Open Access Research article

Copy number variants in locally raised Chinese chicken genomes determined using array comparative genomic hybridization

Ming Tian, Yanqiang Wang, Xiaorong Gu, Chungang Feng, Suyun Fang, Xiaoxiang Hu* and Ning Li*

Author Affiliations

State Key Laboratory for Agrobiotechnology, China Agricultural University, Beijing, 100193, China

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BMC Genomics 2013, 14:262  doi:10.1186/1471-2164-14-262

Published: 17 April 2013

Additional files

Additional file 1:

CNVs detected in each sample and the number of duplicated and deleted CNV loci.

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Additional file 2:

CNVRs overlap in gene content.

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Additional file 3:

The distribution of CNVRs in individuals, including the proportion of CNVRs involving a gain of DNA and the proportion involving a loss of DNA.

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Additional file 4:

The distribution of exon, intron and intergenic regions in chicken genome (GGA1-28 and GGA32).

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Additional file 5:

Biological processes enriched in CNVRs. Additional file 5–1 Clustering of CNVRs with an Ensembl ID as identified using the DAVID Functional Annotation tool. Additional file 5–2 Classification of gene functions for all Ensembl ID genes from Additional file 5–1 annotated by DAVID. Additional file 5–3 Classification of gene functions for the LS, QY, SQ, and WC breeds. Additional file 5–4 Classification of gene functions for the locally raised Chinese chicken breeds other than LS, QY, SQ, and WC.

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Additional file 6:

Validation by qPCR for the 24 loci in QY and WJ and the summary of the statistical analysis qPCR results. A total of 16 samples for each of the two breeds were analyzed using qPCR for 24 loci. Each sample DNA was adjusted to 10 ng/μl using a NanoDrop 2000 instrument. The QY-F, -5, -7, -9 and WJ-F, -30, -33, -35 samples were from females, whereas the QY-M, -52, -91, -93 and WJ-M, -61, -62, -71 samples were from males. The QY-F, QY-M, WJ-F, WJ-M samples were the same as those used in the aCGH analysis.

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