Analysis of the Transcriptome of Bovine Embryos Obtained from Sex Sorted and Non-Sorted Semen by RNA-Sequencing

Sperm sorting to preselect the sex of offspring prior to conception is a technological tool that is now widely applied in cattle, however the implications of the approach for embryo development are not fully appreciated. To understand if there maybe differences in the function of key genes expressed in the developing bovine embryo that are affected by the FACs sorting procedure, we analysed RNA-seq profiles of 4 pools of 3 bovine embryos (blastocyst at Day 7) produced from both sexed and non sexed semen of the same bull. RNA samples were amplified with the Ovation RNA-Seq System V2, which uses Ribo-SPIA technology (NuGEN). cDNA libraries were made using the Illumina TruSeq sample preparation kit. Samples were sequenced on an Illumina Hi-Seq2000 to generate paired end reads of 100bp to allow alternative isoforms to be identified.  Reads were mapped against the reference bovine genome (UMD 3.1) using TopHat and transcripts reconstructed by Cufflinks. Preliminary results showed 164887 potential gene loci and 252644 putative isoforms. Initial differential expression analysis has been performed and novel transcripts and isoforms will be investigated and compared to the current genome annotation. This investigation will identify new transcripts and potential changes in expression during preimplantation embryonic development.