Global integrated omics expression analyses of abiotic stress signaling HSF transcription factor genes in Oryza sativa L.: An in silico approach

Muthuramalingam, Pandiyan; Jeyasri, Rajendran; Bharathi, Ravichandran Kavitha Anbu Snega; Suba, Vellaichami; Pandian, Shunmugiah Karutha; Ramesh, Manikandan

doi:10.1016/j.ygeno.2019.06.006

Cited by 17 publications

(15 citation statements)

References 42 publications

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“…Recent advances in omics have enabled us to decipher complex regulatory networks about plants' stress resistance, specifically cold tolerance [28][29][30][31]. Through an integrated approach, previously published reports characterized multiple metabolite synthesis pathways, i.e., glucosinolate metabolism [29] and flavonoid biosynthesis [8,30] in Arabidopsis, anthocyanin biosynthesis in maize [23], and combined abiotic stress responses (CAbS) in rice [32]. However, cold tolerance mechanisms remain largely unclear in maize regarding the metabolome.…”

Section: Introductionmentioning

confidence: 99%

Metabolic Insight into Cold Stress Response in Two Contrasting Maize Lines

Zhang

Cao

et al. 2022

Life

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Maize (Zea mays L.) is sensitive to a minor decrease in temperature at early growth stages, resulting in deteriorated growth at later stages. Although there are significant variations in maize germplasm in response to cold stress, the metabolic responses as stress tolerance mechanisms are largely unknown. Therefore, this study aimed at providing insight into the metabolic responses under cold stress at the early growth stages of maize. Two inbred lines, tolerant (B144) and susceptible (Q319), were subjected to cold stress at the seedling stage, and their corresponding metabolic profiles were explored. The study identified differentially accumulated metabolites in both cultivars in response to induced cold stress with nine core conserved cold-responsive metabolites. Guanosine 3′,5′-cyclic monophosphate was detected as a potential biomarker metabolite to differentiate cold tolerant and sensitive maize genotypes. Furthermore, Quercetin-3-O-(2″′-p-coumaroyl)sophoroside-7-O-glucoside, Phloretin, Phloretin-2′-O-glucoside, Naringenin-7-O-Rutinoside, L-Lysine, L-phenylalanine, L-Glutamine, Sinapyl alcohol, and Feruloyltartaric acid were regulated explicitly in B144 and could be important cold-tolerance metabolites. These results increase our understanding of cold-mediated metabolic responses in maize that can be further utilized to enhance cold tolerance in this significant crop.

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Section: Introductionmentioning

confidence: 99%

Metabolic Insight into Cold Stress Response in Two Contrasting Maize Lines

Zhang

Cao

et al. 2022

Life

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“…TFs play a prominent role in plant stress signaling and transduce the various signal transduction pathways. In addition, TFs interacting with the cis -regulatory elements were present in the promoter regions of stress-responsible genes, which have differentially regulated the expression of several downstream genes exhibiting the enhancement of abiotic stress tolerance [ 17 , 84 ]. So far, approximately 58 TF families have been categorized [ 85 ].…”

Section: Influence Of Salinity Stress In Plantsmentioning

confidence: 99%

“…cellular differentiation, plant development, seed storage, callus formation, somatic embryogenesis, seed development, biosynthesis of secondary metabolites, and control the plant cell metabolisms [ 17 , 84 , 86 , 87 ]. Furthermore, the mentioned TFs also play a major role in various abiotic stress mechanisms such as cold, submergence, drought, UV, temperature, desiccation, heavy metals, wounding, osmotic stress, and particularly salinity stress [ 17 , 84 , 88 , 89 , 90 , 91 ]. These TFs and their functional role and abiotic stress regulation, mainly salinity stress, are summarized in Supplementary Table S2 .…”

Section: Influence Of Salinity Stress In Plantsmentioning

confidence: 99%

“…These issues alarm to throw more light on plant stress biologists to evaluate the biochemical and molecular stress machinery and their signaling network in rice. Significantly, the available whole rice genome and transcriptome projects [ 15 ], multi-omics approaches [ 16 , 17 ], bioinformatic platforms [ 18 ], agricultural practicing elements [ 19 , 20 , 21 , 22 ], breeding [ 23 ], and recent literature pave the way to identify and annotate the stress-responsive key players with their regulatory functions and also provide the deeper molecular insights. These integrated approaches and holistic strategies used for the dissection of dynamic networks and altering the repercussions in plants support them in controlling abiotic stresses, particularly salinity stress.…”

Section: Introductionmentioning

confidence: 99%

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Multi-Omics and Integrative Approach towards Understanding Salinity Tolerance in Rice: A Review

Muthuramalingam

Jeyasri

Rakkammal

et al. 2022

Biology

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Rice (Oryza sativa L.) plants are simultaneously encountered by environmental stressors, most importantly salinity stress. Salinity is the major hurdle that can negatively impact growth and crop yield. Understanding the salt stress and its associated complex trait mechanisms for enhancing salt tolerance in rice plants would ensure future food security. The main aim of this review is to provide insights and impacts of molecular-physiological responses, biochemical alterations, and plant hormonal signal transduction pathways in rice under saline stress. Furthermore, the review highlights the emerging breakthrough in multi-omics and computational biology in identifying the saline stress-responsive candidate genes and transcription factors (TFs). In addition, the review also summarizes the biotechnological tools, genetic engineering, breeding, and agricultural practicing factors that can be implemented to realize the bottlenecks and opportunities to enhance salt tolerance and develop salinity tolerant rice varieties. Future studies pinpointed the augmentation of powerful tools to dissect the salinity stress-related novel players, reveal in-depth mechanisms and ways to incorporate the available literature, and recent advancements to throw more light on salinity responsive transduction pathways in plants. Particularly, this review unravels the whole picture of salinity stress tolerance in rice by expanding knowledge that focuses on molecular aspects.

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“…In addition, the use of high-throughput techniques has been employed such as expression reads by RNA-Seq, random and targeted mutagenesis, gene shifting, complementation, and synthetic promoter trapping approaches make many avenues for functional analyses of AbS responsive genes and tolerance mechanisms [ 77 ]. Transcription factors (TFs) are crucially important in knowing the appropriate molecular processes and pathways that are involved in plant growth and survival under AbS conditions [ 78 , 79 , 80 ]. AbS are the quantitative and multiple genes associated in nature, these stress molecular cross-talks and their pathway interconnections are found under AbS conditions.…”

Section: Bioinformatics and Functional Omics Approach To Explore The Abs Tolerance Mechanismmentioning

confidence: 99%

An Overview of Abiotic Stress in Cereal Crops: Negative Impacts, Regulation, Biotechnology and Integrated Omics

Jeyasri

Muthuramalingam

Satish

et al. 2021

Plants

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Abiotic stresses (AbS), such as drought, salinity, and thermal stresses, could highly affect the growth and development of plants. For decades, researchers have attempted to unravel the mechanisms of AbS for enhancing the corresponding tolerance of plants, especially for crop production in agriculture. In the present communication, we summarized the significant factors (atmosphere, soil and water) of AbS, their regulations, and integrated omics in the most important cereal crops in the world, especially rice, wheat, sorghum, and maize. It has been suggested that using systems biology and advanced sequencing approaches in genomics could help solve the AbS response in cereals. An emphasis was given to holistic approaches such as, bioinformatics and functional omics, gene mining and agronomic traits, genome-wide association studies (GWAS), and transcription factors (TFs) family with respect to AbS. In addition, the development of omics studies has improved to address the identification of AbS responsive genes and it enables the interaction between signaling pathways, molecular insights, novel traits and their significance in cereal crops. This review compares AbS mechanisms to omics and bioinformatics resources to provide a comprehensive view of the mechanisms. Moreover, further studies are needed to obtain the information from the integrated omics databases to understand the AbS mechanisms for the development of large spectrum AbS-tolerant crop production.

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Global integrated omics expression analyses of abiotic stress signaling HSF transcription factor genes in Oryza sativa L.: An in silico approach

Cited by 17 publications

References 42 publications

Metabolic Insight into Cold Stress Response in Two Contrasting Maize Lines

Metabolic Insight into Cold Stress Response in Two Contrasting Maize Lines

Multi-Omics and Integrative Approach towards Understanding Salinity Tolerance in Rice: A Review

An Overview of Abiotic Stress in Cereal Crops: Negative Impacts, Regulation, Biotechnology and Integrated Omics

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