Identification of Copy Number Variants in Braque Français type Pyrénées”dog using CanineHD array

Copy number variants (CNVs) are an important source of genetic variation complementary to single nucleotide polymorphisms (SNPs). Only a few studies have been conducted in dogs on CNVs derived from high-density SNP array data, and many canine breeds still remain uncharacterised, e.g. the Braque Français, type Pyrénées breed (BRA). Therefore, in an effort to more comprehensively investigate the canine genome for CNVs, we used a high-density genome-wide array (170 K) to discover additional CNVs in BRA. A total of 48 BRA individuals (27 females, 21 males) were sampled. After excluding SNPs which were unmapped or mapped to sex chromosomes, a total of 167,183 markers were used. A total of 1047 CNVs were detected using PennCNV, with an average length of 107.123 kb and an average number of 40.3 CNVs per sample. The CNAM univariate segmentation of SVS identified 1638 CNVs with an average length of 110.41 kb and the average number of 63 CNVs per sample. By aggregating the overlapping CNVs from PennCNV, a total of 181 CNVRs were identified. The CNVs identified with SVS were aggregated into 280 CNVRs. Intersecting the two CNVR datasets, a total of 45 CNVRs, ranging from 3.5 kb to 458,716 kb in length were detected in 26 dog samples. Among the stringent CNVRs, 42 CNVRs were defined as pure deletions, and only 3 as loss/gain, meaning that both deletions and duplications were observed. Results overlap moderately in comparison with previous studies on CNVs in dogs, leading to the identification of 16 novel CNVRs. A total of 159 genes were annotated in the CNVRs. Some of these genes are associated with well-known phenotypes in dogs, such as: SOX8 involved in sex determination, SLC38A2 related to hypoxia adaptation, MYOG associated with the development of functional skeletal muscle. Moreover, the gene ontology enrichment analysis provided information on biological processes and cellular components related with muscle structure development and muscle cell differentiation. These are interesting results considering that BRA is a dog breed used for tracking, hunting, pointing and retrieving feathered game. These are hardy dogs, strong, adequately muscled but without heaviness. We can hypothesise that selection for such hunting behaviour, for which particular anatomical features are required, could have shaped, at least in part, the genetic background of this breed and, consequently, the frequency/presence of the detected CNVRs in these genes.