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

The overall goal of this project has been to understand how plants can remember certain events and recall these "memories" when needed - for example when they are attacked by insects or microorganisms. Research over the last 10-20 years has shown that plants have a molecular memory enabling them to adapt to changing environments much faster than what classical genetic adaptation and evolution would suggest. In this Toppforsk project, we have studied molecular memory mechanisms in connection with climate adaptation and plant defense in three very different plants: Norway spruce (Picea abies), woodland strawberry (Fragaria vesca) and the model plant Arabidopsis thaliana. Studies of plant molecular memories are linked to the research field called epigenetics. Epigenetics can be described as a meeting place between heredity and the environment, and epigenetic mechanisms enable plants to quickly adapt to changes in the environment. Epigenetic mechanisms regulate gene expression even if there are no changes to the genetic code itself. Still, epigenetic changes can be inherited to the next generation of cells or individuals. In this project we have studied the basic molecular memory mechanisms that regulate gene expression in plants. Such basic research is important also for applied plant research, such as genetic breeding of spruce, strawberry, and other crop plants. When spruce and strawberry plants are treated with various chemicals, we observe increased resistance to attack, even if the treatment does not activate plant defenses directly. However, when treated plants are infected or attacked weeks or months after treatment, they activate their defenses much faster and more vigorously than untreated control plants. This phenomenon is called defense priming and is a form of inducible plant defense. Our hypothesis has been that epigenetic mechanisms are involved in defense priming. Through a series of scientific articles, we have described defense priming in spruce with emphasis on gene expression and chemical plant defenses. Among other things, we have described how small RNA molecules (so-called microRNA) help regulate gene expression in spruce trees that have been primed by methyl jasmonate application on the stem bark. In wild strawberries, we have investigated the strength of defense priming by infecting primed plants with gray mold fungus (Botrytis cinerea), a plant pathogen that can cause serious disease in strawberries. Primed plants had higher expression of defense genes than non-primed control plants, and some of the priming chemicals we used also increased plant resistance. R-beta-homoserine was particularly interesting, since treatment with this substance increased plant resistance even when plants were treated at the seed stage. Epigenetic mechanisms also help control how plants relate to their abiotic environment. Correct timing of bud break in the spring can, for example, be a matter of life and death, and is extra important in times of rapid climate change. In the project, we have continued previous research at NIBIO on the epigenetic mechanisms that control climate adaptation in spruce. We have studied gene expression in so-called epithypes, i.e., spruce plants originating from genetically identical embryos that have been allowed to develop at different temperatures. We have also studied epigenetic mechanisms in woodland strawberry through similar studies of gene expression and phenotypic differences in epitypes generated at different temperatures. The work with climate adaptations in strawberry has mainly been carried out by a doctoral student who is expected to defend his dissertation during the spring of 2022. During the project period, we have also been part of a group that has described the genome of the spruce bark beetle. The publication of the spruce bark beetle genome in 2021 was an important milestone in the effort to understand the interactions between spruce defense and this important pest.

Oppnådde virkninger: Vi har etablert samarbeid med toneangivende forskere i Storbritannia (Univ. Sheffield) og Finland (Univ. Helsinki). Delvis på grunn av dette samarbeidet har vi i prosjektperioden publisert på et høyere internasjonalt nivå enn vi gjorde før Toppforsk-prosjektet. Av 16 publiserte artikler i internasjonale tidsskrifter med fagfellevurdering i løpet av prosjektet er fem i Nivå 2-tidsskrifter. Ytterligere to artikler er publisert i tidsskrift med høy "impact factor" men som er klassifisert på Nivå 1 i det norske systemet (Trends in Ecology and Evolution, IF 17,7; Annual Review of Phytopathology, IF 13,1). Potensielle effekter: Vår forskning på mekanismene bak aktivering/priming av plantenes eget forsvar har bidratt til utviklingen av mer bærekraftig beskyttelse av matplanter og skogstrær. Kjemisk plantevern er lite bærekraftig og fører til forurensning, tap av biologisk mangfold og pesticidresistens i insekter og sopper.

We propose to build an internationally prominent research group to characterize the epigenetic modifications involved in (i) primed defenses and (ii) climatic adaptation in plants. These are novel research themes of great basic and applied interest, with important implications for e.g. crop protection and mitigation of climate change. These two cross-cutting research themes are closely integrated in the proposed study, as both will focus on the same plant species and are hypothesized to involve similar underlying molecular mechanisms. Defense priming and climatic adaptation are manifested by phenotypic and gene transcription changes that last months 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 will focus on three complementary but very different plant species: Norway spruce, woodland strawberry, and Arabidopsis. The conifer Norway spruce is one of the most economically important tree species in Europe and is emerging as a gymnosperm model species with a sequenced genome and defined genetic material at our disposal. The woodland strawberry is also an emerging model species for the species-rich and economically important Rosaceae family, which includes many important edible plants. Arabidopsis is the general plant model and is the most amendable of all plants for functional studies and thus ideally suited to transfer knowledge to Norway spruce and strawberry. The assembled research group has a long history of pioneering research on induced/primed plant defenses and epigenetic regulation of climatic adaptation in plants, with several previous and ongoing FRIMEDBIO grants.