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

Xia, Hui; Huang, Weixia; Xiong, Jie; Yan, Shuaigang; Tao, Tao; Li, Jiajia; Wu, Jinhong; Luo, Lijun

doi:10.3389/fpls.2017.00011

Cited by 22 publications

(28 citation statements)

References 54 publications

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“…This is in accordance with our finding that dose-insensitive salt-induced DMMs appeared more commonly in sites that could facilitate perturbation in the expression of genes that hypothetically could be part of a molecular response to salinity, as reported elsewhere [65]. There is evidence from previous studies to suggest that salt-induced DMMs can play important roles in evoking metabolic differences between seedlings growing under control and saline conditions [25,26,29,34,64,66], although the markers found in these works were either few in number or else identified from a single genotype. The provision here of a robust list of consistent, salt-responsive DMMs therefore provides a useful starting point from which to gather a more holistic picture of DNA methylation-mediated regulation of molecular responses to salt exposure.…”

Section: Salt-induced Changes In Dna Methylation May Influence Gene Rsupporting

confidence: 92%

Salt Stress Induces Non-CG Methylation in Coding Regions of Barley Seedlings (Hordeum vulgare)

et al. 2018

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Salinity can negatively impact crop growth and yield. Changes in DNA methylation are known to occur when plants are challenged by stress and have been associated with the regulation of stress-response genes. However, the role of DNA-methylation in moderating gene expression in response to salt stress has been relatively poorly studied among crops such as barley. Here, we assessed the extent of salt-induced alterations of DNA methylation in barley and their putative role in perturbed gene expression. Using Next Generation Sequencing, we screened the leaf and root methylomes of five divergent barley varieties grown under control and three salt concentrations, to seek genotype independent salt-induced changes in DNA methylation. Salt stress caused increased methylation in leaves but diminished methylation in roots with a higher number of changes in leaves than in roots, indicating that salt induced changes to global methylation are organ specific. Differentially Methylated Markers (DMMs) were mostly located in close proximity to repeat elements, but also in 1094 genes, of which many possessed gene ontology (GO) terms associated with plant responses to stress. Identified markers have potential value as sentinels of salt stress and provide a starting point to allow understanding of the functional role of DNA methylation in facilitating barley's response to this stressor.

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Section: Salt-induced Changes In Dna Methylation May Influence Gene Rsupporting

confidence: 92%

Salt Stress Induces Non-CG Methylation in Coding Regions of Barley Seedlings (Hordeum vulgare)

et al. 2018

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“…All transgenic plants and WPB106 (wild type, WT) were grown in the greenhouse at 28–35 °C, in Shanghai, or in fields at the station of the Shanghai Academy of Agricultural Sciences under normal growth conditions. For salinity stress at the seedling stage, seedlings of rice were cultivated in normal nutrient solution for 5 days after germination on a 96-well plate (Xia et al 2017 ). They were placed in a growth chamber (14 h of daytime at 30 °C and 10 hat night at 20 °C with 70% relative humidity).…”

Section: Methodsmentioning

confidence: 99%

Enhanced rice salinity tolerance via CRISPR/Cas9-targeted mutagenesis of the OsRR22 gene

et al. 2019

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Salinity is one of the most important abiotic stress affecting the world rice production. The cultivation of salinity-tolerant cultivars is the most costeffective and environmentally friendly approach for salinity control. In recent years, CRISPR/Cas9 systems have been widely used for target-site genome editing; however, their application for the improvement of elite rice cultivars has rarely been reported. Here, we report the improvement of the rice salinity tolerance by engineering a Cas9-OsRR22-gRNA expressing vector, targeting the OsRR22 gene in rice. Nine mutant plants were identified from 14 T 0 transgenic plants. Sequencing showed that these plants had six mutation types at the target site, all of which were successfully transmitted to the next generations. Mutant plants without transferred DNA (T-DNA) were obtained via segregation in the T1 generations. Two T2 homozygous mutant lines were further examined for their salinity tolerance and agronomic traits. The results showed that, at the seedling stage, the salinity tolerance of T2 homozygous mutant lines was significantly enhanced compared to wild-type plants. Furthermore, no significantly different agronomic traits were found between T2 homozygous mutant lines and wild-type plants. Our results indicate CRISPR/ Cas9 as a useful approach to enhance the salinity tolerance of rice.

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“…Seedlings of WA-CMS and its maintainer line were transplanted to a 96-well plate 3 days after germination and cultivated in a nutrient solution (Xia et al, 2017 ). They were placed in a growth chamber (14 h of light at 30°C and 10 h of darkness at 20°C with 70% relative humidity).…”

Section: Methodsmentioning

confidence: 99%

RNA Editing Responses to Oxidative Stress between a Wild Abortive Type Male-Sterile Line and Its Maintainer Line

et al. 2017

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RNA editing of mitochondrial gene transcripts plays a central role during plant development and evolutionary adaptation. RNA editing has previously been reported to differ between the rice cytoplasmic male sterile (CMS) line and its maintainer line, which has been suggested as a cause for their different performances under environmental stress. To specifically test this hypothesis, a wild abortive (WA) CMS line (Huhan-1A) and its maintainer line (Huhan-1B) were utilized to investigate performances in response to oxidative stress, as well as RNA editing efficiencies on transcripts of six selected mitochondrial genes. Compared to the maintainer line, Huhan-1A represented both lower plant height and total antioxidant capacity, possessed higher total soluble protein and chlorophyll contents, accumulated less H2O2 content on the 3rd day after treatment (DAT), and exhibited higher survival ratio after re-watering. Furthermore, a total of 90 editing sites were detected on transcripts of six mitochondrial genes (atp9, nad2, nad7, nad9, ccmB, and ccmC) in both Huhan-1A and Huhan-1B on the 0, 1st, and 3rd DAT. Forty-eight sites were furthermore determined as stress-responsive sites (SRS). Generally, in response to oxidative stress, SRS in Huhan-1A increased the resulting editing efficiencies, while SRS in Huhan-1B decreased the resulting editing efficiencies. In addition, 33 and 22 sites at ccmB and ccmC were differentially edited between Huhan-1A and Huhan-1B, respectively, on the 0, 1st, and 3rd DAT. Editing efficiencies of ccmB and ccmC were generally lower in Huhan-1A (ccmB, 37.3–47.8%; ccmC, 41.2–52.3%) than those in Huhan-1B (ccmB, 82.6–86.5%; ccmC, 81.0–82.9%). Deficiencies of RNA editing in Huhan-1A at ccmB and ccmC could lead to the loss of transmembrane domains in their protein structures. Consequently, differences in RNA editing at ccmB and ccmC between the WA-CMS line and its maintainer line partially explained their different performances under stress. Moreover, we detected differences in expressions of pentatricopeptide repeat (PPR) genes between both lines, as well as significant correlations with RNA editing. Our study indicated potential associations of RNA editing and PPR genes in rice tolerance to abiotic stresses. However, the underlying molecular mechanisms of stress-adaptation, which are attributed to RNA editing on transcripts of mitochondrial genes, require further investigation.

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

Cited by 22 publications

References 54 publications

Salt Stress Induces Non-CG Methylation in Coding Regions of Barley Seedlings (Hordeum vulgare)

Salt Stress Induces Non-CG Methylation in Coding Regions of Barley Seedlings (Hordeum vulgare)

Enhanced rice salinity tolerance via CRISPR/Cas9-targeted mutagenesis of the OsRR22 gene

RNA Editing Responses to Oxidative Stress between a Wild Abortive Type Male-Sterile Line and Its Maintainer Line

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