Division of Biotechnology and Plant Health

Beyond the genome: epigenetics of defense priming and climatic adaptation in plants

Active Last updated: 13.10.2017
End: jul 2021
Start: jul 2016

In this project we study epigenetic modifications involved in defenses priming against pests and pathogens and climatic adaptation in plants. These are novel research questions of great interest, both from a basic scientific perspective and from a climate change and crop protection perspective. Healthy, vigorous plants with flexible phenotypes that are well adapted to shifting environmental conditions provide better yield and more efficient carbon sequestration from the atmosphere, with less pesticide use. Understanding the molecular mechanisms of the epigenetic machinery will help inform how epigenetics may be exploited in plant breeding and crop management practices.

Status Active
Start - end date 01.07.2016 - 01.07.2021
Project manager Paal Krokene
Division Division of Biotechnology and Plant Health
Department Molecular Plant Biology
Total budget 25000000

The two research themes in this project (defense priming and climatic adaptation) are closely integrated since they focus on the same plant species and are hypothesized to involve similar underlying molecular mechan­isms. Defense priming and environ­mentally induced climatic adaptation are both manifested by phenotypic and gene transcription changes that last weeks to years, but without any change to the genotype. Thus, we hypothesize that both phenom­ena are established and maintained by one or more components of the plants’ epigenetic machin­ery. The primary objective of this proposal is thus to determine changes in gene expression, non-coding RNAs, metabolites, and DNA and histone modifi­cations that contribute to defense priming and climatic adaptation in plants.

We study 3 complementary but very different plant species with different life histories:

1. The conifer Norway spruce (Picea abies) is one of the most economically important tree species in Europe and is a gymnosperm model species with a sequenced genome and defined genetic material at our disposal.

2. The woodland strawberry (Fragaria vesca) is also a model species for the species-rich and economic­ally important Rosaceae family, which includes apples, pears, plums, almonds, raspberry, and the cultivated garden strawberry.

3. Arabidopsis (Arabidopsis thaliana) is the general plant model and is the most amendable of all plants for functional studies and thus ideally suited to transfer knowledge to economically and ecologically important plants such as Norway spruce and strawberry.


Publications in the project

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Kva hadde vel julaan vore utan eit grønt, glitrande juletre? Men det er ikkje ei sjølvfølgje at julegran kan hoggast alle stadar i Noreg. Grana er nemleg eit utsett treslag som er i ein stadig kamp mot insekt og sopp for å overleve. Heldigvis har grana nokre overraskande knep i bakhand som sender fiendane på dør, fortel seniorforskar og granekspert Paal Krokene frå Norsk institutt for bioøkonomi (NIBIO).


Redigering av gener gjer at vi står framfor ein heilt ny debatt om bioteknologi, seier Bioteknologirådets leiar Kristin Halvorsen.

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Main conclusion: Epigenetic memory affects the timing of bud burst phenology and the expression of bud burstrelated genes in genetically identical Norway spruce epitypes in a manner usually associated with ecotypes. In Norway spruce, a temperature-dependent epigenetic memory established during embryogenesis affects the timing of bud burst and bud set in a reproducible and predictable manner. We hypothesize that the clinal variation in these phenological traits, which is associated with adaptation to growth under frost-free conditions, has an epigenetic component. In Norway spruce, dehydrins (DHNs) have been associated with extreme frost tolerance. DHN transcript levels decrease gradually prior to flushing, a time when trees are highly sensitive to frost. Furthermore, EARLY BUD BREAK 1 genes (EBB1) and the FT-TFL1- LIKE 2-gene (PaFTL2) were previously suggested to be implied in control of bud phenology. Here we report an analysis of transcript levels of 12 DHNs, 3 EBB1 genes and FTL2 in epitypes of the same genotype generated at different epitype-inducing temperatures, before and during spring bud burst. Earlier flushing of epitypes originating from embryos developed at 18 C as compared to 28 C, was associated with differential expression of these genes between epitypes and between buds and last year’s needles. The majority of these genes showed significantly different expressions between epitypes in at least one time point. The general trend in DHN expression pattern in buds showed the expected reduction in transcript levels when approaching flushing, whereas, surprisingly, transcript levels peaked later in needles, mainly at the moment of bud burst. Collectively, our results demonstrate that the epigenetic memory of temperature during embryogenesis affects bud burst phenology and expression of the bud burst-related DHN, EBB1 and FTL2 genes in genetically identical Norway spruce epitypes.


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.