Epigenetic and transcriptional landscape of stress memory in woodland strawberry

Bedfiles of differentially methylated regions (DMRs) that were detected in stressed mother plants (M) and their (themselves unstressed) clonal daughter plants that were formed via stolon formation (St1, St2, St3). The M plants were grown and sampled in vitro and the St1, St2, St3 plants in the green house. The DMRs were called using the the EpiDiverse/dmr bioinformatic analysis pipeline (Nunn et al., 2021).

Stress assays in vitro

One-month-old seedlings were transferred to a fresh MS media and growth chambers at 24^oC/21^oC (day/night),16 h light/8 h dark, as control conditions. For heat-stress, plants were exposed to 30^oC (day/night) for one week followed by 2 days of recovery (24^oC/21^oC) on fresh medium as well as the control plants. Then, the plates were transferred to 37^oC (day/night) for 1 week with 2 recovery days (Figure 1A). We sampled aerial parts of plants for the molecular analyses. To reduce variability resulting from individual plants, three biological replicates of 5 pooled plants were collected per condition. Samples were harvested in 1.5 mL tubes between 9:00-11:00 a.m. and immediately frozen in liquid nitrogen and stored at -80^oC until required.

Greenhouse propagation assays

In vitro plants after heat and control treatment were transferred to soil (one plant per pot) in square plastic pots (size: 12x12x10 cm) and to a greenhouse with long day conditions (24^oC/21^oC day/night and 60%-70% humidity).

Twelve mother plants (M) from control (CM; n=12) and heat-stress (HM; n=12) conditions were used for asexual propagation. From each mother plant, the two first stolons (St) were kept for producing the daughter plants of the first asexual propagation (St1) in individual pots. After two weeks, following root formation, the stolons were cut to get independent daughter plants from their mother plant (M). This process was continued until St3.

The DMRs can also be visualized here: https://jbrowse.agroscope.info/jbrowse/?data=fragaria_sub

And the raw bisulfite sequencing data can be found here: https://www.ebi.ac.uk/ena/browser/text-search?query=ERP135585

 How many daughter plants per stolon? One stolon produce a chain of daughter plants.