A review on applications of plant network biology to understand the drought stress response in economically important cereal crops

Thanmalagan, Raja Rajeswary; Jayaprakash, Aiswarya; Roy, Abhijeet Deb; Arunachalam, Annamalai; Lakshmi, P.T.V.

doi:10.1016/j.plgene.2021.100345

Cited by 16 publications

(6 citation statements)

References 183 publications

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“…Plants adapt to drought through a series of morphological, physiological, biochemical, metabolic and molecular changes when water is lacking ( Baozhu et al, 2022 ; Thanmalagan et al, 2022 ). Plant species such as soybean can reduce the damage caused by water loss by increasing the contents of endogenous hormones, inhibiting photosynthesis, altering their morphology and structure, slowing their growth and reducing their biomass ( Ramirez-Villegas et al, 2018 ; Du et al, 2020 ).…”

Section: Introductionmentioning

confidence: 99%

Transcriptomic and Metabolomic Analyses Reveal Key Metabolites, Pathways and Candidate Genes in Sophora davidii (Franch.) Skeels Seedlings Under Drought Stress

et al. 2022

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Soil aridification and desertification are particularly prominent in China’s karst areas, severely limiting crop yields and vegetation restoration. Therefore, it is very important to identify naturally drought-tolerant plant species. Sophora davidii (Franch.) Skeels is resistant to drought and soil infertility, is deeply rooted and is an excellent plant material for soil and water conservation. We studied the transcriptomic and metabolomic changes in S. davidii in response to drought stress (CK, control; LD, mild drought stress; MD, moderate drought stress; and SD, severe drought stress). Sophora davidii grew normally under LD and MD stress but was inhibited under SD stress; the malondialdehyde (MDA), hydrogen peroxide (H2O2), soluble sugar, proline, chlorophyll a, chlorophyll b and carotenoid contents and ascorbate peroxidase (APX) activity significantly increased, while the superoxide dismutase (SOD), peroxidase (POD) and catalase (CAT) activities and soluble protein content significantly decreased. In the LD/CK, MD/CK and SD/CK comparison groups, there were 318, 734 and 1779 DEGs, respectively, and 100, 168 and 281 differentially accumulated metabolites, respectively. Combined analysis of the transcriptomic and metabolomic data revealed the metabolic regulation of S. davidii in response to drought stress. First, key candidate genes such as PRR7, PRR5, GI, ELF3, PsbQ, PsaK, INV, AMY, E2.4.1.13, E3.2.1.2, NCED, PP2C, PYL, ABF, WRKY33, P5CS, PRODH, AOC3, HPD, GPX, GST, CAT and SOD1 may govern the drought resistance of S. davidii. Second, three metabolites (oxidised glutathione, abscisic acid and phenylalanine) were found to be related to drought tolerance. Third, several key candidate genes and metabolites involved in 10 metabolic pathways were identified, indicating that these metabolic pathways play an important role in the response to drought in S. davidii and possibly other plant species.

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Section: Introductionmentioning

confidence: 99%

Transcriptomic and Metabolomic Analyses Reveal Key Metabolites, Pathways and Candidate Genes in Sophora davidii (Franch.) Skeels Seedlings Under Drought Stress

et al. 2022

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“…Most of the genes have minor effects for DT. The complex nature of DT makes it difficult to improve the cultivars without a complete understanding of gene networks ( Thanmalagan et al, 2022 ). Plants adopt several mechanisms to cope with DS ( Fang and Xiong, 2015 ; Muiruri et al, 2021 ; Panda et al, 2021 ).…”

Section: Drought Tolerance Mechanism In Ramiementioning

confidence: 99%

Improving Drought Stress Tolerance in Ramie (Boehmeria nivea L.) Using Molecular Techniques

Rasheed

Jie²,

Nawaz³

et al. 2022

Front. Plant Sci.

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Ramie is one of the most significant fiber crops and contributes to good quality fiber. Drought stress (DS) is one of the most devastating abiotic factors which is accountable for a substantial loss in crop growth and production and disturbing sustainable crop production. DS impairs growth, plant water relation, and nutrient uptake. Ramie has evolved a series of defense responses to cope with DS. There are numerous genes regulating the drought tolerance (DT) mechanism in ramie. The morphological and physiological mechanism of DT is well-studied; however, modified methods would be more effective. The use of novel genome editing tools like clustered regularly interspaced short palindromic repeats (CRISPR) is being used to edit the recessive genes in crops to modify their function. The transgenic approaches are used to develop several drought-tolerant varieties in ramie, and further identification of tolerant genes is needed for an effective breeding plan. Quantitative trait loci (QTLs) mapping, transcription factors (TFs) and speed breeding are highly studied techniques, and these would lead to the development of drought-resilient ramie cultivars. The use of hormones in enhancing crop growth and development under water scarcity circumstances is critical; however, using different concentrations and testing genotypes in changing environments would be helpful to sort the tolerant genotypes. Since plants use various ways to counter DS, investigating mechanisms of DT in plants will lead to improved DT in ramie. This critical review summarized the recent advancements on DT in ramie using novel molecular techniques. This information would help ramie breeders to conduct research studies and develop drought tolerant ramie cultivars.

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“…Furthermore, genome sequence data are invaluable reference tools for high-throughput “omics” studies involving many aspects of plant biology. Consequently, innumerable transcriptomics, proteomics, and metabolomics studies on plant responses to drought have been published and reviewed ( Cramer et al., 2011 ; Ngara and Ndimba, 2014 ; Shanker et al., 2014 ; Barkla, 2016 ; Ngara et al., 2021 ; Singh et al., 2022 ; Thanmalagan et al., 2022 ). In addition, the generalised functional catalogue of plant genes outlined by Bevan et al.…”

Section: Introductionmentioning

confidence: 99%

The roles of plant proteases and protease inhibitors in drought response: a review

Moloi

Ngara

2023

Front. Plant Sci.

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Upon exposure to drought, plants undergo complex signal transduction events with concomitant changes in the expression of genes, proteins and metabolites. For example, proteomics studies continue to identify multitudes of drought-responsive proteins with diverse roles in drought adaptation. Among these are protein degradation processes that activate enzymes and signalling peptides, recycle nitrogen sources, and maintain protein turnover and homeostasis under stressful environments. Here, we review the differential expression and functional activities of plant protease and protease inhibitor proteins under drought stress, mainly focusing on comparative studies involving genotypes of contrasting drought phenotypes. We further explore studies of transgenic plants either overexpressing or repressing proteases or their inhibitors under drought conditions and discuss the potential roles of these transgenes in drought response. Overall, the review highlights the integral role of protein degradation during plant survival under water deficits, irrespective of the genotypes’ level of drought resilience. However, drought-sensitive genotypes exhibit higher proteolytic activities, while drought-tolerant genotypes tend to protect proteins from degradation by expressing more protease inhibitors. In addition, transgenic plant biology studies implicate proteases and protease inhibitors in various other physiological functions under drought stress. These include the regulation of stomatal closure, maintenance of relative water content, phytohormonal signalling systems including abscisic acid (ABA) signalling, and the induction of ABA-related stress genes, all of which are essential for maintaining cellular homeostasis under water deficits. Therefore, more validation studies are required to explore the various functions of proteases and their inhibitors under water limitation and their contributions towards drought adaptation.

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A review on applications of plant network biology to understand the drought stress response in economically important cereal crops

Cited by 16 publications

References 183 publications

Transcriptomic and Metabolomic Analyses Reveal Key Metabolites, Pathways and Candidate Genes in Sophora davidii (Franch.) Skeels Seedlings Under Drought Stress

Transcriptomic and Metabolomic Analyses Reveal Key Metabolites, Pathways and Candidate Genes in Sophora davidii (Franch.) Skeels Seedlings Under Drought Stress

Improving Drought Stress Tolerance in Ramie (Boehmeria nivea L.) Using Molecular Techniques

The roles of plant proteases and protease inhibitors in drought response: a review

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