Inter- and intra-breed genome-wide copy number diversity in a large cohort of European equine breeds.
Copy number variation
Horse
SNP genotyping array
Structural variation
Journal
BMC genomics
ISSN: 1471-2164
Titre abrégé: BMC Genomics
Pays: England
ID NLM: 100965258
Informations de publication
Date de publication:
22 Oct 2019
22 Oct 2019
Historique:
received:
29
05
2019
accepted:
25
09
2019
entrez:
24
10
2019
pubmed:
24
10
2019
medline:
27
2
2020
Statut:
epublish
Résumé
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. 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 = 1755) belonging to eight European horse breeds, varying from draught horses to several warmblood populations. After quality control, 152,640 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 1 bp) 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. 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.
Sections du résumé
BACKGROUND
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
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 = 1755) belonging to eight European horse breeds, varying from draught horses to several warmblood populations. After quality control, 152,640 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 1 bp) 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
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.
Identifiants
pubmed: 31640551
doi: 10.1186/s12864-019-6141-z
pii: 10.1186/s12864-019-6141-z
pmc: PMC6805398
doi:
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
759Subventions
Organisme : FP7 Research for the Benefit of SMEs
ID : 606142
Organisme : Stiftelsen Hästforskning
ID : H1147215
Références
PLoS Genet. 2014 Oct 23;10(10):e1004712
pubmed: 25340504
Nat Genet. 2008 Aug;40(8):1004-9
pubmed: 18641652
G3 (Bethesda). 2016 Jul 07;6(7):2213-23
pubmed: 27207956
Nature. 2010 Apr 1;464(7289):704-12
pubmed: 19812545
Anim Genet. 2010 Dec;41 Suppl 2:64-71
pubmed: 21070278
Nature. 2018 Jun;558(7708):73-79
pubmed: 29875488
Nucleic Acids Res. 2017 Jan 4;45(D1):D183-D189
pubmed: 27899595
Genet Sel Evol. 2009 Jan 05;41:5
pubmed: 19284689
Nat Genet. 2016 Feb;48(2):152-8
pubmed: 26691985
Genome. 2018 Oct;61(10):767-770
pubmed: 30184439
Genome Biol. 2016 Jun 06;17(1):122
pubmed: 27268795
PLoS One. 2013 Sep 30;8(9):e75071
pubmed: 24098679
PLoS Genet. 2014 Dec 04;10(12):e1004830
pubmed: 25474574
BMC Genomics. 2017 Jul 27;18(1):565
pubmed: 28750625
PLoS One. 2006 Dec 20;1:e85
pubmed: 17183716
BMC Genomics. 2014 Mar 19;15:210
pubmed: 24640994
BMC Genomics. 2015 Apr 22;16:330
pubmed: 25896665
Genome Res. 2015 Aug;25(8):1114-24
pubmed: 26149421
Genomics. 2018 May;110(3):143-148
pubmed: 28917637
Nature. 2012 Aug 30;488(7413):642-6
pubmed: 22932389
PLoS Genet. 2013;9(1):e1003211
pubmed: 23349635
BMC Genet. 2018 Jul 30;19(1):49
pubmed: 30060732
Anim Reprod Sci. 2016 Aug;171:81-6
pubmed: 27334685
PLoS One. 2016 Apr 12;11(4):e0152966
pubmed: 27070818
Genetics. 2016 Oct;204(2):423-434
pubmed: 27729493
Nucleic Acids Res. 2016 Jan 4;44(D1):D827-33
pubmed: 26602686
Genome. 2018 Jan;61(1):7-14
pubmed: 28961404
BMC Genomics. 2017 Dec 19;18(1):977
pubmed: 29258433
Anim Genet. 2016 Jun;47(3):334-44
pubmed: 26932307
Front Genet. 2017 Aug 23;8:108
pubmed: 28878807
Nat Genet. 2007 Nov;39(11):1318-20
pubmed: 17906623
PLoS One. 2014 Jan 30;9(1):e86860
pubmed: 24497987
Methods. 2001 Dec;25(4):402-8
pubmed: 11846609
BMC Genomics. 2012 Dec 27;13:733
pubmed: 23270433
Sci Rep. 2016 Mar 23;6:23161
pubmed: 27005566
J Anim Breed Genet. 2018 Feb;135(1):73-83
pubmed: 29345072
Genome Res. 2012 May;22(5):899-907
pubmed: 22383489
Nature. 2008 Nov 6;456(7218):18-21
pubmed: 18987709
BMC Genomics. 2011 Aug 16;12:414
pubmed: 21846351
BMC Genomics. 2012 Feb 17;13:78
pubmed: 22340285
Bioinformatics. 2010 Mar 15;26(6):841-2
pubmed: 20110278
PLoS One. 2014 Jan 28;9(1):e87115
pubmed: 24489850
Anim Genet. 2013 Apr;44(2):206-8
pubmed: 22582820
BMC Genomics. 2018 May 29;19(1):410
pubmed: 29843606
BMC Genomics. 2013 Jul 18;14:487
pubmed: 23865711
Nat Rev Genet. 2013 Feb;14(2):125-38
pubmed: 23329113
Nature. 2006 Nov 23;444(7118):444-54
pubmed: 17122850