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Divergent DNA methylation patterns associated with gene expression in rice cultivars with contrasting drought and salinity stress response.

ABSTRACT: DNA methylation is an epigenetic mechanism that play an important role in gene regulation in response to environmental conditions. The understanding of DNA methylation at the whole genome level can provide insights into the regulatory mechanisms underlying abiotic stress response/adaptation. We report DNA methylation patterns and their influence on transcription in three rice (Oryza sativa) cultivars (IR64, stress-sensitive; Nagina 22, drought-tolerant; Pokkali, salinity-tolerant) via an integrated analysis of whole genome bisulphite sequencing and RNA sequencing. We discovered extensive DNA methylation at single-base resolution in rice cultivars, identified the sequence context and extent of methylation at each site. Overall, methylation levels were significantly different in the three rice cultivars. Numerous differentially methylated regions (DMRs) among different cultivars were identified and many of which were associated with differential expression of genes important for abiotic stress response. Transposon-associated DMRs were found coupled to the transcript abundance of nearby protein-coding gene(s). Small RNA (smRNA) abundance was found to be positively correlated with hypermethylated regions. These results provide insights into interplay among DNA methylation, gene expression and smRNA abundance, and suggest a role in abiotic stress adaptation in rice.

SUBMITTER: Garg R

PROVIDER: S-EPMC4598828 | biostudies-literature | 2015

REPOSITORIES: biostudies-literature

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Divergent DNA methylation patterns associated with gene expression in rice cultivars with contrasting drought and salinity stress response.

Garg Rohini R Narayana Chevala Vvs V Shankar Rama R Jain Mukesh M

Scientific reports 20151009

DNA methylation is an epigenetic mechanism that play an important role in gene regulation in response to environmental conditions. The understanding of DNA methylation at the whole genome level can provide insights into the regulatory mechanisms underlying abiotic stress response/adaptation. We report DNA methylation patterns and their influence on transcription in three rice (Oryza sativa) cultivars (IR64, stress-sensitive; Nagina 22, drought-tolerant; Pokkali, salinity-tolerant) via an integra ...[more]

PMID: 26449881

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Project description: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.

Project description:Silicon (Si) application has great potential to improve salt tolerance in a variety of crop plants. However, it is unclear how Si influences the responses of contrasting rice cultivars when exposed to excessive salt. Here, we investigated the functions of Si in alleviating the negative effects of salt stress on two contrasting rice cultivars, namely BRRI dhan48 (salt-sensitive) and Binadhan-10 (salt-tolerant). Rice seedlings was pre-treated with three doses of Si (as silicic acid; 0, 1 and 2 mM) for 14 days at one-day interval before being exposed to salt stress (10 dSm-1) in a sustained water bath system. The results demonstrated that the seedlings of BRRI dhan48 and Binadhan-10, respectively exhibited substantial reductions in shoot height (16 and 9%), shoot fresh weight (64 and 43%) and shoot dry weight (50 and 39%) under salinity. Intriguingly, BRRI dhan48 pre-treated with 1 and 2 mM Si, respectively, showed a higher increase in shoot height (SH) (by 25.90 and 26.08%) as compared with Binadhan-10 (by 3 and 8%) under salt stress compared with their respective controls. Data revealed that a comparatively higher improvement in the growth performances of the salt-induced Si pre-treated BRRI dhan48 than that of Binadhan-10. For example, 1 and 2 mM of Si treatments significantly attributed to elevated leaf relative water content (RWC) (13 and 22%), proline (138 and 165%), chlorophyll a (42 and 44%), chlorophyll b (91 and 72%), total chlorophyll (58 and 53%) and carotenoids (33 and 29%), and recovery in the reductions of electrolyte leakage (13 and 21%), malondialdehyde content (23 and 30%) and shoot Na+/K+ ratio (22 and 52%) in BRRI dhan48 compared with Si-untreated control plants under salt stress. In addition, we found salt-tolerant Binadhan-10 also had enhanced RWC (9 and 19%), proline (12 and 26%) with pre-treatment with 1 and 2 mM of Si, respectively, under salt stress, while no significant differences were noticed in the case of photosynthetic pigments and Na+/K+ ratio. Our results showed that Si supplementation potentiated higher salt-tolerance ability in the salt-sensitive BRRI dhan48 as compared with salt-tolerant Binadhan-10. Thus, Si application could be highly beneficial in the growth recovery of the salinity-affected salt-sensitive high yielding rice cultivars in the saline-prone areas.

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Divergent DNA methylation patterns associated with gene expression in rice cultivars with contrasting drought and salinity stress response.

Publications

Divergent DNA methylation patterns associated with gene expression in rice cultivars with contrasting drought and salinity stress response.

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