RNA-Seq Analysis of Chicken Primordial Germ Cells (PGCs) for Identification of Sexually Dimorphic Gene Expression and Downstream Metabolic Pathways

We are using RNA-seq to analyze the transcriptomes of chicken PGCs cultured in feeder-less culture medium. We are interested in finding genes differentially expressed in undifferentiated PGCs that distinguish genders and if particular gene networks might underlie differential growth patterns observed between male and female PGCs in-vitro. Our analyses also included PGCs from layers and broilers. High throughput Illumina sequencing reads were used to generate RPKM (Reads Per Kilobase per Million) values and analyzed using ArrayStar (DNAStar ver 13) and fRNAkenstein tools in CyVerse. We identified autosomal, W-linked, Z-linked, and unannotated genes which show sexually dimorphic expression in both breeds. For example, the FOXN1 gene is expressed 2-fold higher in female PGCs. FOXN1 is a member of the Forkhead family of transcription factors some of which have been shown to be differentially expressed in a sex-specific manner in chicken gonads. Our data suggest that this differential expression appears to also exist prior to gonadogenesis. Similarly, LOC1008596602 is W linked gene with no known function that is expressed 3 fold higher in male PGCs vs female. We are interested in detecting the downstream pathways connecting the functional role of these differentially expressed genes between the sexes and between the two different types of chickens.