Chilling-Mediated DNA Methylation Changes during Dormancy and Its Release Reveal the Importance of Epigenetic Regulation during Winter Dormancy in Apple (Malus x domestica Borkh.)

Abstract

Winter dormancy is a well known mechanism adopted by temperate plants, to mitigate the chilling temperature of winters. However, acquisition of sufficient chilling during winter dormancy ensures the normal phenological traits in subsequent growing period. Thus, low temperature appears to play crucial roles in growth and development of temperate plants. Apple, being an important temperate fruit crop, also requires sufficient chilling to release winter dormancy and normal phenological traits, which are often associated with yield and quality of fruits. DNA cytosine methylation is one of the important epigenetic modifications which remarkably affect the gene expression during various developmental and adaptive processes. In present study, methylation sensitive amplified polymorphism was employed to assess the changes in cytosine methylation during dormancy, active growth and fruit set in apple, under differential chilling conditions. Under high chill conditions, total methylation was decreased from 27.2% in dormant bud to 21.0% in fruit set stage, while no significant reduction was found under low chill conditions. Moreover, the demethylation was found to be decreased, while methylation increased from dormant bud to fruit set stage under low chill as compared to high chill conditions. In addition, RNA-Seq analysis showed high expression of DNA methyltransferases and histone methyltransferases during dormancy and fruit set, and low expression of DNA glcosylases during active growth under low chill conditions, which was in accordance with changes in methylation patterns. The RNA-Seq data of 47 genes associated with MSAP fragments involved in cellular metabolism, stress response, antioxidant system and transcriptional regulation showed correlation between methylation and their expression. Similarly, bisulfite sequencing and qRT-PCR analysis of selected genes also showed correlation between gene body methylation and gene expression. Moreover, significant association between chilling and methylation changes was observed, which suggested that chilling acquisition during dormancy in apple is likely to affect the epigenetic regulation through DNA methylation.

Chilling‐responsive DEMETER‐LIKE DNA demethylase mediates in poplar bud break

“…In chestnut ( Castanea sativa ), the bud formation during winter dormancy and bud break during spring are accompanied by an increment and a decrease, respectively, of genomic DNA (gDNA) methylation (Santamaría et al ). Similarly, in apple ( Malus × domestica ), the transition from dormant bud to fruit set is accompanied by a progressive decrease of gDNA methylation (Kumar et al ). It has been proposed that the mechanisms of winter dormancy in trees and vernalization in herbaceous plants show similarities (Brunner et al ; Rios et al ).…”

Cross-talk between active DNA demethylation, resetting of cellular metabolism and shoot apical growth in poplar bud break

“…In apple, Kumar et al (2016) (14) found that reduced genomic DNA methylation during bud break affects the expression of genes involved in many cellular metabolic processes. Taken together these observations suggest a conserved mechanism controlling growth-dormancy cycles in deciduous trees.…”

Overexpression of DEMETER, a DNA demethylase, promotes early apical bud maturation in poplar

“…Indeed, gene activation by DMLs is necessary for the response of plants to biotic and abiotic stresses (Bharti, Mahajan, Vishwakarma, Bhardwaj, & Yadav, ; Le et al, ; Yu et al, ) and for plant development (Gehring et al, ; Liu et al, ). Epigenetic regulation of adaptive responses of forest tree species to the environment, such as changes in DNA methylation, has been implicated in the switch from active growth to dormancy (Conde, González‐Melendi, & Allona, ; Kumar, Rattan, & Singh, ; Santamaría et al, ; R. Zhu et al, ), possibly one of the most critical developmental transitions for the survival of perennial plants. Here, we report the identification, phylogenetic and expression analyses and phenological studies of a chestnut 5mC DNA DML, whose overexpression promotes apical bud maturation in poplar.…”