An initial map of chromosomal segmental copy number variations in the chickenReport as inadecuate




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BMC Genomics

, 11:351

First Online: 03 June 2010Received: 02 July 2009Accepted: 03 June 2010

Abstract

BackgroundChromosomal segmental copy number variation CNV has been recently recognized as a very important source of genetic variability. Some CNV loci involve genes or conserved regulatory elements. Compelling evidence indicates that CNVs impact genome functions. The chicken is a very important farm animal species which has also served as a model for biological and biomedical research for hundreds of years. A map of CNVs in chickens could facilitate the identification of chromosomal regions that segregate for important agricultural and disease phenotypes.

ResultsNinety six CNVs were identified in three lines of chickens Cornish Rock broiler, Leghorn and Rhode Island Red using whole genome tiling array. These CNVs encompass 16 Mb 1.3% of the chicken genome. Twenty six CNVs were found in two or more animals. Whereas most small sized CNVs reside in none coding sequences, larger CNV regions involve genes for example prolactin receptor, aldose reductase and zinc finger proteins. These results suggest that chicken CNVs potentially affect agricultural or disease related traits.

ConclusionAn initial map of CNVs for the chicken has been described. Although chicken genome is approximately one third the size of a typical mammalian genome, the pattern of chicken CNVs is similar to that of mammals. The number of CNVs detected per individual was also similar to that found in dogs, mice, rats and macaques. A map of chicken CNVs provides new information on genetic variations for the understanding of important agricultural traits and disease.

AbbreviationsaCGHarray comparative genome hybridization

AKR1Baldo-keto reductase 1B

CD8αCD8 antigen alpha chain

aCGHarray comparative genome hybridization

CHRMcholinergic receptor muscarinic

CNVcopy number variation

CNVRCNV region

ESTexpressed sequence tag

GAPDHglyceraldehyde 3-phosphate dehydrogenase

Mbmillion base pair

PCCApropionyl coenzyme A carboxylase

PCRpolymerase chain reaction

PRLRprolactin receptor

qPCRquantitative real time PCR

RT-qPCRquantitative real time reverse transcriptase-PCR

SNPsingle nucleotide polymorphism

THRSPthyroid hormone responsive spot 14

ZFRzinc finger RNA binding protein.

Electronic supplementary materialThe online version of this article doi:10.1186-1471-2164-11-351 contains supplementary material, which is available to authorized users.

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Author: Xiaofei Wang - Samuel Nahashon - Tromondae K Feaster - Ann Bohannon-Stewart - Nathaniel Adefope

Source: https://link.springer.com/article/10.1186/1471-2164-11-351



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