Profiling of N6-Methyladenosine (m6A) Modification Landscape in Response to Drought Stress in Apple (Malus prunifolia (Willd.) Borkh)

Abstract

Drought stress is a significant environmental factor limiting crop growth worldwide. <i>Malus prunifolia</i> is an important apple species endemic to China and is used for apple cultivars and rootstocks with great drought tolerance. N⁶-methyladenosine (m⁶A) is a common epigenetic modification on messenger RNAs (mRNAs) in eukaryotes which is critical for various biological processes. However, there are no reports on m⁶A methylation in apple response to drought stress. Here, we assessed the m⁶A landscape of <i>M. prunifolia</i> seedlings in response to drought and analyzed the association between m⁶A modification and transcript expression. In total, we found 19,783 and 19,609 significant m⁶A peaks in the control and drought treatment groups, respectively, and discovered a UGUAH (H: A/U/C) motif. In <i>M. prunifolia</i>, under both control and drought conditions, peaks were highly enriched in the 3' untranslated region (UTR) and coding sequence (CDS). Among 4204 significant differential m⁶A peaks in drought-treated <i>M. prunifolia</i> compared to control-treated <i>M. prunifolia</i>, 4158 genes with m⁶A modification were identified. Interestingly, a large number of hypermethylated peaks (4069) were stimulated by drought treatment compared to hypomethylation. Among the hypermethylated peak-related genes, 972 and 1238 differentially expressed genes (DEGs) were up- and down-regulated in response to drought, respectively. Gene ontology (GO) analyses of differential m⁶A-modified genes revealed that GO slims related to RNA processing, epigenetic regulation, and stress tolerance were significantly enriched. The m⁶A modification landscape depicted in this study sheds light on the epigenetic regulation of <i>M. prunifolia</i> in response to drought stress and indicates new directions for the breeding of drought-tolerant apple trees.