Coordination of m(6)A mRNA methylation and gene transcriptome in rice response to cadmium stress

N(6)-methyladenosine (m(6)A) is the most prevalent internal modification present in the mRNAs of all higher eukaryotes. However, the role of the m(6)A methylomes in rice is still poorly understood. With the development of the MeRIP-seq technique, the in-depth identification of mRNAs with m(6)A modification has become feasible. A study suggested that m(6)A modification is crucial for posttranscriptional regulation related to Cd(2+)-induced malignant transformation, but the association between m(6)A modification in plants and Cd tolerance has not been reported. We investigated the m(6)A methylomes in the roots of a cadmium (Cd)-treated group and compared them with the roots in the control (CK) group by m(6)A sequencing of cv. 9311 and cv. Nipponbare (NIP) plants. The results indicated that Cd leads to an altered modification profile in 3,406 differential m(6)A peaks in cv. 9311 and 2,065 differential m(6)A peaks in cv. NIP. KEGG pathway analysis of the genes with differentially modified m(6)A peaks indicated that the “phenylalanine”, “tyrosine and tryptophan biosynthesis”, “glycine”, “adherens junctions”, “glycerophospholipid metabolism” and “threonine metabolism” signalling pathways may be associated with the abnormal root development of cv. 9311 rice due to exposure to Cd. The “arginine”, “proline metabolism”, “glycerolipid”, and “protein processing in endoplasmic reticulum” metabolism pathways were significantly enriched in genes with differentially modified m(6)A peaks in cv. NIP. Unlike that in Arabidopsis, the m(6)A-modified nucleotide position on mRNAs (m(6)A peak) distribution in rice exhibited a preference towards both the stop codon and 3′ untranslated regions (3′ UTRs). These findings provide a resource for plant RNA epitranscriptomic studies and further increase our knowledge on the function of m(6)A modification in RNA in plants. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12284-021-00502-y.