Genome-Wide Differences in DNA Methylation Changes in Two Contrasting Rice Genotypes in Response to Drought Conditions

Abstract

Differences in drought stress tolerance within diverse rice genotypes have been attributed to genetic diversity and epigenetic alterations. DNA methylation is an important epigenetic modification that influences diverse biological processes, but its effects on rice drought stress tolerance are poorly understood. In this study, methylated DNA immunoprecipitation sequencing and an Affymetrix GeneChip rice genome array were used to profile the DNA methylation patterns and transcriptomes of the drought-tolerant introgression line DK151 and its drought-sensitive recurrent parent IR64 under drought and control conditions. The introgression of donor genomic DNA induced genome-wide DNA methylation changes in DK151 plants. A total of 1190 differentially methylated regions (DMRs) were detected between the two genotypes under normal growth conditions, and the DMR-associated genes in DK151 plants were mainly related to stress response, programmed cell death, and nutrient reservoir activity, which are implicated to constitutive drought stress tolerance. A comparison of the DNA methylation changes in the two genotypes under drought conditions indicated that DK151 plants have a more stable methylome, with only 92 drought-induced DMRs, than IR64 plants with 506 DMRs. Gene ontology analyses of the DMR-associated genes in drought-stressed plants revealed that changes to the DNA methylation status of genotype-specific genes are associated with the epigenetic regulation of drought stress responses. Transcriptome analysis further helped to identify a set of 12 and 23 DMR-associated genes that were differentially expressed in DK151 and IR64, respectively, under drought stress compared with respective controls. Correlation analysis indicated that DNA methylation has various effects on gene expression, implying that it affects gene expression directly or indirectly through diverse regulatory pathways. Our results indicate that drought-induced alterations to DNA methylation may influence an epigenetic mechanism that regulates the expression of unique genes responsible for drought stress tolerance.

Differentially Methylated Epiloci Generated from Numerous Genotypes of Contrasting Tolerances Are Associated with Osmotic-Tolerance in Rice Seedlings

“…However, studies using a limited number of rice genotypes exhibited inconsistent results. E.g., one study reported very similar general methylation levels between DK151 (tolerant genotype) and IR64 (susceptible genotype) (Wang et al, 2011), while other studies reported lower DNA methylation levels or hypo-methylation in drought-tolerant genotypes under both normal and stressed conditions (Gayacharan and Joel, 2013; Zheng et al, 2013; Wang W. et al, 2016). These inconsistent results are suggested to be due to genotype-specific manners of DNA methylation (Karan et al, 2012).…”

“…E.g., 64212 (N22/IR64) and 35723 (PK/IR64) differentially methylated regions (DMR) were identified between two pairs of different cultivars via whole genome bisulphite sequencing, which covered 57.9 and 38.5% protein coding genes annotated in the reference genome (Garg et al, 2015). Furthermore, large proportions of DMRs detected between two cultivars were reported not stress-relevant, as they were not in response to drought-stress (Wang W. et al, 2016). It is therefore difficult to determine whether these differences in DNA methylation between two genotypes are associated with their contrasting tolerances or merely with a different genetic background.…”

“…Researchers also aspired to disclose the associations between DNA methylation and stress-tolerance via artificial generation of DNA methylation differences between two genotypes of contrasting tolerances (Wang et al, 2011; Gayacharan and Joel, 2013; Gao et al, 2014; Ferreira et al, 2015; Garg et al, 2015; Wang W. et al, 2016). However, DNA methylation is genotype-specific (Karan et al, 2012).…”

“…Results could be therefore varied among studies that utilize different genotypes (Wang et al, 2011; Gayacharan and Joel, 2013; Zheng et al, 2013). Additionally, there were always severe epigenetic variations between two genotypes (Wang et al, 2011; Karan et al, 2012; Garg et al, 2015; Wang W. et al, 2016). It is a challenge to separate tolerance-associated epigenetic variance from neutral genotype-specific variance between a single tolerant and a single susceptible genotype (Wang W. et al, 2016).…”

Protective Role of Putrescine against Picloram Induced Genomic Instability and DNA Methylation in Phaseolus vulgaris

“…The results indicated that putrescine had the antagonistic effect against picloram. Recently, several studies have indicated that stress positively contributed to tolerance as alter genes expression by DNA methylation and histone modifications (Wang et al, 2016;Feng et al, 2016). In additional, the present study evaluated the protective role of putrescine against picloram genotoxicity.…”