Next Article in Journal
Using the Footfall Sound of Dairy Cows for Detecting Claw Lesions
Previous Article in Journal
Development and Function of the Intestinal Microbiome and Potential Implications for Pig Production
Article Menu

Export Article

Open AccessCommunication
Animals 2019, 9(3), 77; https://doi.org/10.3390/ani9030077

A Genome-Wide Detection of Copy Number Variations Using SNP Genotyping Arrays in Braque Français Type Pyrénées Dogs

1
Dipartimento Scienze Agrarie, Alimentari e Forestali, University of Palermo, 90128 Palermo, Italy
2
Club Italiano Braque Français Type Pyrénées, 58011 Capalbio, Italy
3
Scuola di Scienze Mediche Veterinarie, University of Camerino, 62024 Matelica, Italy
4
Centro Interuniversitario di Ricerca e di Consulenza sulla Genetica e la Clinica del Cane, 62024 Matelica, Italy
5
Consiglio Nazionale delle Ricerche-Istituto di Biologia e Biotecnologia Agraria, 20133 Milano, Italy
6
Dipartimento di Scienze Veterinarie, University of Pisa, 56100 Pisa, Italy
*
Author to whom correspondence should be addressed.
Received: 8 January 2019 / Revised: 21 February 2019 / Accepted: 28 February 2019 / Published: 1 March 2019
(This article belongs to the Section Animal Genetics and Genomics)
Full-Text   |   PDF [836 KB, uploaded 7 March 2019]   |  

Simple Summary

Copy 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.

Abstract

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. View Full-Text
Keywords: copy number variation (CNV); canine high-density SNP array; Braque Français type Pyrénées dogs copy number variation (CNV); canine high-density SNP array; Braque Français type Pyrénées dogs
Figures

Figure 1

This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited (CC BY 4.0).

Supplementary material

SciFeed

Share & Cite This Article

MDPI and ACS Style

Di Gerlando, R.; Mastrangelo, S.; Sardina, M.T.; Ragatzu, M.; Spaterna, A.; Portolano, B.; Biscarini, F.; Ciampolini, R. A Genome-Wide Detection of Copy Number Variations Using SNP Genotyping Arrays in Braque Français Type Pyrénées Dogs. Animals 2019, 9, 77.

Show more citation formats Show less citations formats

Note that from the first issue of 2016, MDPI journals use article numbers instead of page numbers. See further details here.

Related Articles

Article Metrics

Article Access Statistics

1

Comments

[Return to top]
Animals EISSN 2076-2615 Published by MDPI AG, Basel, Switzerland RSS E-Mail Table of Contents Alert
Back to Top