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Inter- and intra-breed genome-wide copy number diversity in a large cohort of European equine breeds
Swedish Univ Agr Sci, Dept Anim Breeding & Genet, Uppsala, Sweden.ORCID iD: 0000-0001-7884-1051
Univ Parma, Dept Vet Sci, Parma, Italy.ORCID iD: 0000-0003-3700-1042
Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Sciences.
Univ Sydney, Fac Life & Environm Sci, Sydney, NSW, Australia.
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2019 (English)In: BMC Genomics, ISSN 1471-2164, E-ISSN 1471-2164, Vol. 20, no 1, article id 759Article in journal (Refereed) Published
Abstract [en]

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 (R) 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 (similar to 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.

Place, publisher, year, edition, pages
BMC , 2019. Vol. 20, no 1, article id 759
Keywords [en]
Copy number variation, Horse, Structural variation, SNP genotyping array
National Category
Genetics Genetics and Breeding in Agricultural Sciences
Identifiers
URN: urn:nbn:se:uu:diva-397040DOI: 10.1186/s12864-019-6141-zISI: 000491861300003PubMedID: 31640551OAI: oai:DiVA.org:uu-397040DiVA, id: diva2:1371731
Funder
Swedish Research Council Formas, 2016-00947Available from: 2019-11-20 Created: 2019-11-20 Last updated: 2019-11-20Bibliographically approved

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