Study On Expression Characteristics Under Conditions Of Pasteurella Multocida Infection And Genetic Effects Of TNFAIP2 In Hainan Black Goat

Respiratory disease is a serious disease in goat farming in tropical and subtropical regions.Pasteurella multocida in goats causes a huge economic loss to the goat farming industry,and the clinicopathological changes are mainly pneumonia and sepsis.The Hainan Black goat,which is influenced by the natural ecological environment in the tropical regions of Hainan,exhibits a wide range of germplasm characteristics,such as good adaptation and high disease resistance.With the continuous development of high-throughput sequencing technology,bioinformatics analysis of multi-omics data has become a new direction to explore the body’s immune response.In this study,we primarily used transcriptome sequencing(RNA-seq)and whole-genome sequencing(WGS)to identify the potential effects of TNFAIP2 on the host immune response induced by Pasteurella multocida(Pm),followed by polymorphism analysis,missense SNP identification,and bioinformatics analysis of TNFAIP2 in Hainan Black goat.This study aimed to elucidate the expression features of the TNFAIP2 gene of the Hainan Black goat under infection with Pm and its genetic effects and to provide a theoretical basis for the study of single nucleotide polymorphisms of TNFAIP2 in Hainan Black goat.The research content of the paper is as follows:(1)RNA-seq was used to analyze the lung gene expression on the second day of Pastocida.The Pm-infected Hainan Black goats showed obvious clinical symptoms.HE staining of infected lung tissue showed features of purulent pneumonia with inflammatory cell infiltration and destruction of lung architecture.Comparing the control group(CK),there were 3,508 differentially expressed genes in the infection group(Pm＿d2),where1,604 genes were up-regulated and 1,904 genes were downregulated,with the TNFAIP2 gene upregulated.Go and KEGG analysis were performed on the differentially expressed genes,and the immune pathways such as cytokine-cytokine receptor interaction,complement,and coagulation cascades were significantly enriched,which indicated that the body triggered immune response after Pm infection.To verify the accuracy of transcriptome sequencing results,nine immune-related genes were selected for RT-q PCR reaction,and the detection results were consistent with the trend of transcriptome sequencing results and the data were reliable.(2)Whole-genome sequencing was performed for 16 Hainan Black goats,and their sequencing data were comparatively analyzed with those of 6 other breeds of goats from different geographic regions.Principal component analysis(PCA)and phylogenetic trees identified seven lineages of all goats.Hainan Black goats is the most similar to the Lei Zhou goats and the least similar to the Boer goats.Hainan Black goats also exhibited higher genetic diversity.Specific SNP analysis and selective sweep analysis revealed potential genetic trait candidate genes in Hainan black goats,and the immune related genes TNFAIP2 and EXOC3L4 to be potential selection genes for the disease.(3)Combined with the above analytical data,SNPs of the TNFAIP2 gene were found to have a potential impact on immune performance in Hainan black goats.Based on the whole genome sequencing data of Hainan black goats,TNFAIP2 exhibited complex genetic polymorphisms with a total of 31 missense mutation sites,25 SNPs sites were present in the variant database,Sanger sequencing and PCR-RFLP methods were used to identify the remaining SNPs sites,and only SNP(c.1451 G>C)was identified successfully.Bioinformatics analysis revealed that a single SNP(c.1451 G>C)mutation had little effect on the goat TNFAIP2 protein.Further linkage disequilibrium and haplotype analysis found strong linkage disequilibrium between four SNPs loci including SNP(c.1451 G>C),SNP(c.1463 G>A),SNP(c.1466 G>A),and SNP(c.1486 T>A)with four haplotypes.