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RNA-sequencing analysis of the OsIMA overexpression and knockdown rice lines and Fe deficiency responsiveness of non-transformant (NT) rice

ABSTRACT: RNA-sequencing analysis of the OsIMA overexpression and knockdown rice lines and Fe deficiency responsiveness of non-transformant (NT) rice

PROVIDER: PRJNA637773 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR11940663_1.fastq.gz	Fastqsanger.gz
	SRR11940663_2.fastq.gz	Fastqsanger.gz
	SRR11940664_1.fastq.gz	Fastqsanger.gz
	SRR11940664_2.fastq.gz	Fastqsanger.gz
	SRR11940665_1.fastq.gz	Fastqsanger.gz

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iTRAQ analyses of Fe-sufficient and Fe-deficient non-transformant and HRZ-knockdown rice roots

Project description:We conducted iTRAQ analyses using soluble proteins extracted from roots of non-transformant rice (NT) and previously generated HRZ-knockdown (HRZi) lines (Kobayashi et al., 2013 Nat Commun 4: 2792) cultivated under Fe-sufficient and Fe-deficient conditions. We identified and quantified 3,033 and 3,525 proteins in replicate 1 and 2, respectively, which totaled 4,884 proteins including 1,698 overlapping proteins between the two replicate experiments.

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Round 2 RNA-sequencing analysis of the OsIMA overexpression and knockdown rice lines and Fe deficiency responsiveness of non-transformant (NT) rice.

Project description:We report the comparison of transcript expression of Fe-sufficient roots of OsIMA overexpression lines IMA1OX-4, IMA2OX-1, OsIMA knockdown lines IMA1i-2, IMA2i-3, and corresponding NT, as well as Fe-deficient roots of NT, by RNA-Seq.

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Round 1 RNA-sequencing analysis of the OsIMA overexpression and knockdown rice lines and Fe deficiency responsiveness of non-transformant (NT) rice.

Project description:Round 1 RNA-sequencing analysis of the OsIMA overexpression and knockdown rice lines and Fe deficiency responsiveness of non-transformant (NT) rice.

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Round 2 RNA-sequencing analysis of the OsIMA overexpression and knockdown rice lines and Fe deficiency responsiveness of non-transformant (NT) rice.

Project description:Round 2 RNA-sequencing analysis of the OsIMA overexpression and knockdown rice lines and Fe deficiency responsiveness of non-transformant (NT) rice.

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Round 1 RNA-sequencing analysis of the OsIMA overexpression and knockdown rice lines and Fe deficiency responsiveness of non-transformant (NT) rice.

Project description:We report the comparison of transcript expression of Fe-sufficient roots and leaves of OsIMA overexpression lines IMA1OX-7, 9, IMA2OX-2, 5 and corresponding NTby RNA-Seq.

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RNA-sequencing analysis of the OsIMA overexpression and knockdown rice lines and Fe deficiency responsiveness of non-transformant (NT) rice

Project description:This SuperSeries is composed of the SubSeries listed below.

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Genotype variation in rice (Oryza sativa L.) tolerance to Fe toxicity might be linked to root cell wall lignification

Project description:Iron (Fe) is an essential element to plants, but can be harmful if accumulated to toxic concentrations. Fe toxicity can be a major nutritional disorder in rice (Oryza sativa) when cultivated under waterlogged conditions, as a result of excessive Fe solubilization of in the soil. However, little is known about the basis of Fe toxicity and tolerance at both physiological and molecular level. Here we aim at understand the genotypic differences in two rice cultivars with contrasting phenotypes under Fe toxicity.

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Effect of OsHRZ knockdown in rice roots under iron sufficiency and deficiency

Project description:Transcriptional profiling of rice genes analyzing the effect of knockdown of OsHRZ1 and OsHRZ2 in HRZ2i lines. NT and HRZ2i lines 1, 2 and 3 (2i-1, 2i-2 and 2i-3, respectively) were treated under iron sufficiency for 7 days (+Fe 7d) or under iron deficiency for 1 day (-Fe 1d) or 7 days (-Fe 7d) in hydroponic culture. Comparison between NT and HRZ2i lines at +Fe 7d, -Fe 1d and -Fe 7d. Biological replicates: 2-3 NT replicates, 3 HRZ2i replicates (one each for 2i-1, 2i-2 and 2i-3) for each treatment.

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Effect of OsHRZ knockdown in rice roots under iron sufficiency and deficiency

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Project description:Temperature-sensitive male sterility is one of the core components for hybrid rice breeding based on two-line system. We previously found that knockout of ARGONAUTE 1d (AGO1d) caused temperature-sensitive male sterility in rice by influencing phased small interfering RNA (phasiRNA) biogenesis and function. However, the specific phasiRNAs and their targets underlying the temperature-sensitive male sterility in ago1d mutant remain to be determined. Here, we demonstrate that the ago1d mutant displays normal female fertility but complete male sterility at low temperature. Through a multi-omics analysis of small RNA, degradome, and transcriptome, we found that 21-nt phasiRNAs account for the greatest proportion of the 21-nt small RNA (sRNA) species in rice anthers and are sensitive to low temperature and markedly down-regulated in ago1d mutant. Moreover, we found that 21-nt phasiRNAs are essential for the mRNA cleavage of a set of fertility- and cold tolerance-associated genes, such as EDT1, TDR, OsPCF5 and OsTCP21, directly or indirectly determined by AGO1d-mediated gene silencing. The loss-of-function of 21-nt phasiRNAs can result in up-regulation of their targets and causes varying degrees of defects in male fertility and grain setting. Our results highlight the essential functions of 21-nt phasiRNAs in temperature-sensitive male sterility in rice and suggest their promising application in two-line hybrid rice breeding in the future.

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