Citation: Laseca, N.; Molina, A.; Valera, M.; Antonini, A.; Demyda-Peyrás, S. Copy Number Variation (CNV): A New Genomic Insight in Horses. Animals 2022, 12, 1435. https://doi.org/10.3390/ ani12111435 Academic Editor: Maria Teresa Sardina Received: 3 May 2022 Accepted: 30 May 2022 Published: 2 June 2022 Publisher’s Note: MDPI stays neutral with regard to jurisdictional claims in published maps and institutional affil- iations. Copyright: © 2022 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https:// creativecommons.org/licenses/by/ 4.0/). animals Article Copy Number Variation (CNV): A New Genomic Insight in Horses Nora Laseca 1 , Antonio Molina 1 , Mercedes Valera 2 , Alicia Antonini 3 and Sebastián Demyda-Peyrás 3,4, * 1 Departamento of Genética, Universidad de Córdoba, Edificio Gregor Mendel, CN-IV KM396, 14071 Córdoba, Spain; ge2lagan@uco.es (N.L.); ge1moala@uco.es (A.M.) 2 Departamento de Agronomía, ETSIA, Universidad de Sevilla, Ctra Utrera Km 1, 41013 Sevilla, Spain; mvalera@us.es 3 Departamento de Producción Animal, Facultad de Ciencias Veterinarias, Universidad Nacional de La Plata, La Plata 1900, Argentina; antonini@fcv.unlp.edu.ar 4 Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), La Plata 1900, Argentina * Correspondence: sdemyda@fcv.unlp.edu.ar Simple Summary: This study aimed to contribute to our knowledge of CNVs, a type of genomic marker in equines, by producing, for the first time, a fine-scale characterization of the CNV regions (CNVRs) in the Pura Raza Española horse breed. We found not only the existence of a unique pattern of genomic regions enriched in CNVs in the PRE in comparison with the data available from other breeds but also the incidence of CNVs across the entire genome. Since these regions could affect the structure and dose of the genes involved, we also performed a gene ontology analysis which revealed that most of the genes overlapping in CNVRs were related to the olfactory pathways and immune response. Abstract: Copy number variations (CNVs) are a new-fangled source of genetic variation that can explain changes in the phenotypes in complex traits and diseases. In recent years, their study has increased in many livestock populations. However, the study and characterization of CNVs in equines is still very limited. Our study aimed to investigate the distribution pattern of CNVs, characterize CNV regions (CNVRs), and identify the biological pathways affected by CNVRs in the Pura Raza Española (PRE) breed. To achieve this, we analyzed high-density SNP genotyping data (670,804 markers) from a large cohort of 654 PRE horses. In total, we identified 19,902 CNV segments and 1007 CNV regions in the whole population. The length of the CNVs ranged from 1.024 kb to 4.55 Mb, while the percentage of the genome covered by CNVs was 4.4%. Interestingly, duplications were more abundant than deletions and mixed CNVRs. In addition, the distribution of CNVs across the chromosomes was not uniform, with ECA12 being the chromosome with the largest percentage of its genome covered (19.2%), while the highest numbers of CNVs were found in ECA20, ECA12, and ECA1. Our results showed that 71.4% of CNVRs contained genes involved in olfactory transduction, olfactory receptor activity, and immune response. Finally, 39.1% of the CNVs detected in our study were unique when compared with CNVRs identified in previous studies. To the best of our knowledge, this is the first attempt to reveal and characterize the CNV landscape in PRE horses, and it contributes to our knowledge of CNVs in equines, thus facilitating the understanding of genetic and phenotypic variations in the species. However, further research is still needed to confirm if the CNVs observed in the PRE are also linked to variations in the specific phenotypical differences in the breed. Keywords: copy number variation regions; functional clustering; SNP genotyping array; horse breed 1. Introduction Copy number variations (CNVs) are defined as a change in the DNA sequence com- pared to a reference assembly due to the loss (deletions) or gain (insertions and duplica- Animals 2022, 12, 1435. https://doi.org/10.3390/ani12111435 https://www.mdpi.com/journal/animals