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.
Highlights
The epigenetic modifications including DNA methylation and histone methylation/acetylation, are the heritable information [1], which modulate the gene expression without changing the DNA sequence
The active removal of cytosine methylation is catalyzed by DEMETER (DME) and REPRESSOR OF SILENCING 1 (ROS1), and their paralogs DEMETER-LIKE 2 (DML2) and DEMETER-LIKE 3 (DML3), which are the members of DNA glycosylase family [10, 16, 17]
Annotation of polymorphic fragments suggests that methylation might regulate the wide range of molecular and cellular functions during dormancy release and fruit set in apple
Summary
The epigenetic modifications including DNA methylation and histone methylation/acetylation, are the heritable information [1], which modulate the gene expression without changing the DNA sequence. Change in methylation pattern and chromatin modification of genomic DNA has been reported in various developmental processes and environmental stresses in plants [5]. These changes in methylation pattern have been associated with transcriptional regulation in various plants [6,7,8,9]. The cytosine methylation in higher plants occur predominantly at CG or CHG sequences (where H represents A, C, or T) [11,12,13,14] and sometimes at CHH sequences [15] Irrespective of these sequence contexts, DNA cytosine methyltransferase, DOMAINS REARRANGED METHYLTRANSFERASE 2 (DRM2) catalyzes the de novo cytosine DNA methylation in plants. The active removal of cytosine methylation is catalyzed by DEMETER (DME) and REPRESSOR OF SILENCING 1 (ROS1), and their paralogs DEMETER-LIKE 2 (DML2) and DEMETER-LIKE 3 (DML3), which are the members of DNA glycosylase family [10, 16, 17]
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