How is epigenetic memory induced in embryos and maintained year after year in long-lived plants?

The climatic adaptation traits of trees are affected by the climate conditions during seed development. This has been shown to be due to epigenetic memory, which affects the plants' growth pattern and gene activities without changing the codes in the genetic material (DNA). In the EpiMemo project, genetically identical Norway spruce trees grown from embryos (seeds) generated by a tissue culture technique called somatic embryogenesis, are studied. Detailed investigations have shown that Norway spruce plants from embryos developed under warmer conditions have later bud break and de-hardening in the spring and later winter bud formation than plants from embryos developed under cooler conditions. We have shown that this is associated with significant differences throughout the year in DNA methylation in genes related to epigenetic mechanisms, biological clocks and control of the growth-dormancy cycle. Specific such genes have different DNA methylation patterns throughout the year in plants from warmer and colder embryo development climates, while other genes have different DNA methylation patterns only at certain times of the year. Consistent with the fact that DNA methylation patterns can influence the activities of genes, these plant groups have significant differences in gene activities for protein-coding genes as well as genes encoding small regulatory RNA molecules that may be involved in the epigenetic memory. Also, in corresponding somatic embryos developed under cooler and warmer conditions, there are significant differences in gene activities and DNA methylation in the mentioned genes. The results so far may indicate that DNA methylation in specific genes and small regulatory RNA molecules play a role in the epigenetic memory of temperature during seed development. This supports that these epigenetic mechanisms may contribute to more rapid climate adaptation in long-lived plants than the long-term climate adaptation occurring through natural selection.

Epigenetic memory may be induced by environmental conditions experienced during embryogenesis. How such a memory affects an organism’s ability to survive and adapt is a topic of great interest. Questions of intense debate are which life stages that are the most sensitive, how altered epigenetic marks are maintained mitotically through a long life and how they alter the phenotype. In EpiMemo we will probe these questions using the long-lived tree species Norway spruce as our experimental system. We will use a unique set of clonal epitype trees with a stable epigenetic memory of the climatic conditions (cold/warm) during embryogenesis and corresponding epitype embryos. To elucidate if the epigenetic memory is associated with differential DNA methylation between epitypes, we will look for stable DNA methylation differences in stem cells of the apical meristems of shoot tips/buds in epitype trees through the annual cycle and in mature embryos. A machine learning pattern recognition approach will be used to distinguish stable DNA methylation differences between epitypes from dynamic changes through the annual cycle. In addition, we will examine mRNA and sRNA gene expression differences (DEG) between epitypes to establish if changes in DNA methylation marks are associated with the observed DEG. We will also study how and when during embryogenesis the epigenetic memory is laid down, by analysing the DNA methylation, mRNA and sRNA expression during different stages of embryogenesis. To verify that DNA methylation differences are causing the phenotypic differences between epitypes we will use targeted editing of DNA methylation of identified target genes by means of transcriptional gene silencing (TGS). Understanding the evolutionary significance of epigenetic memory in climatic adaptation will reveal how perennial plants may epigenetically adjust their annual cycle to local climate changes more rapidly than classical natural selection can cope with.