| 1. |
- Al Azzawi, Tiba Nazar Ibrahim, et al.
(author)
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Evaluation of Iraqi Rice Cultivars for Their Tolerance to Drought Stress
- 2020
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In: Agronomy. - : MDPI. - 2073-4395. ; 10:11
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Journal article (peer-reviewed)abstract
- Drought stress is a serious problem around the globe and particularly in the Republic of Iraq. Rice is the third most consumed crop for the Iraqi people; however, its cultivation and production is very low due to several challenges including drought. The current study was performed to evaluate five Iraqi rice cultivars along with relevant (drought-tolerant and drought-susceptible) controls under drought stress, either by treatment with 10% PEG (polyethylene glycol) or through water withholding to induce natural drought stress. The phenotypes of all the cultivars were evaluated and the transcriptional responses of key drought-responsive candidate genes, identified through the EST-SSR marker-based approach, were studied. We also studied transcript accumulation of drought-related transcriptional factors, such as OsGRASS23, OsbZIP12, and OsDREB2A. Moreover, the reference cultivars also included a drought-tolerant inter-specific cultivar Nerica 7 (a cross between Oryza sativa ssp. indica X O. glaberrima). Among the cultivars, the more drought-tolerant phenotypic characteristics and higher transcript accumulation of drought-related marker genes OsE647 and OsE1899 and transcriptional factors OsGRASS23, OsbZIP12, and OsDREB2A were observed in four (out of five) significantly drought-tolerant Iraqi cultivars; Mashkab, followed by Furat, Yasmen, and Amber 33. On another note, Amber Barka was found to be significantly drought susceptible. Mashkab and Amber Barka were found to be the most drought-tolerant and-susceptible cultivars, respectively. The identified tolerant cultivars may potentially serve as a genetic source for the incorporation of drought-tolerant phenotypes in rice.
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| 2. |
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| 3. |
- Falak, Noreen, et al.
(author)
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Transcription Factors as the "Blitzkrieg" of Plant Defense : A Pragmatic View of Nitric Oxide's Role in Gene Regulation
- 2021
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In: International Journal of Molecular Sciences. - : MDPI. - 1661-6596 .- 1422-0067. ; 22:2
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Research review (peer-reviewed)abstract
- Plants are in continuous conflict with the environmental constraints and their sessile nature demands a fine-tuned, well-designed defense mechanism that can cope with a multitude of biotic and abiotic assaults. Therefore, plants have developed innate immunity, R-gene-mediated resistance, and systemic acquired resistance to ensure their survival. Transcription factors (TFs) are among the most important genetic components for the regulation of gene expression and several other biological processes. They bind to specific sequences in the DNA called transcription factor binding sites (TFBSs) that are present in the regulatory regions of genes. Depending on the environmental conditions, TFs can either enhance or suppress transcriptional processes. In the last couple of decades, nitric oxide (NO) emerged as a crucial molecule for signaling and regulating biological processes. Here, we have overviewed the plant defense system, the role of TFs in mediating the defense response, and that how NO can manipulate transcriptional changes including direct post-translational modifications of TFs. We also propose that NO might regulate gene expression by regulating the recruitment of RNA polymerase during transcription.
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| 4. |
- Hussain, Adil, et al.
(author)
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CRISPR/Cas9-mediated gene editing in grain crops
- 2020
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In: Recent Advances in Grain Crops Research. - : IntechOpen. - 9781789854503 - 9781789854497 - 9781789856439 ; , s. 1-12
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Book chapter (other academic/artistic)abstract
- The development of reliable and efficient techniques for making precise targeted changes in the genome of living organisms has been a long-standing objective of researchers throughout the world. In plants, different methods, each with several different variations, have been developed for this purpose, though many of them are hampered either by providing only temporary modification of gene function or unpredictable off-target results. The recent discovery of clustered regularly interspaced short palindromic repeats (CRISPRs) and the CRISPR-associated 9 (Cas9) nucleases started a new era in genome editing. Basically, the CRISPR/Cas system is a natural immune response of prokaryotes to resist foreign genetic elements entering via plasmids and phages. Through this naturally occurring gene editing system, bacteria create DNA segments known as CRISPR arrays that allow them to "remember" foreign genetic material for protection against it and other similar sequences in the future. This system has now been adopted by researchers in laboratory to create a short guide RNA that binds to specific target sequences of DNA in eukaryotic genome, and the Cas9 enzyme cuts the DNA at the targeted location. Once cut, the cell's endogenous DNA repair machinery is used to add, delete, or replace pieces of genetic material. Though CRISPR/Cas9 technology has been recently developed, it has started to be regularly used for gene editing in plants as well as animals to good success. It has been proved as an efficient transgene-free technique. A simple search on PubMed (NCBI) shows that among all plants, 80 different studies published since 2013 involved CRISPR/Cas9-mediated genome editing in rice. Of these, 20, 13, and 24 papers have been published in 2019, 2018, and 2017, respectively. Furthermore, 20 different studies published since 2014 utilized CRISPR/Cas9 system for gene editing in wheat, where five of these studies were published in 2019 and seven were published in 2018. Genomes of other grain crops edited through this technique include maize, sorghum, barley, etc. This indicates the high utility of this technique for gene editing in grain crops. Here we emphasize on CRISPR/Cas9-mediated gene editing in rice, wheat, and maize.
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| 5. |
- Hussain, Adil, et al.
(author)
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Nitric oxide mediated transcriptome profiling reveals activation of multiple regulatory pathways in Arabidopsis thaliana
- 2016
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In: Frontiers in Plant Science. - : Frontiers Media S.A.. - 1664-462X. ; 7
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Journal article (peer-reviewed)abstract
- Imbalance between the accumulation and removal of nitric oxide and its derivatives is a challenge faced by all plants at the cellular level, and is especially important under stress conditions. Exposure of plants to various biotic and abiotic stresses causes rapid changes in cellular redox tone potentiated by the rise in reactive nitrogen species that serve as signaling molecules in mediating defensive responses. To understand mechanisms mediated by these signaling molecules, we performed a large-scale analysis of the Arabidopsis transcriptome induced by nitrosative stress. We generated an average of 84 and 91 million reads from three replicates each of control and 1 mM S-nitrosocysteine (CysNO)-infiltrated Arabidopsis leaf samples, respectively. After alignment, more than 95% of all reads successfully mapped to the reference and 32,535 genes and 55,682 transcripts were obtained. CysNO infiltration caused differential expression of 6436 genes (3448 up-regulated and 2988 down-regulated) and 6214 transcripts (3335 up-regulated and 2879 down-regulated) 6 h post-infiltration. These differentially expressed genes were found to be involved in key physiological processes, including plant defense against various biotic and abiotic stresses, hormone signaling, and other developmental processes. After quantile normalization of the FPKM values followed by student's T-test (P < 0.05) we identified 1165 DEGs (463 up-regulated and 702 down-regulated) with at least 2-folds change in expression after CysNO treatment. Expression patterns of selected genes involved in various biological pathways were verified using quantitative real-time PCR. This study provides comprehensive information about plant responses to nitrosative stress at transcript level and would prove helpful in understanding and incorporating mechanisms associated with nitrosative stress responses in plants.
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| 6. |
- Hussain, Adil, et al.
(author)
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Nitric oxide synthase in the plant kingdom
- 2021
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In: Nitric oxide in plant biology. - : Elsevier. - 9780128187975 ; , s. 43-52
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Book chapter (peer-reviewed)abstract
- After the discovery of nitric oxide (NO) as an important signaling molecule in plants, its involvement has been reported in several key physiological processes. At the cellular level, slight alterations in the quantity of NO or its various adducts, also known as reactive nitrogen intermediates (RNIs), have phenomenal implications. In plants this highly reactive, diatomic gaseous molecule regulates a plethora of physiological processes ranging from development, to reproduction, and defense against biotic and abiotic stresses. In animals, NO is produced enzymatically via the nitric oxide synthase (NOS) enzyme. However, after decades of research, it is now clear that in plants there is not one but several routes for NO production. Interestingly the discovery of a NOS enzyme in plants has remained an attractive topic of research for plant scientists over the years; the enzyme still remains elusive. In this chapter we briefly discuss the different pathways responsible for NO production in plants with special emphasis on the enzymatic production. We also discuss the NOS enzyme and its presence in lower and higher plants.
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| 7. |
- Imran, Qari Muhammad, et al.
(author)
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Abiotic stress in plants, stress perception to molecular response and role of biotechnological tools in stress resistance
- 2021
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In: Agronomy. - : MDPI. - 2073-4395. ; 11:8
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Journal article (peer-reviewed)abstract
- Plants, due to their sessile nature, face several environmental adversities. Abiotic stresses such as heat, cold, drought, heavy metals, and salinity are serious threats to plant production and yield. To cope with these stresses, plants have developed sophisticated mechanisms to avoid or resist stress conditions. A proper response to abiotic stress depends primarily on how plants perceive the stress signal, which in turn leads to initiation of signaling cascades and induction of resistance genes. New biotechnological tools such as RNA-seq and CRISPR-cas9 are quite useful in identifying target genes on a global scale, manipulating these genes to achieve tolerance, and helping breeders to develop stress-tolerant cultivars. In this review, we will briefly discuss the adverse effects of key abiotic stresses such as cold, heat, drought, and salinity. We will also discuss how plants sense various stresses and the importance of biotechnological tools in the development of stress-tolerant cultivars.
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| 8. |
- Imran, Qari Muhammad, et al.
(author)
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Nitric oxide responsive heavy metal-associated gene AtHMAD1 contributes to development and disease resistance in Arabidopsis thaliana
- 2016
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In: Frontiers in Plant Science. - : Frontiers Media S.A.. - 1664-462X. ; 7
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Journal article (peer-reviewed)abstract
- Exposure of plants to different biotic and abiotic stress condition instigates significant change in the cellular redox status; resulting in the elevation of reactive nitrogen species that play signaling role in mediating defense responses. Heavy metal associated (HMA) domain containing genes are required for spatio-temporal transportation of metal ions that bind with various enzymes and co-factors within the cell. To uncover the underlying mechanisms mediated by AtHMA genes, we identified 14 Arabidopsis HMA genes that were differentially expressed in response to nitrosative stress through RNA-seq analysis. Of those 14 genes, the expression of eight HMA genes was significantly increased, whereas that of six genes was significantly reduced. We further validated the RNA-seq results through quantitative real-time PCR analysis. Gene ontology analysis revealed the involvement of these genes in biological processes such as hemostasis and transport. The majority of these nitric oxide (NO)-responsive AtHMA gene products are carrier/transport proteins. AtHMAD1 (At1g51090) showed the highest fold change to S-nitrosocystein. We therefore, further investigated its role in oxidative and nitrosative mediated stress conditions and found that AtHMAD1 has antagonistic role in shoot and root growth. Characterization of AtHMAD1 through functional genomics showed that the knock out mutant athmad1 plants were resistant to virulent Pseudomonas syringae (DC3000) and showed early induction and high transcript accumulation of pathogenesis related gene. Furthermore, inoculation of athamd1 with avirulent strain of the same bacteria showed negative regulation of R-gene mediated resistance. These results were supported by hypersensitive cell death response and cell death induced electrolyte leakage. AtHMAD1 was also observed to negatively regulate systemic acquired resistance SAR as the KO mutant showed induction of SAR marker genes. Overall, these results imply that NO-responsive AtHMA domain containing genes may play an important role in plant development and immunity.
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| 9. |
- Imran, Qari Muhammad, et al.
(author)
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NO and ROS crosstalk and acquisition of abiotic stress tolerance
- 2021
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In: Nitric oxide in plant biology. - : Elsevier. - 9780128187975 ; , s. 477-491
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Book chapter (peer-reviewed)abstract
- Nitric oxide (NO) and H2O2, known as signaling molecules, particularly regulate various cellular processes under stress conditions. Abiotic stress, like other stresses, leads to the production of reactive oxygen and nitrogen species (ROS and RNS, respectively). The interaction or crosstalk between these two redox molecules is important for the regulation of cellular processes. Increasing evidence has suggested that NO transfers its bioactivity through posttranslational modifications, the major among them is S-nitrosation, the covalent attachment of an NO moiety to a cysteine thiol that can bring conformational changes in proteins and hence in their functions. S-nitrosation of the tripeptide glutathione (GSH) results in the formation of S-nitrosoglutathione (GSNO), which is a relatively stable reservoir of NO. The formation of GSNO, therefore, determines cellular redox status, crucial for normal metabolic activities, and is regulated by key enzyme GSNO reductase (GSNOR) in plants. Here, we overview the importance of H2O2 and NO as signaling molecules in plants and their roles in stress tolerance. We also discuss crosstalk between H2O2 and NO and its importance in abiotic stress tolerance, with examples of salt, cold, drought, metal, and heat tolerance. The accumulated data from the cited research has important implications for the improved productivity of many crop plants.
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| 10. |
- Imran, Qari Muhammad, et al.
(author)
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Transcriptome profile of NO-induced Arabidopsis transcription factor genes suggests their putative regulatory role in multiple biological processes
- 2018
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In: Scientific Reports. - : Nature Publishing Group. - 2045-2322. ; 8
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Journal article (peer-reviewed)abstract
- TFs are important proteins regulating plant responses during environmental stresses. These insults typically induce changes in cellular redox tone driven in part by promoting the production of reactive nitrogen species (RNS). The main source of these RNS is nitric oxide (NO), which serves as a signalling molecule, eliciting defence and resistance responses. To understand how these signalling molecules regulate key biological processes, we performed a large scale S-nitrosocysteine (CySNO)-mediated RNA-seq analysis. The DEGs were analysed to identify potential regulatory TFs. We found a total of 673 (up- and down-regulated) TFs representing a broad range of TF families. GO-enrichment and MapMan analysis suggests that more than 98% of TFs were mapped to the Arabidopsis thaliana genome and classified into pathways like hormone signalling, protein degradation, development, biotic and abiotic stress, etc. A functional analysis of three randomly selected TFs, DDF1, RAP2.6, and AtMYB48 identified a regulatory role in plant growth and immunity. Loss-of-function mutations within DDF1 and RAP2.6 showed compromised basal defence and effector triggered immunity, suggesting their positive role in two major plant defence systems. Together, these results imply an important data representing NO-responsive TFs that will help in exploring the core mechanisms involved in biological processes in plants.
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