Understanding the early cold response mechanism in IR64 indica rice variety through comparative transcriptome analysis

Dasgupta, Pratiti; Das, A. K.; Datta, Sambit; Banerjee, Ishani; Tripathy, Sucheta; Chaudhuri, Shubho

doi:10.1186/s12864-020-06841-2

Cited by 27 publications

(18 citation statements)

References 101 publications

(109 reference statements)

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“…In the present study, JAZ1, ICE1, dehydration-responsive elementbinding protein 1A/1B/1C (CBF1/2/3), LHY, CCA1, and COR27 were all overexpressed and interacted with each other, which played an important role in adapting to low temperature (Li et al 2016). Furthermore, to compare with a previous publication, the DEGs involved in the CBF pathway under cold stress could also be found in rice through comparative transcriptome analysis (Dasgupta et al 2020), which indicated the confidence and applicability of our results.…”

Section: Discussionsupporting

confidence: 58%

“…These DEGs were related to the inhibition of photosynthesis and the primary biological processes (Ke et al 2020). To identify early responsive events in Oryza sativa under cold stress, a transcriptome profile was performed to identify 516 DEGs that were involved in Ca 2+ and ROS-mediated signaling, and the DREB/CBF pathway (Dasgupta et al 2020).…”

Section: Introductionmentioning

confidence: 99%

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Identification Of Arabidopsis genes associated with cold tolerance based on integrated bioinformatics analysis

Guo¹,

Liu

Jiang³

et al. 2021

Journal of Plant Interactions

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Cold stress is a major environmental factor that limits plant growth and productivity. Plants have evolved various strategies to adapt to these environmental conditions. To better explain the mechanisms used to survive environmental challenges, we retrieved the cold-responsive genes of Arabidopsis thaliana from the Gene Expression Omnibus (GEO) database. The GEO raw data were normalized by the quantile method, and then the differentially expressed genes (DEGs) under cold stress were screened using the robust rank aggregation (RRA) algorithm, including 261 upregulated and 177 downregulated genes out of more than 20,000 genes. Further, the integrated bioinformatics analyses of PUBMED, PANTHER, DAVID, and STRING indicated that the upregulated DEGs were involved in cellular response to red light, negative regulation of circadian rhythm, photoprotection, monosaccharide transport, cold acclimation, and phosphate ion homeostasis, while the downregulated DEGs were associated with the indole glucosinolate biosynthetic process, regulation of RNA splicing, water transport, cell wall modification, cell wall loosening, cellular water homeostasis, and cell wall homeostasis. Furthermore, the up-regulated DEGs had about four times protein-protein-interactions (PPIs) than the down-regulated DEGs, and the cold-responsive genes were identified using Cytoscape software. Furthermore, qRT-PCR of low-temperatureresponsive protein 78 (LTI78), transducin family protein (SWA1), and arginine methyltransferase 11 (PRMT11) were performed to validate the outcome of integrated bioinformatics analysis. Our work will improve our knowledge of cold-responsive mechanisms and these DEGs might be targets for plant cold stress-resistance research.

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Section: Discussionsupporting

confidence: 58%

Section: Introductionmentioning

confidence: 99%

Identification Of Arabidopsis genes associated with cold tolerance based on integrated bioinformatics analysis

Guo¹,

Liu

Jiang³

et al. 2021

Journal of Plant Interactions

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“…Cold weather accounts for serious reductions in crop yield every year, since many agriculturally important crops, including rice ( Oryza sativa ) and peanut, are chilling sensitive and can only be cultivated in tropical or subtropical regions ( Wu et al, 2020 ). Despite the molecular mechanisms of cold-induced reprogramming of gene expression and the metabolite accumulation pattern were extensively studied in model plants ( Hoermiller et al, 2016 ; Jin et al, 2017 ; Pagter et al, 2017 ; Dasgupta et al, 2020 ), only a handful of reports were related to peanut ( Jiang et al, 2020 ; Wu et al, 2020 ; Zhang H. et al, 2020 ). In this study, we attempted to decipher the regulatory mechanisms of peanut in response to cold stress through combining transcriptome with metabolome analysis.…”

Section: Discussionmentioning

confidence: 99%

Integrated Transcriptomics and Metabolomics Analysis Reveal Key Metabolism Pathways Contributing to Cold Tolerance in Peanut

et al. 2021

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Low temperature (non-freezing) is one of the major limiting factors in peanut (Arachis hypogaea L.) growth, yield, and geographic distribution. Due to the complexity of cold-resistance trait in peanut, the molecular mechanism of cold tolerance and related gene networks were largely unknown. In this study, metabolomic analysis of two peanut cultivars subjected to chilling stress obtained a set of cold-responsive metabolites, including several carbohydrates and polyamines. These substances showed a higher accumulation pattern in cold-tolerant variety SLH than cold-susceptible variety ZH12 under cold stress, indicating their importance in protecting peanut from chilling injuries. In addition, 3,620 cold tolerance genes (CTGs) were identified by transcriptome sequencing, and the CTGs were most significantly enriched in the “phenylpropanoid biosynthesis” pathway. Two vital modules and several novel hub genes were obtained by weighted gene co-expression network analysis (WGCNA). Several key genes involved in soluble sugar, polyamine, and G-lignin biosynthetic pathways were substantially higher and/or responded more quickly in SLH (cold tolerant) than ZH12 (cold susceptible) under low temperature, suggesting they might be crucial contributors during the adaptation of peanut to low temperature. These findings will not only provide valuable resources for study of cold resistance in peanut but also lay a foundation for genetic modification of cold regulators to enhance stress tolerance in crops.

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“…Stress perception leads to a complex network of gene expression. Important abiotic stresses such as drought, cold, salinity induce common gene networks including transcription factors, protein kinases, receptor-like kinases, hormone signaling, and genes associated with the production of osmoprotectants (DasGupta et al, 2020;Todaka et al, 2015). However, it is important to improve tolerance to drought, salinity, and cold in most cultivated rice varieties (Menguer et al, 2017).…”

Section: Discussionmentioning

confidence: 99%

“…Rice DREB1 gene family (OsDREB1) is upregulated in the early phase (2 -6 hours) of the cold stress at 4 -10 o C (DasGupta et al, 2020;Doubouzet et al, 2003;Pradhan et al, 2019;Yun et al, 2010). To check if OsDREB genes play a synergistic effect in stress tolerance displayed by RD29a:DREB1a transgenic plants, normalized read counts for OsDREB1 and OsDREB2 genes were compared between genotypes and treatment (Figure S2).…”

Section: Rice Dreb Genesmentioning

confidence: 99%

Phenotypic and transcriptomic analysis reveals early stress responses in transgenic rice expressing Arabidopsis DREB1a

Berchembrock

Pathak

Maurya

et al. 2022

Preprint

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Overexpression of Arabidopsis Dehydration Response Element Binding 1a (DREB1a) is a well-known approach for developing salinity, cold and/or drought stress tolerance. However, understanding of the genetic mechanisms associated with DREB1a expression in rice is generally limited. In this study, DREB1a associated early responses were investigated in a transgenic rice line harboring cold-inducible DREB1a at a gene stacked locus. While the function of other genes in the stacked locus was not relevant to stress tolerance, this study demonstrates DREB1a can be colocalized with other genes for multigenic trait enhancement. As expected, the transgenic lines displayed improved tolerance to salinity stress and water withholding when compared to non-transgenic controls. RNA sequencing and transcriptome analysis showed upregulation of complex transcriptional networks and metabolic reprogramming as DREB1a expression led to the upregulation of multiple transcription factor gene families, suppression of photosynthesis and induction of secondary metabolism. In addition to the detection of previously described mechanisms such as production of protective molecules, potentially novel pathways were also revealed. These include jasmonate, auxin, and ethylene signaling, induction of JAZ and WRKY regulons, trehalose synthesis and polyamine catabolism. These genes regulate various stress responses and ensure timely attenuation of the stress signal. Furthermore, genes associated with heat stress response were downregulated in DREB1a overexpressing lines, suggesting antagonism between heat and dehydration stress pathways. In summary, through a complex transcriptional network, multiple stress signaling pathways are induced by DREB1a that presumably lead to early perception and rapid response towards stress tolerance as well as attenuation of the signal to prevent deleterious effects of the runoff response.

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Understanding the early cold response mechanism in IR64 indica rice variety through comparative transcriptome analysis

Cited by 27 publications

References 101 publications

Identification Of Arabidopsis genes associated with cold tolerance based on integrated bioinformatics analysis

Identification Of Arabidopsis genes associated with cold tolerance based on integrated bioinformatics analysis

Integrated Transcriptomics and Metabolomics Analysis Reveal Key Metabolism Pathways Contributing to Cold Tolerance in Peanut

Phenotypic and transcriptomic analysis reveals early stress responses in transgenic rice expressing Arabidopsis DREB1a

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