Transcriptome Sequencing of a Hybrid Between Two Trifolium Species

Novel patterns of transcription may be induced after hybridization, as the regulatory machinery of two different species are combined in the one nucleus. Theoretically, hybrids should have had an additive gene expression pattern and not deviated significantly from their mid-parent value. We decided to analyse the transcriptome, via RNAseq, of two F₁ hybrids between Trifolium pallescens (P48) and T. occidentale (O39). The transcriptome sequencing was performed with an Illumina HiSeq SQ, using stem nodal tissue. At the time of analysis there were no sequences available for either parent and so Medicago truncatula was used as a reference sequence and for variant detection. Expression divergence analysis according to Rapp et al (2009); allele specific expression and cis trans regulation analysis was performed. The parents had very similar expression profiles; however, P48 expressed more genes at higher levels than O39. Differentially expressed genes in the hybrids had low levels of additive expression, the majority showed parental level expression dominance. Transgressive genes showed cis x trans regulatory divergence more often than cis + trans regulatory divergence. The overrepresentation of parental level dominance in favour of the female transcript is possibly the result of dominant gene action, potentially regulated by a cis x trans mechanisms

Rapp, R. A., Udall, J. A., and Wendel, J. F. (2009). Genomic expression dominance in allopolyploids. BMC Biology 7: 18