Salt Stress Induced Variation in DNA Methylation Pattern and Its Influence on Gene Expression in Contrasting Rice Genotypes

Abstract

BackgroundSalinity is a major environmental factor limiting productivity of crop plants including rice in which wide range of natural variability exists. Although recent evidences implicate epigenetic mechanisms for modulating the gene expression in plants under environmental stresses, epigenetic changes and their functional consequences under salinity stress in rice are underexplored. DNA methylation is one of the epigenetic mechanisms regulating gene expression in plant’s responses to environmental stresses. Better understanding of epigenetic regulation of plant growth and response to environmental stresses may create novel heritable variation for crop improvement.Methodology/Principal FindingsMethylation sensitive amplification polymorphism (MSAP) technique was used to assess the effect of salt stress on extent and patterns of DNA methylation in four genotypes of rice differing in the degree of salinity tolerance. Overall, the amount of DNA methylation was more in shoot compared to root and the contribution of fully methylated loci was always more than hemi-methylated loci. Sequencing of ten randomly selected MSAP fragments indicated gene-body specific DNA methylation of retrotransposons, stress responsive genes, and chromatin modification genes, distributed on different rice chromosomes. Bisulphite sequencing and quantitative RT-PCR analysis of selected MSAP loci showed that cytosine methylation changes under salinity as well as gene expression varied with genotypes and tissue types irrespective of the level of salinity tolerance of rice genotypes.Conclusions/SignificanceThe gene body methylation may have an important role in regulating gene expression in organ and genotype specific manner under salinity stress. Association between salt tolerance and methylation changes observed in some cases suggested that many methylation changes are not “directed”. The natural genetic variation for salt tolerance observed in rice germplasm may be independent of the extent and pattern of DNA methylation which may have been induced by abiotic stress followed by accumulation through the natural selection process.

Comprehensive gene expression analysis of the DNA (cytosine-5) methyltransferase family in rice (Oryza sativa L.)

“…There was great variation in the expression activities of rice MTases under specific conditions of abiotic stress. Both in roots and shoots, our data did not deviate as reported previously (Teerawanichpan et al, 2009;Karan et al, 2012). The OsCMT1 gene was significantly downregulated (P < 0.0001) in roots under both salt and osmotic stresses.…”

Tissue-Specific Response to Experimental Demethylation at Seed Germination in the Non-Model Herb Erodium cicutarium

“…Nevertheless, different investigations have used different compounds and protocols (see e.g., [21][22][23][24]), and, occasionally, variations in the magnitude of the observed response are reported when different genetic lines or source populations are used (e.g., [21][22][23]). In addition to such a genotype-specific response, we should note that the magnitude of methylation changes in response to DNMTi treatment and/or experimental stress is usually analyzed in a single tissue, yet global methylation is known to differ between tissues and developmental stages [1], and changes in DNA methylation in response to stress can differ between tissues of treated individuals (see e.g., [3,[25][26][27][28]). Above and below-ground plant organs are highly differentiated, and experience distinctive environments, thus, exploring variation in methylation between them might be particularly useful when trying to interpret plant responses to certain soil stress factors such as drought or salinity (see e.g., [25,26]).…”

Determination of DNA Methylation Levels with CRED-RA Technique in the Genome of Sunflower Seedlings (Helianthus annuus L.) Subjected to Zinc Stress

“…It means that methylatedcytosine is not on double strands of DNA or inner methylated cytosine on a single strand. It wasaccepted as non-methylatedcytosine according to the previous studies [22,23]. According to this, non-methylation seemed to be present in all concentrations of zinc stress.…”

“…Table 3 [20][21][22][23]. According to these, methylation band profile was scored as the presence (1) or absence (0).…”