Copy Number Variation (CNV): A New Genomic Insight in Horses

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.

Advancements in copy number variation screening in herbivorous livestock genomes and their association with phenotypic traits

“…To identify genes that may be influenced by CNVRs within the genome, an annotation analysis of genes associated with CNVRs revealed that olfactory-related functions, specifically olfactory transduction and olfactory receptor activity, were frequently affected. This observation aligns with previous findings in various species, including cattle ( 119 ), sheep ( 62 , 111 ), horses ( 34 , 115 , 120 ) and humans ( 121 – 123 ), where genes affected by copy number variation have shown enrichment for olfactory-related functions. In the case of humans, the sense of smell is considered a minor aspect of overall health and may not be closely linked with adaptation.…”

“…Furthermore, they constructed an autosomal map of CNVRs in horses. In addition, Laseca et al ( 34 ) analyzed high-density SNP genotyping data from 654 horses, identifying a total of 19,902 CNV segments and 1,007 CNV regions, with CNVs covering 4.4% of the equine genome.…”

Identification of Copy Number Variations in Four Horse Breed Populations in South Korea

“…To characterize the CNVRs identified in this study in more detail, we compared them to those identified in ten previous studies that used various methods [ 13 , 15 , 33 , 34 , 35 , 38 , 39 , 40 , 41 , 42 ]. A total of 2519 CNVRs were identified across all 11 studies: 1844 (73.2%) CNVRs were identified in our study and the previous studies, and 675 (26.8%) CNVRs were identified only in this study ( Table S3 ).…”

“…Doan et al (2012) published the first study to detect genome-wide CNVs in horses, using a whole-exome tiling array and an array-comparative genomic hybridization platform. Since the development of high-density SNP arrays for horses [ 7 , 11 ], CNVs could be also assessed throughout the genomes of various horse breeds, of which some studies investigated potential associations with traits of interest in horses, including body size and genetic risk factors for insect-bite hypersensitivity [ 12 , 13 , 14 , 15 ].…”

Genome-wide copy number variation detection in a large cohort of diverse horse breeds by whole-genome sequencing

“…Several CNV-overlapping candidate genes were discovered to be associated with thermal adaptation in Jinjiang horses ( 12 ). Recent CNV survey studies utilized European horse breeds ( 13 ), Criollo Argentino horses ( 14 ), South Korean horse breeds ( 15 ), and purebred Spanish horses ( 16 ). However, all of these studies mentioned above were conducted either using PCRs, microarrays, or SNP chips and to our best knowledge, only a few studies were conducted using whole-genome sequencing to detect CNVs in horse populations ( 17 , 18 ).…”