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.
Highlights
Plant epigenetics has received considerable attention for both basic and applied research in recent years because understanding of the epigenetic regulation of plant growth and development could create new genetic variation for improving crop productivity as well as adaptation to stress environment [1]
We assessed the epigenetic consequences of salinity stress in rice genotypes with contrasting salt tolerance behavior
The amount of DNA methylation was more in shoot compared to root (Table 1), indicating unique biological functions performed by each tissue in response to salt stress
Summary
Plant epigenetics has received considerable attention for both basic and applied research in recent years because understanding of the epigenetic regulation of plant growth and development could create new genetic variation for improving crop productivity as well as adaptation to stress environment [1]. Epigenetics refers to heritable variation in gene regulation resulting from covalent modifications of DNA and its associated chromatin proteins without changing the underlying nucleotide sequences [2]. Such epigenetic modifications are reversible and can alter the phenotypic appearance [3]. Cytosine methylation is a conserved epigenetic mechanism involved in many important biological processes, including transposon proliferation, genomic imprinting, and regulation of gene expression [4,5] It is usually associated with inactivation of genes while demethylation results in gene activation [6]. Better understanding of epigenetic regulation of plant growth and response to environmental stresses may create novel heritable variation for crop improvement
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