N6‐methyladenosine RNA modification regulates cotton drought response in a Ca(2+) and ABA‐dependent manner

N(6)‐methyladenosine (m(6)A) is the most prevalent internal modification present in mRNAs, and is considered to participate in a range of developmental and biological processes. Drought response is highly regulated at the genomic, transcriptional and post‐transcriptional levels. However, the biological function and regulatory mechanism of m(6)A modification in the drought stress response is still poorly understood. We generated a transcriptome‐wide m(6)A map using drought‐resistant and drought‐sensitive varieties of cotton under different water deficient conditions to uncover patterns of m(6)A methylation in cotton response to drought stress. The results reveal that m(6)A represents a common modification and exhibit dramatic changes in distribution during drought stress. More 5'UTR m(6)A was deposited in the drought‐resistant variety and was associated with a positive effect on drought resistance by regulating mRNA abundance. Interestingly, we observed that increased m(6)A abundance was associated with increased mRNA abundance under drought, contributing to drought resistance, and vice versa. The demethylase GhALKBH10B was found to decrease m(6)A levels, facilitating the mRNA decay of ABA signal‐related genes (GhZEP, GhNCED4 and GhPP2CA) and Ca(2+) signal‐related genes (GhECA1, GhCNGC4, GhANN1 and GhCML13), and mutation of GhALKBH10B enhanced drought resistance at seedling stage in cotton. Virus‐induced gene silencing (VIGS) of two Ca(2+)‐related genes, GhECA1 and GhCNGC4, reduced drought resistance with the decreased m(6)A enrichment on silenced genes in cotton. Collectively, we reveal a novel mechanism of post‐transcriptional modification involved in affecting drought response in cotton, by mediating m(6)A methylation on targeted transcripts in the ABA and Ca(2+) signalling transduction pathways.