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Gondalia N, Quiroz LF, Lai L, Singh AK, Khan M, Brychkova G, McKeown PC, Chatterjee M, Spillane C. Harnessing promoter elements to enhance gene editing in plants: perspectives and advances. PLANT BIOTECHNOLOGY JOURNAL 2025; 23:1375-1395. [PMID: 40013512 PMCID: PMC12018835 DOI: 10.1111/pbi.14533] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2024] [Revised: 10/20/2024] [Accepted: 11/16/2024] [Indexed: 02/28/2025]
Abstract
Genome-edited plants, endowed with climate-smart traits, have been promoted as tools for strengthening resilience against climate change. Successful plant gene editing (GE) requires precise regulation of the GE machinery, a process controlled by the promoters, which drives its transcription through interactions with transcription factors (TFs) and RNA polymerase. While constitutive promoters are extensively used in GE constructs, their limitations highlight the need for alternative approaches. This review emphasizes the promise of tissue/organ specific as well as inducible promoters, which enable targeted GE in a spatiotemporal manner with no effects on other tissues. Advances in synthetic biology have paved the way for the creation of synthetic promoters, offering refined control over gene expression and augmenting the potential of plant GE. The integration of these novel promoters with synthetic systems presents significant opportunities for precise and conditional genome editing. Moreover, the advent of bioinformatic tools and artificial intelligence is revolutionizing the characterization of regulatory elements, enhancing our understanding of their roles in plants. Thus, this review provides novel insights into the strategic use of promoters and promoter editing to enhance the precision, efficiency and specificity of plant GE, setting the stage for innovative crop improvement strategies.
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Affiliation(s)
- Nikita Gondalia
- Agriculture, Food Systems and Bioeconomy Research Centre, Ryan InstituteUniversity of GalwayGalwayIreland
| | - Luis Felipe Quiroz
- Agriculture, Food Systems and Bioeconomy Research Centre, Ryan InstituteUniversity of GalwayGalwayIreland
| | - Linyi Lai
- Agriculture, Food Systems and Bioeconomy Research Centre, Ryan InstituteUniversity of GalwayGalwayIreland
| | - Avinash Kumar Singh
- Agriculture, Food Systems and Bioeconomy Research Centre, Ryan InstituteUniversity of GalwayGalwayIreland
| | - Moman Khan
- Agriculture, Food Systems and Bioeconomy Research Centre, Ryan InstituteUniversity of GalwayGalwayIreland
| | - Galina Brychkova
- Agriculture, Food Systems and Bioeconomy Research Centre, Ryan InstituteUniversity of GalwayGalwayIreland
| | - Peter C. McKeown
- Agriculture, Food Systems and Bioeconomy Research Centre, Ryan InstituteUniversity of GalwayGalwayIreland
| | - Manash Chatterjee
- Agriculture, Food Systems and Bioeconomy Research Centre, Ryan InstituteUniversity of GalwayGalwayIreland
- Viridian Seeds Ltd.CambridgeUK
| | - Charles Spillane
- Agriculture, Food Systems and Bioeconomy Research Centre, Ryan InstituteUniversity of GalwayGalwayIreland
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Li F, Xue M, Guo D, Zhu L, Li Y, Xie L. A Truncated Endogenous U6 Promoter Enables High-Efficiency CRISPR Editing in Flax ( Linum usitatissimum L.). PLANTS (BASEL, SWITZERLAND) 2025; 14:1142. [PMID: 40219210 PMCID: PMC11991013 DOI: 10.3390/plants14071142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2025] [Revised: 03/28/2025] [Accepted: 04/04/2025] [Indexed: 04/14/2025]
Abstract
Functional U6 promoters are widely utilized in CRISPR gene editing systems for crops. The identification of endogenous U6 promoter activity and the establishment of CRISPR/Cas9 gene editing systems in various crops can enhance the efficiency and accuracy of gene editing in molecular breeding. In this study, four U6 snRNAs were identified in the genome of the oil flax (Linum usitatissimum L.) cultivar Longya 10, which exhibit high homology with the promoter regions of Arabidopsis thaliana U6 snRNA. We cloned and constructed fusion expression vectors with U6 promoter-driven dual-luciferase reporter genes. Transient transformation of flax and Nicotiana benthamiana was performed to measure the relative activity of dual luciferase. The U6-4 on chromosome 14 showed the highest transcriptional activity. Truncations of varying lengths from the 5' end of this promoter were tested, revealing that a 342 bp U6 promoter fragment possesses high transcriptional activity and an optimal length. Subsequently, we constructed a CRISPR/Cas9 gene editing vector with LuU6-5P/AtU6-P driving LusPDS sgRNA. Agrobacterium-mediated infection of flax hypocotyls yielded transgenic albino flax shoots. DNA from these shoots was used as a template to amplify LusPDS fragments, which were then sequenced. Sequencing analysis revealed that CRISPR/Cas9 vectors using Lu14U6-4-5P achieved higher editing frequencies at LusPDS compared to AtU6-P-driven systems.
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Affiliation(s)
- Feifei Li
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumqi 830046, China; (F.L.); (M.X.); (D.G.); (L.Z.); (Y.L.)
| | - Min Xue
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumqi 830046, China; (F.L.); (M.X.); (D.G.); (L.Z.); (Y.L.)
| | - Dongliang Guo
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumqi 830046, China; (F.L.); (M.X.); (D.G.); (L.Z.); (Y.L.)
| | - Leilei Zhu
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumqi 830046, China; (F.L.); (M.X.); (D.G.); (L.Z.); (Y.L.)
| | - Yuandong Li
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumqi 830046, China; (F.L.); (M.X.); (D.G.); (L.Z.); (Y.L.)
| | - Liqiong Xie
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumqi 830046, China; (F.L.); (M.X.); (D.G.); (L.Z.); (Y.L.)
- College of Smart Agriculture, Xinjiang University, Urumqi 830046, China
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Garcia-Oliveira AL, Ortiz R, Sarsu F, Rasmussen SK, Agre P, Asfaw A, Kante M, Chander S. The importance of genotyping within the climate-smart plant breeding value chain - integrative tools for genetic enhancement programs. FRONTIERS IN PLANT SCIENCE 2025; 15:1518123. [PMID: 39980758 PMCID: PMC11839310 DOI: 10.3389/fpls.2024.1518123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/29/2024] [Accepted: 11/25/2024] [Indexed: 02/22/2025]
Abstract
The challenges faced by today's agronomists, plant breeders, and their managers encompass adapting sustainably to climate variability while working with limited budgets. Besides, managers are dealing with a multitude of issues with different organizations working on similar initiatives and projects, leading to a lack of a sustainable impact on smallholder farmers. To transform the current food systems as a more sustainable and resilient model efficient solutions are needed to deliver and convey results. Challenges such as logistics, labour, infrastructure, and equity, must be addressed alongside adapting to increasingly unstable climate conditions which affect the life cycle of transboundary pathogens and pests. In this context, transforming food systems go far beyond just farmers and plant breeders and it requires substantial contributions from industry, global finances, transportation, energy, education, and country developmental sectors including legislators. As a result, a holistic approach is essential for achieving sustainable and resilient food systems to sustain a global population anticipated to reach 9.7 billion by 2050 and 11.2 billion by 2100. As of 2021, nearly 193 million individuals were affected by food insecurity, 40 million more than in 2020. Meanwhile, the digital world is rapidly advancing with the digital economy estimated at about 20% of the global gross domestic product, suggesting that digital technologies are increasingly accessible even in areas affected by food insecurity. Leveraging these technologies can facilitate the development of climate-smart cultivars that adapt effectively to climate variation, meet consumer preferences, and address human and livestock nutritional needs. Most economically important traits in crops are controlled by multiple loci often with recessive alleles. Considering particularly Africa, this continent has several agro-climatic zones, hence crops need to be adapted to these. Therefore, targeting specific loci using modern tools offers a precise and efficient approach. This review article aims to address how these new technologies can provide a better support to smallholder farmers.
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Affiliation(s)
- Ana Luísa Garcia-Oliveira
- Genetic Resources Program, Alliance Bioversity International and International Center for Tropical Agriculture (CIAT), Cali, Colombia
| | - Rodomiro Ortiz
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Alnarp, Sweden
| | - Fatma Sarsu
- Plant Breeding and Genetics Section, Joint FAO/IAEA Center, International Atomic Energy Agency, Vienna, Austria
| | | | - Paterne Agre
- Yam Breeding Unit, International Institute of Tropical Agriculture, Ibadan, Nigeria
| | - Asrat Asfaw
- Yam Breeding Unit, International Institute of Tropical Agriculture, Ibadan, Nigeria
| | - Moctar Kante
- Genetics, Genomics, and Crop Improvement Division, International Potato Center, Lima, Peru
| | - Subhash Chander
- Oilseeds Section, Department of Genetics & Plant Breeding, CCS Haryana Agricultural University, Hisar, India
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Zhou L, Zeng X, Yang Y, Li R, Zhao Z. Applications and Prospects of CRISPR/Cas9 Technology in the Breeding of Major Tropical Crops. PLANTS (BASEL, SWITZERLAND) 2024; 13:3388. [PMID: 39683180 DOI: 10.3390/plants13233388] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2024] [Revised: 11/27/2024] [Accepted: 11/29/2024] [Indexed: 12/18/2024]
Abstract
China is a major producer of tropical crops globally, boasting rich varieties and diverse functions. Tropical crops account for two-thirds of the plant species in this country. Many crops and their products, such as oil palm, rubber, banana, sugarcane, cassava, and papaya are well known to people. Most of these products are irreplaceable and possess special functions. They not only supply important raw materials for people's daily life and for industrial and agricultural production but also contribute to the economic growth in the tropical and subtropical regions of China. However, the modern molecular breeding of these crops is severely hampered by their biological characteristics and genetic complexity. Issues such as polyploidy, heterozygosity, vegetative propagation, long juvenile periods, and large plant sizes result in time consuming, low efficiency, and slow progress in conventional breeding of the major tropical crops. The development of genome-editing technologies has brought a new way in tropical crops breeding. As an emerging gene-editing technology, the CRISPR-Cas9 system has been widely used in plants, adopted for its higher targeting efficiency, versatility, and ease of usage. This approach has been applied in oil palm, rubber, banana, sugarcane, cassava, and papaya. This review summarized the delivery patterns, mutation detection, and application of the CRISPR-Cas9 system in tropical crop breeding, discussed the existing problems, and addressed prospects for future applications in this field, providing references to relevant studies.
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Affiliation(s)
- Lixia Zhou
- National Key Laboratory for Tropical Crop Breeding, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
- Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang 571339, China
| | - Xianhai Zeng
- National Key Laboratory for Tropical Crop Breeding, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
- Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang 571339, China
| | - Yaodong Yang
- National Key Laboratory for Tropical Crop Breeding, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
- Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang 571339, China
| | - Rui Li
- National Key Laboratory for Tropical Crop Breeding, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
- Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang 571339, China
| | - Zhihao Zhao
- National Key Laboratory for Tropical Crop Breeding, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
- Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
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Masani MYA, Norfaezah J, Bahariah B, Fizree MDPMAA, Sulaiman WNSW, Shaharuddin NA, Rasid OA, Parveez GKA. Towards DNA-free CRISPR/Cas9 genome editing for sustainable oil palm improvement. 3 Biotech 2024; 14:166. [PMID: 38817736 PMCID: PMC11133284 DOI: 10.1007/s13205-024-04010-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Accepted: 05/18/2024] [Indexed: 06/01/2024] Open
Abstract
The CRISPR/Cas9 genome editing system has been in the spotlight compared to programmable nucleases such as ZFNs and TALENs due to its simplicity, versatility, and high efficiency. CRISPR/Cas9 has revolutionized plant genetic engineering and is broadly used to edit various plants' genomes, including those transformation-recalcitrant species such as oil palm. This review will comprehensively present the CRISPR-Cas9 system's brief history and underlying mechanisms. We then highlighted the establishment of the CRISPR/Cas9 system in plants with an emphasis on the strategies of highly efficient guide RNA design, the establishment of various CRISPR/Cas9 vector systems, approaches of multiplex editing, methods of transformation for stable and transient techniques, available methods for detecting and analyzing mutations, which have been applied and could be adopted for CRISPR/Cas9 genome editing in oil palm. In addition, we also provide insight into the strategy of DNA-free genome editing and its potential application in oil palm.
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Affiliation(s)
- Mat Yunus Abdul Masani
- Malaysian Palm Oil Board (MPOB), 6, Persiaran Institusi, Bandar Baru Bangi, 43000 Kajang, Selangor Malaysia
| | - Jamaludin Norfaezah
- Malaysian Palm Oil Board (MPOB), 6, Persiaran Institusi, Bandar Baru Bangi, 43000 Kajang, Selangor Malaysia
| | - Bohari Bahariah
- Malaysian Palm Oil Board (MPOB), 6, Persiaran Institusi, Bandar Baru Bangi, 43000 Kajang, Selangor Malaysia
| | | | | | - Noor Azmi Shaharuddin
- Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, UPM, 43400 Serdang, Malaysia
| | - Omar Abdul Rasid
- Malaysian Palm Oil Board (MPOB), 6, Persiaran Institusi, Bandar Baru Bangi, 43000 Kajang, Selangor Malaysia
| | - Ghulam Kadir Ahmad Parveez
- Malaysian Palm Oil Board (MPOB), 6, Persiaran Institusi, Bandar Baru Bangi, 43000 Kajang, Selangor Malaysia
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Kharbikar L, Konwarh R, Chakraborty M, Nandanwar S, Marathe A, Yele Y, Ghosh PK, Sanan-Mishra N, Singh AP. 3Bs of CRISPR-Cas mediated genome editing in plants: exploring the basics, bioinformatics and biosafety landscape. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2023; 29:1825-1850. [PMID: 38222286 PMCID: PMC10784264 DOI: 10.1007/s12298-023-01397-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Revised: 11/21/2023] [Accepted: 11/22/2023] [Indexed: 01/16/2024]
Abstract
The recent thrust in research has projected the type II clustered regularly interspaced short palindromic repeats and associated protein 9 (CRISPR-Cas9) system as an avant-garde plant genome editing tool. It facilitates the induction of site-specific double-stranded DNA cleavage by the RNA-guided DNA endonuclease (RGEN), Cas9. Elimination, addition, or alteration of sections in DNA sequence besides the creation of a knockout genotype (CRISPRko) is aided by the CRISPR-Cas9 system in its wild form (wtCas9). The inactivation of the nuclease domain generates a dead Cas9 (dCas9), which is capable of targeting genomic DNA without scissoring it. The dCas9 system can be engineered by fusing it with different effectors to facilitate transcriptional activation (CRISPRa) and transcriptional interference (CRISPRi). CRISPR-Cas thus holds tremendous prospects as a genome-manipulating stratagem for a wide gamut of crops. In this article, we present a brief on the fundamentals and the general workflow of the CRISPR-Cas system followed by an overview of the prospects of bioinformatics in propelling CRISPR-Cas research with a special thrust on the available databases and algorithms/web-accessible applications that have aided in increasing the usage and efficiency of editing. The article also provides an update on the current regulatory landscape in different countries on the CRISPR-Cas edited plants to emphasize the far-reaching impact of the genomic editing technology. Supplementary Information The online version contains supplementary material available at 10.1007/s12298-023-01397-3.
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Affiliation(s)
- Lalit Kharbikar
- ICAR - National Institute of Biotic Stress Management (NIBSM), Raipur, India
- International Centre for Genetic Engineering and Biotechnology (ICGEB), New Delhi, India
| | - Rocktotpal Konwarh
- Department of Biotechnology, Addis Ababa Science and Technology University, Addis Ababa, Ethiopia
- Baba Kinaram Research Foundation (BKRF), Bramsthan, Mau, Uttar Pradesh India
| | - Monoswi Chakraborty
- Institute of Bioinformatics and Applied Biotechnology, Biotech Park, Bengaluru, Karnataka India
- International Centre for Genetic Engineering and Biotechnology (ICGEB), New Delhi, India
| | - Shweta Nandanwar
- ICAR - National Institute of Biotic Stress Management (NIBSM), Raipur, India
| | - Ashish Marathe
- ICAR - National Institute of Biotic Stress Management (NIBSM), Raipur, India
| | - Yogesh Yele
- ICAR - National Institute of Biotic Stress Management (NIBSM), Raipur, India
| | - Probir Kumar Ghosh
- ICAR - National Institute of Biotic Stress Management (NIBSM), Raipur, India
| | - Neeti Sanan-Mishra
- International Centre for Genetic Engineering and Biotechnology (ICGEB), New Delhi, India
| | - Anand Pratap Singh
- Baba Kinaram Research Foundation (BKRF), Bramsthan, Mau, Uttar Pradesh India
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Hu C, Liu F, Sheng O, Yang Q, Dou T, Dong T, Li C, Gao H, He W, Liu S, Deng G, Yi G, Bi F. Efficient and transgene-free genome editing in banana using a REG-2 promoter-driven gene-deletion system. MOLECULAR HORTICULTURE 2023; 3:16. [PMID: 37789476 PMCID: PMC10514973 DOI: 10.1186/s43897-023-00065-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2023] [Accepted: 08/07/2023] [Indexed: 10/05/2023]
Affiliation(s)
- Chunhua Hu
- Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization (Ministry of Agriculture and Rural Affairs), Guangdong Provincial Key Laboratory of Tropical and Subtropical Fruit Tree Research, Guangzhou, China
| | - Fan Liu
- Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization (Ministry of Agriculture and Rural Affairs), Guangdong Provincial Key Laboratory of Tropical and Subtropical Fruit Tree Research, Guangzhou, China
- College of Life Sciences, South China Agricultural University, Guangzhou, China
| | - Ou Sheng
- Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization (Ministry of Agriculture and Rural Affairs), Guangdong Provincial Key Laboratory of Tropical and Subtropical Fruit Tree Research, Guangzhou, China
| | - Qiaosong Yang
- Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization (Ministry of Agriculture and Rural Affairs), Guangdong Provincial Key Laboratory of Tropical and Subtropical Fruit Tree Research, Guangzhou, China
| | - Tongxin Dou
- Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization (Ministry of Agriculture and Rural Affairs), Guangdong Provincial Key Laboratory of Tropical and Subtropical Fruit Tree Research, Guangzhou, China
| | - Tao Dong
- Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization (Ministry of Agriculture and Rural Affairs), Guangdong Provincial Key Laboratory of Tropical and Subtropical Fruit Tree Research, Guangzhou, China
| | - Chunyu Li
- Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization (Ministry of Agriculture and Rural Affairs), Guangdong Provincial Key Laboratory of Tropical and Subtropical Fruit Tree Research, Guangzhou, China
| | - Huijun Gao
- Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization (Ministry of Agriculture and Rural Affairs), Guangdong Provincial Key Laboratory of Tropical and Subtropical Fruit Tree Research, Guangzhou, China
| | - Weidi He
- Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization (Ministry of Agriculture and Rural Affairs), Guangdong Provincial Key Laboratory of Tropical and Subtropical Fruit Tree Research, Guangzhou, China
| | - Siwen Liu
- Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization (Ministry of Agriculture and Rural Affairs), Guangdong Provincial Key Laboratory of Tropical and Subtropical Fruit Tree Research, Guangzhou, China
| | - Guiming Deng
- Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization (Ministry of Agriculture and Rural Affairs), Guangdong Provincial Key Laboratory of Tropical and Subtropical Fruit Tree Research, Guangzhou, China
| | - Ganjun Yi
- Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization (Ministry of Agriculture and Rural Affairs), Guangdong Provincial Key Laboratory of Tropical and Subtropical Fruit Tree Research, Guangzhou, China.
- Maoming Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Maoming, China.
| | - Fangcheng Bi
- Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization (Ministry of Agriculture and Rural Affairs), Guangdong Provincial Key Laboratory of Tropical and Subtropical Fruit Tree Research, Guangzhou, China.
- Maoming Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Maoming, China.
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Wan L, Wang Z, Zhang X, Zeng H, Ren J, Zhang N, Sun Y, Mi T. Optimised Agrobacterium-Mediated Transformation and Application of Developmental Regulators Improve Regeneration Efficiency in Melons. Genes (Basel) 2023; 14:1432. [PMID: 37510336 PMCID: PMC10378916 DOI: 10.3390/genes14071432] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Revised: 06/27/2023] [Accepted: 07/10/2023] [Indexed: 07/30/2023] Open
Abstract
Melon (Cucumis melo L.) is a protected crop in China with high economic value. Agrobacterium-mediated genetic transformation is a powerful tool to improve agronomic traits and obtain elite germplasm. However, current transformation protocols in melons are inefficient and highly genotype-dependent. To improve transformation in melon, we tested different infiltration methods for Agrobacterium-mediated transformation. Among these methods, micro-brushing and sonication for 20 s, followed by vacuum infiltration at -1.0 kPa for 90 s, resulted in the strongest green fluorescent protein signal and increased the proportion of infected explants. We transformed melon with developmental regulatory genes AtGRF5, AtPLT5, AtBBM, AtWUS, AtWOX5, and AtWIND1 from Arabidopsis and estimated regeneration frequencies as the number of regenerating shoots/total number of inoculated explants in the selection medium. The overexpression of AtGRF5 and AtPLT5 in melon resulted in transformation efficiencies of 42.3% and 33% in ZHF and 45.6% and 32.9% in Z12, respectively, which were significantly higher than those of the control. AtGRF5 and AtPLT5 expression cassettes were added to CRISPR/Cas9 genome-editing vectors to obtain transgenic phytoene desaturase CmPDS knockout mutants. Using AtGRF5 or AtPLT5, multi-allelic mutations were observed at CmPDS target sites in recalcitrant melon genotypes. This strategy enables genotype-flexible transformation and promotes precise genome modification technologies in melons.
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Affiliation(s)
- Lili Wan
- Institute of Crop, Wuhan Academy of Agricultural Sciences, Wuhan 430065, China
| | - Zhuanrong Wang
- Institute of Crop, Wuhan Academy of Agricultural Sciences, Wuhan 430065, China
| | - Xuejun Zhang
- Research Center of Hami Melon, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, China
- Hainan Sanya Crops Breeding Trial Center, Xinjiang Academy of Agricultural Sciences, Sanya 572019, China
| | - Hongxia Zeng
- Institute of Crop, Wuhan Academy of Agricultural Sciences, Wuhan 430065, China
| | - Jian Ren
- Institute of Crop, Wuhan Academy of Agricultural Sciences, Wuhan 430065, China
| | - Na Zhang
- Institute of Crop, Wuhan Academy of Agricultural Sciences, Wuhan 430065, China
| | - Yuhong Sun
- Institute of Crop, Wuhan Academy of Agricultural Sciences, Wuhan 430065, China
| | - Tang Mi
- Institute of Crop, Wuhan Academy of Agricultural Sciences, Wuhan 430065, China
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Ahmad N, Fatima S, Mehmood MA, Zaman QU, Atif RM, Zhou W, Rahman MU, Gill RA. Targeted genome editing in polyploids: lessons from Brassica. FRONTIERS IN PLANT SCIENCE 2023; 14:1152468. [PMID: 37409308 PMCID: PMC10318174 DOI: 10.3389/fpls.2023.1152468] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Accepted: 04/11/2023] [Indexed: 07/07/2023]
Abstract
CRISPR-mediated genome editing has emerged as a powerful tool for creating targeted mutations in the genome for various applications, including studying gene functions, engineering resilience against biotic and abiotic stresses, and increasing yield and quality. However, its utilization is limited to model crops for which well-annotated genome sequences are available. Many crops of dietary and economic importance, such as wheat, cotton, rapeseed-mustard, and potato, are polyploids with complex genomes. Therefore, progress in these crops has been hampered due to genome complexity. Excellent work has been conducted on some species of Brassica for its improvement through genome editing. Although excellent work has been conducted on some species of Brassica for genome improvement through editing, work on polyploid crops, including U's triangle species, holds numerous implications for improving other polyploid crops. In this review, we summarize key examples from genome editing work done on Brassica and discuss important considerations for deploying CRISPR-mediated genome editing more efficiently in other polyploid crops for improvement.
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Affiliation(s)
- Niaz Ahmad
- National Institute for Biotechnology and Genetic Engineering College, Pakistan Institute of Engineering and Applied Sciences (PIEAS), Faisalabad, Pakistan
| | - Samia Fatima
- National Institute for Biotechnology and Genetic Engineering College, Pakistan Institute of Engineering and Applied Sciences (PIEAS), Faisalabad, Pakistan
| | - Muhammad Aamer Mehmood
- Department of Bioinformatics & Biotechnology, Government College University Faisalabad, Faisalabad, Pakistan
| | - Qamar U. Zaman
- Hainan Yazhou Bay Seed Laboratory, Sanya Nanfan Research Institute of Hainan University, Sanya, China
- College of Tropical Crops, Hainan University, Haikou, China
| | - Rana Muhammad Atif
- National Center of Genome Editing, Center of Advanced Studies, Agriculture and Food Security, University of Agriculture, Faisalabad, Pakistan
- Department of Plant Breeding and Genetics, University of Agriculture Faisalabad, Faisalabad, Pakistan
| | - Weijun Zhou
- Ministry of Agriculture and Rural Affairs Key Lab of Spectroscopy Sensing, Institute of Crop Science, Zhejiang University, Hangzhou, China
| | - Mehboob-ur Rahman
- National Institute for Biotechnology and Genetic Engineering College, Pakistan Institute of Engineering and Applied Sciences (PIEAS), Faisalabad, Pakistan
| | - Rafaqat Ali Gill
- Key Laboratory for Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, China
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Zhou J, Luan X, Liu Y, Wang L, Wang J, Yang S, Liu S, Zhang J, Liu H, Yao D. Strategies and Methods for Improving the Efficiency of CRISPR/Cas9 Gene Editing in Plant Molecular Breeding. PLANTS (BASEL, SWITZERLAND) 2023; 12:1478. [PMID: 37050104 PMCID: PMC10097296 DOI: 10.3390/plants12071478] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 03/21/2023] [Accepted: 03/22/2023] [Indexed: 06/19/2023]
Abstract
Following recent developments and refinement, CRISPR-Cas9 gene-editing technology has become increasingly mature and is being widely used for crop improvement. The application of CRISPR/Cas9 enables the generation of transgene-free genome-edited plants in a short period and has the advantages of simplicity, high efficiency, high specificity, and low production costs, which greatly facilitate the study of gene functions. In plant molecular breeding, the gene-editing efficiency of the CRISPR-Cas9 system has proven to be a key step in influencing the effectiveness of molecular breeding, with improvements in gene-editing efficiency recently becoming a focus of reported scientific research. This review details strategies and methods for improving the efficiency of CRISPR/Cas9 gene editing in plant molecular breeding, including Cas9 variant enzyme engineering, the effect of multiple promoter driven Cas9, and gRNA efficient optimization and expression strategies. It also briefly introduces the optimization strategies of the CRISPR/Cas12a system and the application of BE and PE precision editing. These strategies are beneficial for the further development and optimization of gene editing systems in the field of plant molecular breeding.
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Affiliation(s)
- Junming Zhou
- College of Life Sciences, Jilin Agricultural University, Changchun 130118, China; (J.Z.); (X.L.); (Y.L.); (L.W.); (J.W.); (S.L.)
| | - Xinchao Luan
- College of Life Sciences, Jilin Agricultural University, Changchun 130118, China; (J.Z.); (X.L.); (Y.L.); (L.W.); (J.W.); (S.L.)
| | - Yixuan Liu
- College of Life Sciences, Jilin Agricultural University, Changchun 130118, China; (J.Z.); (X.L.); (Y.L.); (L.W.); (J.W.); (S.L.)
| | - Lixue Wang
- College of Life Sciences, Jilin Agricultural University, Changchun 130118, China; (J.Z.); (X.L.); (Y.L.); (L.W.); (J.W.); (S.L.)
| | - Jiaxin Wang
- College of Life Sciences, Jilin Agricultural University, Changchun 130118, China; (J.Z.); (X.L.); (Y.L.); (L.W.); (J.W.); (S.L.)
| | - Songnan Yang
- College of Agronomy, Jilin Agricultural University, Changchun 130118, China; (S.Y.); (J.Z.)
| | - Shuying Liu
- College of Life Sciences, Jilin Agricultural University, Changchun 130118, China; (J.Z.); (X.L.); (Y.L.); (L.W.); (J.W.); (S.L.)
| | - Jun Zhang
- College of Agronomy, Jilin Agricultural University, Changchun 130118, China; (S.Y.); (J.Z.)
| | - Huijing Liu
- College of Life Sciences, Jilin Agricultural University, Changchun 130118, China; (J.Z.); (X.L.); (Y.L.); (L.W.); (J.W.); (S.L.)
| | - Dan Yao
- College of Life Sciences, Jilin Agricultural University, Changchun 130118, China; (J.Z.); (X.L.); (Y.L.); (L.W.); (J.W.); (S.L.)
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Effects of Different Gene Editing Modes of CRISPR/Cas9 on Soybean Fatty Acid Anabolic Metabolism Based on GmFAD2 Family. Int J Mol Sci 2023; 24:ijms24054769. [PMID: 36902202 PMCID: PMC10003299 DOI: 10.3390/ijms24054769] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Revised: 02/21/2023] [Accepted: 02/23/2023] [Indexed: 03/06/2023] Open
Abstract
Δ12-fatty acid dehydrogenase (FAD2) is the essential enzyme responsible for catalyzing the formation of linoleic acid from oleic acid. CRISPR/Cas9 gene editing technology has been an essential tool for molecular breeding in soybeans. To evaluate the most suitable type of gene editing in soybean fatty acid synthesis metabolism, this study selected five crucial enzyme genes of the soybean FAD2 gene family-GmFAD2-1A, GmFAD2-1B, GmFAD2-2A, GmFAD2-2B, and GmFAD2-2C-and created a CRISPR/Cas9-mediated single gene editing vector system. The results of Sanger sequencing showed that 72 transformed plants positive for T1 generation were obtained using Agrobacterium-mediated transformation, of which 43 were correctly edited plants, with the highest editing efficiency of 88% for GmFAD2-2A. The phenotypic analysis revealed that the oleic acid content of the progeny of GmFAD2-1A gene-edited plants had a higher increase of 91.49% when compared to the control JN18, and the rest of the gene-edited plants in order were GmFAD2-2A, GmFAD2-1B, GmFAD2-2C, and GmFAD2-2B. The analysis of gene editing type has indicated that base deletions greater than 2bp were the predominant editing type in all editing events. This study provides ideas for the optimization of CRISPR/Cas9 gene editing technology and the development of new tools for precise base editing in the future.
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Ma Z, Ma L, Zhou J. Applications of CRISPR/Cas genome editing in economically important fruit crops: recent advances and future directions. MOLECULAR HORTICULTURE 2023; 3:1. [PMID: 37789479 PMCID: PMC10515014 DOI: 10.1186/s43897-023-00049-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Accepted: 01/10/2023] [Indexed: 10/05/2023]
Abstract
Fruit crops, consist of climacteric and non-climacteric fruits, are the major sources of nutrients and fiber for human diet. Since 2013, CRISPR/Cas (Clustered Regularly Interspersed Short Palindromic Repeats and CRISPR-Associated Protein) genome editing system has been widely employed in different plants, leading to unprecedented progress in the genetic improvement of many agronomically important fruit crops. Here, we summarize latest advancements in CRISPR/Cas genome editing of fruit crops, including efforts to decipher the mechanisms behind plant development and plant immunity, We also highlight the potential challenges and improvements in the application of genome editing tools to fruit crops, including optimizing the expression of CRISPR/Cas cassette, improving the delivery efficiency of CRISPR/Cas reagents, increasing the specificity of genome editing, and optimizing the transformation and regeneration system. In addition, we propose the perspectives on the application of genome editing in crop breeding especially in fruit crops and highlight the potential challenges. It is worth noting that efforts to manipulate fruit crops with genome editing systems are urgently needed for fruit crops breeding and demonstration.
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Affiliation(s)
- Zhimin Ma
- Peking University Institute of Advanced Agricultural Sciences, Weifang, 261000, Shandong, China
| | - Lijing Ma
- Peking University Institute of Advanced Agricultural Sciences, Weifang, 261000, Shandong, China
| | - Junhui Zhou
- Peking University Institute of Advanced Agricultural Sciences, Weifang, 261000, Shandong, China.
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May D, Paldi K, Altpeter F. Targeted mutagenesis with sequence-specific nucleases for accelerated improvement of polyploid crops: Progress, challenges, and prospects. THE PLANT GENOME 2023:e20298. [PMID: 36692095 DOI: 10.1002/tpg2.20298] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Accepted: 11/20/2022] [Indexed: 06/17/2023]
Abstract
Many of the world's most important crops are polyploid. The presence of more than two sets of chromosomes within their nuclei and frequently aberrant reproductive biology in polyploids present obstacles to conventional breeding. The presence of a larger number of homoeologous copies of each gene makes random mutation breeding a daunting task for polyploids. Genome editing has revolutionized improvement of polyploid crops as multiple gene copies and/or alleles can be edited simultaneously while preserving the key attributes of elite cultivars. Most genome-editing platforms employ sequence-specific nucleases (SSNs) to generate DNA double-stranded breaks at their target gene. Such DNA breaks are typically repaired via the error-prone nonhomologous end-joining process, which often leads to frame shift mutations, causing loss of gene function. Genome editing has enhanced the disease resistance, yield components, and end-use quality of polyploid crops. However, identification of candidate targets, genotyping, and requirement of high mutagenesis efficiency remain bottlenecks for targeted mutagenesis in polyploids. In this review, we will survey the tremendous progress of SSN-mediated targeted mutagenesis in polyploid crop improvement, discuss its challenges, and identify optimizations needed to sustain further progress.
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Affiliation(s)
- David May
- Agronomy Department, University of Florida Institute of Food and Agricultural Sciences, Gainesville, FL, USA
- DOE Center for Advanced Bioenergy and Bioproducts Innovation, Gainesville, FL, USA
| | - Katalin Paldi
- Agronomy Department, University of Florida Institute of Food and Agricultural Sciences, Gainesville, FL, USA
- DOE Center for Advanced Bioenergy and Bioproducts Innovation, Gainesville, FL, USA
| | - Fredy Altpeter
- Agronomy Department, University of Florida Institute of Food and Agricultural Sciences, Gainesville, FL, USA
- DOE Center for Advanced Bioenergy and Bioproducts Innovation, Gainesville, FL, USA
- Plant Cellular and Molecular Biology Program, Genetics Institute, University of Florida Institute of Food and Agricultural Sciences, Gainesville, FL, USA
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Kor SD, Chowdhury N, Keot AK, Yogendra K, Chikkaputtaiah C, Sudhakar Reddy P. RNA Pol III promoters-key players in precisely targeted plant genome editing. Front Genet 2023; 13:989199. [PMID: 36685866 PMCID: PMC9845283 DOI: 10.3389/fgene.2022.989199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Accepted: 11/15/2022] [Indexed: 01/05/2023] Open
Abstract
The clustered regularly interspaced short palindrome repeat (CRISPR)/CRISPR-associated protein Cas) system is a powerful and highly precise gene-editing tool in basic and applied research for crop improvement programs. CRISPR/Cas tool is being extensively used in plants to improve crop yield, quality, and nutritional value and make them tolerant to environmental stresses. CRISPR/Cas system consists of a Cas protein with DNA endonuclease activity and one CRISPR RNA transcript that is processed to form one or several short guide RNAs that direct Cas9 to the target DNA sequence. The expression levels of Cas proteins and gRNAs significantly influence the editing efficiency of CRISPR/Cas-mediated genome editing. This review focuses on insights into RNA Pol III promoters and their types that govern the expression levels of sgRNA in the CRISPR/Cas system. We discussed Pol III promoters structural and functional characteristics and their comparison with Pol II promoters. Further, the use of synthetic promoters to increase the targeting efficiency and overcome the structural, functional, and expressional limitations of RNA Pol III promoters has been discussed. Our review reports various studies that illustrate the use of endogenous U6/U3 promoters for improving editing efficiency in plants and the applicative approach of species-specific RNA pol III promoters for genome editing in model crops like Arabidopsis and tobacco, cereals, legumes, oilseed, and horticultural crops. We further highlight the significance of optimizing these species-specific promoters' systematic identification and validation for crop improvement and biotic and abiotic stress tolerance through CRISPR/Cas mediated genome editing.
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Affiliation(s)
- Sakshi Dharmendra Kor
- International Crops Research Institute for the Semi-Arid Tropics, Hyderabad, Telangana, India
| | - Naimisha Chowdhury
- Biological Sciences and Technology Division, CSIR-North East Institute of Science and Technology (CSIR-NEIST), Jorhat, Assam, India
| | - Ajay Kumar Keot
- Biological Sciences and Technology Division, CSIR-North East Institute of Science and Technology (CSIR-NEIST), Jorhat, Assam, India,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Kalenahalli Yogendra
- International Crops Research Institute for the Semi-Arid Tropics, Hyderabad, Telangana, India
| | - Channakeshavaiah Chikkaputtaiah
- Biological Sciences and Technology Division, CSIR-North East Institute of Science and Technology (CSIR-NEIST), Jorhat, Assam, India,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Palakolanu Sudhakar Reddy
- International Crops Research Institute for the Semi-Arid Tropics, Hyderabad, Telangana, India,*Correspondence: Palakolanu Sudhakar Reddy, ,
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Jogam P, Sandhya D, Alok A, Shekhawat MS, Peddaboina V, Singh K, Allini VR. A grobacterium-mediated genetic transformation and cloning of candidate reference genes in suspension cells of Artemisia pallens Wall. ex DC. 3 Biotech 2022; 12:194. [PMID: 35910289 PMCID: PMC9334505 DOI: 10.1007/s13205-022-03251-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Accepted: 07/05/2022] [Indexed: 11/01/2022] Open
Abstract
A reliable and stable Agrobacterium-mediated genetic transformation system for Artemisia pallens has been developed using cell suspension cultures derived from cotyledon explants. Cotyledon, attached cotyledon, and compound leaves were found to be suitable for the induction of callus among five different types of explants tested. The yellow friable callus derived from attached cotyledon was used to initiate suspension cultures in Suspension Culture Medium (SCM) which was supplemented with 2,4-dichlorophenoxyacetic acid (2,4-D) at 2.0 mg L-1 and in combination with different concentrations of Zeatin (ZEA) at 0.25 mg L-1. Two different shock treatments, cold shock (at 4 ℃) for 20 min and heat shock (at 45 ℃) treatment for 5 min, heat shock treatment increased the transformation efficiency. The supplementation of Pluronic F-68 (0.05%) significantly enhanced the transformation efficiency of suspension cultures, whereas Silwet L-77 (0.05%) leads to more browning of the cells and reduced the transformation efficiency. The maximum GUS intensity was recorded with an optimal intensity of blue spots in the transformed cells. The highest GUS fluorometric activity measured was 879.4 ± 113.7 nmol 4MU/mg/min in transformed cell suspension cultures. The hygromycin-resistant calli showed intense blue color in GUS histochemical assay. The transgene integration into the plant genome was confirmed by polymerase chain reaction (PCR) using uidA specific primers in six hygromycin-resistant cell lines. The partial coding sequence of three candidate reference genes, i.e., ADP-ribosylation factor (Arf), β-actin (Act), and ubiquitin (Ubi), and carotenoid biosynthesis pathway gene, i.e., Phytoene desaturase (Pds) were cloned, sequenced, and submitted to NCBI for the first time. The quantitative mRNA expression of the transgene (uidA) and internal ApPds gene were evaluated in transgenic callus lines. The present Agrobacterium-mediated genetic transformation protocol could help in better understanding of the metabolic pathways of this medicinally important plant and its genetic improvement. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-022-03251-x.
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Affiliation(s)
- Phanikanth Jogam
- Department of Biotechnology, Kakatiya University, Warangal, Telangana 506009 India
| | - Dulam Sandhya
- Department of Biotechnology, Kakatiya University, Warangal, Telangana 506009 India
| | - Anshu Alok
- Department of Biotechnology, Punjab University, Chandigarh, 160014 India
| | - Mahipal S. Shekhawat
- Biotechnology Unit, Kanchi Mamunivar Government Institute for Postgraduate Studies and Research, Puducherry, 605008 India
| | | | - Kashmir Singh
- Department of Biotechnology, Punjab University, Chandigarh, 160014 India
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