Dormant but Active: Chilling Accumulation Modulates the Epigenome and Transcriptome of Prunus avium During Bud Dormancy

Abstract

Temperate deciduous fruit tree species like sweet cherry ( Prunus avium ) require long periods of low temperatures to trigger dormancy release and flowering. In addition to sequence-based genetic diversity, epigenetic variation may contribute to different chilling requirements among varieties. For the low chill variety ‘Royal Dawn’ and high chill variety ‘Kordia’, we studied the methylome of floral buds during chilling accumulation using MethylC-seq to identify differentially methylated regions (DMRs) during chilling hours (CH) accumulation, followed by transcriptome analysis to correlate changes in gene expression with DNA methylation. We found that during chilling accumulation, DNA methylation increased from 173 CH in ‘Royal Dawn’ and 443 CH in ‘Kordia’ and was mostly associated with the CHH context. In addition, transcriptional changes were observed from 443 CH in ‘Kordia’ with 1,210 differentially expressed genes, increasing to 4,292 genes at 1,295 CH. While ‘Royal Dawn’ showed approximately 5,000 genes differentially expressed at 348 CH and 516 CH, showing a reprogramming that was specific for each genotype. From conserved upregulated genes that overlapped with hypomethylated regions and downregulated genes that overlapped with hypermethylated regions in both varieties, we identified genes related to cold-sensing, cold-signaling, oxidation-reduction process, metabolism of phenylpropanoids and lipids, and a MADS-box SVP-like gene. As a complementary analysis, we used conserved and non-conserved DEGs that presented a negative correlation between DNA methylations and mRNA levels across all chilling conditions, obtaining Gene Ontology (GO) categories related to abiotic stress, metabolism, and oxidative stress. Altogether, this data indicates that changes in DNA methylation precedes transcript changes and may occur as an early response to low temperatures to increase the cold tolerance in the endodormancy period, contributing with the first methylome information about the effect of environmental cues over two different genotypes of sweet cherry.

Bud endodormancy in deciduous fruit trees: advances and prospects

“…DNA methylation and small interfering RNA (siRNA) might be involved in the regulation of MADS-box genes in sweet cherry during the dormancy transition 100 . More recently, Rothkegel et al demonstrated that DNA methylation might act as an early sensor of low temperature, leading to genotype-specific reprogramming and thus changing gene expression 105 .…”

Identification of DNA Methylation and Transcriptomic Profiles Associated With Fruit Mealiness in Prunus persica (L.) Batsch

“…From methylome results, both in normal and mealy fruits, cytosine methylation was higher in the CpG context, followed by CHG and CHH, coinciding with previous methylome studies of Arabidopsis thaliana, apple (Malus domestica borkh. ), Populus euphratica and sweet cherry (Prunus avium L.), showing that different pathways regulate DNA methylation (Lister et al, 2008;Daccord et al, 2017;Su et al, 2018;Rothkegel et al, 2020). Three biological replicates were considered as three independent fruits.…”

“…A more recent study in tomato also showed that cytosine demethylation by a DNA glycosylase SIDML2/ROS1 is necessary for the activation of ripening-induced genes and inhibition of ripening-repressed genes, revealing a critical role for DNA methylation during fruit ripening ( Lang et al, 2017 ). In addition, changes in DNA methylation can be further used for the identification of novel markers, which will consider the genetic background, together with changing environmental conditions, as recently studied in Prunus ( Prudencio et al, 2018 ; Rothkegel et al, 2020 ). In this sense, molecular approaches associated with agronomical traits should be implemented together with classical genetics in order to support breeding programs ( García-Gómez et al, 2021 ).…”

Integrative Analysis of Gene Expression and miRNAs Reveal Biological Pathways Associated with Bud Paradormancy and Endodormancy in Grapevine

“…This model does not explain; however, the role of transcriptional regulators and environmental factors that affect induction of endodormancy, such as, the MADS-box transcription factors or temperature dependent growth cessation [ 15 , 16 ]. Recent work in cherry trees, suggests that epigenetic regulation could play a vital role in dormancy transitions resulting in large-scale transcriptomic modification and an increase in expression of chromatin remodeling proteins [ 13 , 14 , 17 ].…”

“…A few miRNAs show a more direct role in dormancy-associated processes. Crosstalk between miR6390 and C-repeat binding factor (CBF ) , dormancy-associated MADS-box (DAM) and flowering locus T (FT2) genes play important roles in regulating endodormancy in pear and cherry flower buds and other trees [ 10 , 17 , 20 , 22 ]. Similarly, both miRNA156 and miRNA172 were found to regulate seed dormancy and flowering time in lettuce ( Lactuca sativa ) and Arabidopsis thaliana in a delay of germination 1 (DOG1) dependent manner [ 21 ].…”