Study The Molecular Networks Between Oxidative And Glycolytic Skeletal Muscles From Landrace And Qingyu Pigs By Integrated Analysis Of Multi-omics Data

Skeletal muscle is a kind of highly heterogeneous tissue.Oxidative and glycolytic skeletal muscles have different sensitivity to human myopathy,and they’re closely related to the economic traits of domestic animals,such as growing development and meat quality.Therefore,to explore the molecular genetic mechanism underlying different phenotypes between oxidative and glycolytic skeletal muscles has important implications for human myopathy treatment and the improvement of economic traits of domestic animals.In this study,pig oxidative skeletal muscles（psoas major muscle,PMM）and skeletal muscles（longissimus dorsi muscle,LDM）were used as experimental material to sequence genome-wide DNA methylation（MeDIP）,mRNA transcriptome,microRNA transcriptome,lncRNA transcriptome,and circRNA transcriptome.After the integrated analysis of these five kinds of omics data,some important molecular genetic networks were identified,which were related to different phenotypes between oxidative and glycolytic skeletal muscles.The main results were listed below:（1）In adult Landrace pigs,PMM have smaller muscle fiber cross-section area,higherthe proportion of fast muscle fiber,higher the content of mitochondrial,and bettermeat quality than its in LDM.（2）A total of 43.79 Gb data were obtained from the six MeDIP libraries,and the highquality reads with>10X sequence depth was more than 34.83%.In the presentstudy,15,633 DMRs were identified between LDM and PMM,and 478 DMRswere in the promoter regions.The potential functions of genes with differentialmethylation statuses in promoter regions were related to GTPase regulator activityand the intracellular signaling cascade.（3）A total of 4,983 probes were identified from the microarray data.Those probeswere uniquely mapped to exons of Ensembl genes.Highly significant negativecorrelations were identified between gene expression levels and methylationlevels in the promoter and gene body regions(r=-0.513,P=5.71×10^-14;r=-0.256,P=3.186×10^-6;respectively).（4）There were 617 genes that were differentially expressed between LDM and PMMlocating in DMRs.The results showed that the expression levels of 340 genesdisplayed a negative correlation with methylation levels.According to the GOanalysis,the hypermethylated and low expressed genes,or hypomethylation andoverexpressed genes between LDM and PMM,were mainly enriched inphosphorylation(36 genes,P=1.25×10^-3),protein kinase activity(29 genes,P=1.33×10^-3),and calcium ion binding(38 genes,P=2.75×10^-3)processes.（5）A total of 175 miRNAs（out of 668 known and conserved miRNAs）weredifferentially expressed between PMM and LDM.The functions of differentiallyexpressed miRNAs were mainly enriched in the intracellular signaling cascade,blood vessel development,and response to oxidative stress.（6）According to the growth curve fitting,Qinyu pigs reached the growth inflectionpoint at 178 days old.In the lncRNA library of the six Qinyu pigs,a total length of74.47 Gb（Gigabases）data were obtained,which were 36 times of the pig genome.（7）A total of 16374 reliably expressed genes between PMM and LDM were obtained,of which 810 genes were differentially expressed between LDM and PMM.Thefunctions of differentially expressed genes（mRNA）between Qinyu pigs LDMand PMM were mainly enriched in fatty acid beta-oxidation,glycolytic process,fatty acid metabolism,and pyruvate metabolism.（8）A total of 4046 lncRNA were identified from LDM and PMM.The cis-regulationtarget genes of differentially expressed lncRNAs were mainly enriched inoxidation-reduction process,fatty acid beta-oxidation,PPAR signaling pathwaysignaling pathway.The tran-regulation target genes of differentially expressedlncRNAs were mainly enriched in the mitochondrial inner membrane,oxidation-reduction process,and PPAR signaling pathway.（9）A total of 808 circRNAs were identified from the six libraries,of which 137circRNAs were differentially expressed between PMM and LDM.The host geneof differentially expressed circRNAs was mainly enriched calcium signalingpathway,ATP metabolic process,fatty acid metabolic process,transition betweenfast and slow fiber signaling pathway.（10）Three kinds of network related to slow muscle fiber and mitochondrialbiogenesis were identified between LDM and PMM.They wereCircRNA9210-miR-23a-MEF2C,CircRNA290-miR-27b-Foxj3,andcircRNA41-miR-217-SIRT1.（11）According to the QTL mapping analysis,362（42.79%）differentially expressedmRNA,57（39.32%）differentially expressed lncRNA target genes,and 74（54.01%）differentially expressed circRNAs host genes were enriched in theQTL traits of pig growth and meat quality.