Abstract
This study used 209 public single nucleotide polymorphism (SNP) arrays for 151 candidate genes of pigs to analyse their association with nine blood component traits (insulin-like growth factor-I, insulin, immuno globulin, lymphocyte, monocyte, eosinophil, basophil, neutrophil and atypical lymph) in 209 Korean native pigs and Yorkshire F 2 hybrids. Of these, 52 SNPs in 49 candidate genes showed significant association with one or more blood component traits. Nineteen of these SNPs were found to be present in blood component QTL regions. The 49 candidate genes corresponding to 52 SNPs with significant effects were detected and used for gene ontology analysis to understand the function of the candidate genes at molecular level. Based on functional classification (biological process, cellular components, and molecular function) of annotated candidates, 34 candidate genes (11 genes of IGF-1, 9 of IS, 9 of IG, 6 of NP, and 3 of EP) were detected. Additionally, eight genes ( PSMB4 , PSME3 , MAPKAPK3 , CTLA4 , CUL7 , GGT1 , IDH3B , and RXRB ) interacting with four immune pathways (immune system, adaptive immune system, Class I MHC-mediated antigen processing and presentation, and antigen processing: ubiquitination and proteasome degradation) were found through pathway and network analyses. The eight candidate genes identified in this study are included in class I MHC-mediated antigen pathway, which is an important factor that determines the success of organ transplantation in addition to the improvement of diseases and immunity of pigs. Therefore, these genes can potentially be used in heterogeneous organ research in future research. Keywords: Association analysis, gene network, pathway, SNP, swine
Highlights
For the success of the swine industry, it is important to produce safe high-quality pigs and prevent or reduce the incidence of infectious diseases in pigs
The association of the 144 single nucleotide polymorphism (SNP) filtered through Quality control (QC) and linkage disequilibrium (LD) with blood component traits was analysed
Based on the blood component traits, SNPs were significantly associated with insulin-like growth factor-1 (IGF-1), with IS, 12 with immuno globulin (IG), 13 with LC, 6 with MC, 13 with NP, 5 with EP, and 7 with atypical lymph (AL) trait
Summary
For the success of the swine industry, it is important to produce safe high-quality pigs and prevent or reduce the incidence of infectious diseases in pigs. As the incidence of diseases worldwide increases, studies are being conducted to improve the capacity of the pig immune system (Schroyen & Tuggle, 2015). Pigs are useful as human biomedical models and in genetic studies that involve the immune system, because they are highly comparable with humans in terms of their anatomy, physiology, genetics and genomics (Lunney, 2007). SNPs have the advantages of relatively high availability and stability compared with microsatellites and other DNA polymorphism markers. SNPs are important markers that can be applied in various fields (e.g. evolution and disease) of the study of livestock (Kijas et al, 2009)
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