Local diversity of drought resistance and resilience in <i>Populus tomentosa</i> correlates with the variation of DNA methylation

Zhou, Jiaxuan; Liang, Xiao; Huang, Rui; Song, Fangyuan; Li, Lianzheng; Fang, Yuanyuan; Lu, Wenjie; Lv, Chenfei; Quan, Mingyang; Zhang, Deqiang; Du, Qingzhang

doi:10.1111/pce.14490

Cited by 13 publications

(8 citation statements)

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“…uralensis. Previous studies revealed that genes related to osmotic and antioxidant regulation rapidly respond to water stress, , and these pathways were also enriched and highlighted in our results.…”

Section: Resultsmentioning

confidence: 99%

“…In addition, DMGs were also enriched in phenylpropanoid and flavonoid biosynthesis pathways (Figure 5), which suggested that drought stress and rewatering changed the methylation status of genes involved in the synthesis of secondary metabolites in G. uralensis. Previous studies revealed that genes related to osmotic and antioxidant regulation rapidly respond to water stress, 31,38 and these pathways were also enriched and highlighted in our results. Differential Metabolite Analysis.…”

Section: Correlation Between Dna Methylation Status and Gene Expressi...mentioning

confidence: 99%

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Multi-Omics Analysis Provides Crucial Insights into the Drought Adaptation of Glycyrrhiza uralensis Fisch

Jiang

Liu

et al. 2023

J. Agric. Food Chem.

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Drought adaptation of plants is closely related to resistance and tolerance to drought stress as well as the ability to recover after the elimination of the stress. Glycyrrhiza uralensis Fisch is a commonly applied herb whose growth and development are greatly affected by drought. Here, we provide the first comprehensive analysis of the transcriptomic, epigenetic, and metabolic responses of G. uralensis to drought stress and rewatering. The hyper-/hypomethylation of genes may lead to up-/downregulated gene expression, and epigenetic changes can be regarded as an important regulatory mechanism of G. uralensis under drought stress and rewatering. Moreover, integrated transcriptome and metabolome analysis revealed that genes and metabolites involved in pathways of antioxidation, osmoregulation, phenylpropanoid biosynthesis, and flavonoid biosynthesis may regulate the drought adaptation of G. uralensis. This work provides crucial insights into the drought adaptation of G. uralensis and offers epigenetic resources for cultivating G. uralensis with high drought adaptation.

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Section: Resultsmentioning

confidence: 99%

Section: Correlation Between Dna Methylation Status and Gene Expressi...mentioning

confidence: 99%

Multi-Omics Analysis Provides Crucial Insights into the Drought Adaptation of Glycyrrhiza uralensis Fisch

Jiang

Liu

et al. 2023

J. Agric. Food Chem.

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“…The complex interplay between genotype and environment combined with the limited number of biological replicates, resulted in limited power of this study to identify causal epigenetic variants. However, Zhou et al [ 45 ] detected a functional relationship between DNA-methylation diversity and drought resistance and resilience in Populus tomentosa by combining epigenome-wide association studies with genome-wide association studies. Further research is needed building on our findings to help understand the mechanisms by which DNA methylation epialleles are generated, maintained and erased, and their functional consequences in plants.…”

Section: Discussionmentioning

confidence: 99%

Genome-wide methylome stability and parental effects in the worldwide distributed Lombardy poplar

Vanden Broeck,

Meese,

Verschelde

et al. 2024

BMC Biol

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Background Despite the increasing number of epigenomic studies in plants, little is known about the forces that shape the methylome in long-lived woody perennials. The Lombardy poplar offers an ideal opportunity to investigate the impact of the individual environmental history of trees on the methylome. Results We present the results of three interconnected experiments on Lombardy poplar. In the first experiment, we investigated methylome variability during a growing season and across vegetatively reproduced generations. We found that ramets collected over Europe and raised in common conditions have stable methylomes in symmetrical CG-contexts. In contrast, seasonal dynamics occurred in methylation patterns in CHH context. In the second experiment, we investigated whether methylome patterns of plants grown in a non-parental environment correlate with the parental climate. We did not observe a biological relevant pattern that significantly correlates with the parental climate. Finally, we investigated whether the parental environment has persistent carry-over effects on the vegetative offspring’s phenotype. We combined new bud set observations of three consecutive growing seasons with former published bud set data. Using a linear mixed effects analysis, we found a statistically significant but weak short-term, parental carry-over effect on the timing of bud set. However, this effect was negligible compared to the direct effects of the offspring environment. Conclusions Genome-wide cytosine methylation patterns in symmetrical CG-context are stable in Lombardy poplar and appear to be mainly the result of random processes. In this widespread poplar clone, methylation patterns in CG-context can be used as biomarkers to infer a common ancestor and thus to investigate the recent environmental history of a specific Lombardy poplar. The Lombardy poplar shows high phenotypic plasticity in a novel environment which enabled this clonal tree to adapt and survive all over the temperate regions of the world.

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“…The complex interplay between genotype and environment combined with the limited number of biological replicates, resulted in limited power of this study to identify causal epigenetic variants. However, Zhou et al [42] detected a functional relationship between DNA-methylation diversity and drought resistance and resilience in Populus tomentosa by combining epigenome-wide association studies with genome-wide association studies. Further research is needed building on our findings to help understand the mechanisms by which DNA methylation epialleles are generated, maintained and erased, and their functional consequences in plants.…”

Section: Discussionmentioning

confidence: 99%

Genome-wide methylome stability and parental effects in the worldwide distributed Lombardy poplar

Broeck

Meese

Verschelde

et al. 2023

Preprint

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Background: Despite the increasing number of epigenomic studies in plants, little is known about the forces that shape the methylome in long-lived woody perennials. The Lombardy poplar offers an ideal opportunity to investigate the impact of the individual environmental history of trees on the methylome. Results: We present the results of three interconnected experiments on Lombardy poplar. In the first experiment, we investigated methylome variability during a growing season and across vegetatively reproduced generations. We found that ramets collected over Europe and raised in common conditions have stable methylomes in symmetrical CG-contexts. In contrast, seasonal dynamics occurred in methylation patterns in CHH-context. In the second experiment, we investigated whether methylome patterns of plants grown in a non-parental environment correlate with the parental climate. We did not observe a biological relevant pattern that significantly correlates with the parental climate. Finally, we investigated whether the parental environment has persistent carry-over effects on the phenotype of the vegetative offspring. We combined new bud set observations of three consecutive growing seasons with former published bud set data. Using a linear mixed effects analysis, we found a statistically significant but weak short-term, parental carry-over effect on the timing of bud set. However, this effect was negligible compared to the direct effects of the offspring environment. Conclusions: Genome-wide cytosine methylation patterns in symmetrical CG-context are stable in Lombardy poplar and appear to be mainly the result of random processes. In this widespread poplar clone, methylation patterns in CG-context can be used as bio-markers to infer a common ancestor and thus to investigate the recent environmental history of a specific Lombardy poplar. The Lombardy poplar shows high phenotypic plasticity in a novel environment which enabled this clonal tree to adapt and survive all over the temperate regions of the world.

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Local diversity of drought resistance and resilience in Populus tomentosa correlates with the variation of DNA methylation

Cited by 13 publications

References 108 publications

Multi-Omics Analysis Provides Crucial Insights into the Drought Adaptation of Glycyrrhiza uralensis Fisch

Multi-Omics Analysis Provides Crucial Insights into the Drought Adaptation of Glycyrrhiza uralensis Fisch

Genome-wide methylome stability and parental effects in the worldwide distributed Lombardy poplar

Genome-wide methylome stability and parental effects in the worldwide distributed Lombardy poplar

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