Genome-wide association study for cytokines and immunoglobulin G in swine

PLoS One. 2013 Oct 2;8(10):e74846. doi: 10.1371/journal.pone.0074846. eCollection 2013.

Abstract

Increased disease resistance through improved immune capacity would be beneficial for the welfare and productivity of farm animals. To identify genomic regions responsible for immune capacity traits in swine, a genome-wide association study was conducted. In total, 675 pigs were included. At 21 days of age, all piglets were vaccinated with modified live classical swine fever vaccine. Blood samples were sampled when the piglets were 20 and 35 days of age, respectively. Four traits, including Interferon-gamma (IFN-γ) and Interleukin 10 (IL-10) levels, the ratio of IFN-γ to IL-10 and Immunoglobulin G (IgG) blocking percentage to CSFV in serum were measured. All the samples were genotyped for 62,163 single nucleotide polymorphisms (SNP) using the Illumina porcineSNP60k BeadChip. After quality control, 46,079 SNPs were selected for association tests based on a single-locus regression model. To tackle the issue of multiple testing, 10,000 permutations were performed to determine the chromosome-wise and genome-wise significance level. In total, 32 SNPs with chromosome-wise significance level (including 4 SNPs with genome-wise significance level) were identified. These SNPs account for 3.23% to 13.81% of the total phenotypic variance individually. For the four traits, the numbers of significant SNPs range from 5 to 15, which jointly account for 37.52%, 82.94%, 26.74% and 24.16% of the total phenotypic variance of IFN-γ, IL-10, IFN-γ/IL-10, and IgG, respectively. Several significant SNPs are located within the QTL regions reported in previous studies. Furthermore, several significant SNPs fall into the regions which harbour a number of known immunity-related genes. Results herein lay a preliminary foundation for further identifying the causal mutations affecting swine immune capacity in follow-up studies.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Classical Swine Fever Virus / physiology
  • Genome-Wide Association Study*
  • Immunoglobulin G / genetics*
  • Interferon-gamma / genetics*
  • Interleukin-10 / genetics*
  • Mutation
  • Polymorphism, Single Nucleotide
  • Swine / genetics*
  • Swine / physiology
  • Swine / virology*
  • Swine Diseases / virology

Substances

  • Immunoglobulin G
  • Interleukin-10
  • Interferon-gamma

Grant support

The authors appreciate the financial support provided by the National Natural Science Foundations of China (30972092), the National High Technology Research and Development Program of China (863 Program 2011AA100302), the National Major Special Project of China on New Varieties Cultivation for Transgenic Organisms (2009ZX08009-146B), the Natural Science Foundations of Beijing (6102016), New-Century Training Programme 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.