Copy Number Variation (CNV): A New Genomic Insight in Horses.
Authors: Laseca Nora, Molina Antonio, Valera Mercedes, Antonini Alicia, Demyda-Peyrás Sebastián
Journal: Animals : an open access journal from MDPI
Summary
Copy number variations (CNVs)—segments of DNA present in differing quantities across individuals—represent an underexplored source of genomic diversity in horses that may underpin breed-specific traits and disease susceptibility. Researchers analysed high-density SNP data from 654 Pura Raza Española horses, identifying 19,902 CNV segments spanning 4.4% of the genome, with lengths ranging from 1.024 kb to 4.55 Mb and a notable predominance of duplications over deletions. Chromosome 12 showed the highest genomic coverage by CNVs (19.2%), whilst chromosomes 20, 12, and 1 harboured the greatest number of CNV regions; notably, 39.1% of detected CNVs were previously unreported in equine literature. Functional analysis revealed that 71.4% of CNV regions contained genes involved in olfactory transduction, olfactory receptor activity, and immune response pathways—categories particularly relevant to breed selection and disease resistance. Whilst this work establishes a comprehensive CNV landscape for the PRE breed and advances our understanding of equine genetic architecture, practitioners should recognise that the phenotypic consequences of these variations remain largely unconfirmed; targeted research linking specific CNVs to observable performance, conformation, or health traits would be necessary before incorporating CNV profiling into breeding programmes or clinical assessment protocols.
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Practical Takeaways
- •This genomic characterization of the PRE breed provides baseline CNV data that could eventually help explain phenotypic differences and disease susceptibility in the breed, though clinical applications require further research
- •The high proportion of novel CNVs (39.1%) suggests CNV variation in horses is still incompletely mapped and warrants continued genomic studies across breeds
- •The predominance of genes related to immune response and olfactory function in CNV regions indicates these traits may be subject to copy number-driven variation in the PRE breed
Key Findings
- •19,902 CNV segments and 1,007 CNV regions identified in 654 PRE horses, covering 4.4% of the genome with lengths ranging from 1.024 kb to 4.55 Mb
- •Duplications were more abundant than deletions, with ECA12 showing the largest percentage of genome coverage at 19.2% and ECA20, ECA12, and ECA1 containing the highest CNV numbers
- •71.4% of CNVRs contained genes involved in olfactory transduction, olfactory receptor activity, and immune response
- •39.1% of CNVs detected were novel when compared with previously identified CNVRs in equines