Influence Of Salmonella Enteritidis Infection On Cecal Genomic Methylation In Chicken Through Whole-Genome Bisulfite Sequencing

Salmonella enteritidis can infect poultry digestive tract,causing acute inflammation of the digestive system and even death,it can also infect people,causing food poisoning,it is a common zoonotic pathogen,which not only affect the healthy development of poultry industry seriously,but also endanger human health.Methylation of gene is an important epigenetic modification.It is reported that DNA methylation plays an important role in maintaining genome stability,regulating gene expression,cell differentiation and growth.In the livestock industry,the importance of DNA methylation is reported more and more,indicating that DNA methylation has great potential in genetical breeding.Whole Genome Bisulfite Sequence is a method which connects next-generation sequencing technology with bisulfite treatment.This method can picture the whole genome methylation map at base resolution,which is an effective way to accurately detect the methylation pattern of genomic DNA.In this experiment,we studied the effects of Salmonella enteritidis infection on cecum of jiningbairi chicken by the way of whole genomic bisulfite sequencing,and the significant gene was validated by bisulfite sequencing PCR The The results show:On average,each sample has 54.78G Clean Data and the number of total data is 109.56G with Q30 up to 82.10%and mapped ratio up to 70%.180,530,750 and 185,362,463 Clean Reads were obtained in the treat group and the control group respectively.The number of methylated C sites was found to be 421,423,014,accounting for 56.1%of the total number of C sites.The number of methylation sites of CG type was the highest in all types（CG,CHG,CHH,H=A/C/T）,which was 87.4%.36823 DMRs were found.In the number of 1,2,3,16,25,31,32,33 and sex chromosomal,the ratio of DMR’s length divided by chromosomal length were less than 0.5%,In the number of 19,23,24 and 26 chromosomes,this ratio is greater than 1%.8,947 significantly different（P<0.001）genes were were found.Among them,the gene number of significantly down is 5307 while significantly up is 3639.In all chromosomes,only 16 and sex chromosome W were significantly up,which shows that Salmonella enteritidis infection had a negetive influence on methylation level of Jiningbairi Chicken.Put 8947 methylated differential genesinto the DAVID database pool.5055 genes were classified and 78 were classified as significant（P<0.01）in which there were 78 biological process,15 cell components,and 16 molecular function.The differential expression gene was analyzed by KEGG Pathway signal pathway,and 16 pathways were significant enrichment（Q<0.05）.Wnt signal pathway was the most significant(P=1.93×10^-5).It was found that mircoRNA had high DMC density among all of genes.The genes of the differently methylation were screened,and the HOX family gene was particularly worthy of attention.