Open Access Highly Accessed Research article

Identification of genome-wide copy number variations among diverse pig breeds by array CGH

Yan Li1, Shuqi Mei2, Xuying Zhang1, Xianwen Peng2, Gang Liu1, Hu Tao1, Huayu Wu2, Siwen Jiang1, Yuanzhu Xiong1 and Fenge Li1*

Author Affiliations

1 Key Laboratory of Pig Genetics and Breeding of Ministry of Agriculture & Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan, 430070, PR China

2 Hubei Key Laboratory of Animal Embryo Engineering and Molecular Breeding, Hubei Academy of Agriculture Science, Wuhan, 430070, PR China

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BMC Genomics 2012, 13:725  doi:10.1186/1471-2164-13-725

Published: 24 December 2012

Additional files

Additional file 1:

Probe summary of the 720 K custom-made CGH array designed by Roche NimbleGen.

Format: XLSX Size: 11KB Download file

Open Data

Additional file 2:

Description of the CNVRs detected by a whole-genome CGH array. The genomic coordinates were expressed in bp and were relative to the Sus scrofa genome sequence assembly (Sscrofa9.2). BLAST was used to query the CNVRs sequences against the Sus scrofa genome sequence (Sscrofa9.2). Sequences were retained as duplicated sequences if they had ≥ 1 kb and ≥ 90% identity and occur at more than one site within the genome. WD: White Duroc (♀); YX: Yangxin (♂); EH: Erhualian (♀); TC: Tongcheng (♀); LW: Large White (♀); PT: Pietrain (♂); LD1: Landrace × DIV pig 1 (♂); LD2: Landrace × DIV pig 2 (♀); DIV1: Chinese new pig line DIV 1 (♀); DIV2: Chinese new pig line DIV 2 (♀); L1: Landrace 1 (♂); L2: Landrace 2 (♂).

Format: XLSX Size: 37KB Download file

Open Data

Additional file 3:

Gene contents of CNVRs.

Format: XLS Size: 320KB Download file

This file can be viewed with: Microsoft Excel Viewer

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Additional file 4:

QTLs overlapped with the CNVRs. All the porcine QTLs within 2 Mb (http://www.animalgenome.org/cgi-bin/QTLdb/SS/download?file=gbpSS_10.2) of our CNVRs were counted.

Format: XLSX Size: 15KB Download file

Open Data

Additional file 5:

The validation of the aCGH results using qPCR method.

Format: XLSX Size: 38KB Download file

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Additional file 6:

The primers of qPCR to validate the CNVRs detected by aCGH.

Format: XLSX Size: 9KB Download file

Open Data