DNA Methylation‐Mediated Reprogramming of Gene Expression and Flowering Under Combined Heat and Drought Stress in Maize

Many molecular mechanism-related details for maize to respond to and tolerate combined high air temperature and natural soil drought (HAT-NSD) stress especially via whole genome-wide DNA methylation (WGDM) are not-yet known. This study focused on addressing molecular mechanisms of maize response to HAT-NSD by multi-level approaches. The main findings included 4315 differentially methylated genes (DMG); DNA motif sequences prone to differential methylation (DM); heterozygous and homozygous variations in SNPs and InDels; differential alternative splicing (AS) events of mRNAs; high- and low-density DM regions on chromosomes; positive and negative correlations between WGDM and whole-genome gene expression, depending on C (CG, CHG and CHH) contexts in gene regions; 4186 differentially expressed genes (DEG); 1607 differentially expressed proteins (DEP); the limited impacts of whole-genome DM on protein abundance via DMG-DEG-DEP type genes; reprogramming of whole-genome gene expression and flowering by whole-genome DM under HAT-NSD, involving differential AS events and feedback from the follow-up effects of the DM; and functions of ZmSOS3-3 and ZmSOS5-2 genes in both HAT-NSD tolerance and flowering. Models of DM-driven reprogramming-feedback gene expression and flowering/tasseling of maize under HAT-NSD were proposed. The findings provide new insights into mechanisms for maize responses to HAT-NSD through WGDM.