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| Selection and Biology Annotations for Mycoplasmal Pneumonia of Swine Candidate Genes Based on QTL |
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Abstract Mycoplasmal pneumonia of swine (MPS, also referred to as 'enzootic pneumonia', EP) caused by Mycoplasma hyopneumoniae (Mhp), is a chronic respiratory disease with the clinical sign of persistent dry cough. Epidemic of MPS has a negative impact on growth rate and feed conversion. The causative agent Mhp is easily infected and it will become worse with co-infections, which always gives rise to huge economic damage to the swine (Sus scrofa) industry, both at home and abroad. At present, most research is centered on pathological diagnosis, immunity, prevention and control. However, these medical treatments and public health measures are incapable of alleviating the negative impacts from MPS. For better solving the occurrence of MPS, we intend to adopt bioinformatics analysis methods to explore MPS from the molecular level for better illustrating its mechanism. For the purpose, this study was mainly based on Gene Ontology (GO) enrichment analysis, KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway analysis, text mining and other bioinformatics tools to complete the PigQTLdb (pig QTL Database) retrieval and biological annotations for MPS candidate genes. The results showed that 47 possible QTLs were associated with MPS with the full use of PigQTLdb, 2 of which were related to MPS susceptibility, and the others were involved in immunity. 38 GO terms linked to MPS were searched by CoPub, a text-mining tool, and then 3 379 genes contained in 47 QTLs were effective after semantic similarities calculation with R programming and GOSim package. Among them, 36 genes were statistically significant. For another, there were 53 genes found in GO enrichment analysis, and 16 genes in 'Asthma' pathway from KEGG analysis. In addition, six candidate genes were from the results of text-mining, including TNFα (tumor necrosis factor), NRAMP1 (natural resistance-associated macrophage protein 1), TCRs (T-cell receptor genes), CYP1A1 (cytochrome P450 family 1 subfamily A member 1), CYP3A29 (cytochrome P450 3A29v4) and SERPING1 (serpin family G member 1). As a result, there were totally 104 optimized genes for the MPS candidate gene set. Special attention should be paid on gene TNF, for it was involved in both GO enrichment analysis and KEGG pathway analysis results, and appeared in the text mining results as well. To be specific, TNF was one of the crucial factors to induce inflammation, which ranked fourth in significance among all candidate genes during calculations. We inferred that TNF and POU5F1 were the candidate genes of vital importance during MPS infections. These findings will offer a new aspect for the further research in the future, though there would be some improvements in the analysis, and these conclusions remained to be proved. In next step, we will make efforts to explain the relationship between MPS and other important economic traits and explore the molecular differences between Chinese indigenous pigs and western imported pigs for further to indicate its heritance mechanism and provide insights for human asthma study one day.
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Received: 05 September 2016
Published: 02 March 2017
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