Identification of genome-wide copy number variations among diverse pig breeds using SNP genotyping arrays

PLoS One. 2013 Jul 23;8(7):e68683. doi: 10.1371/journal.pone.0068683. Print 2013.


Copy number variations (CNVs) are important forms of genetic variation complementary to SNPs, and can be considered as promising markers for some phenotypic and economically important traits or diseases susceptibility in domestic animals. In the present study, we performed a genome-wide CNV identification in 14 individuals selected from diverse populations, including six types of Chinese indigenous breeds, one Asian wild boar population, as well as three modern commercial foreign breeds. We identified 63 CNVRs in total, which covered 9.98 Mb of polymorphic sequence and corresponded to 0.36% of the genome sequence. The length of these CNVRs ranged from 3.20 to 827.21 kb, with an average of 158.37 kb and a median of 97.85 kb. Functional annotation revealed these identified CNVR have important molecular function, and may play an important role in exploring the genetic basis of phenotypic variability and disease susceptibility among pigs. Additionally, to confirm these potential CNVRs, we performed qPCR for 12 randomly selected CNVRs and 8 of them (66.67%) were confirmed successfully. CNVs detected in diverse populations herein are essential complementary to the CNV map in the pig genome, which provide an important resource for studies of genomic variation and the association between various economically important traits and CNVs.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Breeding*
  • DNA Copy Number Variations / genetics*
  • Genome / genetics*
  • Genotyping Techniques / methods*
  • Polymorphism, Single Nucleotide / genetics*
  • Real-Time Polymerase Chain Reaction
  • Reproducibility of Results
  • Sus scrofa / genetics*

Grant support

The authors appreciate the financial support provided by Program for Changjiang Scholar and Innovation Research Team in University (IRT1191), the National High Technology Research and Development Program of China (863 Program 2011AA100302), the National Natural Science Foundations of China (31272419, 31201779), New-Century Training Program Foundation for the Talents by the State Education Commission of China (NETC-10-0783) and Scientific Research Foundation for the Returned Overseas Chinese Scholars of State Education Ministry. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.