Abstract
BACKGROUND: Plant growth depends on synergistic interactions between internal and external signals, and yield potential of crops is a manifestation of how these complex factors interact, particularly at critical stages of development. As an initial step towards developing a systems-level understanding of the biological processes underlying the expression of overall agronomic potential in cereal crops, a high-resolution transcriptome analysis of rice was conducted throughout life cycle of rice grown under natural field conditions. RESULTS: A wide range of gene expression profiles based on 48 organs and tissues at various developmental stages identified 731 organ/tissue specific genes as well as 215 growth stage-specific expressed genes universally in leaf blade, leaf sheath, and root. Continuous transcriptome profiling of leaf from transplanting until harvesting further elucidated the growth-stage specificity of gene expression and uncovered two major drastic changes in the leaf transcriptional program. The first major change occurred before the panicle differentiation, accompanied by the expression of RFT1, a putative florigen gene in long day conditions, and the downregulation of the precursors of two microRNAs. This transcriptome change was also associated with physiological alterations including phosphate-homeostasis state as evident from the behavior of several key regulators such as miR399. The second major transcriptome change occurred just after flowering, and based on analysis of sterile mutant lines, we further revealed that the formation of strong sink, i.e., a developing grain, is not the major cause but is rather a promoter of this change. CONCLUSIONS: Our study provides not only the genetic basis for functional genomics in rice but also new insight into understanding the critical physiological processes involved in flowering and seed development, that could lead to novel strategies for optimizing crop productivity.
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Claims 9
Claim · model-written summary
Gene expression profiling identified 731 organ/tissue specific genes in rice
- Taxon
- rice
Oryza sativae0 - Organ / stage
- leaf blade, leaf sheath, and roote1
- Outcome
- organ/tissue specific genese1
- Value
- 731e1
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“a high-resolution transcriptome analysis of rice was conducted”
e1“A wide range of gene expression profiles based on 48 organs and tissues at various developmental stages identified 731 organ/tissue specific genes as well as 215 growth stage-specific expressed genes universally in leaf blade, leaf sheath, and root”
Claim · model-written summary
Gene expression profiling identified 215 growth stage-specific expressed genes in rice
- Taxon
- riceOryza sativae0
- Organ / stage
- leaf blade, leaf sheath, and roote1
- Outcome
- growth stage-specific expressed genese1
- Value
- 215e1
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“a high-resolution transcriptome analysis of rice was conducted”
e1“A wide range of gene expression profiles based on 48 organs and tissues at various developmental stages identified 731 organ/tissue specific genes as well as 215 growth stage-specific expressed genes universally in leaf blade, leaf sheath, and root”
Claim · model-written summary
Continuous leaf transcriptome profiling in rice uncovered two major drastic changes in the leaf transcriptional program
- Taxon
- riceOryza sativae0
- Organ / stage
- leafe2
- Outcome
- two major drastic changes in the leaf transcriptional programe2
- Value
- twoe2
- Qualifier
- from transplanting until harvestinge2
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“a high-resolution transcriptome analysis of rice was conducted”
e2“Continuous transcriptome profiling of leaf from transplanting until harvesting further elucidated the growth-stage specificity of gene expression and uncovered two major drastic changes in the leaf transcriptional program”
Claim · model-written summary
The first major leaf transcriptome change in rice occurred before panicle differentiation
- Taxon
- riceOryza sativae0
- Outcome
- first major changee3
- Qualifier
- before the panicle differentiatione3
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“a high-resolution transcriptome analysis of rice was conducted”
e3“The first major change occurred before the panicle differentiation, accompanied by the expression of RFT1, a putative florigen gene in long day conditions, and the downregulation of the precursors of two microRNAs”
Claim · model-written summary
The first leaf transcriptome change in rice was accompanied by expression of RFT1, a putative florigen gene
- Taxon
- riceOryza sativae0
- Gene
- RFT1e3
- Outcome
- the expression of RFT1e3
- Qualifier
- a putative florigen gene in long day conditionse3
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“a high-resolution transcriptome analysis of rice was conducted”
e3“The first major change occurred before the panicle differentiation, accompanied by the expression of RFT1, a putative florigen gene in long day conditions, and the downregulation of the precursors of two microRNAs”
Claim · model-written summary
The precursors of two microRNAs were downregulated during the first leaf transcriptome change in rice
- Taxon
- riceOryza sativae0
- Outcome
- precursors of two microRNAse3
- Direction
- downregulatione3
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“a high-resolution transcriptome analysis of rice was conducted”
e3“The first major change occurred before the panicle differentiation, accompanied by the expression of RFT1, a putative florigen gene in long day conditions, and the downregulation of the precursors of two microRNAs”
Claim · model-written summary
The transcriptome change was associated with physiological alterations in phosphate-homeostasis state, shown by miR399
- Taxon
- riceOryza sativae0
- Gene
- miR399e4
- Outcome
- phosphate-homeostasis statee4
Not reportedDirection
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“a high-resolution transcriptome analysis of rice was conducted”
e4“This transcriptome change was also associated with physiological alterations including phosphate-homeostasis state as evident from the behavior of several key regulators such as miR399”
Claim · model-written summary
The second major leaf transcriptome change in rice occurred just after flowering
- Taxon
- riceOryza sativae0
- Outcome
- second major transcriptome changee5
- Qualifier
- just after floweringe5
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“a high-resolution transcriptome analysis of rice was conducted”
e5“The second major transcriptome change occurred just after flowering, and based on analysis of sterile mutant lines, we further revealed that the formation of strong sink, i.e., a developing grain, is not the major cause but is rather a promoter of this change”
Claim · model-written summary
Developing grain formation is not the major cause of the second transcriptome change but promotes it
- Taxon
- riceOryza sativae0
- Material
- sterile mutant linese5
- Outcome
- second major transcriptome changee5
- Qualifier
- the formation of strong sink, i.e., a developing grain, is not the major cause but is rather a promotere5
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“a high-resolution transcriptome analysis of rice was conducted”
e5“The second major transcriptome change occurred just after flowering, and based on analysis of sterile mutant lines, we further revealed that the formation of strong sink, i.e., a developing grain, is not the major cause but is rather a promoter of this change”