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Genome-wide analysis of structural variants reveals genetic differences in Chinese pigs

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  • Ruifei Yang
  • Suyun Fang
  • Jing Wang
  • Chunyuan Zhang
  • Ran Zhang
  • Di Liu
  • Yiqiang Zhao
  • Xiaoxiang Hu
  • Ning Li

Abstract

Pigs have experienced long-term selections, resulting in dramatic phenotypic changes. Structural variants (SVs) are reported to exert extensive impacts on phenotypic changes. We built a high resolution and informative SV map based on high-depth sequencing data from 66 Chinese domestic and wild pigs. We inferred the SV formation mechanisms in the pig genome and used SVs as materials to perform a population-level analysis. We detected the selection signals on chromosome X for northern Chinese domestic pigs, as well as the differentiated loci across the whole genome. Analysis showed that these loci differ between southern and northern Chinese domestic pigs. Our results based on SVs provide new insights into genetic differences in Chinese pigs.

Suggested Citation

  • Ruifei Yang & Suyun Fang & Jing Wang & Chunyuan Zhang & Ran Zhang & Di Liu & Yiqiang Zhao & Xiaoxiang Hu & Ning Li, 2017. "Genome-wide analysis of structural variants reveals genetic differences in Chinese pigs," PLOS ONE, Public Library of Science, vol. 12(10), pages 1-18, October.
    • Handle: RePEc:plo:pone00:0186721
    DOI: 10.1371/journal.pone.0186721
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    1. Kevin P. Mouillesseaux & David S. Wiley & Lauren M. Saunders & Lyndsay A. Wylie & Erich J. Kushner & Diana C. Chong & Kathryn M. Citrin & Andrew T. Barber & Youngsook Park & Jun-Dae Kim & Leigh Ann Sa, 2016. "Notch regulates BMP responsiveness and lateral branching in vessel networks via SMAD6," Nature Communications, Nature, vol. 7(1), pages 1-12, December.
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