RNA-seq analysis in progeny leaves on rice seed treatd with heat
Ontology highlight
ABSTRACT:
ORGANISM(S): Oryza sativa
PROVIDER: GSE218077 | GEO | 2025/03/31
REPOSITORIES: GEO
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Project description:RNA-seq analysis in progeny leaves on rice seed treatd with heat
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Project description:We report the relationship between transgenerational growth and profiling of DNA methylation in rice seeds treated with heat.
2025-05-20 | GSE203487 | GEO
Project description:Protein lysine acylation, such as succinylation and acetylation are important posttranslational modification (PTM) mechanisms, with key roles in the regulation of diverse metabolic and cellular processes. Antibody-based affinity enrichment, high-resolution LC-MS/MS analysis and integrated bioinformatics analysis, were used to characterize the lysine succinylome (Ksuc) and acetylome (Kace) in rice leaves. Rice (Oryza sativa., Wuyunjing 7) was kindly provided byJiangsu Academy of Agricultural Sciences, Jiangsu Province, China. Rice seeds were surface-sterilized with 5% NaClO for 20 min, washed extensively with distilled water and then germinated in distilled water at 28ºC for 2 days. Germinated seeds were cultivated on half-strength ammonium-free Murashige and Skoog (MS) medium. For oxidative stress treatments, 14-days-old rice seedlings were transferred to 1/2 MS medium in the absence or presence of 1 mM H2O2 for 6 days. Rice seedlings were then harvested for protein extraction.
2018-07-23 | PXD007175 | Pride
Project description:In this study, we focused on a super rice variety, WFYT025, which is widely used in China. Therefore, we took the flag leaves of WFYT025 and its two parents for high-throughput transcriptome sequencing, trying to find some genes related to photosynthesis or transpiration and development of seeds. The aim of our study is (1) we investigated the length, width, and leaf area of flag leaves for WFYT025 and its parents. MPH and HPH were estimated for the heterosis of flag leaf. (2) We selected the flag leaves of hybrid rice WFYT025 and its parents for transcriptome sequencing, the first day and the tenth days after flowering in the environment of early rice and middle rice, respectively. (3) we referred to further investigate the gene regulatory network. Several major sub-networks were found to represents interactions among genes with similar expression profiles via gene regulatory network analysis.
2021-06-02 | GSE175967 | GEO
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:affy_rice_2012_01 - ivt - One of the key questions for future agriculture will be to save agronomical relevant biodiversity. To do so, it is important to select the best crop cultivars that will germinate efficiently (good seed vigor) and for a long period of time (good seed longevity). Surprisingly, while mankind rely heavily on cereals, very few studies have identified genes positively related to cereal seed vigor and longevity. To close this scientific gap, we aimed to identify genes positively involved in rice seed vigor and longevity. We thus used a “controlled deterioration treatment (Tesnier et al., 2002) to mimic natural seed ageing. Seeds are first equilibrated at 25°C and 85% relative hygrometry during three days. Then, during 15 days, three different batch of seeds are either (i) kept at 25°C and 85% RH (control seeds), (ii) placed at 40°C and 85% RH (loss of seed vigor) or (iii) placed at 45°C and 85% RH (loss of germination capacity). Finally, seeds are equilibrated at 25°C and 32% RH during three days. Using this CDT treatment, we obtained rice seeds with contrasted seed vigor or germination capacity. We extracted the total RNA from the embryos and we analysed their transcriptome using the Affymetrix Rice Genome Array.-We applied a Controlled Deterioration Treatment (CDT) to seeds from the reference rice cultivar Nipponbare. First, all seeds are equilibrated at 25°C and 85% relative hygrometry. Then, depending on the treatment, seeds are placed at 25, 40 or 45°C in 85% relative hygrometry before being finally equilibrated at 25°C and 32% relative hygrometry. The germination of the three seed batches was measured during five days with one measure every 8h. Seeds placed at 25°C during the whole experiment were similar to control seeds kept in the fridge and germinated at nearly 100% in 48h. Seeds placed at 40°C during 15 days germinate at 74% but show altered seedling phenotypes (loss of seed vigor). Finally, seeds placed at 45°C do not germinate.
2013-09-01 | GSE46342 | GEO
Project description:affy_rice_2012_01 - ovation - One of the key questions for future agriculture will be to save agronomical relevant biodiversity. To do so, it is important to select the best crop cultivars that will germinate efficiently (good seed vigor) and for a long period of time (good seed longevity). Surprisingly, while mankind rely heavily on cereals, very few studies have identified genes positively related to cereal seed vigor and longevity. To close this scientific gap, we aimed to identify genes positively involved in rice seed vigor and longevity. We thus used a “controlled deterioration treatment (Tesnier et al., 2002) to mimic natural seed ageing. Seeds are first equilibrated at 25°C and 85% relative hygrometry during three days. Then, during 15 days, three different batch of seeds are either (i) kept at 25°C and 85% RH (control seeds), (ii) placed at 40°C and 85% RH (loss of seed vigor) or (iii) placed at 45°C and 85% RH (loss of germination capacity). Finally, seeds are equilibrated at 25°C and 32% RH during three days. Using this CDT treatment, we obtained rice seeds with contrasted seed vigor or germination capacity. We extracted the total RNA from the embryos and we analysed their transcriptome using the Affymetrix Rice Genome Array.-We applied a Controlled Deterioration Treatment (CDT) to seeds from the reference rice cultivar Nipponbare. First, all seeds are equilibrated at 25°C and 85% relative hygrometry. Then, depending on the treatment, seeds are placed at 25, 40 or 45°C in 85% relative hygrometry before being finally equilibrated at 25°C and 32% relative hygrometry. The germination of the three seed batches was measured during five days with one measure every 8h. Seeds placed at 25°C during the whole experiment were similar to control seeds kept in the fridge and germinated at nearly 100% in 48h. Seeds placed at 40°C during 15 days germinate at 74% but show altered seedling phenotypes (loss of seed vigor). Finally, seeds placed at 45°C do not germinate.
2013-09-01 | GSE46334 | GEO
Project description:Straw return is crucial for the sustainable development of rice planting. To investigate the response of rice leaves to rice straw return, we analyzed the physiological index of rice leaves and measured differentially expressed protein (DEPs) and differentially expressed metabolites (DEMs) levels in rice leaves by the use of proteomics and metabolomics approaches. The results showed that, compared with no rice straw return, rice straw return significantly decreased the dry weight of rice plants and nonstructural carbohydrate contents and destroyed the chloroplast ultrastructure. In rice leaves under rice straw return, 329 DEPs were upregulated, 303 DEPs were downregulated, 44 DEMs were upregulated, and 71 DEMs were downregulated. These DEPs and DEMs were mainly involved in various molecular processes, including photosynthesis, carbon fixation in photosynthetic organisms, glycolysis, and the citric acid cycle. Rice straw return promoted the accumulation of osmotic adjustment substances, such as organic acids, amino acids, and other substances, and reduced the material supply and energy production of carbon metabolism, thus inhibiting the growth of rice.
2022-09-12 | PXD035835 | Pride
Project description:Seed germination is a complicated physiological process, during which structures of mitochondria and plastids are recovered, and metabolisms are re-activated (Han and Yang, 2015). It has been shown that metabolism reactivation is very important for rice germination (He et al., 2011b;Han et al., 2014a). It is still unknown if protein acetylation involved in and regulate these metabolisms during rice seed germination. To answer this question, we globally profiled the acetylome in rice embryos from the germinating seeds. A number of acetylated enzymes were identified. The results provide more information about the metabolism regulation in germinating seeds.
2016-01-26 | PXD002739 | Pride