Enrichment And Verification Of Differentially Expressed Genes And MiRNAs In Bursa Of Fabricius In Two Breeds Of Duck

Genetic effect is one of the main factors that affect animals’ disease resistance. The previous researches indicated that the local duck breeds tend to exhibit stronger ability in disease resistance when comparing with the meat duck breeds by intensively artificial selected. The developments of immune organs in the two breeds of ducks have divergent status in different development stages and the indexes related to immune functions reflect the immune effects are also different. The objective of this study was to research the reason for why they exhibit differences in disease resistance between local and breeded meat ducks, we chose the bursa of Fabricius of Jianchang duck (JCF) and the Nonghua meat duck (PKF) to be the experimental subjects. Through analyzing the digital gene expression profile (DGE) and small RNA sequencing of JCF and PKF at week 4, we obtained differentially expressed genes and miRNAs and tested partial of the differentially expressed genes and miRNAs by the qRT-PCR. We further conjoint analyzed between differentially expressed genes and miRNAs to find the key genes and miRNAs that affect the divergence in disease resistance between the two duck breeds. It would provide more reference data and information in duck immune regulation mechanism and disease resistant breeding research. The results show that:The DGE data showed that, there were 18870755 raw reads and 18438616 clean reads after filtering in JCF. And there were 14281414 raw reads and 13983876 clean reads after filtering in PKF. Compared with PKF, there were 95 up-regulated genes and 100 down-regulated genes in JCF. The GO analysis found that the differentially expressed genes mainly be enrichment to the metabolic pathways and ribosome components. Through the analysis of the KEGG the differentially expressed genes mainly were enriched in spliceosome, RNA transport, RNA degradation process, Jak-STAT signaling pathway, TNF signaling pathway and B cell receptor signaling pathway. The results of the verification of differentially expressed genes by qRT-PCR showed that there were 7 genes experiment value had the same trends with the predicted value at W3. At W4 and W5, there were 3 genes experiment value had the same trends with the predicted value, respectively.The small RNA Seq data showed that, there were 11496755 raw reads and 8234150 clean reads after filtering in JCF. And there were 11962192 raw reads and 8105240 clean reads after filtering in PKF. Compared with PKF, there were 23 up-regulated miRNAs and 41 down-regulated miRNAs in JCF. The GO analysis showed that the differentially expressed miRNAs mainly be enrichment to the cell components. Through the analysis of the KEGG the pathways of metabolic pathways, pathway in cancer, intestinal immune network for IgA production, cytokine-cytokine receptor interaction, influenza A were enriched. The results of the verification of differentially expressed miRNAs by qRT-PCR showed that there were 7 miRNAs experiment value had the same trends with the predicted value at W3.The conjoint analysis between 195 differentially expressed genes and 64 different miRNAs showed that when the expression of miRNAs changed, the mRNA expression of target genes had corresponding significant changes. The results of GO analysis between differentially expressed miRNA and target genes showed that the main enrichment of target genes to the metabolic process: KEGG enrichment analysis found that enrichment of target genes mainly in the ribosome signal pathway and endoplasmic reticulum protein and RNA degradation process.In conclusion, there are 195 differentially expressed genes and 64 miRNAs in the bursa of Fabricius between Jianchang duck and Nonghua meat duck. It makes the basis of difference in resistance to disease between the two kinks of ducks through the molecular process and main signaling pathways related to immune response of differentially expressed genes and miRNAs target genes, such as Antigen processing and presentation, Cytokine-cytokine receptor interaction and B cell receptor signaling pathway. Our researches are the foundation of the further revealing about immune regulation mechanism of duck.