Comparative transcriptome analysis of different root types of a salinity sensitive rice cultivar under salinity stress
Ontology highlight
ABSTRACT:
ORGANISM(S): Oryza sativa
PROVIDER: GSE86860 | GEO | 2021/09/23
REPOSITORIES: GEO
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Project description:Differences in gene expression were compared among nodal roots, S-type lateral roots, and L-type lateral roots of salinity tolerant and sensitive rice varieties.
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Project description:Climate change is affecting crop production due to soil salinization and water scarcity, and is predicted to worsen in the coming years. Rice is a major staple food and the most salt-sensitive cereal. High salinity in the soil triggers several adaptive responses in rice to cope with osmotic and ionic stress at the physiological, cellular and molecular levels. A major QTL for salinity tolerance, named Saltol, is present on chromosome 1 of Indian rice landrace varieties such as Pokkali and Nona Bokra. In this study, we characterized the physiological and early proteomic responses to salinity in FL478, an inbred rice line harboring the Saltol region. For this, plantlets were cultured in hydroponic cultures with 100 mM NaCl and evaluated at 6, 24 and 48h. At the physiological level, salinity significantly reduced shoot length after 48 h, whereas root length significantly increased. Moreover, the Na+/K+ ratio was maintained at lower levels in the shoots compared to the roots FL478 plantlets. On the other hand, roots showed a faster and more coordinated proteomic response than shoots, which was evident from only 6h of treatment. These responses were markedly related with transcription- and translation-related proteins. Moreover, roots exhibited a higher accumulation of stress-related proteins in response to salinity treatment, like peroxidase and SalT, which are both present in the Saltol QTL. Both, physiological and proteomic response, showed that roots respond in a highly adaptive manner to salinity stress compared to shoots, which suggests that this tissue is critical to the tolerance observed in varieties harbouring the Saltol region.
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Project description:Cell-type specific transcriptional profiles were generated by FACS (Fluorescence Activated Cell Sorting) sorting of roots that express cell-type specific GFP-reporters. Five different GFP-reporter lines were utilized allowing us to obtain transcriptional profiles for cells in all radial zones of the root. FACS cell populations were isolated from roots grown under standard conditions or roots that had been transfered to -Fe media for 24 hours. Little is known about how developmental cues affect the way cells interpret their environment. Here we characterize the transcriptional response of different cell layers and developmental stages of the Arabidopsis root to high salinity and find that transcriptional responses are highly constrained by developmental parameters. These transcriptional changes lead to the differential regulation of specific biological functions in subsets of cell-layers, several of which correspond to observable physiological changes. We show that known stress pathways primarily control semi-ubiquitous responses and use mutants that disrupt epidermal patterning to reveal cell-layer specific and inter-cell-layer effects. By performing a similar analysis using iron-deprivation we identify common cell-type specific stress responses and environment-independent biological functions that define each cell type. Keywords: Cell-type specific analysis using FACS
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Project description:Soil salinity presents a notable challenge to agriculture and to increasing the use marginal lands for farming. Here we provide a detailed analysis of the physiology, chemistry and gene expression patterns in roots and shoots of Camelina sativa in response to salt stress. Salt treatment reduced shoot, but not root length. Root and shoot weight were affected by salt, as was photosynthetic capacity. Salt treatment did not alter micro-element concentration in shoots, but increased macro-element (Ca and Mg) levels. Gene expression patterns in shoots indicated that salt stress may have led to shuttling of Na+ from the cytoplasm to the tonoplast and to an increase in K+ and Ca+2 import into the cytoplasm. In roots, gene expression patterns indicated that Na+ was exported from the cytoplasm by the SOS pathway and that K+ was imported in response to salt. Genes encoding proteins involved in chelation and storage were highly up-regulated in shoots, while metal detoxification appeared to involve various export mechanisms in roots. In shoots, genes involved in secondary metabolism leading to lignin, anthocyanin and wax production were up-regulated, probably to improve desiccation tolerance. Partial genome expression partitioning was observed in roots and shoots based on the expression of homeologous genes from the three C. sativa genomes. Genome I and II were involved in the response to salinity stress to about the same degree, while about 10 % more differentially-expressed genes were associated with Genome III. This study has provided valuable information and insight into the response of camelina to salt stress. Examination of this data and comparison to similar studies in more halophytic species will allow development of even more salt-tolerant varieties of this emerging industrial crop.
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Project description:Cell-type specific transcriptional profiles were generated by FACS (Fluorescence Activated Cell Sorting) sorting of roots that express cell-type specific GFP-reporters. Six different GFP-reporter lines were utilized allowing us to obtain transcriptional profiles for cells in all radial zones of the root. FACS cell populations were isolated from roots grown under standard conditions or roots that had been transfered to media supplemented with 140 mM NaCl for 1 hour. Cells are amazingly adept at integrating both external and internal cues to regulate transcriptional states. While internal processes such as differentiation and cell-type specification are generally understood to have an important impact on gene expression, very little is known about how cells utilize these developmental cues to regulate responses to external stimuli. Here we use the response to a well characterized environmental stress, high salinity, to obtain a global view of the role that cell identity plays in guiding transcriptional responses in the root of Arabidopsis. Our analysis is based on three microarray data sets we have generated that explore transcriptional changes spatially among 6 cell layers and 4 longitudinal regions or temporally along 5 time points after salt treatment. We show that the majority of the response to salt stress is cell-type specific resulting in the differential regulation of unique biological functions in subsets of cell layers. To understand the regulatory mechanisms controlling these responses we have analyzed cis-element enrichment in the promoters of salt responsive genes and demonstrate that known stress regulatory elements likely control responses to salt occurring in multiple cell types. Despite the extensive shift in transcriptional state that salt stress elicits, we are able to identify several biological processes that consistently define each cell layer and find that transcriptional regulators of cell-identity tend to exhibit robust cell-type specific expression. Finally, using mutants that disrupt cell-type specification in the epidermis, we reveal cell autonomous and non-autonomous effects when cell identity is altered. Together, these data elucidate a novel intersection between physiology and development and expand our understanding of how transcriptional states are regulated in a multi-cellular context. Keywords: Cell-type specific analysis using FACS
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Project description:In order to understand molecular mechanisms of salt stress tolerance in rice several researches have been reported, however there are still unclear processes involved in salt tolerance. For reaching to a better perspective of the molecular mechanisms, we designed a comprehensive transcriptome study consisting contrasting genotypes, different tissues and different sampling time points. Two contrasting genotypes were selected and grown in Yoshida hydroponic medium for 14 days under controlled conditions. For salinity stress half of the seedlings were under 150 mM NaCl and after 6 and 54 h the treated and untreated samples were harvested in three replications from roots and shoots separately
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Project description:Roots make the first contact with the soil environment and are the first responders of stress. These root behaviors are quantifiable and adaptive. The response of rice varieties in mechanical and salinity stress was measured in a novel experimental setup that mimics the soil environment. We analyzed the response of roots by means of SAC (Stress Adaptation Coefficient) in 28 rice varieties that include high-yield salt tolerant varieties as well as geographically isolated native rice varieties. cDNA microarray of IR64 root-tip shows about 6000 common transcripts to be differentially regulated among the two stresses and common pathways were identified. Overall, our study indicates that there is an important commonality in the molecular basis of salt and mechanical stress and presents an easy-to-perform early establishment stress screen for rice varieties.
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