Transcriptome analysis of knockout mutants of rice seed dormancy gene OsVP1 and Sdr4

Chen, Wenqiang; Liu, Da-Pu; Li, Zhixin; Chen, Kai; Luo, Jianxun; Xu, Jianlong

doi:10.1007/s00299-022-02958-8

Cited by 3 publications

(3 citation statements)

References 58 publications

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“…The pyrabactin resistance 1 ( PYR1 )/ PYR1‐like / regulatory components of ABA receptors ( PYR/PYL/RCAR ) family members of wheat TaPYL4 have been reported to promote seed dormancy when overexpressed (Mega et al, 2019). Viviparous‐1 ( Vp1 ) (homologous to ABSCISIC ACID INSENSITIVE3 of Arabidopsis thaliana , ABI3 ) plays a major regulatory role in seed dormancy, with mutants of vp1/abi3 in maize, rice, and Arabidopsis displaying weak dormancy and are prone to PHS (McCarty et al, 1991; Nambara et al, 1995; Chen et al, 2020). Previous studies have demonstrated a positive correlation between the expression level of TaVP1 and wheat dormancy (Yang et al, 2007; Chang et al, 2009; Feng et al, 2017).…”

Section: Introductionmentioning

confidence: 99%

TaSRO1 interacts with TaVP1 to modulate seed dormancy and pre‐harvest sprouting resistance in wheat

Liu,

Li,

Wang

et al. 2024

JIPB

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Dormancy is an adaptive trait that prevents seeds from germinating under unfavorable environmental conditions. Seeds with weak dormancy undergo pre‐harvest sprouting (PHS) which decreases grain yield and quality. Understanding the genetic mechanisms that regulate seed dormancy and resistance to PHS is crucial for ensuring global food security. In this study, we illustrated the function and molecular mechanism of TaSRO1 in the regulation of seed dormancy and PHS resistance by suppressing TaVP1. The tasro1 mutants exhibited strong seed dormancy and enhanced resistance to PHS, whereas the mutants of tavp1 displayed weak dormancy. Genetic evidence has shown that TaVP1 is epistatic to TaSRO1. Biochemical evidence has shown that TaSRO1 interacts with TaVP1 and represses the transcriptional activation of the PHS resistance genes TaPHS1 and TaSdr. Furthermore, TaSRO1 undermines the synergistic activation of TaVP1 and TaABI5 in PHS resistance genes. Finally, we highlight the great potential of tasro1 alleles for breeding elite wheat cultivars that are resistant to PHS.This article is protected by copyright. All rights reserved.

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Section: Introductionmentioning

confidence: 99%

TaSRO1 interacts with TaVP1 to modulate seed dormancy and pre‐harvest sprouting resistance in wheat

Liu,

Li,

Wang

et al. 2024

JIPB

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“…With the development of omics technology, such as transcriptomics and metabolomics, these have been widely used to fully understand the effects of gene knockout on the body [27][28][29]. Transcriptomic profiling is a powerful tool that identifies gene expression signatures [30].…”

Section: Introductionmentioning

confidence: 99%

Combined Transcriptome and Metabolome Analysis of Smooth Muscle of Myostatin Knockout Cattle

Wang

et al. 2023

IJMS

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Myostatin (MSTN), a growth and differentiation factor, plays an important role in regulating skeletal muscle growth and development. MSTN knockout (MSTN-KO) leads to skeletal muscle hypertrophy and regulates metabolic homeostasis. Moreover, MSTN is also detected in smooth muscle. However, the effect of MSTN-KO on smooth muscle has not yet been reported. In this study, combined metabolome and transcriptome analyses were performed to investigate the metabolic and transcriptional profiling in esophageal smooth muscles of MSTN-KO Chinese Luxi Yellow cattle (n = 5, 24 months, average body weight 608.5 ± 17.62 kg) and wild-type (WT) Chinese Luxi Yellow cattle (n = 5, 24 months, average body weight 528.25 ± 11.03 kg). The transcriptome was sequenced using the Illumina Novaseq™ 6000 sequence platform. In total, 337 significantly up- and 129 significantly down-regulated genes were detected in the MSTN-KO cattle compared with the WT Chinese Luxi Yellow cattle. Functional enrichment analysis indicated that the DEGs were mainly enriched in 67 signaling pathways, including cell adhesion molecules, tight junction, and the cGMP-PKG signaling pathway. Metabolomics analysis by liquid chromatography-tandem mass spectrometry (LC-MS/MS) identified 130 differential metabolites between the groups, with 56 up-regulated and 74 down-regulated in MSTN knockout cattle compared with WT cattle. Differential metabolites were significantly enriched in 31 pathways, including glycerophospholipid metabolism, histidine metabolism, glutathione metabolism, and purine metabolism. Transcriptome and metabolome were combined to analyze the significant enrichment pathways, and there were three metabolically related pathways, including histidine metabolism, purine metabolism, and arginine and proline metabolism. These results provide important references for in-depth research on the effect of MSTN knockout on smooth muscle.

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“…The precise genome editing enabled by CRISPR/Cas9 has the potential to greatly enhance the quality and yield of agricultural production, while also facilitating the creation of new and improved varieties of rice with enhanced traits [ 28 , 29 , 30 , 31 , 32 ]. In recent years, the beneficial integration of CRISPR/Cas9 and high-throughput transcriptome sequencing technology (RNA-seq) has opened up new possibilities for investigating gene function [ 33 , 34 ]. Simultaneously, with the development of molecular biology technology, RNA-seq has been widely used in the study of gene expression levels and regulatory networks [ 35 , 36 , 37 ].…”

Section: Introductionmentioning

confidence: 99%

Improving Rice Leaf Shape Using CRISPR/Cas9-Mediated Genome Editing of SRL1 and Characterizing Its Regulatory Network Involved in Leaf Rolling through Transcriptome Analysis

Han

Yang

et al. 2023

IJMS

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Leaf rolling is a crucial agronomic trait to consider in rice (Oryza sativa L.) breeding as it keeps the leaves upright, reducing interleaf shading and improving photosynthetic efficiency. The SEMI-ROLLED LEAF 1 (SRL1) gene plays a key role in regulating leaf rolling, as it encodes a glycosylphosphatidylinositol-anchored protein located on the plasma membrane. In this study, we used CRISPR/Cas9 to target the second and third exons of the SRL1 gene in the indica rice line GXU103, which resulted in the generation of 14 T0 transgenic plants with a double-target mutation rate of 21.4%. After screening 120 T1 generation plants, we identified 26 T-DNA-free homozygous double-target mutation plants. We designated the resulting SRL1 homozygous double-target knockout as srl1-103. This line exhibited defects in leaf development, leaf rolling in the mature upright leaves, and a compact nature of the fully grown plants. Compared with the wild type (WT), the T2 generation of srl1-103 varied in two key aspects: the width of flag leaf (12.6% reduction compared with WT) and the leaf rolling index (48.77% increase compared with WT). In order to gain a deeper understanding of the involvement of SRL1 in the regulatory network associated with rice leaf development, we performed a transcriptome analysis for the T2 generation of srl1-103. A comparison of srl1-103 with WT revealed 459 differentially expressed genes (DEGs), including 388 upregulated genes and 71 downregulated genes. In terms of the function of the DEGs, there seemed to be a significant enrichment of genes associated with cell wall synthesis (LOC_Os08g01670, LOC_Os05g46510, LOC_Os04g51450, LOC_Os10g28080, LOC_Os04g39814, LOC_Os01g71474, LOC_Os01g71350, and LOC_Os11g47600) and vacuole-related genes (LOC_Os09g23300), which may partially explain the increased leaf rolling in srl1-103. Furthermore, the significant downregulation of BAHD acyltransferase-like protein gene (LOC_Os08g44840) could be the main reason for the decreased leaf angle and the compact nature of the mutant plants. In summary, this study successfully elucidated the gene regulatory network in which SRL1 participates, providing theoretical support for targeting this gene in rice breeding programs to promote variety improvement.

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Transcriptome analysis of knockout mutants of rice seed dormancy gene OsVP1 and Sdr4

Cited by 3 publications

References 58 publications

TaSRO1 interacts with TaVP1 to modulate seed dormancy and pre‐harvest sprouting resistance in wheat

TaSRO1 interacts with TaVP1 to modulate seed dormancy and pre‐harvest sprouting resistance in wheat

Combined Transcriptome and Metabolome Analysis of Smooth Muscle of Myostatin Knockout Cattle

Improving Rice Leaf Shape Using CRISPR/Cas9-Mediated Genome Editing of SRL1 and Characterizing Its Regulatory Network Involved in Leaf Rolling through Transcriptome Analysis

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