Gene expression signatures of rice floral organs before and after pollination under heat and combined drought and heat stress
Ontology highlight
ABSTRACT:
ORGANISM(S): Oryza sativa
PROVIDER: GSE57154 | GEO | 2015/05/31
SECONDARY ACCESSION(S): PRJNA245798
REPOSITORIES: GEO
Similar Datasets
Project description:A heat and drought tolerant rice cultivar (N22) was grown in the field under control and drought conditions during the dry season in 2013. Drought was applied during early grain filling and resulted in simultaneous heat stress, leading to reduced grain yield and quality. Total RNA was extracted from developing seeds under stress and control (fully flooded) conditions and RNA-seq analysis was performed. These samples are a part of a bigger experiment analysing the responses of three contrasting rice cultivars (N22, Dular, Anjali) to combined heat and drought stress including different organs (developing seeds, flag leaves, flowering spikelets) and developmental stages (early grain filling, flowering) at the transcriptomic level.
2020-11-04 | GSE153030 | GEO
Project description:Rice is susceptible to both heat and drought stress, in particular during flowering and grain filling, when both grain yield and quality may be severely compromised. However, under field conditions, these two stresses rarely occur separately. Under well-watered conditions, plants avoid heat stress by transpirational cooling, while this is not possible under drought conditions. Although investigating combined heat and drought stress is clearly more agronomically relevant than analyzing the effects of the single stresses, only a few studies of this stress combination, in particular under field conditions, have been published. Furthermore, little is known about how plants respond during recovery from drought stress, which also determines plant survival. To address these knowledge gaps, three rice cultivars differing in heat and drought tolerance were grown in the field under control and drought conditions in three consecutive years. Drought was applied either during flowering or during early grain filling, resulting in simultaneous heat stress, leading to reduced grain yield and quality. Analysis by gas chromatography-mass spectrometry (GC-MS) showed distinct metabolic profiles for the three investigated organs (flag leaves, flowering spikelets, developing seeds). The metabolic responses of the plants also strongly differed between cultivars and organs, and between stress and rewatering conditions. Correlation analysis identified potential metabolic markers for grain yield and quality under combined heat and drought stress from stress- and rewatering-regulated metabolites and from metabolites with constitutive differences between the cultivars. These results show that GC-MS can resolve metabolic responses to combined heat and drought stress and subsequent rewatering in different organs of field-grown rice. The metabolite profiles can be used to identify potential marker metabolites for yield stability and grain quality that are expected to improve breeding efforts towards climate change resilient rice.
2019-04-25 | MTBLS801 | MetaboLights
Project description:Rice reproductive development is highly sensitive to high temperature stress. In rice flowering occurs over a period of at least 5 days. Heat stress alters the global gene expression dynamics in panicle especially during pollen development, anthesis and grain filling. Some of the rice genotypes like Nagina 22 show better spikelet fertility and grain filling compared to high yielding and popular rice cultivars like IR 64. We carried out microarray analysis of 8 days heat stressed panicles of Nagina22, heat and drought tolerant aus rice cultivar and IR64, a heat susceptible indica genotype along with unstressed samples of Nagina22 and IR64 so as to understand the transcriptome dynamics in these two genotypes under heat stress and to identify the genes important for governing heat stress tolerance in rice.
2021-01-31 | GSE136746 | GEO
Project description:Heat stress drastically affects anther tissues resulting in poor plant fertility, necessitating an urgent need to determine the key proteins associated in the response of anthers to heat stress. Employing quantitative proteome analysis, we identified several cultivar-specific protein alterations in anthers of Moroberekan (Japonica, heat sensitive), IR64 (Indica, moderately heat tolerant), and Nagina 22 (Aus, heat tolerant) rice types following short-term (ST_HS; one cycle of 42°C, 4 hours before anthesis) and long-term (LT_HS; 6 cycles of 38°C, 6 hours before anthesis) heat treatments. The protein numbers were higher in Nagina 22 than IR 64 and Moroberekan anthers under unstressed and heat stress. The proteins upregulated in long-term heat stress in Nagina 22 were enriched in biological processes related to unfolded protein binding and carboxylic acid metabolism, including amino acid metabolism. In short-term heat stress, Nagina 22 anthers were enriched in proteins associated with vitamin E biosynthesis while proteins downregulated were related to ribosomal proteins. The expression of Hsp20, DnaJ, and Hsp101 was predominantly observed in Nagina 22. Overall, the heat response in Nagina 22 was associated with its capacity for adequate metabolic control and cellular homeostasis which may be critical for its higher reproductive thermotolerance
2023-02-17 | PXD035952 | Pride
Project description:Purpose: understanding the complex genetic control of heat tolerance can be reached using whole transcriptome sequencing (RNA-seq) that is currently the most powerful tool to identify genes differentially regulated. Heat responses differ greatly between sensitive and tolerant genotypes, mainly in terms of the amount of genes and pathways involved in the response and differences in the expression level of constitutive genes in many pathways. The present study aims to compare the molecular response of Brazilian flooded rice cultivars with variable sensitivity to heat stress at anthesis stage and to discuss the possible processes involved in heat tolerance. Methods: Panicle mRNA profiles of cultivars IRGA 428 (sensitive) and BR-IRGA 409 (tolerant) were generated by deep sequencing, in triplicate (each replicate is composed of two plants), under three days of heat stress and control condition at anthesis stage, using Illumina Hiseq 2500. The sequence reads from each sample that passed quality filters were mapped independently, generating contigs that were aligned with the reference genome sequences in rice (cv. MH63-indica). The transcripts were analyzed at the expression level with statistic test (EdgeR – Rstudio) to identify the significant changes in the expression level of the genes for each treatment condition and cultivar follow by identification of metabolic pathways (MapMan and Cytoscape) based on different programs. Results: Using an optimized data analysis workflow, we identified 16,871 transcripts in the rice spikelet of sensitive and tolerant cultivars with HISAT workflow. Using filtered and aligned reads, transcript levels were used to find differentially expressed genes (DEGs) at different thermal condition and cultivars. We identified 2,064 genes for BR-IRGA 409 and 1,078 genes for IRGA 428 that showed a significant change in expression in response to heat stress (LogFC ≥0.5 and adjusted p-value <0.001). When it was examined the multi-factor responsive genes, that is genes with an interaction between cultivar and heat stress (multi-factor analysis - cultivars vs control and high temperature), it was identified 65 DEGs in response to heat stress (LogFC ≥0.5 and adjusted p-value <0.001). Comparison of our data set with other RNA-seq studies shows a significant overlap in heat responsive genes (hypergeometric enrichment test). This core set of genes common among RNA-seq studies indicates that it may be associated with basal response to heat. In the present study, genes related to light reaction pathway were induced in the panicle of the cultivar IRGA 428, while these genes in cultivar BR-IRGA 409 were already expressed highly in control conditions. The basal level of these genes in BR-IRGA 409 was as high as the heat-induced level in the sensitive IRGA 428. Photosynthesis is known to occur in rice panicles, but little has been reported about the photosynthetic characteristics of such panicles. To cope with heat stress, plants have developed a sophisticated mechanism to repair photosystem damage. Therefore, in IRGA 428 the induction of these genes suggests the activation of a repair mechanism to reverse damage on the photosynthetic apparatus caused by the heat stress. The difference in basal levels of the photosynthetic genes may be a contributing factor to the differences in spikelet fertility between the cultivars under heat stress. Conclusion: This is the first study to evaluate the heat tolerance of Brazilian rice cultivars. In panicle tissue, most canonical heat responsive genes, such as HSF family, small HSP family and FKBP family, show a similar response in both Brazilian cultivars, despite the fact that these cultivars have not been specifically selected for heat tolerance. The response of photosynthetic genes to heat stress is a major difference between the cultivars BR-IRGA 409 and IRGA 428. This study indicates that the higher basal expression of photosynthetic genes in the panicle provides improved spikelet fertility under heat stress. This may provide potential markers that can be used to identify heat tolerant genotypes among rice breeding programs. This study emphasizes that the characterization of heat stress responses in individual cultivars provides insights into both the basic mechanisms of heat response and assists with understanding the complex phenomenon of responses to high temperature stress.
2018-08-29 | GSE119109 | GEO
Project description:Heat shock factors (Hsfs) are known to regulate heat and drought stress response by controlling the expression of heat shock proteins and oxidative stress responsive genes. Loss-of-function of OsHSFA2e gene resulted in increased sensitivity of rice plants to drought and heat stress. To identify the targets of OsHSFA2e and dissect the stress response pathway regulated by it, we performed transcriptome profiling of Oshsfa2e mutant plants under drought stress as well as well-watered conditions by RNA-sequencing.
2015-01-16 | GSE65025 | GEO
Project description:Drought and heat are major abiotic stresses frequently coinciding to threaten rice production. Although hundreds of stress-related genes have been identified in the past two decades, very few genes have been confirmed to confer resistance to multiple stresses in crops. Here we report ONAC023, identified through NAC-centered gene regulatory network and genetic association analyses, is a hub stress-regulator that integrates the regulations of both drought and heat tolerance in rice. The loss-of-function mutant of ONAC023 showed significantly increased sensitivity to drought and heat stresses, whereas the overexpression of ONAC023 confers drought and heat tolerance at both seedling and reproductive stages. Notably, drought and heat stresses activated the function of ONAC023 not only by the induction of ONAC023 transcript but also by the nuclear accumulation of ONAC023 protein through a remorin-importin-α-assisted translocation. Under drought or heat stress, ONAC023 can directly target and promote the expression of functionally diverse downstream genes, such as OsPIP2;7, PGL3, OsFKBP20-1b, and OsSF3B1, which are involved in various stress-responsive processes including water transport, reactive oxygen species homeostasis, and alternative splicing (AS). Furthermore, genome-wide AS profiling revealed that the loss of ONAC023 function led to alternation of the encoding outcomes of thousands of AS transcripts under drought and heat stresses. These results manifested that ONAC023 is fine tuned to positively regulate drought and heat tolerance through the integration of multiple stress-responsive processes. Our findings provide not only an underlying connection between drought and heat responses, but also a promising candidate for engineering multi-stress-resilient rice.
2024-06-13 | GSE183241 | GEO
Project description:Systems responses of mature leaves from 4 reference cultivars of a larger collection of European potato cultivars (Solanum tuberosum L.) are investigated by metabolome profiling and RNA-Sequencing. The chosen reference cultivars, Milva, Alegria, Desiree, and Saturna, vary in ascending order in regard to drought tolerance. Systems analyses are based on 3 independent field trials and 3 paralleled greenhouse trials. Robust responses across all cultivars and conditions to natural seasonal drought stress comprise proline, raffinose, galactinol, arabitol, arabinonic acid, chlorogenic acid, and 102 transcripts which consist to a high proportion of heat shock proteins and genes with signaling or regulatory functions, such as a homolog of abscisic acid receptor PYL4. Constitutive differences of the tolerant cultivars, Desiree and Saturna, compared to the sensitive cultivars include arbutin (hydroquinone-beta-D-glucopyranoside), octopamine (p-hydroxyphenylethanolamine), ribitol and 248 differential transcripts. Many of these transcripts are disease related, receptor kinases, or regulatory genes, for example a homolog of the Arabidopsis FOUR LIPS MYB-regulator of stomatal cell proliferation. Functional enrichment analyses imply that heat stress is a major acclimation component of potato leaves to agronomical relevant drought stress. Enhanced leaf heat stress is a result of drought caused by loss of transpiration cooling. This effect and CO2-limitation are the main dilemmas of drought- or ABA-induced stomatal closure. Constitutive differences between tolerant and sensitive cultivars indicate partially synergistic interactions of drought and biotic stress responses. We suggest that drought tolerance of the potato reference cultivars may be caused by general resistance mechanisms which are part of previously selected pathogen tolerance. Transcriptome profiling by RNA-sequencing of 48 leaf samples from 4 potato cultivars grown under control or drought stress conditions in 6 independent experiments
2016-07-06 | E-GEOD-77826 | biostudies-arrayexpress
Project description:Gene expression signatures of rice floral organs before and after pollination under heat and combined drought and heat stress
| PRJNA245798 | ENA
Project description:Plants evolved several acquired tolerance traits for drought stress adaptation to maintain the cellular homeostasis. The combination of constitutive and acquired traits governs drought tolerance, which is crucial for maintaining crop productivity under drought. Drought affects protein synthesis, to uncover the translational landscape with response to drought stress in rice, polysome bound mRNA sequencing at anthesis stage in resistant APO and sensitive IR64 genotypes were performed. Our results demonstrate that drought tolerant genotype maintains higher transcripts bound to poly-ribosomes which facilitate higher protien synthesis which impacted on photosynthesis, spikelet fertility, seed filing and yield under drought stress. We identified many novel LncRNAs and relevant genes associated with translation which can play important role in manitaing grain protein content with drought tolerance.
2024-03-20 | GSE232522 | GEO