Comparison of the heat stress induced variations in DNA methylation between heat-tolerant and heat-sensitive rapeseed seedlings

Gao, Guizhen; Li, Jun; Li, Hao; Li, Feng; Xu, Kun; Yan, Guiqin; Chen, Biyun; Qiao, Jiangwei; Wu, Xiaoming

doi:10.1270/jsbbs.64.125

Cited by 96 publications

(68 citation statements)

References 51 publications

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“…We also considered another possible explanation, i.e., whether epigenetic modifications such as DNA methylation and histone modification were responsible for the different Pi starvation responses of BnaSPX1 paralogs. It was shown that an adverse environment can induce genome-wide changes in DNA methylation status, specifically in stress-related genes in B. napus (Gao et al, 2014; Verkest et al, 2015). As such, epigenetic modification analysis between these two genes will be performed in the future.…”

Section: Discussionmentioning

confidence: 99%

Genome-Wide Identification and Characterization of SPX Domain-Containing Members and Their Responses to Phosphate Deficiency in Brassica napus

Yang

Ding

et al. 2017

Front. Plant Sci.

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The importance of SPX domain-encoding proteins to phosphate (Pi) homeostasis and signaling pathways has been well-documented in rice and Arabidopsis. However, global information and responses of SPX members to P stress in allotetraploid Brassica napus, one of the world’s major oil crops that is sensitive to P deficiency, remain undefined. We identified a total of 69 SPX domain-containing genes in the B. napus genome. Based on the domain organizations, these genes were classified into four distinct subfamilies—SPX (11), SPX-EXS (43), SPX-MFS (8), and SPX-RING (7)—that represented clear orthologous relationships to their family members in Arabidopsis. A cis-element analysis indicated that 2 ∼ 4 P1BS elements were enriched in the promoter of SPX subfamily genes except BnaSPX4s. RNA-Seq analysis showed that BnaSPX genes were differentially expressed in response to Pi deficiency. Furthermore, quantitative real-time reverse transcription PCR revealed that nine SPX subfamily genes were significantly induced by Pi starvation and recovered rapidly after Pi refeeding. A functional analysis of two paralogous BnaSPX1 genes in transgenic Arabidopsis indicated their functional divergence during long-term evolution. This comprehensive study on the abundance, molecular characterization and responses to Pi deficiency of BnaSPX genes provides insights into the structural and functional diversities of these family members in B. napus and provides a solid foundation for future functional studies of BnaSPX genes.Highlight: The genome-wide identification and characterization of SPX genes in B. napus and their responses to Pi deficiency provide comprehensive insights into the structural and functional diversities of the family members in B. napus and their potential in Pi homeostasis and signaling responsiveness to Pi stress.

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Section: Discussionmentioning

confidence: 99%

Genome-Wide Identification and Characterization of SPX Domain-Containing Members and Their Responses to Phosphate Deficiency in Brassica napus

Yang

Ding

et al. 2017

Front. Plant Sci.

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“…Genome-wide DNA methylation under various abiotic and biotic stresses have been recorded for various plant species (Kou et al, 2011; Wang et al, 2011, 2015; Karan et al, 2012; Colaneri and Jones, 2013; Fan et al, 2013; Shan et al, 2013; Gao et al, 2014). 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).…”

Section: Introductionmentioning

confidence: 99%

“…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).…”

Section: Introductionmentioning

confidence: 99%

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

et al. 2017

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DNA methylation plays an essential role in plant responses to environmental stress. Since drought develops into a rising problem in rice cultivation, investigations on genome-wide DNA methylation in responses to drought stress and in-depth explorations of its association with drought-tolerance are required. For this study, 68 rice accessions were used for an evaluation of their osmotic-tolerance related to 20% PEG6000 simulated physiological traits. The tolerant group revealed significantly higher levels of total antioxidant capacity and higher contents of H2O2 in both normal and osmotic-stressed treatments, as well as higher survival ratios. We furthermore investigated the DNA methylation status in normal, osmotic-stressed, and re-watering treatments via the methylation-sensitive amplification polymorphism (MSAP). The averaged similarity between two rice accessions from tolerant and susceptible groups was approximately 50%, similar with that between two accessions within the tolerant/susceptible group. However, the proportion of overall tolerance-associated epiloci was only 5.2% of total epiloci. The drought-tolerant accessions revealed lower DNA methylation levels in the stressed condition and more de-methylation events when they encountered osmotic stress, compared to the susceptible group. During the recovery process, the drought-tolerant accessions possessed more re-methylation events. Fourteen differentially methylated epiloci (DME) were, respectively, generated in normal, osmotic-stressed, and re-watering treatments. Approximately, 35.7% DME were determined as tolerance-associated epiloci. Additionally, rice accessions with lower methylation degrees on DME in the stressed conditions had a higher survival ratio compared to these with higher methylation degrees. This result is consistent with the lower DNA methylation levels of tolerant accessions observed in the stressed treatment. Methylation degrees on a differentially methylated epilocus may further influence gene regulation in the rice seedling in response to the osmotic stress. All these results indicate that DME generated from a number of genotypes could have higher probabilityies for association with stress-tolerance, rather than DME generated from two genotypes of contrasting tolerance. The DME found in this study are suspected to be good epigenetic markers for the application in drought-tolerant rice breeding. They could also be a valuable tool to study the epigenetic differentiation in the drought-tolerance between upland and lowland rice ecotypes.

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“…As reviewed by various researchers (Chen, Li et al., ; Chen, Müller et al., ; Liu, Feng et al., ; Ohama, Sato, Sinozaki, & Yamaguchi‐Shinozaki, ), the evidences are emerging that illustrate contribution of DNA methylation, chromatin modification and ncRNAs to regulate HS‐responsive gene(s) and their complex networks rendering plants acclimatized to HS. A large number of epigenetically governed HS‐responsive regulatory genes have been recently uncovered in different plant species including Arabidopsis (Naydenov et al., ), rice (Folsom, Begcy, Hao, Wang, & Walia, ), cotton (Min et al., ) and Brassica napus (Gao et al., ). However, further understanding of HS response in grain legumes at epigenetic level demands greater attention.…”

Section: Advancements In Proteomics Metabolomics and Epigenomicsmentioning

confidence: 99%

Integrated “omics” approaches to sustain global productivity of major grain legumes under heat stress

2017

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Grain legumes serve as key sources of dietary protein to the global human population. Consequence of high-temperature (HT) stress is increasingly evident as drastically lost production of different crops including grain legumes worldwide, thus putting the global food security under great threat. In a changing climate scenario, cool season-adapted grain legumes frequently encounter heat stress (HS) during their reproductive phase, thus witnessing serious yield losses. To combat the emerging challenges of HT stress, an integrated approach demanding collaborative efforts from various disciplines of plant science should be in place. This review summarizes major impacts of HT stress on grain legume, and captures the relevance of crop genetic resources to HS tolerance in these crops. Measurement of physiological traits assumes key place in view of ever-increasing precision of next-generation phenotyping assays. We also discuss the significance of genetic inheritance and QTL discovery and evolving "omics" science for developing HS tolerance grain legume crops.

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Comparison of the heat stress induced variations in DNA methylation between heat-tolerant and heat-sensitive rapeseed seedlings

Cited by 96 publications

References 51 publications

Genome-Wide Identification and Characterization of SPX Domain-Containing Members and Their Responses to Phosphate Deficiency in Brassica napus

Genome-Wide Identification and Characterization of SPX Domain-Containing Members and Their Responses to Phosphate Deficiency in Brassica napus

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

Integrated “omics” approaches to sustain global productivity of major grain legumes under heat stress

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