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Genome-wide transcriptomic analysis reveals the gene regulatory network that controlled by SRL1 in regulating rice leaf rolling

ABSTRACT: Genome-wide transcriptomic analysis reveals the gene regulatory network that controlled by SRL1 in regulating rice leaf rolling

PROVIDER: PRJNA604718 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR11014445_1.fastq.gz	Fastqsanger.gz
	SRR11014445_2.fastq.gz	Fastqsanger.gz
	SRR11014446_1.fastq.gz	Fastqsanger.gz
	SRR11014446_2.fastq.gz	Fastqsanger.gz
	SRR11014447_1.fastq.gz	Fastqsanger.gz

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Similar Datasets

Genome-wide transcriptomic analysis reveals the gene regulatory network that controlled by SRL1 in regulating rice leaf rolling

Project description:To understand the gene regulatory network that controlled by SRL1, we analyzed the transcriptomic data that generated from the mature leaves (60 days after germination) of the SRL1 knockout mutants srl1-KO and the control non-KO. We carried out the RNA-seq with three biological replicates of srl1-KO and non-KO respectively.

2020-02-05 | GSE144729 | GEO

Transcriptome evidence provides insight into Hox gene regulating rolling behavior in oniscidea

Project description:Behavior of rolling in oniscidea species had been reported as a sign to protect themselves to increase their survival rates, but the molecular mechanisms of rolling behaviors were still largely unknown. So we deeply characterized the molecular differences in rolling oniscidea samples and stretching oniscidea samples by transcriptome sequencing strategy (RNA-seq). Bulk RNA sequencing was performed with rolling and streching oniscidea samples. And our study suggests that Hox genes' expression levels could play an essential role in regulating neuron system development in oniscidea animals.

2021-01-26 | GSE156323 | GEO

Physiological and genome-wide expression analysis of cold-induced leaf rolling at the seedling stage in rice (Oryza sativa L.)

Project description:Leaf rolling and discoloration are two chilling injury symptoms that are widely adopted as indicators for evaluation of cold tolerance at the seedling stage in rice, respectively. However, their relationship has not been well investigated, in particular the mechanism on how low temperature causes leaf rolling at a genome-wide level. In this study, a cold-tolerant japonica cultivar Lijiangxintuanheigu and a cold-sensitive indica cultivar Sanhuangzhan-2 were subjected to different low temperature treatments and physiological and genome-wide gene expression analysis were conducted. Our results showed that leaf rolling happened at temperatures lower than 11℃, but discoloration appeared at moderately low temperatures, such as 13℃. Chlorophyll contents of the two cultivars significantly decreased under 13℃, but didn’t change under 11℃. Contrastly, their relative water contents and the relative electrolyte leakages decreased significantly. Genome-wide gene expression profiling of LTH revealed that the calcium signaling related genes and the genes related to ABA degradation significantly changed under 11℃. Moreover, numerous genes in DREB, MYB, bZIP, NAC, Zin finger, bHLH, WRKY gene families were differently expressed. Furthermore, many aquaporin genes, the key genes in trehalose and starch synthesis were down-regulated under 11℃. These results suggest that the two chilling injury symptoms are controlled by different mechanisms. Cold-induced leaf rolling is associated with calcium and ABA signaling pathways, and subjected to regulation of multiple transcription regulators. The suppression of aquaporin genes and reduced accumulation of soluble sugars under cold stress result in reduction of water potential in cells and consequently, leaf rolling.

2019-03-30 | GSE112547 | GEO

Transcriptomic analysis of OsRUS1 overexpression rice lines with rapid and dynamic leaf rolling morphology

Project description:OsRUS1-GFP overexpression (OsRUS1-OX) transgenic rice lines were generated using ZH-11 wildtype. Under well-watered conditions, the leaves of OsRUS1-OX transgenic rice lines could roll in about four minutes under sunlight, and the rolled leaves of OsRUS1-OX transgenic rice lines could expand in about seven minutes if the sunlight was shaded, while the leaves of wildtype ZH-11 expanded all the times at the same conditions. The mechanism behind the light-responded rapid and dynamic leaf rolling phenotype of OsRUS1-OX transgenic rice lines is unknown. Therefore, in order to understand this mechanism the RNA-Seq approach was used to explore the expressed genes difference between OsRUS1-OX and ZH-11.

2019-03-27 | GSE128886 | GEO

Semi-Rolled Leaf2 modulates rice leaf rolling by regulating abaxial side cell differentiation.

Project description:Moderate leaf rolling maintains the erectness of leaves and minimizes the shadowing between leaves which is helpful to establish ideal plant architecture. Here, we describe asrl2(semi-rolled leaf2) rice mutant, which has incurved leaves due to the presence of defective sclerenchymatous cells on the abaxial side of the leaf and displays narrow leaves and reduced plant height. Map-based cloning revealed that SRL2 encodes a novel plant-specific protein of unknown biochemical function.SRL2 was mainly expressed in the vascular bundles of leaf blades, leaf sheaths, and roots, especially in their sclerenchymatous cells. The transcriptional activities of several leaf development-related YABBY genes were significantly altered in the srl2 mutant. Double mutant analysis suggested that SRL2 and SHALLOT-LIKE1(SLL1)/ROLLED LEAF9(RL9) function in distinct pathways that regulate abaxial-side leaf development. Hence, SRL2 plays an important role in regulating leaf development, particularly during sclerenchymatous cell differentiation.

| S-EPMC4809286 | biostudies-literature

Transcriptome evidence provides insight into Hox gene regulating rolling behavior in oniscidea

Project description:Transcriptome evidence provides insight into Hox gene regulating rolling behavior in oniscidea

| PRJNA657520 | ENA

<i>DRB2</i> Modulates Leaf Rolling by Regulating Accumulation of MicroRNAs Related to Leaf Development in Rice.

Project description:As an important agronomic trait in rice (Oryza sativa), moderate leaf rolling helps to maintain the erectness of leaves and minimize shadowing between leaves, leading to improved photosynthetic efficiency and grain yield. However, the molecular mechanisms underlying rice leaf rolling still need to be elucidated. Here, we isolated a rice mutant, rl89, showing adaxially rolled leaf phenotype due to decreased number and size of bulliform cells. We confirmed that the rl89 phenotypes were caused by a single nucleotide substitution in OsDRB2 (LOC_Os10g33970) gene encoding DOUBLE-STRANDED RNA-BINDING2. This gene was constitutively expressed, and its encoded protein was localized to both nucleus and cytoplasm. Yeast two-hybrid assay showed that OsDRB2 could interact with DICER-LIKE1 (DCL1) and OsDRB1-2 respectively. qRT-PCR analysis of 29 related genes suggested that defects of the OsDRB2-miR166-OsHBs pathway could play an important role in formation of the rolled leaf phenotype of rl89, in which OsDRB2 mutation reduced miR166 accumulation, resulting in elevated expressions of the class III homeodomain-leucine zipper genes (such as OsHB1, 3 and 5) involved in leaf polarity and/or morphology development. Moreover, OsDRB2 mutation also reduced accumulation of miR160, miR319, miR390, and miR396, which could cause the abnormal leaf development in rl89 by regulating expressions of their target genes related to leaf development.

| S-EPMC9570175 | biostudies-literature

Decoding the PITX2 controlled genetic network in atrial fibrillation

Project description:Decoding the PITX2 controlled genetic network in atrial fibrillation

| PRJNA759904 | ENA

Transcriptomic analysis of OsRUS1 overexpression rice lines with rapid and dynamic leaf rolling morphology

Project description:Transcriptomic analysis of OsRUS1 overexpression rice lines with rapid and dynamic leaf rolling morphology

| PRJNA529208 | ENA

Heterodimer formed by ROC8 and ROC5 modulates leaf rolling in rice.

Project description:Moderately rolled leaf is one of the target traits of the ideal plant architecture in rice breeding. Many genes, including homeodomain leucine zipper IV transcription factors ROC5 and ROC8, regulating rice leaf rolling have been cloned and functionally analysed. However, the molecular mechanism by which these genes modulate leaf-rolling remains largely elusive. In this study, we demonstrated the transcription activation activity of both ROC8 and ROC5. Overexpressing ROC8 caused adaxially rolled leaves due to decreased number and size of bulliform cells, whereas knockout of ROC8 induced abaxially rolled leaves due to increased number and size of bulliform cells. ROC8 and ROC5 each could form homodimer, but ROC8 interacted preferably with ROC5 to forms a heterodimer. Importantly, we showed that the ROC8-ROC5 heterodimer rather than the homodimer of ROC8 or ROC5 was functional as neither overexpressing ROC8 in the ROC5 mutant nor overexpressing ROC5 in the ROC8-knockout line could rescue the mutant phenotype. This was further partially supported by the identification of a large number of common differentially expressed genes in single and double mutants of roc8 and roc5. ROC8 and ROC5 were functionally additive as the phenotype of abaxially rolled leaves was stronger in the roc5roc8 double mutant than in their single mutants. Our results provide evidence for the role of dimerization of ROC members in regulating leaf rolling of rice.

| S-EPMC8633501 | biostudies-literature

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