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Integrated analysis of microRNA and mRNA expression profiles of rice seedlings in response to zinc deficiency and recovery

ABSTRACT: Integrated analysis of microRNA and mRNA expression profiles of rice seedlings in response to zinc deficiency and recovery

PROVIDER: PRJNA542268 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR9036800_1.fastq.gz	Fastqsanger.gz
	SRR9036800_2.fastq.gz	Fastqsanger.gz
	SRR9036810_1.fastq.gz	Fastqsanger.gz
	SRR9036810_2.fastq.gz	Fastqsanger.gz
	SRR9036801_1.fastq.gz	Fastqsanger.gz

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Integrated analysis of microRNA and mRNA expression profiles of rice seedlings in response to zinc deficiency and recovery (mRNA-seq)

Project description:Integrated analysis of microRNA and mRNA expression profiles of rice seedlings in response to zinc deficiency and recovery (mRNA-seq)

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Integrated analysis of microRNA and mRNA expression profiles of rice seedlings in response to zinc deficiency and recovery (miRNA-seq)

Project description:Integrated analysis of microRNA and mRNA expression profiles of rice seedlings in response to zinc deficiency and recovery (miRNA-seq)

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Integrated analysis of microRNA and mRNA expression profiles of rice seedlings in response to zinc deficiency and recovery (mRNA-seq)

Project description:Using Illumina’s high-throughput small RNA sequencing and RNA sequencing, miRNAs and mRNAs differentially expressed under Zn deficiency and Zn resupply conditions were identified in shoots and roots of rice seedlings. A total of 68 miRNAs were identified to be differentially expressed under Zn deficiency and/or Zn resupply, and 38 of them were novel miRNAs. The Zn-responsive miRNAs were predicted to target a total of 799 genes. The transcriptome sequencing identified a total of 360 differentially expressed genes (DEGs) under Zn deficiency in shoots and roots, and 97 of them were recovered after Zn resupply treatment. Twelve DEGs were found to be potential targets genes of several Zn-responsive miRNAs like miR171g-5p, miR397b-5p, miR398a-5p, and miR528-5p.

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Integrated analysis of microRNA and mRNA expression profiles of rice seedlings in response to zinc deficiency and recovery (miRNA-seq)

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Integrated analyses of miRNAome and transcriptome reveal zinc deficiency responses in rice seedlings.

Project description:BACKGROUND:Zinc (Zn) deficiency is one of the most widespread soil constraints affecting rice productivity, but the molecular mechanisms underlying the regulation of Zn deficiency response is still limited. Here, we aim to understand the molecular mechanisms of Zn deficiency response by integrating the analyses of the global miRNA and mRNA expression profiles under Zn deficiency and resupply in rice seedlings by integrating Illumina's high-throughput small RNA sequencing and transcriptome sequencing. RESULTS:The transcriptome sequencing identified 360 genes that were differentially expressed in the shoots and roots of Zn-deficient rice seedlings, and 97 of them were recovered after Zn resupply. A total of 68 miRNAs were identified to be differentially expressed under Zn deficiency and/or Zn resupply. The integrated analyses of miRNAome and transcriptome data showed that 12 differentially expressed genes are the potential target genes of 10 Zn-responsive miRNAs such as miR171g-5p, miR397b-5p, miR398a-5p and miR528-5p. Some miRNA genes and differentially expressed genes were selected for validation by quantitative RT-PCR, and their expressions were similar to that of the sequencing results. CONCLUSION:These results provide insights into miRNA-mediated regulatory pathways in Zn deficiency response, and provide candidate genes for genetic improvement of Zn deficiency tolerance in rice.

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Integrated analysis of microRNA and mRNA expression profiles of rice seedlings in response to zinc deficiency and recovery

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

2020-01-08 | GSE131004 | GEO

Transcriptional profiling of shoots and roots in japonica and indica rice seedlings under salt stress and recovery stage

Project description:Rice seedlings at 3-leaf stage were used for expression analysis in control and salt stressed (incloudling salt treatment for 3, 24hrs and recovery from salt stress for 24hrs) samples. Samples of shoots and roots from biological replicates of both genotypes were generated and the expression profiles were determined using Phalanx Rice OneArray＠ v1.

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