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Identification of global copy number variations among diverse pig breeds by a CGH array


ABSTRACT: A CNV map in pigs could facilitate the identification of chromosomal regions that segregate for important economic and disease phenotypes. The goal of this study was to identify CNV regions (CNVRs) in pigs based on a custom array comparative genome hybridization (aCGH). We carried out a custom-made array comparative genome hybridization (aCGH) experiment in order to identify copy number variations (CNVs) in the pig genome analysing animals of diverse pig breeds (White Duroc, Yangxin, Erhualian, Tongcheng, Large White, Pietrain, Landrace and Chinese new pig line DIV ) using a tiling oligonucleotide array with ~720,000 probes designed on the pig genome (Sus scrofa genome version 9.0). In this study, a custom-made tiling oligo-nucleotide 720k array was used with a median probe spacing of 2506 bp for screening 12 pigs with a female Duroc as the reference. 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 (♂).

ORGANISM(S): Sus scrofa

SUBMITTER: Fenge Li 

PROVIDER: E-GEOD-41488 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

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

Li Yan Y   Mei Shuqi S   Zhang Xuying X   Peng Xianwen X   Liu Gang G   Tao Hu H   Wu Huayu H   Jiang Siwen S   Xiong Yuanzhu Y   Li Fenge F  

BMC genomics 20121224


<h4>Background</h4>Recent studies have shown that copy number variation (CNV) in mammalian genomes contributes to phenotypic diversity, including health and disease status. In domestic pigs, CNV has been catalogued by several reports, but the extent of CNV and the phenotypic effects are far from clear. The goal of this study was to identify CNV regions (CNVRs) in pigs based on array comparative genome hybridization (aCGH).<h4>Results</h4>Here a custom-made tiling oligo-nucleotide array was used  ...[more]

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