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. 2017 Aug 1;34(8):2035-2040.
doi: 10.1093/molbev/msx150.

Small RNAs Reflect Grandparental Environments in Apomictic Dandelion

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Free PMC article

Small RNAs Reflect Grandparental Environments in Apomictic Dandelion

Lionel Morgado et al. Mol Biol Evol. .
Free PMC article

Abstract

Plants can show long-term effects of environmental stresses and in some cases a stress "memory" has been reported to persist across generations, potentially mediated by epigenetic mechanisms. However, few documented cases exist of transgenerational effects that persist for multiple generations and it remains unclear if or how epigenetic mechanisms are involved. Here, we show that the composition of small regulatory RNAs in apomictic dandelion lineages reveals a footprint of drought stress and salicylic acid treatment experienced two generations ago. Overall proportions of 21 and 24 nt RNA pools were shifted due to grandparental treatments. While individual genes did not show strong up- or downregulation of associated sRNAs, the subset of genes that showed the strongest shifts in sRNA abundance was significantly enriched for several GO terms including stress-specific functions. This suggests that a stress-induced signal was transmitted across multiple unexposed generations leading to persistent changes in epigenetic gene regulation.

Keywords: Taraxacum officinale; drought stress; epigenetic inheritance; salicylic acid; small RNA; transgenerational effects.

Figures

<sc>Fig</sc>. 1
Fig. 1
Length composition for the read libraries: all sRNAs (A and D), mapped to annotated TEs (B and E) and mapped to gene-annotated transcripts (C and F) (mean ± SE). Bottom panels (D, E, and F) are enlargements of top panels showing P values from permutation tests performed for 21 and 24 nt sRNA size classes. P values larger than 0.1 are labeled “NS” (not significant). Treatment groups (C: control; D: drought; S: salicylic acid) refer to grandparental treatments.
<sc>Fig</sc>. 2
Fig. 2
Spatial accumulation of 21 and 24 nt sRNA reads in gene-mapping transcripts. Lines represent density distributions of sRNA mapping location along the transcript. Each gene-mapping transcript was scaled to a length of 1000 bp and sRNA mapping positions (pooled replicates) inside each transcript were transformed accordingly. The counts for each transcript were afterwards collapsed into a single transcript model by calculating the averaged number of sRNA hits for each transcript coordinate across all length-normalized transcripts. Color code for treatment groups: control (green), drought (blue), and SA (red).
<sc>Fig</sc>. 3
Fig. 3
Distribution for sRNA fold change in gene-mapping transcripts after grandparental drought stress (A) and salicylic acid (B) against control. Bar plots show p values of GO term enrichment tests (blue: enrichment test in set of genes with reduced sRNAs after stress; orange: enrichment test in set of genes with increased sRNAs after stress), in the case of the drought (C) and the salicylic acid (D) sets. Grey bars indicate P values obtained from random bootstrapping (absence of enrichment), which can be affected by biases in the dandelion reference transcriptome in comparison to the Arabidopsis reference gene set. Error bars indicate 95% bootstrap confidence intervals.

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