Oryza sativa
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PROVIDER: PRJNA378155 | ENA |
REPOSITORIES: ENA
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Project description:The profiling was conducted with the Rice 3'-Tiling 135k Microarray designed from 31,439 genes deposited at IRGSP, RAP2 database (http://rapdb.lab.nig.ac.jp). We have identified and characterized a T-DNA insert rice mutant (Osfuct) with loss of α1,3-fucosyltransferase function. Matrix-assisted laser desorption/ionization time-of-flight analyses of the N-glycan revealed the lack of α1,3-fucose in the N-glycan structure of rice Osfuct mutant. The mutant displayed the pleiotropic developmental defects such as diminished growth, shorter plant height, less number of tillers, shorter panicle lengths and internode, impaired anther and pollen development. In addition, the anther was curved, pollen grains shapes were shriveled, pollen viability and pollen number per anther was dramatically decreased in Osfuct mutant. The complementation test of Osfuct mutant clearly exhibited that the phenotype is caused by the loss of α1,3-fucosyltransferase function bescause complementation line is rescued. Transcriptome profiling data revealed that several genes essential in plant developmental processes were significantly altered in Osfuct mutant including protein kinases, transcription factors, genes involved in metabolism, genes related to protein synthesis and hypothetical proteins. Moreover, Osfuct mutant exhibited the enhanced salt insensitivity. Taken together, these findings demonstrated that Osfuct plays a critical role in growth, anther, pollen development and salt stress response.
2018-06-06 | GSE110873 | GEO
Project description:- Pollen tube growth is important process for successful double fertilization, which is critical for grain yield in crop plants. Despite much progress in identification of rapid alkalization factors (RALFs) which serve as ligand for signaling transduction during fertilization in Arabidopsis, there is no functional study of RALF in mono-cotyledon plant. - We functionally characterized two pollen specific RALF in rice (Oryza sativa) using multiple CRISPR/Cas9 induced loss-of-function mutants, peptide treatment, expression analyses, tag reporter lines. - OsRALF17 is specifically expressed in pollen and pollen tube as the strongest level among 41 RALF members in rice. Exogenously applied OsRALF17 inhibits pollen tube germination and elongation at high concentration, but enhances tube elongation at low concentration, indicating the regulation of growth balance. Double mutant of OsRALF17 with OsRALF19 exhibit almost male sterile, with defect on pollen germination and tube elongation. - Our study revealed that functionally-redundant OsRALF17 and 19 peptides binds to the OsMTD2, CrRLK1L family member, and transmits ROS signal for pollen tube germination and integrity maintenance in rice. We provide new insights into the role of RALF and expanding our understanding of the biological role of RALF in regulating rice fertilization.
2023-09-21 | PXD037597 | Pride
Project description:Pollen tube growth is essential for successful fertilization and stable crop yields. We constructed loss-of-function/knock-out mutants that simultaneously target two rice genes using the CRISPR/Cas9 mutagenesis system. The selected OsRALF17 and OsRALF19 genes are strongly expressed in rice bicellular/tricellular pollen and have essential functions in the pollen tube growth. For the corresponding transcriptomic analysis, we sampled mature pollen anthers from a control group and an OsRALF17/19 knock-out mutant.
2023-09-29 | E-MTAB-12295 | biostudies-arrayexpress
Project description:DNA methylation is an important epigenetic modification that regulates various plant developmental processes. Rice seed integument determines the seed size. However, the role of DNA methylation in its development remains largely unknown. Here, we report the first dynamic DNA methylomic profiling of rice maternal integument before and after pollination by using a whole-genome bisulfite deep sequencing approach. Analysis of DNA methylation patterns identified 4238 differentially methylated regions underpin 4112 differentially methylated genes, including GW2, DEP1, RGB1 and numerous other regulators participated in maternal integument development. Bisulfite sanger sequencing and qRT-PCR of six differentially methylated genes revealed extensive occurrence of DNA hypomethylation triggered by double fertilization at IAP compared with IBP, suggesting that DNA demethylation might be a key mechanism to activate numerous maternal controlling genes. These results presented here not only greatly expanded the rice methylome dataset, but also shed novel insight into the regulatory roles of DNA methylation in rice seed maternal integument development.
2017-10-10 | GSE95107 | GEO
Project description:Oryza longistaminata is an African wild rice species that possesses special traits for breeding applications. Self-incompatibility is the main cause of sterility in O. longistaminata, but here we demonstrated that its pollen fertility and vitality are normal. Lipid and carbohydrate metabolism were active throughout pollen development. In this study, transcriptomics quantitative analysis was used to investigate the profiles of genes related to lipid and carbohydrate metabolism in 4-, 6- and 8.5-mm O. longistaminata spikelets before flowering. We documented cytological changes throughout important stages of anther development, including changes in reproductive cells as they formed mature pollen grains through meiosis and mitosis. RNA-seq and proteome association analysis indicated that fatty acids were converted to sucrose after the 6-mm spikelet stage, based on the abundance of most key enzymes of the glyoxylate cycle and gluconeogenesis. In conclusion, our study provides novel insights into the pollen viability of O. longistaminata at the transcriptome level, which can be used to improve the efficiency of male parent pollination in hybrid rice breeding applications.
2021-07-31 | GSE181045 | GEO
Project description:In this study, we analyzed the early response of two rice cultivars to infection by RSV (Rice stripe virus) and its carrier at the transcriptome level using next-generation deep-sequencing techniques. We investigated the alteration in gene expression between a disease-resistant cultivar and a susceptible cultivar before and after inoculation with RSV by co-culturing with Laodelphax striatellus for 48 h. Our study provides insight at the molecular level into the mechanism of development of rice stripe disease, which contributes to our understanding of the rice-RSV interaction.
2013-08-21 | E-MTAB-4392 | biostudies-arrayexpress
Project description:Transcriptional profiling of MIT knockdown plants. MIT is a mitochondrial Fe transporter essential for rice growth and development. The goal was to determine the effects of MIT on global rice gene expression.
2011-04-07 | GSE28428 | GEO
Project description:5 leaves old rice plantlets were infected with Magnaporthe grisea spores and zero, two hours and twenty four houres after infection samples were collected
2014-01-31 | GSE50454 | GEO
Project description:A biological phenomenon in which hybrids exhibit superior phenotypes from its parental inbred lines known as heterosis, has been widely exploited in plant breeding and extensively used in crop improvement. Hybrid rice has immense potential to increase yield over other rice varieties and hence is crucial in meeting increasing demand of rice globally. Moreover, the molecular basis of heterosis is still not fully understood and hence it becomes imperative to unravel its genetic and molecular basis. In this context, RNA sequencing technology (RNA-Seq) was employed to sequence transcriptomes of two rice hybrids, Ajay and Rajalaxmi, their parental lines, CRMS31A (sterile line, based on WA-CMS) and CRMS32A (sterile line based on Kalinga-CMS) respectively along with the common restorer line of both hybrids, IR-42266-29-3R at two critical rice developmental stages viz., panicle initiation (PI) and grain filling (GF). Identification of differentially expressed genes (DEGs) at PI and GF stages will further pave the way for understanding heterosis. In addition, such kind of study would help in better understanding of heterosis mechanism and genes up-regulated and down-regulated during the critical stages of rice development for higher yield.
2015-08-02 | E-MTAB-4291 | biostudies-arrayexpress
Project description:The small RNAs presented here were produced as a preliminary exploration of small RNAs in rice, and as such, various tissues and stress conditions were sampled. Small RNAs present in these samples were all mapped to the rice genome TIGR version 5. The total number of distinct mapped sequences are 12879 for Run 1 and 88508 for Run 2. The total number of sequence reads were respectively 70406 and 191682. The datasets contain Oryza sativa var Nipponbar endogenous small RNA sequences in the size range 18 to 34 nt. Plants were grown in a Conviron Environmental Chamber at high light intensity using both high pressure sodium and metal halide lamps for 10.5 hr at 28 degrees C and for 13.5 hr at 26 degrees C in the dark. RNA was extracted from rice tissues at various stages of development and under different abiotic and biotic stresses. The small RNAs presented here were all mapped to the rice genome TIGR version 5. The total number of distinct mapped sequences are 12879 for Run 1 and 88508 for Run 2. The total number of sequence reads were respectively 70406 and 191682.
2009-06-08 | GSE16248 | GEO