Sammendrag
Epigenetic memory in Norway spruce affects the timing of bud burst and bud set,
vitally important adaptive traits for this long-lived forest species. Epigenetic memory is
established in response to the temperature conditions during embryogenesis. Somatic
embryogenesis at different epitype inducing (EpI) temperatures closely mimics the natural
processes of epigenetic memory formation in seeds, giving rise to epigenetically different
clonal plants in a reproducible and predictable manner, with respect to altered bud
phenology. MicroRNAs (miRNAs) and other small non-coding RNAs (sRNAs) play an
essential role in the regulation of plant gene expression and may affect this epigenetic
mechanism. We used NGS sequencing and computational in silico methods to identify
and profile conserved and novel miRNAs among small RNAs in embryogenic tissues
of Norway spruce at three EpI temperatures (18, 23 and 28◦C). We detected three
predominant classes of sRNAs related to a length of 24 nt, followed by a 21–22 nt class
and a third 31 nt class of sRNAs. More than 2100 different miRNAs within the prevailing
length 21–22 nt were identified. Profiling these putative miRNAs allowed identification of
1053 highly expressed miRNAs, including 523 conserved and 530 novels. 654 of these
miRNAs were found to be differentially expressed (DEM) depending on EpI temperature.
For most DEMs, we defined their putative mRNA targets. The targets represented
mostly by transcripts of multiple-repeats proteins, like TIR, NBS-LRR, PPR and TPR
repeat, Clathrin/VPS proteins, Myb-like, AP2, etc. Notably, 124 DE miRNAs targeted
203 differentially expressed epigenetic regulators. Developing Norway spruce embryos
possess a more complex sRNA structure than that reported for somatic tissues. A
variety of the predicted miRNAs showed distinct EpI temperature dependent expression
patterns. These putative EpI miRNAs target spruce genes with a wide range of functions,
including genes known to be involved in epigenetic regulation, which in turn could provide
a feedback process leading to the formation of epigenetic marks. We suggest that TIR,
NBS and LRR domain containing proteins could fulfill more general functions for signal
transduction from external environmental stimuli and conversion them into molecular
response. Fine-tuning of the miRNA production likely participates in both developmental
regulation and epigenetic memory formation in Norway spruce.
Vis fullstendig beskrivelse