Differential Gene Expression in Diploid Sexual, Diploid Apomictic and Triploid Apomictic Species of Boechera

Among other processes, apomixis in many Boechera species is characterized by a meiotic 1st division restitution. To better understand the molecular biology of this form of apomeiosis, we focused on RNASeq gene expression data from immature pistils of diploid sexual B. stricta, the diploid apomicts B. lignifera and B. retrofracta x exilis and the triploid hybrid apomict B. gunnisoniana x sp. We specifically addressed the following questions: 1) Can we find a uniform response to drought-stress among the four species in question? 2) Are there genes, associated with apomixis, that can be found across diploid and triploid species of apomictic Boechera? 3) Do triploid Boechera apomicts exhibit differences in gene expression, compared to their diploid congenerics? 4) Can we find genes showing differential expression specific to reversals from apomeiosis to meiosis in B. lignifera (which was suggested by DIC microscopy results)? Bayesian analysis of differential expression based on normalized expression data was used to identify genes adhering to 8 respective models, each assuming differential expression between different sets of samples. Evidence of species-specific drought stress responses was not clear from principle component analyses, and consistently, none of the 26072 genes analysed in our study were expressed in a pattern conforming to a uniform drought stress response across the four species. We were able to find genes that were expressed across all apomicts, compared to the sexual B. stricta. Additionally, the triploid hybrid apomict B. gunnisoniana x sp. contains more than 100 genes that are differentially expressed compared to the diploid species considered here. Finally, we found 125 genes that show differential expression specific to a potential reversal from apomeiosis to meiosis. A subset of the differentially-expressed genes in the respective model groups will be discussed.