Transcriptome changes caused by RBP-P mutations in rice seed
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PROVIDER: PRJNA481311 | ENA |
REPOSITORIES: ENA
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Project description:Two RBP-P mutants, P1MH and P3MH, carrying G401S and A252T point mutations, respectively, were obtained by TILLING studies (http://www.shigen.nig.ac.jp/rice/oryzabase). The A252T mutation site in P3MH lies within the linker sequence between the two RRM domains while the G401S substitutions in P1MH is located in the glycine-rich C-terminal region. Those mutations results in varying degrees of reduced RNA binding and/or protein-protein interactive properties of RBP-P. Transcriptome analysis on the dehulled 10-14 days old developing seeds from wild type, P1MH and P3MH mutants indicates that partial loss of RBP-P function caused the differential expression of storage protein genes and relevant genes involved in several essential biological processes during rice development.
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Project description:Transcriptome changes caused by Tudor-SN mutations in rice seed
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Project description:One OsTudor-SN mutant, EM1084, carrying E503K point mutation and one associated WT-OsTSN complemented transgenic (pHL8042/EM1084 ) were applied in this study. EM1084 was obtained by TILLING studies (http://www.shigen.nig.ac.jp/rice/oryzabase). The E503K mutation site in EM1084 lies within the SN3 domain, while the EM1084 complemented transgenic plant was complemented with the full-length WT OsTSN gene driven by native OsTSN promoter. This mutation results in affecting storage protein mRNA localization and, in turn, with a strong reduction in grain weight and storage protein accumulation. Transcriptome analysis on the dehulled 10-14 days old developing seeds from wild type, EM1084 and pHL8042/EM1084 indicates that partial loss of Tudor-SN function caused the differential expression of storage protein genes and relevant genes involved in several essential biological processes during rice development.
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Project description:Understanding the molecular mechanisms underlying early seed development is important for improving grain yield and quality in crop plants. To investigate the molecular mechanisms that occur during early seed development, we performed comparative label-free quantitative proteomic analysis on developing WT rice seeds between 0 and 1 day after pollination (DAP). A total of 5231 proteins were identified, and 902 proteins showed differential accumulation between 0 and 1 DAP seeds. Further analysis focused on the proteins preferentially expressed at 1 DAP and revealed an enrichment of proteins involved in DNA replication and pyrimidine biosynthetic pathways. Notably, the transcript of OsCTPS1, a cytidine triphosphate synthase known to play an essential role in early endosperm development, did not differ between 0 and 1 DAP, but OsCTPS1 protein accumulated more specifically at 1 DAP than at 0 DAP. We then found that inhibiting phosphorylation increased the stability of this protein. Furthermore, in osctps1-2, minichromosome maintenance (MCM) proteins were significantly reduced compared to WT at 1 DAP, and mutations in OsMCM5 caused defects in seed development. In this study, we tried to understand the molecular mechanisms of early seed development at the post-transcriptional regulation.
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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