Unknown,Transcriptomics,Genomics,Proteomics

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RNA-seq of Norwegian spruce embryos exposed to gamma radiation

ABSTRACT: Conifers such as Picea abies (Norway spruce) are among the most radiosensitive plant species, yet the molecular impact of ionising radiation on their stem cells remains poorly understood. This study examines the transcriptomic response of embryogenic stem cells to gamma radiation, focusing on mechanisms that influence stem cell viability and maintenance of stemness. Clonal callus cultures were generated in vitro and exposed to chronic gamma radiation at dose rates of 1, 10, 20, 40, and 100 mGy h⁻¹ for 144 hours. Total RNA was extracted at the end of the exposure period from both irradiated and control samples. Strand-specific RNA sequencing was performed to quantify dose-dependent changes in gene expression. The dataset provides a resource for studying molecular responses to ionising radiation in conifers, with particular relevance to DNA damage repair, oxidative stress responses, chromatin modification, protein homeostasis, and hormone signalling pathways. This work contributes to understanding how ecologically and economically important tree species may respond to environmental radiation exposure at the cellular level.

INSTRUMENT(S): Illumina HiSeq 4000

ORGANISM(S): Picea abies

SUBMITTER: Gareth Gillard

PROVIDER: E-MTAB-15297 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Project description:In the summer of 2012, one year after the 3.11 accident at Fukushima Daiichi nuclear power plant following the Great Tohoku Earthquake, a project was initiated to examine the effects of low-level gamma radiation on rice plants. The site of the experiment was the highly contaminated Iitate village in Fukushima prefecture of Japan. The basic experimental strategy was to expose healthy rice seedlings to continuous low-dose gamma radiation and examine the morphological and molecular genetic changes therien. Selected gene expression profiles of internal control, DNA replication/repair, oxidative stress, photosynthesis, and defense/stress functions were examined by semi-quantitative RT-PCR. Results revealed that low-level gamma radiation affects the expression of numerous genes, in particular showing the early (6 h) induction in DNA repair/damage-related genes and the late (72 h) induction of a previously described marker gene for defense/stress responses. Based on these results, which confirmed our data from preliminary experiments using detached rice leaves for radiation exposure, we proceeded for DNA microarray analysis. Using the established dye-swap approach, we analyzed the differentially expressed genes at 6 and 72 h time points using a whole rice genome 4 x 44 K custom chip. Obtained results showed that exposure to low-level gamma radiation differentially regulated 4481 (induced) and 3740 (suppressed) and 2291 (induced) and 1474 (suppressed) rice leaf genes at 6 and 72 h post-exposure, respectively, by at least two-fold changes. MapMan bioinformatics tool was also used to produce diagrams of the potential pathways, based on the input gene expression data of highly changed genes, operating downstream of the gamma radiation perception by rice plant.Inventory of a large number of gamma radiation-responsive genes in leaves provide new information and increased knowledge on novel regulatory processes in rice. The highly contaminated Iitate Farm (ITF), which is located 31 Km from the damaged nuclear power plant and having a background radiation level over 100 times (~ 5 microSv/h) than normal, was the designated place for the re-examination of low-level gamma radiation experiments using rice as a model system. As our group had a decade of experience and data on the effects of gamma radiation on leaf segments, the experimental was designed in such a way so as to expose whole rice plants to gamma radiation being emitted from the contaminated ground and examine the morphological and molecular genetic changes in the leaves under a dose-dependent manner.

Project description:Sugarcane is a crop widely used worldwide for bioenergy production, and its genetic breeding is highly dependent on tissue culture techniques. Auxin biosynthesis and transport are critical processes for in vitro tissue culture development, but the regulatory responses associated with these processes are still poorly understood in plants. We investigated the role of auxin transport during somatic embryo differentiation in sugarcane callus using an auxin transport inhibitor through a high-throughput proteomic approach. Four concentrations of 2,3,5-triiodobenzoic acid (TIBA 0, 1, 10, and 100 µM) were tested on sugarcane embryogenic callus during the pre-maturation phase of somatic embryogenesis. Pre-maturation treatment with 100 µM TIBA inhibited the differentiation of embryogenic callus into somatic embryos. Then, embryogenic callus from control and 100 µM TIBA treatments were compared via proteomic analysis. A total of 1221 proteins were found, of which 740 were differentially accumulated (DAP) in the 100 µM TIBA/Control comparison. Among the DAPs, 33 were unique to the control treatment, 31 were unique to the 100 µM TIBA pre-maturation treatment, and 415 down-regulated and 261 up-regulated. Inhibition of auxin transport impaired the accumulation and predicted protein‒protein interactions involved in embryonic development, translation, ubiquitination, and energy metabolism. The levels of spermidine synthase and spermidine were reduced, suggesting an association between auxin and polyamines during embryonic development in vitro. The down-regulation of the proteins chaperone BOBBER1, Cullin-associated NEDD8-dissociated protein 1, and Receptor-like kinase TMK2 could be associated with auxin responses and the predicted interactions between proteasome members found during the differentiation of somatic embryos. These new findings demonstrate the role of auxin transport in downstream responses during somatic embryo differentiation and open new avenues for exploring the potential of sugarcane for biotechnological purposes.

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RNA-seq of Norwegian spruce embryos exposed to gamma radiation

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