RNA sequencing as a tool for understanding biological complexity of abiotic stress in plants

Malik, V. S.

doi:10.1007/s13562-015-0326-6

Cited by 10 publications

(5 citation statements)

References 14 publications

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“…RNA-seq technology has higher sensitivity to capture low and high-level gene expression than array technologies [8]. RNA-seq can not only detect information about the relationship between a gene and its products, but also isolate genes that are difficult to handle by biochemistry [9]. The technique has been widely used to identify key pathways and differential gene expression in a variety of plant species involved in regulation during abiotic stress, such as drought stress [10], salt stress [11], heat stress [12], cold stress [13].…”

Section: Introductionmentioning

confidence: 99%

Transcriptome analysis on responses of orchardgrass (Dactylis glomerata L.) leaves to a short term flooding

et al. 2020

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Background Orchardgrass (Dactylis glomerata L.) is a popular cool-season perennial grass with a high production value, and orchardgrass seed is the fourth top-selling forage grass seed in the world. However, its yield and quality are often affected by flooding. To date, the molecular responses of orchardgrass to flooding were poorly understood. Results Here, we performed mRNA-seq to explore the transcriptomic responses of orchardgrass to a short term flooding (8 h and 24 h). There were 1454 and 565 differentially expressed genes identified in the 8 h and 24 h of flooding, respectively, compared to well control. GO functional enrichment analysis showed that oxidoreductase activity and oxidation-reduction process were highly present, suggesting that flooding induced the response to oxygen stress. Pathways enrichment analysis highlights the importance of glutathione metabolism, peroxidase, glycolysis and plant hormone signal transduction in response to flooding acclimation. Besides, the ROS clearance system is activated by significantly expressed glutathione S-transferase and genes encoding SOD and CAT (CAT1 and CDS2). The significant positive correlation between RNA sequencing data and a qPCR analysis indicated that the identified genes were credible. Conclusion In the process of orchardgrass response to flooding stress, multiple differential genes and biological processes have participated in its acclimation to flooding, especially the biological processes involved in the removal of ROS. These results provide a basis for further research on the adaptation mechanism of orchardgrass to flood tolerance.

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Section: Introductionmentioning

confidence: 99%

Transcriptome analysis on responses of orchardgrass (Dactylis glomerata L.) leaves to a short term flooding

et al. 2020

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“…Plants have developed sophisticated mechanisms to survive these adverse conditions, including differential expression of numerous genes [ 33 ]. The analysis of these transcriptomic changes has been utilized as a powerful for investigating the molecular regulatory mechanisms induced by abiotic and biotic stresses [ 18 ].…”

Section: Discussionmentioning

confidence: 99%

“…RNA sequencing (RNA-Seq) is widely recognized as a powerful NGS-based method enabling the comprehensive profiling of gene expression. Analysis of the transcriptome can provide new insights into the genetic and molecular bases of abiotic stress tolerance in diverse plant species [ 18 ].…”

Section: Introductionmentioning

confidence: 99%

Transcriptome Profiling of a Soybean Mutant with Salt Tolerance Induced by Gamma-ray Irradiation

Kang,

Chowdhury,

Kang

et al. 2024

Plants

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Salt stress is a significant abiotic stress that reduces crop yield and quality globally. In this study, we utilized RNA sequencing (RNA-Seq) to identify differentially expressed genes (DEGs) in response to salt stress induced by gamma-ray irradiation in a salt-tolerant soybean mutant. The total RNA library samples were obtained from the salt-sensitive soybean cultivar Kwangan and the salt-tolerant mutant KA-1285. Samples were taken at three time points (0, 24, and 72 h) from two tissues (leaves and roots) under 200 mM NaCl. A total of 967,719,358 clean reads were generated using the Illumina NovaSeq 6000 platform, and 94.48% of these reads were mapped to 56,044 gene models of the soybean reference genome (Glycine_max_Wm82.a2.v1). The DEGs with expression values were compared at each time point within each tissue between the two soybeans. As a result, 296 DEGs were identified in the leaves, while 170 DEGs were identified in the roots. In the case of the leaves, eight DEGs were related to the phenylpropanoid biosynthesis pathway; however, in the roots, Glyma.03G171700 within GmSalt3, a major QTL associated with salt tolerance in soybean plants, was differentially expressed. Overall, these differences may explain the mechanisms through which mutants exhibit enhanced tolerance to salt stress, and they may provide a basic understanding of salt tolerance in soybean plants.

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“…Non-Target-Site Herbicide Resistance in Sunflower plants (Duhoux et al, 2015) since it may yield information about the affiliations between genes and their products and allow isolation of genes for traits whose biochemistry is difficult (Malik, 2016). It offers several advantages over other transcriptome techniques such as high sensitivity and specificity in the detection of lower abundance transcripts and the possibility of discriminating highly similar sequences.…”

Section: High Throughput Sequencingmentioning

confidence: 99%

Decoding Non-Target-Site Herbicide Resistance in Sunflower: The Beginning of the Story

Gil

Nestares

2019

Helia

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In the last years, many efforts have been made to develop sunflower cultivars showing important agronomical characteristics such as herbicide resistance. These approaches have been focused mainly on resistance to herbicides with the same mode of action, that is acetohydroxyacid synthase (AHAS) inhibitors. To date, four induced and natural AHAS mutations have been found that confer resistance to these herbicides and many of these alleles are being used for the production of sunflower hybrids resistant to herbicides and to develop different non-transgenic technologies for weed control. However, little is known about the bases of non-target-site-based resistance (NTSR) developing cross-resistance to herbicides with different modes of action in sunflower. These mechanisms diminish the number of active herbicide molecules that reach the target and are generally polygenic. Elucidating the nature of NTSR would allow evaluating maximal efficiency conditions for the herbicide and would enable to establish weed management strategies in sunflower crop. Nowadays, mining of NTSR genes can be more easily accomplished taking advantage of up-to-date omics-based approaches: high-throughput techniques involving genomics, transcriptomics, proteomics and metabolomics. Considering the difficulties in the discovery of new compounds with a broad spectrum of weed control, it results essential to broaden the use of former herbicides which are highly efficient and ecologically desirable. Full understanding of NTSR mechanisms in sunflower would allow detecting specific genes potentially useful as biotechnological tools for the phytoremediation of herbicides and modern plant breeding.

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RNA sequencing as a tool for understanding biological complexity of abiotic stress in plants

Cited by 10 publications

References 14 publications

Transcriptome analysis on responses of orchardgrass (Dactylis glomerata L.) leaves to a short term flooding

Transcriptome analysis on responses of orchardgrass (Dactylis glomerata L.) leaves to a short term flooding

Transcriptome Profiling of a Soybean Mutant with Salt Tolerance Induced by Gamma-ray Irradiation

Decoding Non-Target-Site Herbicide Resistance in Sunflower: The Beginning of the Story

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