Abstract
BackgroundGene expression inheritance patterns in Arabidopsis hybrid plants were investigated for correlation with the presence of transposable elements (TEs) and small RNA profile.ResultsThe presence of TEs in a gene and the expression of small RNA matching a gene were both found to be associated with non-additive mRNA inheritance patterns in hybrids. Expression levels below mid-parent values in the hybrids were associated with low mRNA expression in parents, with the presence of small RNA from both strands, and with the presence of TEs. High-parent dominance of mRNA levels was found to be associated with high parental mRNA expression levels, the absence of TEs, and for some genes, with small RNA fragments that are predominantly from the sense strand. These small RNAs exhibit a broader size distribution than siRNA and reduced nucleotide end bias, which are consistent with an origin from degraded mRNA. Thus, increased as well as decreased gene expression in hybrids relative to the parental mean is associated with gene expression levels, TE presence and small RNA fragments with differing characteristics.ConclusionsThe data presented here is consistent with a role for differential mRNA decay kinetics as one mechanism contributing to high-parent dominance in gene expression. Our evidence is also consistent with trans repression by siRNA and TEs as the cause of low-parent dominance.Electronic supplementary materialThe online version of this article (doi:10.1186/s12870-015-0549-7) contains supplementary material, which is available to authorized users.
Highlights
Gene expression inheritance patterns in Arabidopsis hybrid plants were investigated for correlation with the presence of transposable elements (TEs) and small RNA profile
We reasoned that the use of a single plant per replicate would facilitate the study of dynamic co-regulation between small RNA and mRNA levels
We show evidence that sense strand small RNA (sssRNA) is associated with high mRNA expression in parents of a cross and with high-parent dominance (HP) inheritance in hybrids
Summary
Gene expression inheritance patterns in Arabidopsis hybrid plants were investigated for correlation with the presence of transposable elements (TEs) and small RNA profile. Hybrid plants can show enhanced growth rate, novel phenotypes or adaptive advantages in diverse environments. They may even have enhanced potential to evolve into new species [1, 2]. One intriguing hypothesis is that variation in gene expression is a driver of hybrid biology. While the underlying mechanisms regulating gene expression in hybrids remain to be discovered, small RNA and transposable elements (TEs) have been proposed as likely agents that may trigger nonadditive inheritance [22, 23]
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