Processes of muscle development and lipid metabolism that plays important roles during fetal growth and development stages, are different in thin- and fat-tailed sheep breeds. Therefore, in order to have a better perception of differentially expressed genes and their pathways in ovine prenatal muscle tissue , the gene expression data from muscle tissue of two thin- and fat-tailed breeds of sheep derived from the gene expression array experiment (Access number: GSE23563) were analyzed. The LIMMA package in R used to identify 691, 410, 404, 290 and 155 differentially expressed genes at 70, 85, 100, 120, and 135 days from gestation, respectively.Also,identification of significant gene clusters was performed for each fetal stage using Cytoscape. Finally,13 genes were recognized as differentially expressed at all 5 stages of sampling; among them, EEF1A2, ITGAM,NINL and RPL39 were confirmed as genes related to fetal weight, involved in the muscle development and lipid metabolism regulation.Also Gene Ontology and KEGG pathway analysis for differentially expressed genes by DAVID led to identification of significant processes and pathways associated with myogenesis, lipid metabolism and nervous and immune system in the developing muscle tissue transcriptome. The results of this study could provide supplementary information revealing genes with significant impact on the formation of muscle and fat tissues during fetal development and also the pathways involved in these biological processes.These genes might provide some evidence on DNA markers associated with some economic traits including birth weight,carcass and meat quality traits in sheep which can be applied in selection and breeding programs.

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