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ABSTRACT:
PROVIDER: PRJNA716503 | ENA |
REPOSITORIES: ENA
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Project description:Salinity stress poses a significant risk to agricultural yield and productivity. Therefore, elucidation of plant salt-response mechanisms has become essential to identify stress-tolerance genes. In the present study, two pearl millet genotypes with contrasting salt-tolerance showed differential morpho-physiological and proteomic responses under 150 mM NaCl, and the genotype IC 325825 could withstand salt-stress better than IP 17224. The salt-tolerance potential of IC 325825 was associated with its ability to maintain ionic, osmotic balance and membrane integrity under stress. The IC 325825 exhibited better growth under salinity as compared to IP 17224 due to higher expression of C4 photosynthesis enzymes, efficient antioxidant system, and lower Na+/K+ ratio. Comparative proteomics analysis revealed greater metabolic perturbation in IP 17224 under salinity, in contrast to IC 325825 that harbored pro-active stress-responsive machinery, allowing its survival and better adaptability under salt-stress. The differentially expressed proteins were in-silico characterized for their functions, subcellular-localization, pathway/ interaction analysis, and relative transcript levels. This study has provided novel insights into salinity stress adaptive mechanisms in pearl millet, demonstrating the power of proteomics-based approaches. The critical proteins identified in the present study could be further explored as potential objects for increasing salt-tolerance in sensitive crop plants.
2022-05-09 | PXD025592 | Pride
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
2023-01-01 | GSE133480 | GEO
Project description:Soil salinity is one of the primary causes of yield decline in rice. Pokkali (Pok) is a highly salt-tolerant landrace whereas IR29, is salt-sensitive but a widely cultivated cultivar. Comparative analysis of these genotypes may offer better understandings of the salinity tolerance mechanism. The published reports largely underscored the importance of transcriptional regulation during salt stress in these genotypes, while, the regulation at translational level is also critically important. Therefore, simultaneous comparison of transcriptional and translational changes between IR29 and Pok could unravel molecular insights into gene regulatory mechanisms that differ between these contrasting genotypes. Using RNA-Seq, we analyzed transcriptome and translatome from the control and salt-exposed Pok and IR29 seedlings. Clear differences were evident both at transcriptional and translational levels between the two genotypes even under control condition. In response to salt stress, 57 DEGs were commonly upregulated both at transcriptional and translational levels in the two genotypes; the number of up/down regulated DEGs in IR29 was comparable at transcriptional and translational levels; whereas in Pok, the number of upregulated DEGs at translational level (544 DEGs) was considerably higher than that at transcriptional level (219 DEGs); contrastingly, the number of downregulated DEGs (58) at translational level was significantly smaller than that at transcriptional level (397 DEGs). We speculate that Pok is more capable of stabilizing mRNA as well as can efficiently load mRNAs on to polysomes for translation under salt stress. Functional analysis showed that Pok is more efficient in maintaining cell wall integrity, detoxifying reactive oxygen species (ROS), translocating molecules and maintaining photosynthesis under salt stress. The present study not only confirmed the known salt stress associated genes, but also identified a number of putative new salt-responsive genes. This study also showed the importance of translational regulation in salt stress and other stresses responsive mechanism.
2019-01-15 | GSE119721 | GEO
Project description:Soil salinity is one of the primary causes of yield decline in rice. Pokkali (Pok) is a highly salt-tolerant landrace whereas IR29, is salt-sensitive but a widely cultivated cultivar. Comparative analysis of these genotypes may offer better understandings of the salinity tolerance mechanism. The published reports largely underscored the importance of transcriptional regulation during salt stress in these genotypes, while, the regulation at translational level is also critically important. Therefore, simultaneous comparison of transcriptional and translational changes between IR29 and Pok could unravel molecular insights into gene regulatory mechanisms that differ between these contrasting genotypes. Using RNA-Seq, we analyzed transcriptome and translatome from the control and salt-exposed Pok and IR29 seedlings. Clear differences were evident both at transcriptional and translational levels between the two genotypes even under control condition. In response to salt stress, 57 DEGs were commonly upregulated both at transcriptional and translational levels in the two genotypes; the number of up/down regulated DEGs in IR29 was comparable at transcriptional and translational levels; whereas in Pok, the number of upregulated DEGs at translational level (544 DEGs) was considerably higher than that at transcriptional level (219 DEGs); contrastingly, the number of downregulated DEGs (58) at translational level was significantly smaller than that at transcriptional level (397 DEGs). We speculate that Pok is more capable of stabilizing mRNA as well as can efficiently load mRNAs on to polysomes for translation under salt stress. Functional analysis showed that Pok is more efficient in maintaining cell wall integrity, detoxifying reactive oxygen species (ROS), translocating molecules and maintaining photosynthesis under salt stress. The present study not only confirmed the known salt stress associated genes, but also identified a number of putative new salt-responsive genes. This study also showed the importance of translational regulation in salt stress and other stresses responsive mechanism.
2019-01-15 | GSE119720 | GEO
Project description:Many plant researchers have applied genomic tools to model species to identify abiotic stress responsive genes that might be useful for improving stress tolerance in crops. However, it is unclear whether this translational approach will be successful given the complexity of abiotic stress tolerance. We carried out a functional genomic (ionomic, transcriptomic and metabolomic) comparison of three model and three forage species of the genus Lotus with varying tolerance to salinity. Transcriptome analysis showed that about 60 % of expressed genes were responsive to salt treatment in one or more of the six species tested, but less than 1 % was responsive in all genotypes. Therefore, genotype-specific responses overshadowed conserved transcriptional responses to salinity and represent an impediment to translational genomics. Fortunately, 'triangulation' from multiple species enabled the identification of a core set of conserved and tolerant-specific responses that could provide durable tolerance across genotypes.
2010-08-10 | E-MEXP-2344 | biostudies-arrayexpress
Project description:Abiotic stresses such as salinity are very important factors limiting rice growth and productivity around the world. Affymetrix rice genome array containing 48,564 japonica and 1,260 indica sequences was used to analyze the gene expression pattern of rice responsive to salinity stress, try to elucidate the difference of genome-wide gene expression profiling of two contrasting rice genotypes in response to salt stress and to discover the salinity related genes and gene interaction and networks. Under salinity condition, the number of differentially expressed genes (DEGs) in 177-103 was more than that in IR64, and most of up-regulated DEGs in 177-103 are response to stress. But in IR64, most of up-regulated DEGs are transcription related genes. The DEGs under salinity showed very strong tissue specificity, the number of DEGs in leaf was more than that in root. A lot of genes differentially expressed by exogenous ABA treatment under salinity condition, such as Leaf senescence protein, 1-deoxy-D-xylulose 5-phosphate synthase 2 precursor and Protein of unknown function DUF26 were induced by ABA and contributed to salinity tolerance.
2015-11-02 | GSE58603 | GEO
Project description:Analysis of root gene expression of salt-tolerant genotypes FL478, Pokkali and IR63731, and salt-sensitive genotype IR29 under control and salinity-stressed conditions during vegetative growth. Results provide insight into the genetic basis of salt tolerance in indica rice. Keywords: stress response
2009-07-16 | GSE14403 | GEO
Project description:Abiotic stresses such as salinity are very important factors limiting rice growth and productivity around the world. Affymetrix rice genome array containing 48,564 japonica and 1,260 indica sequences was used to analyze the gene expression pattern of rice responsive to salinity stress, try to elucidate the difference of genome-wide gene expression profiling of two contrasting rice genotypes in response to salt stress and to discover the salinity related genes and gene interaction and networks. Under salinity condition, the number of differentially expressed genes (DEGs) in 177-103 was more than that in IR64, and most of up-regulated DEGs in 177-103 are response to stress. But in IR64, most of up-regulated DEGs are transcription related genes. The DEGs under salinity showed very strong tissue specificity, the number of DEGs in leaf was more than that in root. A lot of genes differentially expressed by exogenous ABA treatment under salinity condition, such as Leaf senescence protein, 1-deoxy-D-xylulose 5-phosphate synthase 2 precursor and Protein of unknown function DUF26 were induced by ABA and contributed to salinity tolerance. In this study, the gene expression patterns across two organs including leaves and roots at seedling stage were characterized under control, salinity, salinity+ABA treatments by using the Affymetrix rice microarray platform based on a salinity tolerant rice line derived from IR64.
2015-11-02 | E-GEOD-58603 | biostudies-arrayexpress
Project description:Oilseed mustard, Brassica juncea, exhibits high levels of genetic variability for salinity tolerance. To obtain the global view of transcriptome and investigate the molecular basis of salinity tolerance in a salt-tolerant variety CS52 of B. juncea, we performed transcriptome sequencing of control and salt-stressed seedlings. De novo assembly of 184 million high-quality paired-end reads yielded 42,327 unique transcripts longer than 300 bp with RPKM ≥1. When compared with non-redundant proteins, we could annotate 67% unigenes obtained in our study. Based on the mapping to expressed sequence tags (ESTs), 52.6% unigenes are novel compared to EST data available for B. juncea and constituent genomes. Differential expression analysis revealed altered expression of 1469 unigenes in response to salinity stress. Of these, 587, mainly associated with ROS detoxification, sulfur assimilation and calcium signaling pathways, are up regulated. Notable of these is RSA1 (SHORT ROOT IN SALT MEDIUM 1) INTERACTING TRANSCRIPTION FACTOR 1 (RITF1) homolog up regulated by >100 folds in response to stress. RITF1, encoding a bHLH transcription factor, is a positive regulator of SOS1 and several key genes involved in scavenging of salt stress-induced reactive oxygen species (ROS). Further, we performed comparative expression profiling of key genes implicated in ion homeostasis and sequestration (SOS1, SOS2, SOS3, ENH1, NHX1), calcium sensing pathway (RITF1) and ROS detoxification in contrasting cultivars, B. juncea and B. nigra, for salinity tolerance. The results revealed higher transcript accumulation of most of these genes in B. juncea var. CS52 compared to salt-sensitive cultivar even under normal growth conditions. Together, these findings reveal key pathways and signaling components that contribute to salinity tolerance in B. juncea var. CS52. We report transcriptome sequencing of two-weeks-old seedlings of B. juncea var. CS52 under normal growth conditions (CTRL) and in response to salinity stress (SS) using Illumina paired-end sequencing
2015-02-28 | E-GEOD-66389 | biostudies-arrayexpress