Genomics and transcriptomics to protect rice (Oryza sativa. L.) from abiotic stressors: -pathways to achieving zero hunger

Ahmad, Masood

doi:10.3389/fpls.2022.1002596

Cited by 8 publications

(20 citation statements)

References 200 publications

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“…In the upcoming years, many more are probably going to be put on the market. Due to the higher proportion of oleic and lower proportion of linolenic fatty acids in high oleic soybeans, the oil has a higher thermal and oxidative stability ( Nonaka et al., 2017 ; Metje-Sprink et al., 2018 ; Ahmad M., 2022 ).…”

Section: Challenges In 21st-century Food Systemsmentioning

confidence: 99%

“…Zinc-finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs), and the CRISPR/Cas system are the three primary categories of genome-editing tools. By causing DNA double-strand breaks, which promote error-prone non-homologous end joining (NHEJ) or homology-directed repair (HDR) at specified genomic loci, ZFNs and TALENs have been used to carry out a variety of genetic changes ( Li et al., 2011 ; Miller et al., 2011 ; Jinek et al., 2012 ; Li et al., 2012 ; Gaj et al., 2013 ; Ahmad M., 2022 ). The DNA cleavage domain of the restriction enzyme FokI and zinc-finger-based DNA recognition modules make up the ZFN family of targeted drugs ( Podevin et al., 2013 ; Pinto-Carbó et al., 2016 ; Verhaegen and De Smet, 2017 ; Ramkumar et al., 2022 ).…”

Section: Why Crispr-cas Ge Better Than Zfns and Talens Genome Editing?mentioning

confidence: 99%

“…Before joining together to cling to particular DNA sequences, each zinc finger locates and bonds to a nucleotide triplet. However, it took nine years from the discovery of ZFNs to the first ZFN-based plant genome editing due to the challenge of developing ZFNs with high sequence affinity and high off-target efficiency ( Zetsche et al., 2015 ; Kim et al., 2016 ; Komor et al., 2016 ; Anzalone et al., 2019 ; Zhang et al., 2019 ; Lin et al., 2020 ; Ahmad M., 2022 ). The transcriptional activator-like effector (TALE) repeats are combined with the FokI restriction enzyme to produce TALENs ( Hua et al., 2022 ; Kumar et al., 2022 ; Randall et al., 2022 ).…”

Section: Why Crispr-cas Ge Better Than Zfns and Talens Genome Editing?mentioning

confidence: 99%

“…However, genome-editing technologies, particularly the CRISPR-(Cas-9) systems, are biotechnological tools for precise genetic change of crops that can cut breeding time while increasing diversity. This article provides a thorough explanation of the Cas9-CRISPR network with an emphasis on how it can be utilized to quickly create crop and plant varieties that are resistant to salinity, drought, and temperature stressors such as wheat, rice, tomato, soybean, oilseeds, potato, and maize ( Laity et al., 2001 ; Puchta, 2005 ; Urnov et al., 2005 ; Scully et al., 2019 ; Rönspies et al., 2021 ; Ahmad M., 2022 ); To develop novel plant types that are resistant to abiotic stress or to apply to other underutilized crops for future food security, which is a major challenge up to 2050 in developing countries ( Figure 1 ) the aforementioned crops contain crucial information on plant genome editing targets.…”

Section: Introductionmentioning

confidence: 99%

“…A growing number of fields, including plant science and crop breeding, characterization of gene function, and crop enhancement are turning to genetic modification as a cutting-edge and precise strategy of genetic modification. This includes editing to change a specific gene inside an organism’s genome ( Anzalone et al., 2019 ; Scully et al., 2019 ; Yu et al., 2019 ; Hahn et al., 2020 ; Menz et al., 2020 ; Schmidt et al., 2020b ; Ahmad M., 2022 ).…”

Section: Introductionmentioning

confidence: 99%

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Plant breeding advancements with “CRISPR-Cas” genome editing technologies will assist future food security

Ahmad

2023

Front. Plant Sci.

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Genome editing techniques are being used to modify plant breeding, which might increase food production sustainably by 2050. A product made feasible by genome editing is becoming better known, because of looser regulation and widespread acceptance. The world’s population and food supply would never have increased proportionally under current farming practices. The development of plants and food production has been greatly impacted by global warming and climate change. Therefore, minimizing these effects is crucial for agricultural production that is sustainable. Crops are becoming more resilient to abiotic stress because of sophisticated agricultural practices and a better understanding of the abiotic stress response mechanism. Both conventional and molecular breeding techniques have been used to create viable crop types both processes are time-consuming. Recently, plant breeders have shown an interest in genome editing approaches for genetic manipulation that use clustered regularly interspaced short palindromic repeats (CRISPR/Cas9). To ensure the security of the food supply in the future, plant kinds with desired traits must be developed. A completely new era in plant breeding has begun because of the revolution in genome editing techniques based on the CRISPR/CRISPR-associated nuclease (Cas9) systems. All plants may effectively target a particular gene or group of loci using Cas9 and single-guide RNA (sgRNA). CRISPR/Cas9 can thereby save time and labor compared to conventional breeding methods. An easy, quick, and efficient method for directly altering the genetic sequences in cells is with the CRISPR and Cas9 systems. The CRISPR-Cas9 system, which was developed from components of the earliest known bacterial immune system, allows for targeted gene breakage and gene editing in a variety of cells/RNA sequences to guide endonuclease cleavage specificity in the CRISPR-Cas9 system. Editing can be directed to practically any genomic site by altering the guide RNA (gRNA) sequence and delivering it to a target cell along with the Cas9 endonuclease. We summarize recent CRISPR/Cas9 plant research findings, investigate potential applications in plant breeding, and make predictions about likely future breakthroughs and approaches to food security through 2050.

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Section: Challenges In 21st-century Food Systemsmentioning

confidence: 99%

Section: Why Crispr-cas Ge Better Than Zfns and Talens Genome Editing?mentioning

confidence: 99%

Section: Why Crispr-cas Ge Better Than Zfns and Talens Genome Editing?mentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 3 more Smart Citations

Plant breeding advancements with “CRISPR-Cas” genome editing technologies will assist future food security

Ahmad

2023

Front. Plant Sci.

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Identification and characterization of abiotic stress-tolerant genes in rice (Oryza sativa L.): a computational approach

Kadam,

Choudhary,

Cheulkar

et al. 2024

J Plant Dis Prot

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Integration of mRNA and miRNA analysis reveals the molecular mechanisms of sugar beet (Beta vulgaris L.) response to salt stress

Zhang,

Wang,

Chen

et al. 2023

Sci Rep

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The continuous increase of saline-alkali areas worldwide has led to the emergence of saline-alkali conditions, which are the primary abiotic stress or hindering the growth of plants. Beet is among the main sources of sugar, and its yield and sugar content are notably affected by saline-alkali stress. Despite sugar beet being known as a salt-tolerant crop, there are few studies on the mechanisms underlying its salt tolerance, and previous studies have mainly delineated the crop’s response to stress induced by NaCl. Recently, advancements in miRNA-mRNA network analysis have led to an increased understanding of how plants, including sugar beet, respond to stress. In this study, seedlings of beet variety "N98122" were grown in the laboratory using hydroponics culture and were exposed to salt stress at 40 days of growth. According to the phenotypic adaptation of the seedlings' leaves from a state of turgidity to wilting and then back to turgidity before and after exposure, 18 different time points were selected to collect samples for analysis. Subsequently, based on the data of real-time quantitative PCR (qRT-PCR) of salt-responsive genes, the samples collected at the 0, 2.5, 7.5, and 16 h time points were subjected to further analysis with experimental materials. Next, mRNA-seq data led to the identification of 8455 differentially expressed mRNAs (DEMs) under exposure to salt stress. In addition, miRNA-seq based investigation retrieved 3558 miRNAs under exposure to salt stress, encompassing 887 known miRNAs belonging to 783 families and 2,671 novel miRNAs. With the integrated analysis of miRNA-mRNA network, 57 miRNA-target gene pairs were obtained, consisting of 55 DEMIs and 57 DEMs. Afterwards, we determined the pivotal involvement of aldh2b7, thic, and δ-oat genes in the response of sugar beet to the effect of salt stress. Subsequently, we identified the miRNAs novel-m035-5p and novel-m0365-5p regulating the aldh gene and miRNA novel-m0979-3p regulating the thic gene. The findings of miRNA and mRNA expression were validated by qRT-PCR.

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Genomics and transcriptomics to protect rice (Oryza sativa. L.) from abiotic stressors: -pathways to achieving zero hunger

Cited by 8 publications

References 200 publications

Plant breeding advancements with “CRISPR-Cas” genome editing technologies will assist future food security

Plant breeding advancements with “CRISPR-Cas” genome editing technologies will assist future food security

Identification and characterization of abiotic stress-tolerant genes in rice (Oryza sativa L.): a computational approach

Integration of mRNA and miRNA analysis reveals the molecular mechanisms of sugar beet (Beta vulgaris L.) response to salt stress

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