Exploring The Association Between Genomic DNA Methylation Similarity And Kinship In Gilts

As an important part of epigenetics,DNA methylation primarily occurs in Cytosine-Phosphate-Guanine(CpG)in mammals,and it plays a great regulatory function in eukaryotes,including genetranscription regulation,stability of genetic material,genomic imprinting,X chromosomeinactivation and embryonic development.Several researches have reported that Singlenucleotide polymorphism(SNP)could affect the DNA methylation pattern of its adjacentCp Gs and contribute to allele specific methylation(ASM),and the methylation pattern of CpGsinASMshowed a positive correlation with kinship.At present,researches on the association between DN A methylation similarity and kinship were limited to few CpGsaround SNP markers,whether the genomic DNA methylation similarity of CpGs coverd the whole genome has a certain association with kinship was little-known.Inthisstudy,Reduced representation bisulfite sequencing(RRBS)was introduced to complete the genomic sequencing of hypothalamus,pituitary and ovary in 10 landrace × large white gilts.By using GATK,the SNP information was detected from the sequenced data and used to conducting a gradient test of Call rate and Minor allele frequency(MAF)with the aim of obtaining the best quality control parameter(BQCP).Based on BQCP,the qualified SNP markers were screened out for constructing a kinship matrix(G matrix).By using Bismark,the DN A methylation information was extracted from the data,and we selected thequalified Cp Gs to compute the DNA methylation similarity.According to above information,we compared the distribution of DNA methylation similarity among genome,chromosomes and gene element levels,and explored the association between kinship and DNA methylation similarity,as well as the impact of SNPs on themethylation pattern of its adjacent Cp Gs in three different tissues.We mainly got the following conclusions:1.In this study,the best quality control parameter of Call rate and MAF were 90% and 0.05,respectively,and its corresponding G matrix values were in the range of 0.694235~0.759088.2.TheDN A methylation similarity of X chromosome,Intron and Intergenic showed a lower level than that of genome,whilethatwas little changed in autosome and displayed a higher level in Upstream,Downstream and Exon.Besides,those similarities were all not affected by kinship and those results were identical in hypothalamus,pituitary and ovary.3.SNP markersinfluenced the methylation pattern of CpGs around them in atissue-specific pattern.While the DN A methylation similarity based on SNP-related Cp Gs was unaffected by kinship.