期刊
G3-GENES GENOMES GENETICS
卷 5, 期 6, 页码 1253-1261出版社
GENETICS SOCIETY AMERICA
DOI: 10.1534/g3.115.018473
关键词
genomic variation; copy number variations; array CGH; pigs
资金
- Program for the National High Technology Research and Development Program of China (863 Program) [2011AA100302, 2013AA102503]
- Changjiang Scholar and Innovation Research Team in University [IRT1191]
- National Natural Science Foundations of China [31272419]
- New-Century Training Program Foundation for the Talents by the State Education Commission of China [NETC-10-0783]
As a major component of genomic variation, copy number variations (CNVs) are considered as promising markers for some phenotypic and economically important traits in domestic animals. Using a custom-designed 1M array CGH (aCGH), we performed CNV discovery in 12 pig samples from one Asian wild boar population, six Chinese indigenous breeds, and two European commercial breeds. In total, we identified 758 CNV regions (CNVRs), covering 47.43 Mb of the pig genome sequence. Of the total porcine genes, 1295 genes were completely or partially overlapped with the identified CNVRs, which enriched in the terms related to sensory perception of the environment, neurodevelopmental processes, response to external stimuli, and immunity. Further probing the potential functions of these genes, we also found a suite of genes related important traits, which make them a promising resource for exploring the genetic basis of phenotype differences among diverse pig breeds. Compared with previous relevant studies, the current study highlights that different platforms can complement each other, and the combined implementation of different platforms is beneficial to achieve the most comprehensive CNV calls. CNVs detected in diverse populations herein are essentially complementary to the CNV map in the pig genome, which would be helpful for understanding the pig genome variants and investigating the associations between various phenotypes and CNVs.
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