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.
Highlights
During winter, perennial fruit trees from temperate regions face unfavorable environmental conditions like low temperatures
For ‘Royal Dawn’ trees, we estimated that chilling requirement (CR) was completed at 516 chilling hours (CH) (2015) and 660 CH (2016) (Figure 1I)
For MethylC-seq of varieties ‘Royal Dawn’ and ‘Kordia’, we isolated genomic DNA from floral buds exposed to different CH accumulation of season 2015 (Figure 1I)
Summary
Perennial fruit trees from temperate regions face unfavorable environmental conditions like low temperatures. The tree ceases its visible growth and enters into dormancy, an adaptative process that sense the environmental cues to increase cold tolerance and to avoid flowering in winter (Lloret et al, 2018). Sweet cherry (Prunus avium L.) belongs to the Rosaceae family and is cultivated in areas of temperate climate, entering into dormancy in autumn to survive the low temperatures of winter. In P. avium and other Rosaceae species, the prolonged exposition to low temperatures in winter and the fulfillment of a chilling requirement (CR), is critical to ensure an optimal flowering in spring and is considered to be specific for each variety or genotype (Campoy et al, 2011). Low chill varieties have the risk of completing this CR earlier in winter, being exposed to spring frost
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