ArticlePloS one2011
Transcriptome phase distribution analysis reveals diurnal regulated biological processes and key pathways in rice flag leaves and seedling leaves.
Article in PloS one, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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16 citing papers in PubMed, 36 citations in OpenAlex.
- DeepCBA: A deep learning framework for gene expression prediction in maize based on DNA sequences and chromatin interactions.Plant communications · 2024Article
- Time of Day Analysis over a Field Grown Developmental Time Course in Rice.Plants (Basel, Switzerland) · 2022Article
- Integration of rhythmic metabolome and transcriptome provides insights into the transmission of rhythmic fluctuations and temporal diversity of metabolism in rice.Science China. Life sciences · 2022Article
- Malectin Domain Protein Kinase (MDPK) Promotes Rice Resistance to Sheath Blight via IDD12, IDD13, and IDD14.International journal of molecular sciences · 2022Article
- Association mapping of drought tolerance and agronomic traits in rice (Oryza sativa L.) landraces.BMC plant biology · 2021Article
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- Rice Biofortification With Zinc and Selenium: A Transcriptomic Approach to Understand Mineral Accumulation in Flag Leaves.Frontiers in genetics · 2020Article
- Kingdom-wide comparison reveals the evolution of diurnal gene expression in Archaeplastida.Nature communications · 2019Article
- Article
- Crosstalk between diurnal rhythm and water stress reveals an altered primary carbon flux into soluble sugars in drought-treated rice leaves.Scientific reports · 2017Article
- Diurnal regulation of RNA polymerase III transcription is under the control of both the feeding-fasting response and the circadian clock.Genome research · 2017Article
- Progressive promoter element combinations classify conserved orthogonal plant circadian gene expression modules.Journal of the Royal Society, Interface · 2014Article
- Article
- Salt overly sensitive pathway members are influenced by diurnal rhythm in rice.Plant signaling & behavior · 2013Article
- A genome scale metabolic network for rice and accompanying analysis of tryptophan, auxin and serotonin biosynthesis regulation under biotic stress.Rice (New York, N.Y.) · 2013Article
- The circadian clock coordinates ribosome biogenesis.PLoS biology · 2013Article
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Authors and funding
16 authors at 6 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Plant diurnal oscillation is a 24-hour period based variation. The correlation between diurnal genes and biological pathways was widely revealed by microarray analysis in different species. Rice (Oryza sativa) is the major food staple for about half of the world's population. The rice flag leaf is essential in providing photosynthates to the grain filling. However, there is still no comprehensive view about the diurnal transcriptome for rice leaves. In this study, we applied rice microarray to monitor the rhythmically expressed genes in rice seedling and flag leaves. We developed a new computational analysis approach and identified 6,266 (10.96%) diurnal probe sets in seedling leaves, 13,773 (24.08%) diurnal probe sets in flag leaves. About 65% of overall transcription factors were identified as flag leaf preferred. In seedling leaves, the peak of phase distribution was from 2:00am to 4:00am, whereas in flag leaves, the peak was from 8:00pm to 2:00am. The diurnal phase distribution analysis of gene ontology (GO) and cis-element enrichment indicated that, some important processes were waken by the light, such as photosynthesis and abiotic stimulus, while some genes related to the nuclear and ribosome involved processes were active mostly during the switch time of light to dark. The starch and sucrose metabolism pathway genes also showed diurnal phase. We conducted comparison analysis between Arabidopsis and rice leaf transcriptome throughout the diurnal cycle. In summary, our analysis approach is feasible for relatively unbiased identification of diurnal transcripts, efficiently detecting some special periodic patterns with non-sinusoidal periodic patterns. Compared to the rice flag leaves, the gene transcription levels of seedling leaves were relatively limited to the diurnal rhythm. Our comprehensive microarray analysis of seedling and flag leaves of rice provided an overview of the rice diurnal transcriptome and indicated some diurnal regulated biological processes and key functional pathways in rice.
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