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. Malus prunifolia 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 M. prunifolia 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 M. prunifolia, 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 M. prunifolia compared to control-treated M. prunifolia, 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 M. prunifolia in response to drought stress and indicates new directions for the breeding of drought-tolerant apple trees.

MdMTA‐mediated m6A modification enhances drought tolerance by promoting mRNA stability and translation efficiency of genes involved in lignin deposition and oxidative stress

“…We speculated that the limitations of sequencing may have caused this undetectable m 6 A modification of these enzymes. Based on our previously published m 6 A-seq datasets (Mao et al, 2021), we found these genes can be modified by m 6 A modification. Therefore, we designed primers based on where m 6 A modification occur in previous results to detect m 6 A levels of these enzymes in MdMTA transgenic plants.…”

Genome-Wide Identification of m6A Writers, Erasers and Readers in Poplar 84K

“…The reader proteins mainly included ECT2/3/4 and CPSF30 [ 6 , 9 ]. m 6 A has been examined in many species, including Arabidopsis [ 11 ], maize [ 12 ], wheat [ 13 ], oat [ 14 ], rice [ 15 ], sea buckthorn and apple [ 16 , 17 ]. Recently, the function of some m 6 A pathway genes in plants has been studied.…”

m6A‐mediated regulation of crop development and stress responses

“…Accordingly, the m 6 A-mediated stress responses have been extensively studied in ª 2022 The Authors. Plant Biotechnology Journal published by Society for Experimental Biology and The Association of Applied Biologists and John Wiley & Sons Ltd., 20, 1447-1455 various crops, including tobacco (Nicotiana tabacum) (Li et al, 2018), rice (Cheng et al, 2021;Shi et al, 2019b;Tian et al, 2021;Zhang et al, 2021a), wheat (Sun et al, 2020;Zhang et al, 2021b), sweet sorghum (Zheng et al, 2021), tomato (Yang et al, 2021), apple (Guo et al, 2021;Mao et al, 2021), and pakchoi (Liu et al, 2020).…”

“…Mutation of m 6 A writers in Arabidopsis induces significant changes in the expression of genes responsive to abiotic and biotic stresses, as revealed by transcriptome analysis (Anderson et al ., 2018 ; Bodi et al ., 2012 ; Hu et al ., 2021a ). Accordingly, the m 6 A‐mediated stress responses have been extensively studied in various crops, including tobacco ( Nicotiana tabacum ) (Li et al ., 2018 ), rice (Cheng et al ., 2021 ; Shi et al ., 2019b ; Tian et al ., 2021 ; Zhang et al ., 2021a ), wheat (Sun et al ., 2020 ; Zhang et al ., 2021b ), sweet sorghum (Zheng et al ., 2021 ), tomato (Yang et al ., 2021 ), apple (Guo et al ., 2021 ; Mao et al ., 2021 ), and pak‐choi (Liu et al ., 2020 ).…”

“…Salt stress induces a drastic alteration in m 6 A methylome in sweet sorghum, leading to the increase in m 6 A modification and mRNA stability of genes related to the salt resistance, which in turn positively regulated the tolerance to salt stress (Zheng et al ., 2021 ). Furthermore, significant changes in m 6 A methylome profile, as well as its correlation with mRNA abundance, have been deciphered in pak‐choi seedling under heat stress (Liu et al ., 2020 ), tomato anther under cold stress (Yang et al ., 2021 ), and apple leaf under drought stress (Mao et al ., 2021 ). These results revealed that m 6 A modification also participates in controlling the responses of crops to temperature and humidity‐induced stresses.…”