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Kim JY, Kim DH, Kim MS, Jung YJ, Kang KK. Physicochemical Properties and Antioxidant Activity of CRISPR/Cas9-Edited Tomato SGR1 Knockout (KO) Line. Int J Mol Sci 2024; 25:5111. [PMID: 38791150 PMCID: PMC11120780 DOI: 10.3390/ijms25105111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Revised: 04/30/2024] [Accepted: 05/01/2024] [Indexed: 05/26/2024] Open
Abstract
Tomatoes contain many secondary metabolites such as β-carotene, lycopene, phenols, flavonoids, and vitamin C, which are responsible for antioxidant activity. SlSGR1 encodes a STAY-GREEN protein that plays a critical role in the regulation of chlorophyll degradation in tomato leaves and fruits. Therefore, the present study was conducted to evaluate the sgr1 null lines based on their physicochemical characteristics, the content of secondary metabolites, and the γ-Aminobutyric acid (GABA) content. The total soluble solids (TSS), titrated acidity (TA), and brix acid ratio (BAR) of the sgr1 null lines were higher than those of the wild type(WT). Additionally, the sgr1 null lines accumulated higher levels of flavor-inducing ascorbic acid and total carotenoids compared to WT. Also, the total phenolic content, total flavonoids, GABA content, and 2,2-diphenyl-1-picrylhydrazyl (DPPH) radical content of the sgr1 null lines were higher than those of the WT. Therefore, these studies suggest that the knockout of the SGR1 gene by the CRISPR/Cas9 system can improve various functional compounds in tomato fruit, thereby satisfying the antioxidant properties required by consumers.
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Affiliation(s)
- Jin Young Kim
- Division of Horticultural Biotechnology, Hankyong National University, Anseong 17579, Republic of Korea; (J.Y.K.); (D.H.K.)
| | - Dong Hyun Kim
- Division of Horticultural Biotechnology, Hankyong National University, Anseong 17579, Republic of Korea; (J.Y.K.); (D.H.K.)
| | - Me-Sun Kim
- Department of Crop Science, College of Agriculture and Life & Environment Sciences, Chungbuk National University, Cheongju 28644, Republic of Korea;
| | - Yu Jin Jung
- Division of Horticultural Biotechnology, Hankyong National University, Anseong 17579, Republic of Korea; (J.Y.K.); (D.H.K.)
- Institute of Genetic Engineering, Hankyong National University, Anseong 17579, Republic of Korea
| | - Kwon Kyoo Kang
- Division of Horticultural Biotechnology, Hankyong National University, Anseong 17579, Republic of Korea; (J.Y.K.); (D.H.K.)
- Institute of Genetic Engineering, Hankyong National University, Anseong 17579, Republic of Korea
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2
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Prasad K, Gadeela H, Bommineni PR, Reddy PS, Tyagi W, Yogendra K. CRISPR/Cas9-mediated mutagenesis of phytoene desaturase in pigeonpea and groundnut. Funct Integr Genomics 2024; 24:57. [PMID: 38478115 DOI: 10.1007/s10142-024-01336-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 02/28/2024] [Accepted: 03/05/2024] [Indexed: 05/01/2024]
Abstract
The CRISPR/Cas9 technology, renowned for its ability to induce precise genetic alterations in various crop species, has encountered challenges in its application to grain legume crops such as pigeonpea and groundnut. Despite attempts at gene editing in groundnut, the low rates of transformation and editing have impeded its widespread adoption in producing genetically modified plants. This study seeks to establish an effective CRISPR/Cas9 system in pigeonpea and groundnut through Agrobacterium-mediated transformation, with a focus on targeting the phytoene desaturase (PDS) gene. The PDS gene is pivotal in carotenoid biosynthesis, and its disruption leads to albino phenotypes and dwarfism. Two constructs (one each for pigeonpea and groundnut) were developed for the PDS gene, and transformation was carried out using different explants (leaf petiolar tissue for pigeonpea and cotyledonary nodes for groundnut). By adjusting the composition of the growth media and refining Agrobacterium infection techniques, transformation efficiencies of 15.2% in pigeonpea and 20% in groundnut were achieved. Mutation in PDS resulted in albino phenotype, with editing efficiencies ranging from 4 to 6%. Sequence analysis uncovered a nucleotide deletion (A) in pigeonpea and an A insertion in groundnut, leading to a premature stop codon and, thereby, an albino phenotype. This research offers a significant foundation for the swift assessment and enhancement of CRISPR/Cas9-based genome editing technologies in legume crops.
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Affiliation(s)
- Kalyani Prasad
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, 502324, India
| | - Harika Gadeela
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, 502324, India
| | - Pradeep Reddy Bommineni
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, 502324, India
| | - Palakolanu Sudhakar Reddy
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, 502324, India
| | - Wricha Tyagi
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, 502324, India
| | - Kalenahalli Yogendra
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, 502324, India.
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Sun X, Lei R, Zhang H, Chen W, Jia Q, Guo X, Zhang Y, Wu P, Wang X. Rapid and sensitive detection of two fungal pathogens in soybeans using the recombinase polymerase amplification/CRISPR-Cas12a method for potential on-site disease diagnosis. PEST MANAGEMENT SCIENCE 2024; 80:1168-1181. [PMID: 37874890 DOI: 10.1002/ps.7847] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Revised: 10/08/2023] [Accepted: 10/24/2023] [Indexed: 10/26/2023]
Abstract
BACKGROUND Diaporthe aspalathi and Diaporthe caulivora are two of the fungal pathogens causing soybean stem canker (SSC) in soybean, which is one of the most widespread diseases in soybean growing regions and can cause 100% loss of yield. Current methods for the detection of fungal pathogens, including morphological identification and molecular detection, are mostly limited by the need for professional laboratories and staff. To develop a detection method for potential on-site diagnosis for two of the fungal pathogens causing SSC, we designed a rapid assay combining recombinase polymerase amplification (RPA) and CRISPR-Cas12a-based diagnostics to specifically detect D. aspalathi and D. caulivora. RESULTS The translation elongation factor 1-alpha gene was employed as the target gene to evaluate the specificity and sensitivity of this assay. The RPA/CRISPR-Cas12a system has excellent specificity to distinguish D. aspalathi and D. caulivora from closely related species. The sensitivities of RPA/CRISPR-Cas12a-based fluorescence detection and lateral flow assay for D. aspalathi and D. caulivora are 14.5 copies and 24.6 copies, respectively. This assay can detect hyphae in inoculated soybean stems at 12 days after inoculation and has a recovery as high as 86% for hyphae-spiked soybean seed powder. The total time from DNA extraction to detection was not more than 60 min. CONCLUSION The method developed for rapid detection of plant pathogens includes DNA extraction with magnetic beads or rapid DNA extraction, isothermal nucleic acid amplification at 39 °C, CRISPR-Cas12a cleavage reaction at 37 °C, and lateral flow assay or endpoint fluorescence visualization at room temperature. The RPA and CRISPR-Cas12a reagents can be preloaded in the microcentrifuge tube to simplify the procedures in the field. Both RPA and CRISPR-Cas12a reaction can be realized on a portable incubator, and the results are visualized using lateral flow strips or portable flashlight. This method requires minimal equipment and operator training, and has promising applications for rapid on-site disease screening, port inspection, or controlling fungal pathogen transmission in crop. © 2023 Society of Chemical Industry.
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Affiliation(s)
- Xiwen Sun
- Chinese Academy of Inspection and Quarantine, Beijing, China
- Shenyang Agricultural University, Shenyang, China
| | - Rong Lei
- Chinese Academy of Inspection and Quarantine, Beijing, China
| | | | - Wujian Chen
- Technical Center of Hangzhou Customs, Hangzhou, China
| | - Qianwen Jia
- School of Life and Health, Dalian University, Dalian, China
| | - Xing Guo
- School of Life and Health, Dalian University, Dalian, China
| | - Yongjiang Zhang
- Chinese Academy of Inspection and Quarantine, Beijing, China
| | - Pinshan Wu
- Chinese Academy of Inspection and Quarantine, Beijing, China
| | - Xinyi Wang
- School of Life and Health, Dalian University, Dalian, China
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Lippolis A, Roland WSU, Bocova O, Pouvreau L, Trindade LM. The challenge of breeding for reduced off-flavor in faba bean ingredients. FRONTIERS IN PLANT SCIENCE 2023; 14:1286803. [PMID: 37965015 PMCID: PMC10642941 DOI: 10.3389/fpls.2023.1286803] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Accepted: 10/17/2023] [Indexed: 11/16/2023]
Abstract
The growing interest in plant protein sources, such as pulses, is driven by the necessity for sustainable food production and climate change mitigation strategies. Faba bean (Vicia faba L.) is a promising protein crop for temperate climates, owing to its remarkable yield potential (up to 8 tonnes ha-1 in favourable growing conditions) and high protein content (~29% dry matter basis). Nevertheless, the adoption of faba bean protein in plant-based products that aim to resemble animal-derived counterparts is hindered by its distinctive taste and aroma, regarded as "off-flavors". In this review, we propose to introduce off-flavor as a trait in breeding programs by identifying molecules involved in sensory perception and defining key breeding targets. We discuss the role of lipid oxidation in producing volatile and non-volatile compounds responsible for the beany aroma and bitter taste, respectively. We further investigate the contribution of saponin, tannin, and other polyphenols to bitterness and astringency. To develop faba bean varieties with diminished off-flavors, we suggest targeting genes to reduce lipid oxidation, such as lipoxygenases (lox) and fatty acid desaturases (fad), and genes involved in phenylpropanoid and saponin biosynthesis, such as zero-tannin (zt), chalcone isomerase (chi), chalcone synthase (chs), β-amyrin (bas1). Additionally, we address potential challenges, including the need for high-throughput phenotyping and possible limitations that could arise during the genetic improvement process. The breeding approach can facilitate the use of faba bean protein in plant-based food such as meat and dairy analogues more extensively, fostering a transition toward more sustainable and climate-resilient diets.
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Affiliation(s)
- Antonio Lippolis
- Plant Breeding, Wageningen University & Research, Wageningen, Netherlands
| | - Wibke S. U. Roland
- Wageningen Food & Biobased Research, Wageningen University & Research, Wageningen, Netherlands
| | - Ornela Bocova
- Plant Breeding, Wageningen University & Research, Wageningen, Netherlands
| | - Laurice Pouvreau
- Wageningen Food & Biobased Research, Wageningen University & Research, Wageningen, Netherlands
| | - Luisa M. Trindade
- Plant Breeding, Wageningen University & Research, Wageningen, Netherlands
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Nivya VM, Shah JM. Recalcitrance to transformation, a hindrance for genome editing of legumes. Front Genome Ed 2023; 5:1247815. [PMID: 37810593 PMCID: PMC10551638 DOI: 10.3389/fgeed.2023.1247815] [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: 06/26/2023] [Accepted: 09/06/2023] [Indexed: 10/10/2023] Open
Abstract
Plant genome editing, a recently discovered method for targeted mutagenesis, has emerged as a promising tool for crop improvement and gene function research. Many genome-edited plants, such as rice, wheat, and tomato, have emerged over the last decade. As the preliminary steps in the procedure for genome editing involve genetic transformation, amenability to genome editing depends on the efficiency of genetic engineering. Hence, there are numerous reports on the aforementioned crops because they are transformed with relative ease. Legume crops are rich in protein and, thus, are a favored source of plant proteins for the human diet in most countries. However, legume cultivation often succumbs to various biotic/abiotic threats, thereby leading to high yield loss. Furthermore, certain legumes like peanuts possess allergens, and these need to be eliminated as these deprive many people from gaining the benefits of such crops. Further genetic variations are limited in certain legumes. Genome editing has the potential to offer solutions to not only combat biotic/abiotic stress but also generate desirable knock-outs and genetic variants. However, excluding soybean, alfalfa, and Lotus japonicus, reports obtained on genome editing of other legume crops are less. This is because, excluding the aforementioned three legume crops, the transformation efficiency of most legumes is found to be very low. Obtaining a higher number of genome-edited events is desirable as it offers the option to genotypically/phenotypically select the best candidate, without the baggage of off-target mutations. Eliminating the barriers to genetic engineering would directly help in increasing genome-editing rates. Thus, this review aims to compare various legumes for their transformation, editing, and regeneration efficiencies and discusses various solutions available for increasing transformation and genome-editing rates in legumes.
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Affiliation(s)
| | - Jasmine M. Shah
- Department of Plant Science, Central University of Kerala, Kasaragod, Kerala, India
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Mainkar P, Manape TK, Satheesh V, Anandhan S. CRISPR/Cas9-mediated editing of PHYTOENE DESATURASE gene in onion ( Allium cepa L.). FRONTIERS IN PLANT SCIENCE 2023; 14:1226911. [PMID: 37701798 PMCID: PMC10494252 DOI: 10.3389/fpls.2023.1226911] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Accepted: 07/28/2023] [Indexed: 09/14/2023]
Abstract
Introduction Clustered regularly interspaced short palindromic repeats (CRISPR)/ CRISPR-associated protein 9 (Cas9) is a precise genome editing tool used to introduce genetic modifications in a wide range of crop species. Thus far, there is no report of CRISPR/Cas9-mediated genome editing in onions (Allium cepa L.). Methods In the present study, we targeted two exons of the gene coding for Phytoene desaturase (AcPDS) in onion cv. Bhima Super. The sgRNA-carrying constructs were co-cultivated with 8-week-old embryogenic calli using an Agrobacterium-mediated transformation protocol and incubated on the media without hygromycin B selection. Results and discussion Out of the total 617 co-cultivated calli, 21 (3.4%) regenerated shoots exhibited three distinct phenotypes: albino, chimeric, and pale green; in comparison to the wild-type non-transformed regenerated shoots. Total chlorophyll content was drastically reduced in albino shoots and significantly decreased in chimeric shoots. Out of the six Cas9 gene PCR-confirmed regenerated shoots, two exhibited the albino phenotype due to insertions/deletions (InDels) and substitution-based mutations in and around the AcPDS target sites. Deep amplicon sequencing revealed a significantly variable InDel frequency between two sgRNAs, ranging from 1.2% to 63.4%, along with a 53.4% substitution frequency. The mutation of the AcPDS gene generated a visually detectable albino phenotype, thus confirming the successful editing of the AcPDS gene. This is the first time a CRISPR/Cas9-mediated genome editing protocol has been successfully established in onion, with the AcPDS gene serving as an example. This study will provide the necessary momentum for researchers to further basic and applied research on onions.
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Affiliation(s)
- Pawan Mainkar
- ICAR-Directorate of Onion and Garlic Research, Pune, Maharashtra, India
| | | | - Viswanathan Satheesh
- Genome Informatics Facility, Office of Biotechnology, Iowa State University, Ames, IA, United States
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Leung HS, Chan LY, Law CH, Li MW, Lam HM. Twenty years of mining salt tolerance genes in soybean. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2023; 43:45. [PMID: 37313223 PMCID: PMC10248715 DOI: 10.1007/s11032-023-01383-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Accepted: 04/12/2023] [Indexed: 06/15/2023]
Abstract
Current combined challenges of rising food demand, climate change and farmland degradation exert enormous pressure on agricultural production. Worldwide soil salinization, in particular, necessitates the development of salt-tolerant crops. Soybean, being a globally important produce, has its genetic resources increasingly examined to facilitate crop improvement based on functional genomics. In response to the multifaceted physiological challenge that salt stress imposes, soybean has evolved an array of defences against salinity. These include maintaining cell homeostasis by ion transportation, osmoregulation, and restoring oxidative balance. Other adaptations include cell wall alterations, transcriptomic reprogramming, and efficient signal transduction for detecting and responding to salt stress. Here, we reviewed functionally verified genes that underly different salt tolerance mechanisms employed by soybean in the past two decades, and discussed the strategy in selecting salt tolerance genes for crop improvement. Future studies could adopt an integrated multi-omic approach in characterizing soybean salt tolerance adaptations and put our existing knowledge into practice via omic-assisted breeding and gene editing. This review serves as a guide and inspiration for crop developers in enhancing soybean tolerance against abiotic stresses, thereby fulfilling the role of science in solving real-life problems. Supplementary Information The online version contains supplementary material available at 10.1007/s11032-023-01383-3.
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Affiliation(s)
- Hoi-Sze Leung
- Center for Soybean Research of the State Key Laboratory of Agrobiotechnology, and School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR People’s Republic of China
| | - Long-Yiu Chan
- Center for Soybean Research of the State Key Laboratory of Agrobiotechnology, and School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR People’s Republic of China
| | - Cheuk-Hin Law
- Center for Soybean Research of the State Key Laboratory of Agrobiotechnology, and School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR People’s Republic of China
| | - Man-Wah Li
- Center for Soybean Research of the State Key Laboratory of Agrobiotechnology, and School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR People’s Republic of China
| | - Hon-Ming Lam
- Center for Soybean Research of the State Key Laboratory of Agrobiotechnology, and School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR People’s Republic of China
- Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, 518000 People’s Republic of China
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Wei T, Jiang L, You X, Ma P, Xi Z, Wang NN. Generation of Herbicide-Resistant Soybean by Base Editing. BIOLOGY 2023; 12:biology12050741. [PMID: 37237553 DOI: 10.3390/biology12050741] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 05/15/2023] [Accepted: 05/17/2023] [Indexed: 05/28/2023]
Abstract
Weeds cause the largest yield loss in soybean production. The development of herbicide-resistant soybean germplasm is of great significance for weed control and yield improvement. In this study, we used the cytosine base editor (BE3) to develop novel herbicide-resistant soybean. We have successfully introduced base substitutions in GmAHAS3 and GmAHAS4 and obtained a heritable transgene-free soybean with homozygous P180S mutation in GmAHAS4. The GmAHAS4 P180S mutants have apparent resistance to chlorsulfuron, flucarbazone-sodium, and flumetsulam. In particular, the resistance to chlorsulfuron was more than 100 times that of with wild type TL-1. The agronomic performance of the GmAHAS4 P180S mutants showed no significant differences to TL-1 under natural growth conditions. In addition, we developed allele-specific PCR markers for the GmAHAS4 P180S mutants, which can easily discriminate homozygous, heterozygous mutants, and wild-type plants. This study demonstrates a feasible and effective way to generate herbicide-resistant soybean by using CRISPR/Cas9-mediated base editing.
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Affiliation(s)
- Tao Wei
- Tianjin Key Laboratory of Protein Sciences, Department of Plant Biology and Ecology, College of Life Sciences, Nankai University, Tianjin 300071, China
- State Key Laboratory of Elemento-Organic Chemistry, Department of Chemical Biology, National Engineering Research Center of Pesticide, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Linjian Jiang
- Key Laboratory of Pest Monitoring and Green Management, MOA, Department of Plant Pathology, College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Xiang You
- Tianjin Key Laboratory of Protein Sciences, Department of Plant Biology and Ecology, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Pengyu Ma
- State Key Laboratory of Elemento-Organic Chemistry, Department of Chemical Biology, National Engineering Research Center of Pesticide, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Zhen Xi
- State Key Laboratory of Elemento-Organic Chemistry, Department of Chemical Biology, National Engineering Research Center of Pesticide, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Ning Ning Wang
- Tianjin Key Laboratory of Protein Sciences, Department of Plant Biology and Ecology, College of Life Sciences, Nankai University, Tianjin 300071, China
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Joshi T, Sehgal H, Mandal SK, Joshi M, Deepa PR, Sharma PK. Nutraceutical and flavor profiles in underutilized desert legumes of India: gene editing strategies towards sustainable food development. JOURNAL OF PLANT BIOCHEMISTRY AND BIOTECHNOLOGY 2023:1-8. [PMID: 37359892 PMCID: PMC10049905 DOI: 10.1007/s13562-023-00836-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Accepted: 03/09/2023] [Indexed: 06/28/2023]
Abstract
Climate change has posed a challenge for food security all over the world in the form of fluctuating crop yields and novel disease outbreaks in plants. Human society's overdependence on a few food crops does not seem a wise precedence. There are numerous underutilized/orphan/neglected legumes growing in the Indian desert regions that can come to the rescue and act as balanced and sustainable sources of nutrients and health-benefitting nutraceuticals. However, challenges such as low plant yield, unidentified metabolic pathways and off-flavor in the food products derived from them prevent the realization of their full potential. Conventional breeding techniques are too slow to achieve the desired modifications and cater to the sharply rising demand for functional foods. The novel gene editing tools like CRISPR-Cas provide more precise tool to manipulate the target genes with or without introduction of foreign DNA and therefore, have better chances to be accepted by governments and societies. The current article reports some of the relevant 'gene editing' success stories with respect to nutraceutical and flavor profiles in the popular legumes. It highlights gaps and future potential, along with areas requiring caution, in underutilized edible legumes of the Indian (semi) arid regions like Prosopis cineraria, Acacia senegal and Cyamopsis tetragonoloba.
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Affiliation(s)
- Tripti Joshi
- Department of Biological Sciences, Birla Institute of Technology and Science (BITS), Pilani Campus, Pilani, Rajasthan 333031 India
| | - Hansa Sehgal
- Department of Biological Sciences, Birla Institute of Technology and Science (BITS), Pilani Campus, Pilani, Rajasthan 333031 India
| | - Sumit Kumar Mandal
- Department of Biological Sciences, Birla Institute of Technology and Science (BITS), Pilani Campus, Pilani, Rajasthan 333031 India
| | - Mukul Joshi
- Department of Biological Sciences, Birla Institute of Technology and Science (BITS), Pilani Campus, Pilani, Rajasthan 333031 India
| | - P. R. Deepa
- Department of Biological Sciences, Birla Institute of Technology and Science (BITS), Pilani Campus, Pilani, Rajasthan 333031 India
| | - Pankaj Kumar Sharma
- Department of Biological Sciences, Birla Institute of Technology and Science (BITS), Pilani Campus, Pilani, Rajasthan 333031 India
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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: 3] [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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11
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Illa-Berenguer E, LaFayette PR, Parrott WA. Editing efficiencies with Cas9 orthologs, Cas12a endonucleases, and temperature in rice. Front Genome Ed 2023; 5:1074641. [PMID: 37032710 PMCID: PMC10080323 DOI: 10.3389/fgeed.2023.1074641] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Accepted: 03/07/2023] [Indexed: 03/19/2023] Open
Abstract
The advent of CRISPR-Cas technology has made it the genome editing tool of choice in all kingdoms of life, including plants, which can have large, highly duplicated genomes. As a result, finding adequate target sequences that meet the specificities of a given Cas nuclease on any gene of interest remains challenging in many cases. To assess target site flexibility, we tested five different Cas9/Cas12a endonucleases (SpCas9, SaCas9, St1Cas9, Mb3Cas12a, and AsCas12a) in embryogenic rice calli from Taipei 309 at 37°C (optimal temperature for most Cas9/Cas12a proteins) and 27°C (optimal temperature for tissue culture) and measured their editing rates under regular tissue culture conditions using Illumina sequencing. StCas9 and AsCas12 were not functional as tested, regardless of the temperature used. SpCas9 was the most efficient endonuclease at either temperature, regardless of whether monoallelic or biallelic edits were considered. Mb3Cas12a at 37°C was the next most efficient endonuclease. Monoallelic edits prevailed for both SaCas9 and Mb3Cas12a at 27°C, but biallelic edits prevailed at 37°C. Overall, the use of other Cas9 orthologs, the use of Cas12a endonucleases, and the optimal temperature can expand the range of targetable sequences.
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Affiliation(s)
- Eudald Illa-Berenguer
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA, United States
- *Correspondence: Eudald Illa-Berenguer,
| | - Peter R. LaFayette
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA, United States
| | - Wayne A. Parrott
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA, United States
- Department of Crop and Soil Sciences, University of Georgia, Athens, GA, United States
- Institute of Plant Breeding, Genetics and Genomics, University of Georgia, Athens, GA, United States
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12
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Adeyinka OS, Tabassum B, Koloko BL, Ogungbe IV. Enhancing the quality of staple food crops through CRISPR/Cas-mediated site-directed mutagenesis. PLANTA 2023; 257:78. [PMID: 36913066 DOI: 10.1007/s00425-023-04110-6] [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: 11/20/2022] [Accepted: 02/28/2023] [Indexed: 06/18/2023]
Abstract
The enhancement of CRISPR-Cas gene editing with robust nuclease activity promotes genetic modification of desirable agronomic traits, such as resistance to pathogens, drought tolerance, nutritional value, and yield-related traits in crops. The genetic diversity of food crops has reduced tremendously over the past twelve millennia due to plant domestication. This reduction presents significant challenges for the future especially considering the risks posed by global climate change to food production. While crops with improved phenotypes have been generated through crossbreeding, mutation breeding, and transgenic breeding over the years, improving phenotypic traits through precise genetic diversification has been challenging. The challenges are broadly associated with the randomness of genetic recombination and conventional mutagenesis. This review highlights how emerging gene-editing technologies reduce the burden and time necessary for developing desired traits in plants. Our focus is to provide readers with an overview of the advances in CRISPR-Cas-based genome editing for crop improvement. The use of CRISPR-Cas systems in generating genetic diversity to enhance the quality and nutritional value of staple food crops is discussed. We also outlined recent applications of CRISPR-Cas in developing pest-resistant crops and removing unwanted traits, such as allergenicity from crops. Genome editing tools continue to evolve and present unprecedented opportunities to enhance crop germplasm via precise mutations at the desired loci of the plant genome.
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Affiliation(s)
- Olawale Samuel Adeyinka
- Department of Chemistry, Physics and Atmospheric Sciences Jackson State University, Jackson, MS, 39217, USA.
| | - Bushra Tabassum
- School of Biological Sciences, University of the Punjab, Lahore, Pakistan
| | | | - Ifedayo Victor Ogungbe
- Department of Chemistry, Physics and Atmospheric Sciences Jackson State University, Jackson, MS, 39217, USA
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13
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Verma V, Kumar A, Partap M, Thakur M, Bhargava B. CRISPR-Cas: A robust technology for enhancing consumer-preferred commercial traits in crops. FRONTIERS IN PLANT SCIENCE 2023; 14:1122940. [PMID: 36824195 PMCID: PMC9941649 DOI: 10.3389/fpls.2023.1122940] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Accepted: 01/16/2023] [Indexed: 06/18/2023]
Abstract
The acceptance of new crop varieties by consumers is contingent on the presence of consumer-preferred traits, which include sensory attributes, nutritional value, industrial products and bioactive compounds production. Recent developments in genome editing technologies provide novel insight to identify gene functions and improve the various qualitative and quantitative traits of commercial importance in plants. Various conventional as well as advanced gene-mutagenesis techniques such as physical and chemical mutagenesis, CRISPR-Cas9, Cas12 and base editors are used for the trait improvement in crops. To meet consumer demand, breakthrough biotechnologies, especially CRISPR-Cas have received a fair share of scientific and industrial interest, particularly in plant genome editing. CRISPR-Cas is a versatile tool that can be used to knock out, replace and knock-in the desired gene fragments at targeted locations in the genome, resulting in heritable mutations of interest. This review highlights the existing literature and recent developments in CRISPR-Cas technologies (base editing, prime editing, multiplex gene editing, epigenome editing, gene delivery methods) for reliable and precise gene editing in plants. This review also discusses the potential of gene editing exhibited in crops for the improvement of consumer-demanded traits such as higher nutritional value, colour, texture, aroma/flavour, and production of industrial products such as biofuel, fibre, rubber and pharmaceuticals. In addition, the bottlenecks and challenges associated with gene editing system, such as off targeting, ploidy level and the ability to edit organelle genome have also been discussed.
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Affiliation(s)
- Vipasha Verma
- Floriculture Laboratory, Agrotechnology Division, Council of Scientific and Industrial Research (CSIR) –Institute of Himalayan Bioresource Technology (IHBT), Palampur, India
| | - Akhil Kumar
- Floriculture Laboratory, Agrotechnology Division, Council of Scientific and Industrial Research (CSIR) –Institute of Himalayan Bioresource Technology (IHBT), Palampur, India
| | - Mahinder Partap
- Floriculture Laboratory, Agrotechnology Division, Council of Scientific and Industrial Research (CSIR) –Institute of Himalayan Bioresource Technology (IHBT), Palampur, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, India
| | - Meenakshi Thakur
- Floriculture Laboratory, Agrotechnology Division, Council of Scientific and Industrial Research (CSIR) –Institute of Himalayan Bioresource Technology (IHBT), Palampur, India
| | - Bhavya Bhargava
- Floriculture Laboratory, Agrotechnology Division, Council of Scientific and Industrial Research (CSIR) –Institute of Himalayan Bioresource Technology (IHBT), Palampur, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, India
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14
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Zhang A, He H, Li Y, Wang L, Liu Y, Luan X, Wang J, Liu H, Liu S, Zhang J, Yao D. MADS-Box Subfamily Gene GmAP3 from Glycine max Regulates Early Flowering and Flower Development. Int J Mol Sci 2023; 24:ijms24032751. [PMID: 36769078 PMCID: PMC9917172 DOI: 10.3390/ijms24032751] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2022] [Revised: 12/30/2022] [Accepted: 01/29/2023] [Indexed: 02/04/2023] Open
Abstract
AP3 has been studied and is reported to affect structural changes in floral organs in various plants. However, the function of the soybean AP3 genes in flower development is unknown. Here, the full-length cDNA sequence of GmAP3 was obtained by RACE and it was verified that it belongs to the MADS-box subfamily by a bioinformatics analysis. The expression of GmAP3 is closely related to the expression of essential enzyme genes related to flower development. Yeast two-hybrid assays demonstrated that GmAP3 interacts with AP1 to determine the identity of flower organ development. A follow-up analysis showed that overexpression of the GmAP3 gene advanced flowering time and resulted in changes in floral organ morphology. The average flowering time of overexpressed soybean and tobacco plants was 6-8 days earlier than that of wild-type plants, and the average flowering time of gene-edited soybean and tobacco plants was 6-11 days later than that of wild-type plants. In conclusion, GmAP3 may directly or indirectly affect the flower development of soybean. The results of this study lay the foundation for further research on the biological functions of MADS transcriptional factors in soybeans.
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Affiliation(s)
- Aijing Zhang
- College of Life Sciences, Jilin Agricultural University, Changchun 130118, China
- College of Agronomy, Jilin Agricultural University, Changchun 130118, China
| | - Haobo He
- College of Life Sciences, Jilin Agricultural University, Changchun 130118, China
| | - Yue Li
- College of Life Sciences, Jilin Agricultural University, Changchun 130118, China
| | - Lixue Wang
- College of Life Sciences, Jilin Agricultural University, Changchun 130118, China
| | - Yixuan Liu
- College of Life Sciences, Jilin Agricultural University, Changchun 130118, China
| | - Xinchao Luan
- College of Life Sciences, Jilin Agricultural University, Changchun 130118, China
| | - Jiaxin Wang
- College of Life Sciences, Jilin Agricultural University, Changchun 130118, China
| | - Huijing Liu
- College of Life Sciences, Jilin Agricultural University, Changchun 130118, China
| | - Shuying Liu
- College of Life Sciences, Jilin Agricultural University, Changchun 130118, China
| | - Jun Zhang
- College of Agronomy, Jilin Agricultural University, Changchun 130118, China
- Correspondence: (J.Z.); (D.Y.)
| | - Dan Yao
- College of Life Sciences, Jilin Agricultural University, Changchun 130118, China
- Correspondence: (J.Z.); (D.Y.)
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Luan T, Wang L, Zhao J, Luan H, Zhang Y, Wang C, Langford PR, Liu S, Zhang W, Li G. A CRISPR/Cas12a-assisted rapid detection platform by biosensing the apxIVA of Actinobacillus pleuropneumoniae. Front Microbiol 2022; 13:928307. [PMID: 36160205 PMCID: PMC9493679 DOI: 10.3389/fmicb.2022.928307] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Accepted: 08/19/2022] [Indexed: 11/13/2022] Open
Abstract
Actinobacillus pleuropneumoniae is an important respiratory pig pathogen that causes substantial losses in the worldwide swine industry. Chronic or subclinical infection with no apparent clinical symptoms poses a challenge for preventing transmission between herds. Rapid diagnostics is important for the control of epidemic diseases. In this study, we formulated an A. pleuropneumoniae species-specific apxIVA-based CRISPR/Cas12a-assisted rapid detection platform (Card) that combines recombinase polymerase amplification (RPA) of target DNA and subsequent Cas12a ssDNase activation. Card has a detection limit of 10 CFUs of A. pleuropneumoniae, and there is no cross-reactivity with other common swine pathogens. The detection process can be completed in 1 h, and there was 100% agreement between the conventional apxIVA-based PCR and Card in detecting A. pleuropneumoniae in lung samples. Microplate fluorescence readout enables high-throughput use in diagnostic laboratories, and naked eye and lateral flow test readouts enable use at the point of care. We conclude that Card is a versatile, rapid, accurate molecular diagnostic platform suitable for use in both laboratory and low-resource settings.
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Affiliation(s)
- Tian Luan
- State Key Laboratory of Veterinary Biotechnology, Division of Bacterial Diseases, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Lu Wang
- College of Veterinary Medicine, Xinjiang Agricultural University, Xinjiang, China
| | - Jiyu Zhao
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, China
| | - Hui Luan
- State Key Laboratory of Veterinary Biotechnology, Division of Bacterial Diseases, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Yueling Zhang
- State Key Laboratory of Veterinary Biotechnology, Division of Bacterial Diseases, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Chunlai Wang
- State Key Laboratory of Veterinary Biotechnology, Division of Bacterial Diseases, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Paul R Langford
- Section of Paediatric Infectious Disease, Department of Infectious Disease, Imperial College London, St. Mary's Campus, London, United Kingdom
| | - Siguo Liu
- State Key Laboratory of Veterinary Biotechnology, Division of Bacterial Diseases, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Wanjiang Zhang
- State Key Laboratory of Veterinary Biotechnology, Division of Bacterial Diseases, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Gang Li
- State Key Laboratory of Veterinary Biotechnology, Division of Bacterial Diseases, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
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Niazian M, Belzile F, Torkamaneh D. CRISPR/Cas9 in Planta Hairy Root Transformation: A Powerful Platform for Functional Analysis of Root Traits in Soybean. PLANTS (BASEL, SWITZERLAND) 2022; 11:1044. [PMID: 35448772 PMCID: PMC9027312 DOI: 10.3390/plants11081044] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 04/07/2022] [Accepted: 04/08/2022] [Indexed: 12/22/2022]
Abstract
Sequence and expression data obtained by next-generation sequencing (NGS)-based forward genetics methods often allow the identification of candidate causal genes. To provide true experimental evidence of a gene's function, reverse genetics techniques are highly valuable. Site-directed mutagenesis through transfer DNA (T-DNA) delivery is an efficient reverse screen method in plant functional analysis. Precise modification of targeted crop genome sequences is possible through the stable and/or transient delivery of clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated protein (CRISPR/Cas) reagents. Currently, CRISPR/Cas9 is the most powerful reverse genetics approach for fast and precise functional analysis of candidate genes/mutations of interest. Rapid and large-scale analyses of CRISPR/Cas-induced mutagenesis is achievable through Agrobacterium rhizogenes-mediated hairy root transformation. The combination of A. rhizogenes hairy root-CRISPR/Cas provides an extraordinary platform for rapid, precise, easy, and cost-effective "in root" functional analysis of genes of interest in legume plants, including soybean. Both hairy root transformation and CRISPR/Cas9 techniques have their own complexities and considerations. Here, we discuss recent advancements in soybean hairy root transformation and CRISPR/Cas9 techniques. We highlight the critical factors required to enhance mutation induction and hairy root transformation, including the new generation of reporter genes, methods of Agrobacterium infection, accurate gRNA design strategies, Cas9 variants, gene regulatory elements of gRNAs and Cas9 nuclease cassettes and their configuration in the final binary vector to study genes involved in root-related traits in soybean.
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Affiliation(s)
- Mohsen Niazian
- Département de Phytologie, Université Laval, Québec City, QC G1V 0A6, Canada; (M.N.); (F.B.)
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec City, QC G1V 0A6, Canada
- Field and Horticultural Crops Research Department, Kurdistan Agricultural and Natural Resources Research and Education Center, Agricultural Research, Education and Extension Organization (AREEO), Sanandaj 6616936311, Iran
| | - François Belzile
- Département de Phytologie, Université Laval, Québec City, QC G1V 0A6, Canada; (M.N.); (F.B.)
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec City, QC G1V 0A6, Canada
| | - Davoud Torkamaneh
- Département de Phytologie, Université Laval, Québec City, QC G1V 0A6, Canada; (M.N.); (F.B.)
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec City, QC G1V 0A6, Canada
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Xu H, Guo Y, Qiu L, Ran Y. Progress in Soybean Genetic Transformation Over the Last Decade. FRONTIERS IN PLANT SCIENCE 2022; 13:900318. [PMID: 35755694 PMCID: PMC9231586 DOI: 10.3389/fpls.2022.900318] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2022] [Accepted: 05/11/2022] [Indexed: 05/13/2023]
Abstract
Soybean is one of the important food, feed, and biofuel crops in the world. Soybean genome modification by genetic transformation has been carried out for trait improvement for more than 4 decades. However, compared to other major crops such as rice, soybean is still recalcitrant to genetic transformation, and transgenic soybean production has been hampered by limitations such as low transformation efficiency and genotype specificity, and prolonged and tedious protocols. The primary goal in soybean transformation over the last decade is to achieve high efficiency and genotype flexibility. Soybean transformation has been improved by modifying tissue culture conditions such as selection of explant types, adjustment of culture medium components and choice of selection reagents, as well as better understanding the transformation mechanisms of specific approaches such as Agrobacterium infection. Transgenesis-based breeding of soybean varieties with new traits is now possible by development of improved protocols. In this review, we summarize the developments in soybean genetic transformation to date, especially focusing on the progress made using Agrobacterium-mediated methods and biolistic methods over the past decade. We also discuss current challenges and future directions.
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Affiliation(s)
- Hu Xu
- Tianjin Genovo Biotechnology Co., Ltd., Tianjin, China
| | - Yong Guo
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Lijuan Qiu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
- *Correspondence: Lijuan Qiu,
| | - Yidong Ran
- Tianjin Genovo Biotechnology Co., Ltd., Tianjin, China
- Yidong Ran,
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