Dataset Information

High-resolution DNA methylome reveals that demethylation enhances adaptability to continuous cropping comprehensive stress in soybean.

ABSTRACT:

Background

Continuous cropping stress involves such factors as biological barriers, allelopathic autotoxicity, deterioration of soil physicochemical properties, and soil fertility imbalance and is regarded as a kind of comprehensive stress limiting soybean yield and quality. Genomic DNA methylation is an important regulatory mechanism for plants to resist various environmental stresses. Therefore, it is especially worthwhile to reveal genomic methylation characteristics under stress and clarify the relationship between DNA methylation status and continuous cropping stress adaptability in soybean.

Results

We generated a genome-wide map of cytosine methylation induced by this kind of comprehensive stress in a tolerant soybean variety (Kang Xian 2, KX2) and a sensitive variety (He Feng, HF55) using whole-genome bisulfite sequencing (WGBS) technology. The expression of DNA demethylase genes was detected using real-time quantitative PCR (qRT-PCR). The functions of differentially methylated genes (DMGs) involved in stress response in biochemical metabolism and genetic information transmission were further assessed based on Gene Ontology (GO) annotation and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis. The results showed that genomic DNA demethylation was closely related to continuous cropping comprehensive stress adaptability in soybean, which was further verified by the increasing expression of DNA demethylases ROS1 and DML. The demethylation of mCpG and mCpHpG (mCpApG preferred) contexts was more critical, which mainly occurred in gene-regulatory regions at the whole-chromosome scale. Moreover, this kind of stress adaptability may be related to various stress responders generated through strengthened glucose catabolism and amino acid and fatty acid anabolism, as well as fidelity transmission of genetic information.

Conclusions

Genomic DNA demethylation was closely associated with continuous cropping comprehensive stress adaptability, highlighting the promising potential of screening continuous cropping-tolerant cultivars by DNA methylation index and further exploring the application of DNA demethylases in soybean breeding.

SUBMITTER: Liang X

PROVIDER: S-EPMC6380062 | biostudies-literature | 2019 Feb

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

High-resolution DNA methylome reveals that demethylation enhances adaptability to continuous cropping comprehensive stress in soybean.

Liang Xilong X Hou Xue X Li Jianying J Han Yiqiang Y Zhang Yuxian Y Feng Naijie N Du Jidao J Zhang Wenhui W Zheng Dianfeng D Fang Shumei S

BMC plant biology 20190218 1

<h4>Background</h4>Continuous cropping stress involves such factors as biological barriers, allelopathic autotoxicity, deterioration of soil physicochemical properties, and soil fertility imbalance and is regarded as a kind of comprehensive stress limiting soybean yield and quality. Genomic DNA methylation is an important regulatory mechanism for plants to resist various environmental stresses. Therefore, it is especially worthwhile to reveal genomic methylation characteristics under stress and ...[more]

PMID: 30777019

Similar Datasets

Project description:The continuous planting of soybeans leads to soil acidification, aggravation of soil-borne diseases, reduction in soil enzyme activity, and accumulation of toxins in the soil. Microorganisms in the rhizosphere play a very important role in maintaining the sustainability of the soil ecosystem and plant health. In this study, two soybean genotypes, one bred for continuous cropping and the other not, were grown in a Mollisol in northeast China under continuous cropping for 7 and 36years in comparison with soybean-maize rotation, and microbial communities in the rhizosphere composition were assessed using high-throughput sequencing technology. The results showed that short- or long-term continuous cropping had no significant effect on the rhizosphere soil bacterial alpha diversity. Short-term continuous planting increased the number of soybean cyst nematode (Heterodera glycines), while long-term continuous planting reduced these numbers. There were less soybean cyst nematodes in the rhizosphere of the tolerant genotypes than sensitive genotypes. In addition, continuous cropping significantly increased the potential beneficial bacterial populations, such as Pseudoxanthomonas, Nitrospira, and Streptomyces compared to rotation and short-term continuous cropping, suggesting that long-term continuous cropping of soybean shifts the microbial community toward a healthy crop rotation system. Soybean genotypes that are tolerant to soybean might recruit some microorganisms that enhance the resistance of soybeans to long-term continuous cropping. Moreover, the network of the two genotypes responded differently to continuous cropping. The tolerant genotype responded positively to continuous cropping, while for the sensitive genotype, topology analyses on the instability of microbial community in the rhizosphere suggested that short periods of continuous planting can have a detrimental effect on microbial community stability, although this effect could be alleviated with increasing periods of continuous planting.

Project description:BackgroundProstate cancer is a clinically heterogeneous disease with a subset of patients rapidly progressing to lethal-metastatic prostate cancer. Current clinicopathological measures are imperfect predictors of disease progression. Epigenetic changes are amongst the earliest molecular changes in tumourigenesis. To find new prognostic biomarkers to enable earlier intervention and improved outcomes, we performed methylome sequencing of DNA from patients with localised prostate cancer and long-term clinical follow-up.MethodsWe used whole-genome bisulphite sequencing (WGBS) to comprehensively map and compare DNA methylation of radical prostatectomy tissue between patients with lethal disease (n = 7) and non-lethal (n = 8) disease (median follow-up 19.5 years). Validation of differentially methylated regions (DMRs) was performed in an independent cohort (n = 185, median follow-up 15 years) using targeted multiplex bisulphite sequencing of candidate regions. Survival was assessed via univariable and multivariable analyses including clinicopathological measures (log-rank and Cox regression models).ResultsWGBS data analysis identified cancer-specific methylation patterns including CpG island hypermethylation, and hypomethylation of repetitive elements, with increasing disease risk. We identified 1420 DMRs associated with prostate cancer-specific mortality (PCSM), which showed enrichment for gene sets downregulated in prostate cancer and de novo methylated in cancer. Through comparison with public prostate cancer datasets, we refined the DMRs to develop an 18-gene prognostic panel. Applying this panel to an independent cohort, we found significant associations between PCSM and hypermethylation at EPHB3, PARP6, TBX1, MARCH6 and a regulatory element within CACNA2D4. Strikingly in a multivariable model, inclusion of CACNA2D4 methylation was a better predictor of PCSM versus grade alone (Harrell's C-index: 0.779 vs. 0.684).ConclusionsOur study provides detailed methylome maps of non-lethal and lethal prostate cancer and identifies novel genic regions that distinguish these patient groups. Inclusion of our DNA methylation biomarkers with existing clinicopathological measures improves prognostic models of prostate cancer mortality, and holds promise for clinical application.

Dataset Information

High-resolution DNA methylome reveals that demethylation enhances adaptability to continuous cropping comprehensive stress in soybean.

Background

Results

Conclusions

Publications

High-resolution DNA methylome reveals that demethylation enhances adaptability to continuous cropping comprehensive stress in soybean.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets