N6‐methyladenosine RNA modification regulates cotton drought response in a Ca2+ and ABA‐dependent manner

Summary 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.