNV patterns, in the genome of some European horse breeds, occurred in specific genomic regions. The results provide support to the hypothesis that high frequency private CNVs residing in genes may potentially be responsible for the diverse phenotypes seen between horse breeds.
Figure 1
Figure 2
Figure 3
Figure 4
Figure 5
This is a list of supplementary files associated with this preprint. Click to download.
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