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 met...
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ftdatacite:10.6084/m9.figshare.c.4406045.v1 2023-05-15T16:02:08+02:00 High-resolution DNA methylome reveals that demethylation enhances adaptability to continuous cropping comprehensive stress in soybean Xilong Liang Hou, Xue Jianying Li Yiqiang Han Yuxian Zhang Naijie Feng Jidao Du Wenhui Zhang Dianfeng Zheng Shumei Fang 2019 https://dx.doi.org/10.6084/m9.figshare.c.4406045.v1 https://springernature.figshare.com/collections/High-resolution_DNA_methylome_reveals_that_demethylation_enhances_adaptability_to_continuous_cropping_comprehensive_stress_in_soybean/4406045/1 unknown Figshare https://dx.doi.org/10.1186/s12870-019-1670-9 https://dx.doi.org/10.6084/m9.figshare.c.4406045 CC BY 4.0 https://creativecommons.org/licenses/by/4.0 CC-BY Biophysics Genetics FOS Biological sciences Molecular Biology 59999 Environmental Sciences not elsewhere classified FOS Earth and related environmental sciences 39999 Chemical Sciences not elsewhere classified FOS Chemical sciences 69999 Biological Sciences not elsewhere classified Plant Biology Collection article 2019 ftdatacite https://doi.org/10.6084/m9.figshare.c.4406045.v1 https://doi.org/10.1186/s12870-019-1670-9 https://doi.org/10.6084/m9.figshare.c.4406045 2021-11-05T12:55:41Z 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. Article in Journal/Newspaper DML DataCite Metadata Store (German National Library of Science and Technology) |
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DataCite Metadata Store (German National Library of Science and Technology) |
op_collection_id |
ftdatacite |
language |
unknown |
topic |
Biophysics Genetics FOS Biological sciences Molecular Biology 59999 Environmental Sciences not elsewhere classified FOS Earth and related environmental sciences 39999 Chemical Sciences not elsewhere classified FOS Chemical sciences 69999 Biological Sciences not elsewhere classified Plant Biology |
spellingShingle |
Biophysics Genetics FOS Biological sciences Molecular Biology 59999 Environmental Sciences not elsewhere classified FOS Earth and related environmental sciences 39999 Chemical Sciences not elsewhere classified FOS Chemical sciences 69999 Biological Sciences not elsewhere classified Plant Biology Xilong Liang Hou, Xue Jianying Li Yiqiang Han Yuxian Zhang Naijie Feng Jidao Du Wenhui Zhang Dianfeng Zheng Shumei Fang High-resolution DNA methylome reveals that demethylation enhances adaptability to continuous cropping comprehensive stress in soybean |
topic_facet |
Biophysics Genetics FOS Biological sciences Molecular Biology 59999 Environmental Sciences not elsewhere classified FOS Earth and related environmental sciences 39999 Chemical Sciences not elsewhere classified FOS Chemical sciences 69999 Biological Sciences not elsewhere classified Plant Biology |
description |
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. |
format |
Article in Journal/Newspaper |
author |
Xilong Liang Hou, Xue Jianying Li Yiqiang Han Yuxian Zhang Naijie Feng Jidao Du Wenhui Zhang Dianfeng Zheng Shumei Fang |
author_facet |
Xilong Liang Hou, Xue Jianying Li Yiqiang Han Yuxian Zhang Naijie Feng Jidao Du Wenhui Zhang Dianfeng Zheng Shumei Fang |
author_sort |
Xilong Liang |
title |
High-resolution DNA methylome reveals that demethylation enhances adaptability to continuous cropping comprehensive stress in soybean |
title_short |
High-resolution DNA methylome reveals that demethylation enhances adaptability to continuous cropping comprehensive stress in soybean |
title_full |
High-resolution DNA methylome reveals that demethylation enhances adaptability to continuous cropping comprehensive stress in soybean |
title_fullStr |
High-resolution DNA methylome reveals that demethylation enhances adaptability to continuous cropping comprehensive stress in soybean |
title_full_unstemmed |
High-resolution DNA methylome reveals that demethylation enhances adaptability to continuous cropping comprehensive stress in soybean |
title_sort |
high-resolution dna methylome reveals that demethylation enhances adaptability to continuous cropping comprehensive stress in soybean |
publisher |
Figshare |
publishDate |
2019 |
url |
https://dx.doi.org/10.6084/m9.figshare.c.4406045.v1 https://springernature.figshare.com/collections/High-resolution_DNA_methylome_reveals_that_demethylation_enhances_adaptability_to_continuous_cropping_comprehensive_stress_in_soybean/4406045/1 |
genre |
DML |
genre_facet |
DML |
op_relation |
https://dx.doi.org/10.1186/s12870-019-1670-9 https://dx.doi.org/10.6084/m9.figshare.c.4406045 |
op_rights |
CC BY 4.0 https://creativecommons.org/licenses/by/4.0 |
op_rightsnorm |
CC-BY |
op_doi |
https://doi.org/10.6084/m9.figshare.c.4406045.v1 https://doi.org/10.1186/s12870-019-1670-9 https://doi.org/10.6084/m9.figshare.c.4406045 |
_version_ |
1766397740955205632 |