The link between small RNA-directed gene regulation and heterosis in Arabidopsis allotetraploids

Hybridization between different species of plants and animals commonly leads to superior levels of biomass, growth rate and stress resistance, because of a phenomenon known as hybrid vigor or heterosis. Despite the evolutionary significance and agricultural importance of this vigor, a true understanding of the genetic and molecular parameters remains unknown. Genome-wide changes in gene expression are well documented in hybrids, and could be under the control of a multitude of epigenetic factors. To examine the relative impact that small RNA (sRNA) directed cleavage of target transcripts has on Arabidopsis hybrid vigor, transcriptome, degradome and small RNA-sequence libraries were produced for five Arabidopsis lines: A. thaliana autotetraploids, A. arenosa, F1 resynthesized allotetraploids, F8 allotetraploids, and the natural allotetraploid A. suecica. Together these RNA libraries allowed for degradome analysis to be performed. This genome-wide approach allows for direct detection of sRNA-directed cleavage of target mRNAs without the need for prior predictions or sequence knowledge. The analysis output provides evidence of sRNA-target pairs that are biologically functioning in vivo at a particular spatial or temporal capacity. When transcriptome or protein expression data is incorporated with degradome analysis, an overall model of expression and regulation patterns can be devised. During this investigation I detected novel and significantly differentiated sRNA-target interactions between the allotetraploids and their parents. Allelic expression frequencies within the allotetraploids allowed for the identification of homoeolog cleavage silencing modifications, along with the classification of cleavage events as being additive, exhibiting parental level dominance, or manifesting transgressive up- or down-regulation. I found that there is a significant amount of homoeolog expression bias that is being influenced by sRNA-mediated cleavage. Bias cleavage was found to not only preferentially eliminate homoeologous transcripts, but also function a buffering action to control threshold concentrations of target mRNA productions. Results from this investigation indicates that sRNA-directed cleavage is contributing to the stimulation of heterosis within Arabidopsis allotetraploids. Integration of what we learned about this sRNA influence with previous reports on circadian rhythm, methylation and histone modification will better our knowledge of the mechanisms driving heterosis.