Transcriptome and DNA methylome analysis of Fragaria nilgerrensis under drought stress. Fragaria nilgerrensis

Fragaria nilgerrensis is a diploid wild strawberry, which is densely covered with yellow-brown sericeous on the whole plant, giving them excellent drought resistance. Hitherto, there is a general lack of in-depth understanding of the mechanism of drought resistance of F. nilgerrensis. We therefore investigated the drought response regulatory networks of F. nilgerrensis based on the integrated analysis of DNA methylation, transcriptome and physiological traits during four continuous time points under drought stress. The results revealed that the most differentially expressed genes (DEGs) and the corresponding physiological changes were found at 8 days (T8) compared with 0 day (T0, control). While the most hypo- and hypermethylated regions were found in T4 and T8 respectively. Then, we investigated the relationship between gene expression and methylation in F. nilgerrensis using integrating analysis and identified 835 differentially methylated expressed genes (DMEGs), which were further divided into four clusters based on methylation and gene expression patterns. The genes with either positive or negative correlation between methylation and gene expression were mainly associated with Kinases, ROS synthesis and scavenging, ABA signal pathway etc. Consistently, the weighted gene co-expression network analysis (WGCNA) revealed the hub role of ABA signaling pathway in drought resistance of F. nilgerrensis. Moreover, the expression of a large number of stress responsive genes were also upregulated, including kinases, dehydration genes, late embryogenesis genes and stress responsible transcription factors. These results would deepen our understanding on drought resistance and its application in breeding in strawberry.