| The porcine meat quality, carcass and reproduction traits are importanteconomic traits, but the development of QTL mapping and candidate geneapproach is slow due to the low heritability and the difficulty of measure.Microarray technology has become one of the most powerful tools forstudying gene expression in genome wide and the related database wasdeveloping as well. However, there are the following limitations in thecurrent microarray experiments. Firstly, most of them are focused on themodel animals (such as mice) or humans, but less were on pigs or otherdomestic animals since poor platforms and high cost. Secondly, the samplesizes of all the experiments are so small, wheras there are frequently manyrepeat or similar studies on the same problem of the model animals orhumans. Moreover, the database of PigQTLdb is becoming perfect, which isthe treasure for the studies of porcine science.Based on all of these, we used the related microarray data of modelanimals or human in the public database of GEO, the method ofmeta-analysis and the PigQTLdb to explore a novel path to study theregulatory mechanisms of porcine essential economic traits. Thus, in thispaper, the research works are included as the following chapters:1. Microarray analysis on Atp7b knockout miceCopper is one of the important mineral elements affecting pigmetabolism and performance, and having an impact on meat quality traitswith iron together. Several studies have used gene expression profiling ofhigh copper effects to identify the key genes in the process, but few focused on the involved pathways and the co-expression patterns of associatedpathways. Here, we employed microarray dataset from the public databaselibrary of GEO (Gene Expression Omnibus), which is associated with livertranscriptome in the early stages of copper accumulation in the mouse modelof Wilson disease under Atp7b knockout. Then, we applied gene setenrichment analysis (GSEA) on the datasets and performed candidatetranscription factors selection. As a result,16up-regulated pathways such astryptophan metabolism and cell cycle and15down-regulated pathways suchas TCA cycle and PPAR signaling pathway were identified as high copperresponsive target pathways in Atp7b knockout mouse liver, most of themwere with no previous reports. Finally, co-expression networks of relatedpathways were constructed with the significant core genes and transcriptionfactors, such as SREBP1and PPAR. These may help us to systematiclyunderstand the molecular mechanisms of the high copper effects in mice liverand to explore the pork quality traits.2. A comparative study of mouse hepatic and intestinal geneexpression profiles under PPARα knockout by gene set enrichmentanalysisBased on meta-analysis of mouse hepatic and intestinal gene expressionprofiles under PPARα knockout, we have identified12PPARα-dependentand4PPARα-independent overlapping pathways in both of two tissues.Among them, most of the pathway is related to metabolic function, such asthe PPARα-dependent fatty acid metabolism pathway, tryptophan metabolismpathway, and pyruvate metabolism pathway and PPARα-independentgluconeogenesis pathway and propionic acid metabolic pathways.Furthermore, PPAR signaling pathway is the significantly down-regulatedpathway for both Atp7b and PPARα knockout condition, so we may furtherstudy the genetic mechanisms of meat quality and carcass traits in thiscandidate pathway level.3. Association study of PPAR signaling pathway and the meat quality and carcass traits in pigsWe have identified13TagSNPs associated with meat quality or carcasstraits QTL in PPAR signaling pathway combining with the database ofPigQTLdb. Then a mixed linear model in the candidate pathway level wasestablished to study the association with10categories of meat quality andcarcass traits in33chosen DLY crossbred population. We found that theadditive effect of the PPAR signaling pathway has significant effects on8categories; then performed a general linear model combined with multivariatemultiple regression analysis and MB-MDR method to study the associationwith SNP loci. For one of the most significantly related traits named fatcontent, we further estimated the values of the additive effect of the PPARsignaling pathway in each sample, which may provide a more accurate theoryfor our further selection. In sum, we set up a new research strategy named asCandidate Pathway Approach (CPA) based on meta-analysis of microarraydatasets in model animals.4. Application of CPA in the study of reproductive traitsHere, we employed microarray dataset of high fertility mouse line andapplied the method of GSEA combining with PigQTLdb to identifysignificant mouse genes in pathway level and further identify the pig geneswithin the reported QTL location related to reproductive performance.5. Meta-analysis on microarray data of early embryonicdevelopment of three mammalian speciesPre-implantation development, also named early embryonicdevelopment, which is the crucial step in successful implantation andpregnancy in mammals and the basic stage for reproductive traits. Here, weemployed the microarray datasets from the public database library of GEOand applied comparative analysis of genome wide temporal gene expressiondata based on statistical analysis and functional annotation for mouse, humanand bovine, demonstrating the discordance between the regulatory mechanisms of these three mammalian pre-implantation development.Further functional analysis and pathway analysis revealed that some majorfactors and related pathways are required for distinctive developmental stages.Among them, the pathway of fatty acid metabolism may be one of ourcandidate pathways for further study of reproductive traits in pigs.To conclude, focused on meat quality, carcass and reproduction traits inpigs, here we have established a study strategy named as Candidate PathwayApproach (CPA) based on meta-analysis on the related microaaray datasets inmodel animals. Firstly, we performed meta-analysis on the related microaaraydatasets in model animals such as humans or mice, and then minedsignificantly associated pathways and genes with the traits of meat quality,carcass and reproduction. Then we used the approach of comparativegenomics combined with Pig QTL database to find out the homologous genesfor pigs in the common pathways and annotate them. These pathways andgenes may be our candidate ones for the study of porcine meat quality,carcass and repoduction traits. We can perform association study with relatedtraits in pathway level. These may be helpful for us to further study thegenetic mechanisms of meat quality, carcass and reproduction traits in pigs. |
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