Finding Candiate Gene Sets Of Porcine Growth Traits By Using Mouse Microarray Datasets Analysis

Growth traits of pigs are of great importance for economic efficiency. However, studying the mechanism of controlling growth and development has confronted challenges and numerous achievements of QTL mapping are also difficult to be applied to genetic improvements of pigs. To better explain the biological process from genes to traits, this study applied parts of candidate gene set approach, aiming to find candidate gene sets that influence the growth traits of pigs. This can provide theoretical support for the breeding practice. Details and results are described below:First, we searched NCBI GEO (Gene Expression Omnibus) database and selected four recently published commercial Affymetrix microarray datasets. They were GSE9484, GSE7863, GSE14710 and GSE10428 which were all about mouse skeletal muscle growth and development. The experimental designs were based on four different factors (Akt1, Galgt2, STAT5, RB1) respectively. The four datasets were applied GSEA to analyze. Because of their different design principles, the first two and the latter two were integrated respectively. There were 24 & 15 and 5 & 1 significantly up- and down-regulated pathways. Among them, valine, leucine and isoleucine degradation and starch and sucrose metabolism pathways were the common integration of the two integrating analysis. So, a total of 27 & 17 up- and down-regulated candidate gene sets were found.Second, the pathway genes in mice were blast to the cDNA database of pigs. Homologous genes were found when the sequence similarity was greater than 75%. What's more, these homologous genes were compared to existing pathway members of pigs and add the novel genes to the gene sets and the non-recurring ones would be formed a new pathway.Finally, members of these candidate gene sets were mapped to QTL database through genetic base, resulting that these gene set members were related to slaughter weight, average daily gain, body weight, protein acceretion rate, scapula length, physis score, age at slaughter, tibia length, ulna length, humerus length, days to 100kg, femur bone mineral density, femur length, lipid accretion rate. The genes which were related to specific growth trait were candidate QTGs. Then, the two existing SNP database, the NCBI's dbSNP database and the Illumina Porcine 60K SNP chip database were used to identify candidate QTN and 314 QTNs were found.In summary, this paper analyzed cDNA microarray of mouse skeletal muscle and used comparative genomics to compare mice and pigs to find growth-related candidate gene sets. Then the members of these gene sets were mapped to the pig QTL database to find growth related candidate QTGs. Finally, using of the existing SNP databases helped to get candidate QTNs. The common pathways and genes can be seen as critical pathways and genes for pig growth which could better understand the growth trait related genes and helped to find new important genes for growth, to provide evidence for pig breeding.