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PROVIDER: PRJNA1290431 | ENA |
REPOSITORIES: ENA
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Project description:Rapid and uniform seed germination is required for modern cropping system. Thus, it is important to optimize germination performance through breeding strategies in maize, in which identification for key regulators is needed. Here, we characterized an AP2/ERF transcription factor, ZmEREB92, as a negative regulator of seed germination in maize. Enhanced germination in ereb92 mutants is contributed by elevated ethylene signaling and starch degradation. Consistently, an ethylene signaling gene ZmEIL7 and an α-amylase gene ZmAMYa2 are identified as direct targets repressed by ZmEREB92. OsERF74, the rice ortholog of ZmEREB92, shows conserved function in negatively regulating seed germination in rice. Importantly, this orthologous gene pair is likely experienced convergently selection during maize and rice domestication. Besides, mutation of ZmEREB92 and OsERF74 both lead to enhanced germination under cold condition, suggesting their regulation on seed germination might be coupled with temperature sensitivity. Collectively, our findings uncovered the ZmEREB92-mediated regulatory mechanism of seed germination in maize and provide breeding targets for maize and rice to optimize seed germination performance towards changing climates.
2023-11-09 | GSE234833 | GEO
Project description:Regulation of seed germination by dormancy relies on a complex network of transcriptional and post‐transcriptional modifications during seed imbibition that controls seed adaptive responses to environmental cues. High‐throughput technologies have brought significant progress in the understanding of this phenomenon and have led to identify major regulators of seed germination, mostly by studying the behaviour of highly differentially expressed genes. However, the actual models of transcriptome analysis cannot catch additive effects of small variations of gene expression in individual signalling or metabolic pathways, which are also likely to control germination. Therefore, the comprehension of the molecular mechanism regulating germination is still incomplete and to gain knowledge about this process we have developed a pathway‐based analysis of transcriptomic Arabidopsis datasets, to identify regulatory actors of seed germination. The method allowed quantifying the level of deregulation of a wide range of pathways in dormant versus non‐dormant seeds. Clustering pathway deregulation scores of germinating and dormant seed samples permitted the identification of mechanisms involved in seed germination such as RNA transport or vitamin B6 metabolism, for example. Using this method, which was validated by metabolomics analysis, we also demonstrated that Col and Cvi seeds follow different metabolic routes for completing germination, demonstrating the genetic plasticity of this process. We finally provided an extensive basis of analysed transcriptomic datasets that will allow further identification of mechanisms controlling seed germination.
2019-05-21 | MTBLS662 | MetaboLights
Project description:Melatonin plays a potential role in multiple plant developmental processes and stress response. However, there are no reports regarding exogenous melatonin promoting rice seed germination under salinity and nor about the underlying molecular mechanisms at genome-wide. Here, we revealed that exogenous application of melatonin conferred roles in promoting rice seed germination under salinity. The putative molecular mechanisms of exogenous melatonin in promoting rice seed germination under high salinity were further investigated through metabolomic and transcriptomic analyses. The results state clearly that the phytohormone contents were reprogrammed, the activities of SOD, CAT, POD were enhanced, and the total antioxidant capacity was activated under salinity by exogenous melatonin. Additionally, melatonin-pre-treated seeds exhibited higher concentrations of glycosides than non-treated seeds under salinity. Furthermore, exogenous melatonin alleviated the accumulation of fatty acids induced by salinity. Genome-wide transcriptomic profiling identified 7160 transcripts that were differentially expressed in NaCl, MT100 and control. Pathway and GO term enrichment analysis revealed that genes involved in the response to oxidative stress, hormone metabolism, heme building, mitochondrion, tricarboxylic acid transformation were altered after melatonin pre-treatment under salinity. This study provides the first evidence of the protective roles of exogenous melatonin in increasing rice seed germination under salt stress, mainly via activation of antioxidants and modulation of metabolic homeostasis.
2020-01-20 | GSE143922 | GEO
Project description:affy_rice_2011_03 - affy_compartimentation_rice_albumen_embryon - During germination, the rice seed goes from a dry quiescent state to an active metabolism. As with all cereals, the rice seed is highly differentiated between the embryo (that will give rise to the future plantlet) and the endosperm (that contains the seed storage compounds and that will degenerate). The molecular mechanisms operating in the rice seed embryo have begun to be described. Yet, very few studies have focused specifically on the endosperm during the germination process. In particular, the endosperm is mostly addressed with regards to its storage proteins but we have detected a large protein diversity by two-dimensional electrophoresis. Similarly, the endosperm is rich in total RNA which suggest that gene expression coming from seed maturation could play a role during the germination process. In this context, we want to compare the transcriptome of the embryo and the endosperm during rice seed germination. -We germinate rice seeds of the first sequenced rice cultivar i.e. Nipponbare during 0, 4, 8, 12, 16 and 24h of imbibition in sterile distilled water. Germination occurs under constant air bubbling, in the dark at 30°C. These rice seeds are then manually dissected into embryo and endosperm fractions. -The embryo-derived samples are abbreviated in “E” while the endosperm samples are abbreviated “A”. The germination time-point is indicated after the letter (e.g. E8 for embryo samples harvested after 8 hours of germination). Finally, the biological repetition number is indicated before the letter and the time digit (e.g. 1-E8 for an embryo sample from the first repetition at 8 hours of imbibition).
2013-07-01 | GSE43780 | GEO
Project description:Chloramphenicol (CAM) is recognized as one such factor that influence the seed germination. However, the mechanism by which CAM induced suppression on rice germination remains uncertain. To investigate the effect of CAM on rice seed germination, changes in the global profile of phosphorylated proteins induced by CAM were analyzed using LC-MS/MS.
2025-03-25 | PXD050963 | JPOST Repository
Project description:affy_rice_2011_03 - affy_compartimentation_rice_albumen_embryon - During germination, the rice seed goes from a dry quiescent state to an active metabolism. As with all cereals, the rice seed is highly differentiated between the embryo (that will give rise to the future plantlet) and the endosperm (that contains the seed storage compounds and that will degenerate). The molecular mechanisms operating in the rice seed embryo have begun to be described. Yet, very few studies have focused specifically on the endosperm during the germination process. In particular, the endosperm is mostly addressed with regards to its storage proteins but we have detected a large protein diversity by two-dimensional electrophoresis. Similarly, the endosperm is rich in total RNA which suggest that gene expression coming from seed maturation could play a role during the germination process. In this context, we want to compare the transcriptome of the embryo and the endosperm during rice seed germination. -We germinate rice seeds of the first sequenced rice cultivar i.e. Nipponbare during 0, 4, 8, 12, 16 and 24h of imbibition in sterile distilled water. Germination occurs under constant air bubbling, in the dark at 30M-BM-0C. These rice seeds are then manually dissected into embryo and endosperm fractions. -The embryo-derived samples are abbreviated in M-bM-^@M-^\EM-bM-^@M-^] while the endosperm samples are abbreviated M-bM-^@M-^\AM-bM-^@M-^]. The germination time-point is indicated after the letter (e.g. E8 for embryo samples harvested after 8 hours of germination). Finally, the biological repetition number is indicated before the letter and the time digit (e.g. 1-E8 for an embryo sample from the first repetition at 8 hours of imbibition). 36 arrays - rice; organ comparison,time course
2013-07-01 | E-GEOD-43780 | biostudies-arrayexpress
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
Project description:Seeds experience several stress responses from dry to germinated state. To determine the regulators contributing to imbibitional tolerance, dynamic transcriptome analyses were conducted at dry (0 h), imbibed (24 h) and germinated (48 h) stages in japonica Jiucaiqing in this study. Results showed that the differentially expressed genes (DEGs) were pronounced in the early stage (0-24 h) than the late stage (24-48 h); 1,452 transcripts were differentially expressed (648 up-regulated and 804 down-regulated) in the early stage and 625 transcripts (230 up-regulated and 395 down-regulated) in the late stage. Gene ontology and MapMan analyses confirmed that 391 and 164 DEGs at the early and late stage respectively involved in stress responses pathway. These DEGs included the abiotic stress-, hormone-, peroxidases-, signaling-, transcription-, proteolysis- and cell wall-related genes. Nearly all the heat stress-related DEGs, e.g. hsp20 and DnaK family proteins, were down-regulated with seed germination, while the peroxidases- and signaling-related DEGs, e.g. calcium-binding proteins, were up-regulated. Many auxins-, abscisic acid- and ethylene-related DEGs, e.g. 9-cis-epoxycarotenoid dioxygenase, OsFBL16 and OsSAUR33, were involved in stress responses during seed germination. Meanwhile, several transcription factors of bZIP and MYB, ethylene responsive element binding protein family (ERF), and heat stress transcription factor family (HSF) were identified during seed germination. The proteolysis-related DEGs, e.g. ubiquitin-related proteins, were significantly regulated during seed germination. The uniformity between transcriptome data, quantitative trait loci co-localizations and quantitative RT-PCR results confirm the crucial roles of the cell wall-related genes on seed germination. The identified stress-responsive might be useful for the improvement of imbibitional tolerance in rice.
2020-04-28 | GSE98338 | GEO
Project description:Wheat seed germination directly affects wheat yield and quality. The wheat grains mainly include embryo and endosperm, and both play important roles in seed germination, seedling survival and subsequent vegetative growth. ABA can positively regulate dormancy induction and then negatively regulates seed germination at low concentrations. H2O2 treatment with low concentration can promote seed germination of cereal plants. Although various transcriptomics and proteomics approaches have been used to investigate the seed germination mechanisms and response to various abiotic stresses in different plant species, an integrative transcriptome analysis of wheat embryo and endosperm response to ABA and H2O2 stresses has not reported so far. We used the elite Chinese bread wheat cultivar Zhenmai 9023 as material and performed the first comparative transcriptome microarray analysis between embryo and endosperm response to ABA and H2O2 treatments during seed germination using the GeneChip® Wheat Genome Array Wheat seed germination includes a great amount of regulated genes which belong to many functional groups. ABA/H2O2 can repress/promote seed germination through coordinated regulating related genes expression. Our results provide new insights into the transcriptional regulation mechanisms of embryo and endosperm response to ABA and H2O2 treatments during seed germination
2014-12-11 | GSE64030 | GEO