Gene expression pattern and molecular mechanisms involved in Shal and Sangsari sheep fertility using RNA-Seq.

Ovulation rate and litter size are the main reproductive traits with high economic value in the sheep breeding industry. In this study, three Shal ewes (multiparous) and three Sangsari ewes (uniparous) at the age of 5 were used. The live weight was between 45 and 50 kg at extremely body condition score of 3. These breeds are marked seasonal reproduction activity and are often bred in semi-closed breeding system. Total RNAs were extracted from the ovarian tissues and RNA sequencing was carried out. The DAVID (Database for Annotation, Visualization and Integrated Discovery) database was then used to annotate genes, and the string database and the cytoscape software were used to investigate their interactions. Then Path-act network analysis and Gene-act network analysis were investigated. The results indicated that 19932 genes were differentially expressed. The 5968 differentially expressed genes were identified in Shal ewe's ovarian tissue compared to Sangsari ewes (FDR <0.05), of which 2921 genes were up-regulated and 3047 genes were down-regulated. Bioinformatics analysis exhibited that most of the biological processes and KEGG (Kyoto Encyclopedia of Genes and Genomes) pathways associated with significant DEGs (Differentially Expressed Genes) in the two studied breeds are associated with oocyte maturation and metabolism. MAPK signaling pathways and Ubiquitin mediated proteolysis are the most important biological pathways associated with reproductive and fertility traits in the Shal breed. AKT3, MAPK8, MAPK9, and RELA genes are also important genes related to the fertility of multiparous sheep. Analysis of ovarian RNA-seq data identified that most of differentially expressed genes were involved in various reproductive processes including folliculogenesis, ovulation, ovarian and embryonic development. The MAPK signaling pathway had the most interaction with other pathways and AKT3 gene could be a powerful candidate gene in the reproduction and fertility of Shal sheep. These results could pave the way for future efforts to address sheep prolificacy barriers.