Abstract
Simple SummaryCopy number variations (CNVs) are important sources of variation in mammalian species. In this study, we used a single nucleotide polymorphisms (SNP) array to detect CNVs in Braque Français, type Pyrénées dogs (BRA). Results overlapped moderately in comparison with previous studies on CNVs in dogs, leading to the identification of 16 novel CNVRs. Several genes were annotated in the CNV regions (CNVRs) detected, some of which related to muscle structure development. This breed is known to be excellent upland game birds dogs. The selection for such hunting behavior could have driven the presence of these genes into the CNVRs. Copy number variations may be of interest to study associations between genomic and phenotypic variation.Copy number variants (CNVs) are an important source of genetic variation complementary to single nucleotide polymorphisms (SNPs). Only few studies have been conducted in dogs on CNVs derived from high-density SNP array data, and many canine breeds still remain uncharacterized, 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 SNP array (170 K) to discover CNVs in BRA. The CNV regions (CNVRs) were identified through the merging of two different CNVRs datasets, obtained separately from SNP data using the PennCNV and SVS software. A total of 45 stringent CNVRs, ranging from 3.5 kb to 458,716 kb in length were detected in 26 dog samples. Results overlapped 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 detected with stringent quality criteria in particular high classification stringency and false discovery rate correction. The gene ontology enrichment analysis provided information on biological processes and cellular components related to muscle structure development and muscle cell differentiation. Considering that BRA is a breed used for speed in hunting and retrieval, for the ability to find feathered game, and for pointing, we can hypothesize that selection for such hunting behavior could have driven, at least in part, the presence of these genes into the CNVRs.
Highlights
The domestication domestication of ofmodern moderndogs dogsstarted startedapproximately approximately15,00015,000years years ago and has resulted ago [1][1]and has resulted in in extraordinary amount of variation in canine forms and functions, theofcreation of an an extraordinary amount of variation in canine forms and functions, through through the creation divergent divergent breeds.withbiological their great biological are model very suitable animals to breeds
After excludingonSNPs chromosomes were obtained from the genomeasequence assembly
To reduce the possible false Copy number variants (CNVs) calls, we considered only those CNVs that contained three or more consecutive single nucleotide polymorphisms (SNPs)
Summary
Withbiological their great biological are model very suitable animals to breeds. With Dogs, their great diversity, are diversity, very suitable animals model to address studies address studiesgenetics, of population genetics, phenotypic diseases, many which are similar of population phenotypic variation and variation diseases,and many of which areofsimilar to human to human[2]. With the completion of theofassembly of genome, the canine genome, high-throughput diseases. With the of the assembly the canine high-throughput sequencing sequencing and genotyping offered a great potentialour to increase our understanding of and genotyping technologiestechnologies offered a great potential to increase understanding of the genomic the genomic of canid variation. Single nucleotide (SNP) data have investigate investigate patternsvariation of genetic variation within and between breeds, examine among relatedness among patterns of genetic within and between breeds, examine relatedness breeds, and breeds, identify selection [3].
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