Multi-omics responses of barley seedlings to low and high linear energy transfer irradiation

Volkova, Polina; Prazyan, Alexandr; Podlutskii, Mikhail; Saburov, Vyacheslav; Kazakova, Elizaveta; Bitarishvili, Sofia; Duarte, Gustavo T.; Shesterikova, Ekaterina; Makarenko, Ekaterina; Lychenkova, Maria; Ben, Cécile; Gentzbittel, Laurent; Kazakov, Evgenii; Moiseev, Alexandr; Diuzhenko, Sergei; Korol, Marina; Bondarenko, Ekaterina

doi:10.1016/j.envexpbot.2023.105600

Cited by 3 publications

(2 citation statements)

References 141 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…An extended multiomics experiment involving ionising radiation with low-and high-LET exposure of winter barley (Hordeum vulgare L.) seedlings was performed [40]. The specific subset of transcriptomic data related to low-LET IRs was analysed in detail and presented in the current article.…”

Section: Methodsmentioning

confidence: 99%

“…Heavy metals, such as chromium, lead, cadmium, and arsenic, also exhibit genotoxic effects, triggering apoptosis in plant cells and increasing the frequency of aberrant cells [36][37][38][39]. Having in mind that adaptation pathways to many stress agents have similar mechanisms [39,40], it is plausible to use ionising radiation as a tool for revealing potential molecular contributors to abiotic and anthropogenic stress resilience.…”

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Comparative Analysis of the Effect of Gamma-, Electron, and Proton Irradiation on Transcriptomic Profile of Hordeum vulgare L. Seedlings: In Search for Molecular Contributors to Abiotic Stress Resilience

Prazyan,

Podlutskii,

Volkova

et al. 2024

Plants

Self Cite

View full text Add to dashboard Cite

The development of adaptation strategies for crops under ever-changing climate conditions is a critically important food security issue. Studies of barley responses to ionising radiation showed that this evolutionarily ancient stress factor can be successfully used to identify molecular pathways involved in adaptation to a range of abiotic stressors. In order to identify potential molecular contributors to abiotic stress resilience, we examined the transcriptomic profiles of barley seedlings after exposure to γ-rays, electrons, and protons. A total of 553 unique differentially expressed genes with increased expression and 124 with decreased expression were detected. Among all types of radiation, the highest number of differentially expressed genes was observed in electron-irradiated samples (428 upregulated and 56 downregulated genes). Significant upregulation after exposure to the three types of radiation was shown by a set of ROS-responsive genes, genes involved in DNA repair, cell wall metabolism, auxin biosynthesis and signalling, as well as photosynthesis-related genes. Most of these genes are known to be involved in plant ROS-mediated responses to other abiotic stressors, especially with genotoxic components, such as heavy metals and drought. Ultimately, the modulation of molecular pathways of plant responses to ionising radiation may be a prospective tool for stress tolerance programmes.

show abstract

Section: Methodsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Comparative Analysis of the Effect of Gamma-, Electron, and Proton Irradiation on Transcriptomic Profile of Hordeum vulgare L. Seedlings: In Search for Molecular Contributors to Abiotic Stress Resilience

Prazyan,

Podlutskii,

Volkova

et al. 2024

Plants

Self Cite

View full text Add to dashboard Cite

show abstract

Advances in barley germplasm diversity characterization through next-generation sequencing approach

Panahi,

Hosseinzadeh Gharajeh,

Mohammadzadeh Jalaly

2024

Genet Resour Crop Evol

View full text Add to dashboard Cite

Using single-sample networks and genetic algorithms to identify radiation-responsive genes in rice affected by heavy ions of the galactic cosmic radiation with different LET values

Zhang,

Wang,

Zhang

et al. 2024

Front. Plant Sci.

View full text Add to dashboard Cite

IntroductionHeavy ions of the galactic cosmic radiation dominate the radiation risks and biological effects for plants under spaceflight conditions. However, the biological effects and sensitive genes caused by heavy ions with different linear energy transfer (LET) values have not been thoroughly studied.MethodsTo comprehensively analyze the biological effects of heavy ions with different LET values on rice under spaceflight conditions, we utilized the Shijian-10 recoverable satellite (SJ-10) to transport the dehydrated rice seeds on a 12.5-day mission in a 252 km low Earth orbit (LEO), and obtained rice plants hit by individual heavy ions with LET values ranging from 18 keV/μm to 213 keV/μm. The transcriptome and methylation sequencing were conducted on above plants, and a bioinformatics pipeline based on single-sample networks (SSNs) and genetic algorithms (GA) was developed to analyze the multi-omics expression profiles in this work. Note that SSNs can depict the gene interaction patterns within a single sample. The LET regression models were constructed from both gene expression and interaction pattern perspectives respectively, and the radiation response genes that played significant roles in the models were identified. We designed a gene selection algorithm based on GA to enhance the performance of LET regression models.ResultsThe experimental results demonstrate that all our models exhibit excellent regression performance (R2 values close to 1), which indicates that both gene expressions and interaction patterns can reflect the molecular changes caused by heavy ions with different LET values. LET-related genes (genes exhibiting strong correlation with LET values) and radiation-responsive genes were identified, primarily involved in DNA damage and repair, oxidative stress, photosynthesis, nucleic acid metabolism, energy metabolism, amino acid/protein metabolism, and lipid metabolism, etc. DNA methylation plays a crucial role in responding to heavy ions stressors and regulates the aforementioned processes.DiscussionTo the best of our knowledge, this is the first study to report the multi-omics changes in plants after exposure to heavy ions with different LET values under spaceflight conditions.

show abstract

Multi-omics responses of barley seedlings to low and high linear energy transfer irradiation

Cited by 3 publications

References 141 publications

Comparative Analysis of the Effect of Gamma-, Electron, and Proton Irradiation on Transcriptomic Profile of Hordeum vulgare L. Seedlings: In Search for Molecular Contributors to Abiotic Stress Resilience

Comparative Analysis of the Effect of Gamma-, Electron, and Proton Irradiation on Transcriptomic Profile of Hordeum vulgare L. Seedlings: In Search for Molecular Contributors to Abiotic Stress Resilience

Advances in barley germplasm diversity characterization through next-generation sequencing approach

Using single-sample networks and genetic algorithms to identify radiation-responsive genes in rice affected by heavy ions of the galactic cosmic radiation with different LET values

Contact Info

Product

Resources

About