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Bhuyan SJ, Kumar M, Ramrao Devde P, Rai AC, Mishra AK, Singh PK, Siddique KHM. Progress in gene editing tools, implications and success in plants: a review. Front Genome Ed 2023; 5:1272678. [PMID: 38144710 PMCID: PMC10744593 DOI: 10.3389/fgeed.2023.1272678] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Accepted: 11/13/2023] [Indexed: 12/26/2023] Open
Abstract
Genetic modifications are made through diverse mutagenesis techniques for crop improvement programs. Among these mutagenesis tools, the traditional methods involve chemical and radiation-induced mutagenesis, resulting in off-target and unintended mutations in the genome. However, recent advances have introduced site-directed nucleases (SDNs) for gene editing, significantly reducing off-target changes in the genome compared to induced mutagenesis and naturally occurring mutations in breeding populations. SDNs have revolutionized genetic engineering, enabling precise gene editing in recent decades. One widely used method, homology-directed repair (HDR), has been effective for accurate base substitution and gene alterations in some plant species. However, its application has been limited due to the inefficiency of HDR in plant cells and the prevalence of the error-prone repair pathway known as non-homologous end joining (NHEJ). The discovery of CRISPR-Cas has been a game-changer in this field. This system induces mutations by creating double-strand breaks (DSBs) in the genome and repairing them through associated repair pathways like NHEJ. As a result, the CRISPR-Cas system has been extensively used to transform plants for gene function analysis and to enhance desirable traits. Researchers have made significant progress in genetic engineering in recent years, particularly in understanding the CRISPR-Cas mechanism. This has led to various CRISPR-Cas variants, including CRISPR-Cas13, CRISPR interference, CRISPR activation, base editors, primes editors, and CRASPASE, a new CRISPR-Cas system for genetic engineering that cleaves proteins. Moreover, gene editing technologies like the prime editor and base editor approaches offer excellent opportunities for plant genome engineering. These cutting-edge tools have opened up new avenues for rapidly manipulating plant genomes. This review article provides a comprehensive overview of the current state of plant genetic engineering, focusing on recently developed tools for gene alteration and their potential applications in plant research.
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Affiliation(s)
- Suman Jyoti Bhuyan
- Department of Biotechnology, Mizoram University (A Central University), Pachhunga University College Campus, Aizawl, Mizoram, India
| | - Manoj Kumar
- Institute of Plant Sciences, Agricultural Research Organization, Volcani Center, Rishon LeZion, Israel
| | - Pandurang Ramrao Devde
- Department of Biotechnology, Mizoram University (A Central University), Pachhunga University College Campus, Aizawl, Mizoram, India
| | - Avinash Chandra Rai
- Institute of Plant Sciences, Agricultural Research Organization, Volcani Center, Rishon LeZion, Israel
| | | | - Prashant Kumar Singh
- Department of Biotechnology, Mizoram University (A Central University), Pachhunga University College Campus, Aizawl, Mizoram, India
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Gafni I, Rai AC, Halon E, Zviran T, Sisai I, Samach A, Irihimovitch V. Expression Profiling of Four Mango FT/TFL1-Encoding Genes under Different Fruit Load Conditions, and Their Involvement in Flowering Regulation. Plants 2022; 11:plants11182409. [PMID: 36145810 PMCID: PMC9506463 DOI: 10.3390/plants11182409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 09/05/2022] [Accepted: 09/14/2022] [Indexed: 11/16/2022]
Abstract
Plant flowering is antagonistically modulated by similar FLOWERING LOCUS T (FT) and TERMINAL FLOWER 1 (TFL1) proteins. In mango (Mangifera indica L.), flowering is induced by cold temperatures, unless the tree is juvenile or the adult tree had a high fruit load (HFL) in the summer. Here, we studied the effects of juvenility and fruit load on the expression of four MiFT/TFL1 genes cloned from the mango ‘Shelly’ cultivar. Ectopic expression of MiFT1 in Arabidopsis resulted in early flowering, whereas over-expression of MiFT2 and the two cloned MiTFL1 genes repressed flowering. Moreover, juvenility was positively correlated with higher transcript levels of MiFT2 and both MiTFL1s. In trees with a low fruit load, leaf MiFT1 expression increased in winter, whereas HFL delayed its upregulation. MiFT2 expression was upregulated in both leaves and buds under both fruit load conditions. Downregulation of both MITFL1s in buds was associated with a decrease in regional temperatures under both conditions; nevertheless, HFL delayed the decrease in their accumulation. Our results suggest that cold temperature has opposite effects on the expression of MiFT1 and the MiTFL1s, thereby inducing flowering, whereas HFL represses flowering by both suppressing MiFT1 upregulation and delaying MiTFL1s downregulation. The apparent flowering-inhibitory functions of MiFT2 are discussed.
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Affiliation(s)
- Itamar Gafni
- Institute of Plant Sciences, Agricultural Research Organization (ARO), The Volcani Center, Rishon LeZion 7528809, Israel
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot 76100, Israel
| | - Avinash Chandra Rai
- Institute of Plant Sciences, Agricultural Research Organization (ARO), The Volcani Center, Rishon LeZion 7528809, Israel
| | - Eyal Halon
- Institute of Plant Sciences, Agricultural Research Organization (ARO), The Volcani Center, Rishon LeZion 7528809, Israel
| | - Tali Zviran
- Institute of Plant Sciences, Agricultural Research Organization (ARO), The Volcani Center, Rishon LeZion 7528809, Israel
| | - Isaac Sisai
- Institute of Plant Sciences, Agricultural Research Organization (ARO), The Volcani Center, Rishon LeZion 7528809, Israel
| | - Alon Samach
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot 76100, Israel
| | - Vered Irihimovitch
- Institute of Plant Sciences, Agricultural Research Organization (ARO), The Volcani Center, Rishon LeZion 7528809, Israel
- Correspondence: ; Tel.: +972-3-9683965; Fax: +972-3-9669583
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Rai AC, Rai A, Shah K, Singh M. Engineered BcZAT12 gene mitigates salt stress in tomato seedlings. Physiol Mol Biol Plants 2021; 27:535-541. [PMID: 33854282 PMCID: PMC7981348 DOI: 10.1007/s12298-021-00948-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2020] [Revised: 01/21/2021] [Accepted: 02/09/2021] [Indexed: 05/14/2023]
Abstract
In salt-prone areas, plant growth and productivity is adversely affected. In the present study, the ZT1-ZT6 transgenic tomato lines having BcZAT12 gene under the regulatory control of the stress inducible Bclea1 promoter were exposed to three salinity levels (50, 100 and 200 mM) at the four leaf stage for 10 days. The transgenic lines showed improved growth in stem height, leaf area, root length and shoot length under saline conditions, as compared to control. Moreover, ZT1 and ZT5 lines showed lower electrolyte leakage and decreased hydrogen peroxide formation, in combination with elevated relative water content, proline and chlorophyll levels. The enzyme activity of catalase was also enhanced in ZT1 and ZT5. These results poses the present lines as an attractive alternative for tomato cultivation in salinity-affected areas.
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Affiliation(s)
- Avinash Chandra Rai
- Institute of Plant Sciences, The Volcani Center, Agricultural Research Organization, 50250 Bet-Dagan, Israel
- Department of Crop Improvement, Indian Institute of Vegetable Research, Shahanshahpur Jakhini, Varanasi, 221 305 U.P. India
| | - Ashutosh Rai
- Department of Crop Improvement, Indian Institute of Vegetable Research, Shahanshahpur Jakhini, Varanasi, 221 305 U.P. India
| | - Kavita Shah
- Institute of Environment and Sustainable Development, Banaras Hindu University, Varanasi, 221 005 U.P. India
| | - Major Singh
- Department of Crop Improvement, Indian Institute of Vegetable Research, Shahanshahpur Jakhini, Varanasi, 221 305 U.P. India
- Directorate of Onion and Garlic Research, Rajgurunagar, Pune, Maharashtra 410505 India
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Singh S, Khemariya P, Rai A, Rai AC, Koley TK, Singh B. Carnauba wax-based edible coating enhances shelf-life and retain quality of eggplant ( Solanum melongena ) fruits. Lebensm Wiss Technol 2016. [DOI: 10.1016/j.lwt.2016.08.004] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Rai AC, Guo B, Lin CH, Zhang J, Pei J, Chen Q. Ozone reaction with clothing and its initiated VOC emissions in an environmental chamber. Indoor Air 2014; 24:49-58. [PMID: 23841649 DOI: 10.1111/ina.12058] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2013] [Accepted: 06/28/2013] [Indexed: 05/03/2023]
Abstract
Human health is adversely affected by ozone and the volatile organic compounds (VOCs) produced from its reactions in the indoor environment. Hence, it is important to characterize the ozone-initiated reactive chemistry under indoor conditions and study the influence of different factors on these reactions. This investigation studied the ozone reactions with clothing through a series of experiments conducted in an environmental chamber under various conditions. The study found that the ozone reactions with a soiled (human-worn) T-shirt consumed ozone and generated VOCs. The ozone removal rate and deposition velocity for the T-shirt increased with the increasing soiling level and air change rate, decreased at high ozone concentrations, and were relatively unaffected by the humidity. The deposition velocity for the soiled T-shirt ranged from 0.15 to 0.29 cm/s. The ozone-initiated VOC emissions included C6-C10 straight-chain saturated aldehydes, acetone, and 4-OPA (4-oxopentanal). The VOC emissions were generally higher at higher ozone, humidity, soiling of T-shirt, and air change rate. The total molar yield was approximately 0.5 in most cases, which means that for every two moles of ozone removed by the T-shirt surface, one mole of VOCs was produced.
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Affiliation(s)
- A C Rai
- School of Mechanical Engineering, Purdue University, West Lafayette, IN, USA
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Shah K, Singh M, Rai AC. Effect of heat-shock induced oxidative stress is suppressed in BcZAT12 expressing drought tolerant tomato. Phytochemistry 2013; 95:109-117. [PMID: 23962802 DOI: 10.1016/j.phytochem.2013.07.026] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2013] [Revised: 06/03/2013] [Accepted: 07/26/2013] [Indexed: 05/27/2023]
Abstract
The transcription factor ZAT12 is a member of stress-responsive C2H2 type zinc finger protein (ZFP) reported to control the expression of stress-activated genes mediated via ROS in plants. BcZAT12-transformed tomato cv. H-86, var. Kashi vishesh (lines ZT1-ZT6) over-expressing the gene product is demonstrated herein to be tolerant to heat-shock (HS)-induced oxidative stress. Results reveal that the relative expression of ZAT12 as well as heat induced Hsp17.4 and Hsp21 gene transcripts increased in transgenic upon exposure to HS. The transformed tomato lines ZT1 and ZT5 had significantly lowered free radical formation, improved electrolyte leakage, relative water content and chlorophyll levels with an enhanced activities of antioxidant enzymes viz. superoxide dismutase, catalase, ascorbate peroxidase and glutathione reductase when exposed to HS. HS-induced oxidative stress by over-expression of the BcZAT12 gene transcripts in tomato as well as by largely enhancing the ROS-scavenging capacity and up regulation of Hsp transcripts. This enables the transgenic tomato plants to acquire a greater ability to counteract HS-induced oxidative stress, being endowed with more reduced antioxidant pools. The use of these HS-tolerant tomato lines could possibly be used for tomato cultivation in the areas affected by sudden temperature changes.
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Affiliation(s)
- Kavita Shah
- Institute of Environment and Sustainable Development, Banaras Hindu University, Varanasi 221005, U.P., India.
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Rai AC, Singh M, Shah K. Engineering drought tolerant tomato plants over-expressing BcZAT12 gene encoding a C₂H₂ zinc finger transcription factor. Phytochemistry 2013; 85:44-50. [PMID: 23079765 DOI: 10.1016/j.phytochem.2012.09.007] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2012] [Revised: 09/15/2012] [Accepted: 09/18/2012] [Indexed: 05/21/2023]
Abstract
Efficient genetic transformation of cotyledonary explants of tomato (Solanum lycopersicum, cv. H-86, Kashi vishesh) was obtained. Disarmed Agrobacterium tumifaciens strain GV 3101 was used in conjugation with binary vector pBinAR containing a construct consisting of the coding sequence of the BcZAT12 gene under the regulatory control of the stress inducible Bclea1a promoter. ZAT12 encodes a C₂H₂ zinc finger protein which confers multiple abiotic stress tolerance to plants. Integration of ZAT12 gene into nuclear genome of individual kanamycin resistant transformed T₀ tomato lines was confirmed by Southern blot hybridization with segregation analysis of T(1) plants showing Mendelian inheritance of the transgene. Expression of ZAT12 in drought-stressed transformed tomato lines was verified in T₂ generation plants using RT-PCR. Of the six transformed tomato lines (ZT1-ZT6) the transformants ZT1 and ZT5 showed maximum expression of BcZAT12 gene transcripts when exposed to 7 days drought stress. Analysis of relative water content (RWC), electrolyte leakage (EL), chlorophyll colour index (CCI), H₂O₂ level and catalase activity suggested that tomato BcZAT12 transformants ZT1 and ZT5 have significantly increased levels of drought tolerance. These results suggest that BcZAT12 transformed tomato cv. H-86 has real potential for molecular breeding programs aimed at augmenting yield of tomato in regions affected with drought stress.
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Affiliation(s)
- Avinash Chandra Rai
- Department of Biochemistry, Faculty of Science, Banaras Hindu University, Varanasi, UP 221005, India.
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Chandra Rai A, Singh M, Shah K. Effect of water withdrawal on formation of free radical, proline accumulation and activities of antioxidant enzymes in ZAT12-transformed transgenic tomato plants. Plant Physiol Biochem 2012; 61:108-14. [PMID: 23127521 DOI: 10.1016/j.plaphy.2012.09.010] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2012] [Accepted: 09/14/2012] [Indexed: 05/20/2023]
Abstract
Water stress often leads to the accumulation of reactive oxygen species (ROS) and their excessive production alters the activities of enzymes involved in their removal. ZAT12 is a member of stress-responsive C(2)H(2) type Zinc Finger Protein (ZFP) reported to control the expression of several stress-activated genes in plants through ROS signaling. The ZAT12-transformed tomato lines (cv. H-86 variety Kashi Vishesh) when subjected to water withdrawal for 7, 14 and 21 days revealed significant and consistent changes in activities of enzymes SOD, CAT, APX, GR and POD paralleled with an increased proline levels. Unlike that in wild-type tomato, the leaf superoxide anion and hydrogen peroxide concentrations in the transformed tomato plants did not alter much, suggesting a well regulated formation of free radicals suppressing oxidative stress in the latter. Results suggest BcZAT12-transformed tomato lines ZT1, ZT2 and ZT6 to be better adapted to drought stress tolerance by accumulation of osmolyte proline and increased antioxidant response triggered by the ZAT12 gene. Therefore, the ZAT12-transformed tomato cv. H-86 lines will prove useful for higher yield of tomato crop in regions affected with severe drought stress.
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Affiliation(s)
- Avinash Chandra Rai
- Division of Vegetable Improvement, Indian Institute of Vegetable Research, Shahanshahpur, Jhakhini, Varanasi, U.P. 221305, India
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