Single-base methylome analysis reveals dynamic epigenomic differences associated with water deficit in apple

Area of Science:

• Plant epigenetics
• Molecular biology
• Genomics

Background:

• Cytosine methylation is crucial for epigenetic regulation in plants.
• Limited understanding exists on DNA methylation dynamics under environmental stress.
• Apple (Malus x domestica) methylome data is scarce, especially concerning stress responses.

Purpose of the Study:

• To map the apple genome's methylome at single-base resolution.
• To analyze DNA methylation changes in response to water deficit stress.
• To investigate the relationship between DNA methylation and gene expression in apple.

Main Methods:

• Whole-genome bisulfite sequencing (WGBS) for single-base resolution methylation mapping.
• Differential gene expression analysis using RNA-sequencing.
• Comparative analysis of methylation patterns in drought-sensitive and drought-tolerant apple cultivars under water deficit.

Main Results:

• The apple genome shows distinct methylation levels: ~54% (CG), ~38% (CHG), and ~8.5% (CHH).
• Water deficit stress induced widespread DNA methylation alterations, particularly in genes encoding transcription factors (TFs) and transposable elements (TEs).
• Promoter hypomethylation correlated with higher gene expression, while gene body methylation showed a positive correlation with expression levels.

Conclusions:

• This study provides a comprehensive methylome map for the apple genome.
• DNA methylation patterns are dynamic and significantly altered by water deficit stress in apple.
• Epigenetic modifications, specifically DNA methylation, play a key role in plant adaptation to abiotic stress, offering targets for crop breeding.