Cytosine methylation in the promoter region of genes involved in cellular oxidation equilibrium pathways affects rice heat tolerance

Abstract

Background High temperatures are detrimental to rice yield and quality, especially at night. Due to the predicted increases in global warming, it is imperative that crops are able to adapt to high night temperatures (HNTs) in the near future. DNA methylation is a potential mechanism for controlling gene activity and cellular phenotype under adversely environment without changing nucleotide sequence.Results Here, we reported that few CG and CHG contexts but CHH context in rice genome was strongly induced by HNT to occur cytosine methylation variation between two coisogenic rice strains with significant difference in heat tolerance. Methylation variations occurred mainly on successive cytosines in the promoter or downstream regions of transcription factors and transposon elements. In contrast to the heat-sensitive rice strain, two basal transcriptional factor TFIID subunit 11 and mediator of RNA polymerase II transcription subunit 31 were fully demethylated in the downstream 358-359 bp and 2-60 bp under HNT in the heat-tolerant strain, respectively. Various genes involved in ABA-related reactive oxygen species (ROS) equilibrium pathways, including the pentatricopeptide repeat domain gene PPR (LOC_Os07g28900) and the homeobox domain gene homeobox (LOC_Os01g19694), were induced by HNT to occur methylation variation on successive cytosines in the gene promoter regions of the heat-tolerant strain. Varidation among the typical heat-tolerant group and heat-sensitive group of rice germplasms, methylation rate of the cytosines in gene promoter region for gene PPR was higher and gene expression was suppressed in the heat-sensitive group, comparing to the heat-tolerant group.Conclusions The CHH context in rice genome was the main context type to occur cytosine methylation variation under HNT between the heat-sensitive and heat-tolerant rice strains. Methylation in the promoter regions of the genes related to abscisic acid-related oxidation and ROS scavenging contributes to rice heat tolerance. These findings provide bases to explain the molecular mechanisms behind rice heat tolerance.