A genome-wide detection of copy number variations using SNP genotyping arrays in braque français type pyrénées dogs

Rosalia Di Gerlando, Salvatore Mastrangelo, Maria Teresa Sardina, Baldassare Portolano, Filippo Biscarini, Marco Ragatzu, Roberta Ciampolini, Andrea Spaterna

Risultato della ricerca: Article

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.
Lingua originaleEnglish
pagine (da-a)77-
Numero di pagine8
RivistaDefault journal
Volume9
Stato di pubblicazionePublished - 2019

All Science Journal Classification (ASJC) codes

  • Animal Science and Zoology
  • veterinary(all)

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@article{6301f5933b61499dba8fe7786cea6928,
title = "A genome-wide detection of copy number variations using SNP genotyping arrays in braque fran{\cc}ais type pyr{\'e}n{\'e}es dogs",
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 Fran{\cc}ais, type Pyr{\'e}n{\'e}es 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.",
keywords = "Animal Science and Zoology, Braque Fran{\cc}ais type Pyr{\'e}n{\'e}es dogs, Canine high-density SNP array, Copy number variation (CNV), Veterinary (all)",
author = "{Di Gerlando}, Rosalia and Salvatore Mastrangelo and Sardina, {Maria Teresa} and Baldassare Portolano and Filippo Biscarini and Marco Ragatzu and Roberta Ciampolini and Andrea Spaterna",
year = "2019",
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TY - JOUR

T1 - A genome-wide detection of copy number variations using SNP genotyping arrays in braque français type pyrénées dogs

AU - Di Gerlando, Rosalia

AU - Mastrangelo, Salvatore

AU - Sardina, Maria Teresa

AU - Portolano, Baldassare

AU - Biscarini, Filippo

AU - Ragatzu, Marco

AU - Ciampolini, Roberta

AU - Spaterna, Andrea

PY - 2019

Y1 - 2019

N2 - 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.

AB - 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.

KW - Animal Science and Zoology

KW - Braque Français type Pyrénées dogs

KW - Canine high-density SNP array

KW - Copy number variation (CNV)

KW - Veterinary (all)

UR - http://hdl.handle.net/10447/352831

UR - https://www.mdpi.com/2076-2615/9/3/77/pdf

M3 - Article

VL - 9

SP - 77-

JO - Default journal

JF - Default journal

ER -