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BMC genomics2019; 20(1); 759; doi: 10.1186/s12864-019-6141-z

Inter- and intra-breed genome-wide copy number diversity in a large cohort of European equine breeds.

Abstract: 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 = 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: 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.
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Publication Date: 2019-10-22 PubMed ID: 31640551PubMed Central: PMC6805398DOI: 10.1186/s12864-019-6141-zGoogle Scholar: Lookup
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  • Journal Article

Summary

This research summary has been generated with artificial intelligence and may contain errors and omissions. Refer to the original study to confirm details provided. Submit correction.

This study examines the variations in gene copy number in different horse breeds to understand how these variations contribute to their evolution and diversity.

Research Methods and Objectives

  • The research aimed to understand the patterns of Copy Number Variation (CNV), population variation, and gene annotation of CNV in horses, and in particular European breeds.
  • They used a large group of individual horses from eight different breeds, including draught horses and several warmblood populations.
  • The Axiom® Equine Genotyping Array was used in the study, which contained 670,796 Single Nucleotide Polymorphisms (SNPs).

Findings

  • The analysis discovered 152,640 SNP CNVs (individual markers that indicate variation in the number of gene copies), 18,800 segment CNVs (consecutive SNP CNVs of the same gain/loss state), and 939 CNV regions (overlapping segment CNVs).
  • Equus caballus chromosome 12 (ECA12) had the most segment CNV gains and losses, but the highest number of segment CNVs were detected on ECA1 and ECA20.
  • Different horse breeds had private SNP CNV gains or losses on specific chromosomes suggesting a possible link to breed characteristics.
  • A total of 10,612 genes were annotated within the CNV regions, which significantly aligned with the biological terms related to cellular processes and immunity.
  • 80 CNV regions overlapped with known Quantitative Trait Loci (QTL) for fertility, coat colour, conformation and temperament, providing potential leads for understanding breed diversity.
  • 67 novel CNV regions were found in this study, which had not previously been reported.

Conclusions

  • The research found that CNV patterns in the genome of various European horse breeds occurred in specific genomic regions.
  • The results support the hypothesis that high frequency private CNVs residing in genes may potentially be responsible for the diverse phenotypes seen between horse breeds.
  • This study would potentially help in studying the genetic basis of phenotypic variations and in horse breeding programs.

Cite This Article

APA
Solé M, Ablondi M, Binzer-Panchal A, Velie BD, Hollfelder N, Buys N, Ducro BJ, François L, Janssens S, Schurink A, Viklund Å, Eriksson S, Isaksson A, Kultima H, Mikko S, Lindgren G. (2019). Inter- and intra-breed genome-wide copy number diversity in a large cohort of European equine breeds. BMC Genomics, 20(1), 759. https://doi.org/10.1186/s12864-019-6141-z

Publication

BMC genomics
ISSN: 1471-2164
NlmUniqueID: 100965258
Country: England
Language: English
Volume: 20
Issue: 1
Pages: 759
PII: 759

Researcher Affiliations

Solé, Marina
  • Department of Animal Breeding & Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden. marina.sole@slu.se.
Ablondi, Michela
  • Department of Veterinary Science, Università di Parma, Parma, Italy.
Binzer-Panchal, Amrei
  • Department of Medical Sciences, Array and Analysis Facility, Uppsala University, Uppsala, Sweden.
Velie, Brandon D
  • Faculty of Life and Environmental Science, University of Sydney, Sydney, NSW, Australia.
Hollfelder, Nina
  • Department of Medical Sciences, Array and Analysis Facility, Uppsala University, Uppsala, Sweden.
Buys, Nadine
  • Livestock Genetics, Department of Biosystems, KU Leuven, 3001, Leuven, Belgium.
Ducro, Bart J
  • Animal Breeding and Genomics, Wageningen University & Research, P.O. Box 338, 6700 AH, Wageningen, the Netherlands.
François, Liesbeth
  • Livestock Genetics, Department of Biosystems, KU Leuven, 3001, Leuven, Belgium.
Janssens, Steven
  • Livestock Genetics, Department of Biosystems, KU Leuven, 3001, Leuven, Belgium.
Schurink, Anouk
  • Animal Breeding and Genomics, Wageningen University & Research, P.O. Box 338, 6700 AH, Wageningen, the Netherlands.
  • Centre for Genetic Resources, the Netherlands (CGN), Wageningen University & Research, P.O. Box 338, 6700 AH, Wageningen, the Netherlands.
Viklund, Åsa
  • Department of Animal Breeding & Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden.
Eriksson, Susanne
  • Department of Animal Breeding & Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden.
Isaksson, Anders
  • Department of Medical Sciences, Array and Analysis Facility, Uppsala University, Uppsala, Sweden.
Kultima, Hanna
  • Department of Medical Sciences, Array and Analysis Facility, Uppsala University, Uppsala, Sweden.
Mikko, Sofia
  • Department of Animal Breeding & Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden.
Lindgren, Gabriella
  • Department of Animal Breeding & Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden.
  • Livestock Genetics, Department of Biosystems, KU Leuven, 3001, Leuven, Belgium.

MeSH Terms

  • Animals
  • Breeding
  • Comparative Genomic Hybridization
  • DNA Copy Number Variations / genetics
  • Europe
  • Evolution, Molecular
  • Genetic Variation
  • Genetics, Population
  • Genome / genetics
  • Genotype
  • Horses / genetics
  • Phenotype
  • Selection, Genetic

Grant Funding

  • 606142 / FP7 Research for the Benefit of SMEs
  • H1147215 / Stiftelsen Hu00e4stforskning

Conflict of Interest Statement

The authors declare that they have no competing interests.

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Citations

This article has been cited 23 times.
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