ArticlePlant molecular biology2013
Transcriptomic analysis of rice (Oryza sativa) endosperm using the RNA-Seq technique.
Article in Plant molecular biology, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 46 papers.
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Who cites it
46 citing papers in PubMed.
- Regulatory Roles of PURPLE FRUIT 1 and OsPa in Pigmentation of Rice Grain.Rice (New York, N.Y.) · 2026Article
- Stage-Specific Transcriptomic Insights into Seed Germination and Early Development inPlants (Basel, Switzerland) · 2025Article
- Characterization of carotenoids and flavonoids in Yangxian pigmented rice varieties through LC‒MS/MS-based targeted metabolomics and multivariate statistics.Current research in food science · 2025Article
- Transcriptome and metabolome analyses reveal regulatory networks associated with nutrition synthesis in sorghum seeds.Communications biology · 2024Article
- Transcriptome Analysis of Sesame (International journal of molecular sciences · 2024Article
- Exploration into Natural Variation Genes Associated with Determinate and Capitulum-like Inflorescence inInternational journal of molecular sciences · 2023Article
- Promoter activity and transcriptome analyses decipher functions of CgbHLH001 gene (Chenopodium glaucum L.) in response to abiotic stress.BMC plant biology · 2023Article
- Transcriptomes across fertilization and seed development in the water lily Nymphaea thermarum (Nymphaeales): evidence for epigenetic patterning during reproduction.Plant reproduction · 2022Article
- miR2105 and the kinase OsSAPK10 co-regulate OsbZIP86 to mediate drought-induced ABA biosynthesis in rice.Plant physiology · 2022Article
- Laser microdissection transcriptome data derived gene regulatory networks of developing rice endosperm revealed tissue- and stage-specific regulators modulating starch metabolism.Plant molecular biology · 2022Article
- Review
- Chemical Characterization, Antitumor, and Immune-Enhancing Activities of Polysaccharide fromMolecules (Basel, Switzerland) · 2021Article
- Systematic analysis of differentially expressedPhysiology and molecular biology of plants : an international journal of functional plant biology · 2021Article
- Review
- Maize kernel development.Molecular breeding : new strategies in plant improvement · 2021Review
- Analysis of Spatio-Temporal Transcriptome Profiles of Soybean (International journal of molecular sciences · 2020Article
- Genome Wide Analysis of the Transcriptional Profiles in Different Regions of the Developing Rice Grains.Rice (New York, N.Y.) · 2020Article
- The dynamic transcriptome of waxy maize (Zea mays L. sinensis Kulesh) during seed development.Genes & genomics · 2020Article
- Article
- Similarities and Differences of Photosynthesis Establishment Related mRNAs and Novel lncRNAs in Early Seedlings (Coleoptile/Cotyledon vs. True Leaf) of Rice andFrontiers in genetics · 2020Article
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Authors and funding
4 authors.
Funding
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Abstract
The endosperm plays an important role in seed formation and germination, especially in rice (Oryza sativa). We used a high-throughput sequencing technique (RNA-Seq) to reveal the molecular mechanisms involved in rice endosperm development. Three cDNA libraries were taken from rice endosperm at 3, 6 and 10 days after pollination (DAP), which resulted in the detection of 21,596, 20,910 and 19,459 expressed gens, respectively. By ERANGE, we identified 10,371 differentially expressed genes (log(2)Ratio ≥1, FDR ≤0.001). The results were compared against three public databases (Gene Ontology, Kyoto Encyclopedia of Genes and Genomes and MapMan) in order to annotate the gene descriptions, associate them with gene ontology terms and to assign each to pathways. A large number of genes related to ribosomes, the spliceosome and oxidative phosphorylation were found to be expressed in the early and middle stages. Plant hormone, galactose metabolism and carbon fixation related genes showed a significant increase in expression at the middle stage, whereas genes for defense against disease or response to stress as well as genes for starch/sucrose metabolism were strongly expressed during the later stages of endosperm development. Interestingly, most metabolic pathways were down-regulated between 3 and 10 DAP except for those involved in the accumulation of material, such as starch/sucrose and protein metabolism. We also identified the expression of 1,118 putative transcription factor genes in endosperm development. The RNA-Seq results provide further systematic understanding of rice endosperm development at a fine scale and a foundation for future studies.
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