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Integrated transcriptomics and miRNAomics provide insights into the regulatory networks associated with coleoptile senescence in rice

ABSTRACT: Purpose: To understand the transcriptional changes during coleoptile senescence, transcriptome libraries were constructed from control and senescence tissues and subjected to Illumina sequencing. Methods: Rice seeds were surface sterilized and submerged for seven days in sterile water. The seeds with coleoptile was transferred to aerobic condition. Senescence progression was monitored and tissues of un-senesced and senesced coleoptiles were harvested. Total RNA was isolated from the harvested tissues. mRNA libraries were generated and sequenced as 101 bp paired-end reads by using Illumina Hiseq 4000. Results: Our analysis revealed that 3166 transcripts were differentially expressed in senescing coleoptile (Day 2) samples as compared to the control. Furthermore, 44 and 273 transcripts showed specific expression in control and day 2 samples, respectively. From the functional category analysis, we observed that 197, 182, 99 and 88 transcripts belonging to signalling, transcription factors, hormone signalling and transporters respectively were differentially expressed during coleoptile senescence . And 15, 12, 3, and 6 transcripts showed senescence specific expression patterns in the transporters, transcription factors, signalling and hormone signalling categories respectively. Conclusions: The present study has generated a comprehensive resource of the molecular networks that enrich our understanding of the fundamental pathways regulating coleoptile senescence in rice.

ORGANISM(S): Oryza sativa

PROVIDER: GSE199139 | GEO | 2022/07/21

REPOSITORIES: GEO

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Integrated transcriptomics and miRNAomics provide insights into the regulatory networks associated with coleoptile senescence in rice.

Project description:Purpose: To understand the miRNAome changes during coleoptile senescence, small RNA libraries were constructed from control and senescence tissues and subjected to Illumina sequencing. Methods: Rice seeds were surface sterilized and submerged for seven days in sterile water. The seeds with coleoptile was transferred to aerobic condition. Senescence progression was monitored and tissues of un-senesced and senesced coleoptiles were harvested. Total RNA was isolated from the harvested tissues. Total four small RNA libraries of coleoptile senescence were constructed and high-throughput sequencing was performed using Illumina GA IIx system . . Results: Small RNA sequencing identified forty-one known and twenty-one novel miRNAs that were differentially expressed during coleoptile senescence. Integration of expression data of transcriptome and miRNAome identified 148 miRNA-mRNA modules, mainly comprised of miRNAs regulating TFs, signaling-associated factors and transporters, thereby demonstrating multi-tiered regulation of coleoptile senescence. Conclusions: The present study has generated a comprehensive resource of the molecular networks that enrich our understanding of the fundamental pathways regulating coleoptile senescence in rice.

2022-07-21 | GSE199238 | GEO

Transcript Profiling of the Aerobic and Anoxic Rice Coleoptile

Project description:Rice (Oryza sativa L.) seeds can germinate in complete absence of oxygen. Under anoxia, the rice coleoptile elongates, reaching a length greater than that of the aerobic one. In this series, we compare the transcriptome of rice coleoptiles grown under aerobic and anaerobic conditions. Lasanthi-Kudahettige, R, et. al. Plant Physiology (2007). Transcript Profiling of the Anoxic Rice Coleoptile. Keywords: stress response

2007-03-19 | GSE6908 | GEO

Transcriptome profiles of the rice coleoptile of wild type and reduced adh activity (rad) mutant

Project description:Normally, rice can elongate the coleoptile under submerged condition. However, reduced adh activity (rad) mutant cannot elongate the coleoptile under submergence. To investigate the change in gene expression, we performed microarray analysis. In this analysis, we used 1 day old seedling of rice. But it is difficult to isolate only coleoptile from rice embryo without any contamination in this stage. Therefore, we applied laser microdissection (LM) technique to this microarray. By use of LM, we isolated coleoptile from rice embryo and use for microarray analysis. As the results, we found that the differences in the gene expression profiles of coleoptile between wild type and rad mutant. Gene expression analysis in coleoptile of wild type and mutant.

2011-04-07 | E-GEOD-26632 | biostudies-arrayexpress

Transcriptome profiles of the rice coleoptile of wild type and reduced adh activity (rad) mutant

2011-04-07 | GSE26632 | GEO

Transcriptional profiling of Triticea seed and vegetative tissues

Project description:Despite their importance, there remains to be few large scale expression-based studies of tissue-specific expression information in the species belonging to the Triticeae. We used the 55K Affymetrix GeneChipÂ® Wheat Genome Array to generate a gene expression atlas of triticale tissues. The global transcriptional profiles of seed tissues (embryo, endosperm, crease, pericarp and epiderm) and vegetative tissues (root, coleoptile, stem and leaf) were analyzed and co-regulated as well as preferentially expressed genes were identified. Data analysis revealed both novel and conserved regulatory factors underlying Triticeae tissue development and function. Triticale seed (embryo, endosperm, crease, pericarp and epiderm) and vegetative tissues (root, coleoptile, leaf and stem) were collected and analyzed using the 55K Affymetrix Wheat Genome array. All seed tissues were collected at the soft dough stage of seed development. Vegetative tissues were collected at multiple stages of development. Root and coleoptile tissues were collected at early development (Zadoks' stage 7), and leaf tissue was collected at five successive stages ranging from seedling to late senescence and stem tissue was collected at four successive stages stages ranging from initial tillering to early senescence. Between two to five biological replicates for each tissue were analyzed.

2014-12-24 | E-GEOD-43127 | biostudies-arrayexpress

Project description:coleoptile sequencing of rice

| PRJNA601920 | ENA

Transcription profiling of rice stigma

Project description:In angiosperms, stigma provides initial nutrients and guidance cues for pollen grain germination and tube growth. However, little is known about genes that regulate these processes in rice. Here we generate rice stigma-specific gene expression profiles through comparing genome-wide expression patterns of hand dissected unpollinated stigma at anthesis with seven tissues including seedling shoot, seedling root, mature anther, ovary at anthesis, seeds of five days after pollination, 10-day-old embryo, 10-day-old endosperm as well as suspension cultured cells by using 57K Affymetrix rice whole genome array. In total, we identified 665 probe sets (550 genes) to be expressed specifically or predominantly in the stigma papillar cells of rice. Real-Time quantitative RT-PCR analysis of 34 selected genes confirmed their stigma-specific expression. The expression of five selected genes was further validated by RNA in situ hybridization. Gene annotation shows that several auxin-signaling components, transporters and stress-related genes are significantly overrepresented in the rice stigma gene set. We also found that genes involved in cell wall metabolism and cellular communication appear to be conserved in the stigma between rice and Arabidopsis. Our results indicate that the stigmas appear to have conserved and novel molecular functions between rice and Arabidopsis. Experiment Overall Design: We generate rice stigma-specific gene expression profiles through comparing genome-wide expression patterns of hand dissected unpollinated stigma at anthesis with seven tissues including seedling shoot, seedling root, mature anther, ovary at anthesis, seeds of five days after pollination, 10-day-old embryo, 10-day-old endosperm as well as suspension cultured cells by using 57K Affymetrix rice whole genome array.

2008-11-08 | E-GEOD-7951 | biostudies-arrayexpress

Succinylome analyses in the germinating rice seed

Project description:The dehulled rice (Oryza sativa L. japonica. cv. Nipponbare) seeds were washed with distilled water for three times and then imbibed with distilled water in dark growth chamber at 26 °C and 70% relative humidity. About 100 embryos (50 mg) of rice seeds were sliced manually and collected at intervals of 24h after imbibitions (HAI), respectively. After frozen with liquid nitrogen, the samples were stored in −80 °C until used for protein extraction.

2016-01-26 | PXD002740 | Pride

The flooding resilience loci SUBMERGENCE 1 and ANAEROBIC GERMINATION 1 interact in rice seedlings established underwater

Project description:Little is known of the consequences of genetic pyramiding of abiotic stress tolerance loci in crops. In rice (Oryza sativa L.), ANAEROBIC GERMINATION1 (AG1) encodes TREHALOSE 6-PHOSPHATE PHOSPHATASE 7 (OsTPP7) that enhances mobilization of endosperm reserves to the embryo, promoting formation of a highly elongated hollow coleoptile in seeds sown directly into shallow paddies. This trait reduces labor costs and herbicide use. SUBMERGENCE1 (SUB1) includes the ethylene-responsive transcription factor SUB1A that confers tolerance to complete submergence by dampening shoot elongation of vegetative-phase plants and enhancing regrowth upon desubmergence. As OsTPP7 and SUB1A-1 mRNAs simultaneously accumulate in shoots, we evaluated the independent contribution and interactions between these loci in rice seeded under complete submergence until the four-leaf stage (14 d). Evaluating growth, carbohydrates, and the transcriptome of shoot tissue of four near-isogenic genotypes uncovered independent and interacting effects including: (a) early enhanced coleoptile elongation by IR64(AG1); (b) precocious transition to phototrophy followed by limited elongation by IR64(SUB1); and (c) delayed phototrophy by IR64(AG1, SUB1). mRNA-sequencing highlighted time-dependent and genotype-specific regulation of mRNAs associated with energy sensing, carbohydrate catabolism, photomorphogenesis, elongation, and defense responses. Although SUB1A did not antagonize AG1 in direct seeding, seedling establishment could be negatively impacted if submergence escape does not occur before the transition to photoautotrophy, due to antithetical regulation of carbohydrate catabolism by AG1 and SUB1.

2020-07-05 | GSE136885 | GEO

Analysis of representative organ specific genes and promoters of rice using 3â ORF oriented long oligomer microarray

Project description:The profiling was conducted with the Rice 3'-Tiling Microarray designed from 27,448 genes deposited at IRGSP, RAP1 database (http://rapdb.lab.nig.ac.jp). In this research, an array of 27,448 rice genes was used to elucidate the transcriptome of 7 tissues or organs of Oryza sativa L. cv. Dongjin including calli, regenerating calli, germinating seeds, leaves, roots, and flowers (before and after pollination) using a rice 3â² ORF tilling microarray. The ratio of standard deviation to the mean of microarray intensities was used to distinguish between organ-specific and constitutively expressed genes. Accordingly, the genes are classified into highly variable, variable, and constitutive groups. To isolate the organ-specific promoters, several genes were selected and validated in planta using reporter gene analysis. We found that the Os01g0702500, Os11g0211800, and Os01g0257300 promoters were active in the calli, germinating seeds, and roots, respectively. The Os08g0135500 promoter was shown to drive transgene expression in various organs of the mature flowers, such as the anther, lemma, and palea, whereas the Os03g0369100 promoter was only active in the anther. Lastly, the Os09g0553100 promoter induced high levels of reporter gene expression in all organs. The gene expression data from representative organs could put a frame work for large dataset collections and then subsequent profiling by subdivision of organ/tissues might be more efficient to find appropriate promoters. A total of 14 chips were used for microarray. Total RNAs were extracted from rice 7 tissues or organs of Oryza sativa L. cv. Dongjin including calli, regenerating calli, germinating seeds, leaves, roots, and flowers (before and after pollination. Experiments were duplicated.

2016-07-28 | E-GEOD-84903 | biostudies-arrayexpress

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