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Kumari M, Checker VG, Kathpalia R, Srivastava V, Singh IK, Singh A. Metabolic engineering for enhanced terpenoid production: Leveraging new horizons with an old technique. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 210:108511. [PMID: 38593484 DOI: 10.1016/j.plaphy.2024.108511] [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: 12/07/2023] [Revised: 02/06/2024] [Accepted: 03/06/2024] [Indexed: 04/11/2024]
Abstract
Terpenoids are a vast class of plant specialized metabolites (PSMs) manufactured by plants and are involved in their interactions with environment. In addition, they add health benefits to human nutrition and are widely used as pharmaceutically active compounds. However, native plants produce a limited amount of terpenes restricting metabolite yield of terpene-related metabolites. Exponential growth in the plant metabolome data and the requirement of alternative approaches for producing the desired amount of terpenoids, has redirected plant biotechnology research to plant metabolic engineering, which requires in-depth knowledge and precise expertise about dynamic plant metabolic pathways and cellular physiology. Metabolic engineering is an assuring tool for enhancing the concentration of terpenes by adopting specific strategies such as overexpression of the key genes associated with the biosynthesis of targeted metabolites, controlling the modulation of transcription factors, downregulation of competitive pathways (RNAi), co-expression of the biosynthetic pathway genes in heterologous system and other combinatorial approaches. Microorganisms, fast-growing host plants (such as Nicotiana benthamiana), and cell suspension/callus cultures have provided better means for producing valuable terpenoids. Manipulation in the biosynthetic pathways responsible for synthesis of terpenoids can provide opportunities to enhance the content of desired terpenoids and open up new avenues to enhance their production. This review deliberates the worth of metabolic engineering in medicinal plants to resolve issues associated with terpenoid production at a commercial scale. However, to bring the revolution through metabolic engineering, further implementation of genome editing, elucidation of metabolic pathways using omics approaches, system biology approaches, and synthetic biology tactics are essentially needed.
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Affiliation(s)
- Megha Kumari
- Department of Plant Molecular Biology, University of Delhi South Campus, Benito Juarez Road, Dhaula Kuan, New Delhi, 110021, India; Department of Botany, Hansraj College, University of Delhi, Delhi, 110007, India
| | | | - Renu Kathpalia
- Department of Botany, Kirori Mal College, University of Delhi, Delhi, 110007, India
| | - Vikas Srivastava
- Department of Botany, School of Life Sciences, Central University of Jammu, Samba, 181143, India
| | - Indrakant Kumar Singh
- Molecular Biology Research Lab, Department of Zoology, Deshbandhu College, University of Delhi, Kalkaji, New Delhi, 110019, India
| | - Archana Singh
- Department of Plant Molecular Biology, University of Delhi South Campus, Benito Juarez Road, Dhaula Kuan, New Delhi, 110021, India; Department of Botany, Hansraj College, University of Delhi, Delhi, 110007, India; Delhi School of Climate Change and Sustainability, Institution of Eminence, Maharishi Karnad Bhawan, University of Delhi, Delhi, India.
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Hernandes-Lopes J, Pinto MS, Vieira LR, Monteiro PB, Gerasimova SV, Nonato JVA, Bruno MHF, Vikhorev A, Rausch-Fernandes F, Gerhardt IR, Pauwels L, Arruda P, Dante RA, Yassitepe JEDCT. Enabling genome editing in tropical maize lines through an improved, morphogenic regulator-assisted transformation protocol. Front Genome Ed 2023; 5:1241035. [PMID: 38144709 PMCID: PMC10748596 DOI: 10.3389/fgeed.2023.1241035] [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: 06/15/2023] [Accepted: 11/20/2023] [Indexed: 12/26/2023] Open
Abstract
The recalcitrance exhibited by many maize (Zea mays) genotypes to traditional genetic transformation protocols poses a significant challenge to the large-scale application of genome editing (GE) in this major crop species. Although a few maize genotypes are widely used for genetic transformation, they prove unsuitable for agronomic tests in field trials or commercial applications. This challenge is exacerbated by the predominance of transformable maize lines adapted to temperate geographies, despite a considerable proportion of maize production occurring in the tropics. Ectopic expression of morphogenic regulators (MRs) stands out as a promising approach to overcome low efficiency and genotype dependency, aiming to achieve 'universal' transformation and GE capabilities in maize. Here, we report the successful GE of agronomically relevant tropical maize lines using a MR-based, Agrobacterium-mediated transformation protocol previously optimized for the B104 temperate inbred line. To this end, we used a CRISPR/Cas9-based construct aiming at the knockout of the VIRESCENT YELLOW-LIKE (VYL) gene, which results in an easily recognizable phenotype. Mutations at VYL were verified in protoplasts prepared from B104 and three tropical lines, regardless of the presence of a single nucleotide polymorphism (SNP) at the seed region of the VYL target site in two of the tropical lines. Three out of five tropical lines were amenable to transformation, with efficiencies reaching up to 6.63%. Remarkably, 97% of the recovered events presented indels at the target site, which were inherited by the next generation. We observed off-target activity of the CRISPR/Cas9-based construct towards the VYL paralog VYL-MODIFIER, which could be partly due to the expression of the WUSCHEL (WUS) MR. Our results demonstrate efficient GE of relevant tropical maize lines, expanding the current availability of GE-amenable genotypes of this major crop.
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Affiliation(s)
- José Hernandes-Lopes
- Genomics for Climate Change Research Center (GCCRC), Universidade Estadual de Campinas, Campinas, Brazil
- Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas, Campinas, Brazil
| | - Maísa Siqueira Pinto
- Genomics for Climate Change Research Center (GCCRC), Universidade Estadual de Campinas, Campinas, Brazil
- Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas, Campinas, Brazil
| | - Letícia Rios Vieira
- Genomics for Climate Change Research Center (GCCRC), Universidade Estadual de Campinas, Campinas, Brazil
- Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas, Campinas, Brazil
| | - Patrícia Brant Monteiro
- Genomics for Climate Change Research Center (GCCRC), Universidade Estadual de Campinas, Campinas, Brazil
- Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas, Campinas, Brazil
| | - Sophia V. Gerasimova
- Genomics for Climate Change Research Center (GCCRC), Universidade Estadual de Campinas, Campinas, Brazil
- Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas, Campinas, Brazil
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Juliana Vieira Almeida Nonato
- Genomics for Climate Change Research Center (GCCRC), Universidade Estadual de Campinas, Campinas, Brazil
- Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas, Campinas, Brazil
| | - Maria Helena Faustinoni Bruno
- Genomics for Climate Change Research Center (GCCRC), Universidade Estadual de Campinas, Campinas, Brazil
- Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas, Campinas, Brazil
| | - Alexander Vikhorev
- Frontier Engineering School, Novosibirsk State University, Novosibirsk, Russia
| | - Fernanda Rausch-Fernandes
- Genomics for Climate Change Research Center (GCCRC), Universidade Estadual de Campinas, Campinas, Brazil
- Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas, Campinas, Brazil
- Embrapa Agricultura Digital, Campinas, Brazil
| | - Isabel R. Gerhardt
- Genomics for Climate Change Research Center (GCCRC), Universidade Estadual de Campinas, Campinas, Brazil
- Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas, Campinas, Brazil
- Embrapa Agricultura Digital, Campinas, Brazil
| | - Laurens Pauwels
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Paulo Arruda
- Genomics for Climate Change Research Center (GCCRC), Universidade Estadual de Campinas, Campinas, Brazil
- Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas, Campinas, Brazil
- Departamento de Genética, Evolução, Microbiologia e Imunologia, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, Brazil
| | - Ricardo A. Dante
- Genomics for Climate Change Research Center (GCCRC), Universidade Estadual de Campinas, Campinas, Brazil
- Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas, Campinas, Brazil
- Embrapa Agricultura Digital, Campinas, Brazil
| | - Juliana Erika de Carvalho Teixeira Yassitepe
- Genomics for Climate Change Research Center (GCCRC), Universidade Estadual de Campinas, Campinas, Brazil
- Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas, Campinas, Brazil
- Embrapa Agricultura Digital, Campinas, Brazil
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Movahedi A, Aghaei-Dargiri S, Li H, Zhuge Q, Sun W. CRISPR Variants for Gene Editing in Plants: Biosafety Risks and Future Directions. Int J Mol Sci 2023; 24:16241. [PMID: 38003431 PMCID: PMC10671001 DOI: 10.3390/ijms242216241] [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: 09/27/2023] [Revised: 10/25/2023] [Accepted: 11/09/2023] [Indexed: 11/26/2023] Open
Abstract
The CRISPR genome editing technology is a crucial tool for enabling revolutionary advancements in plant genetic improvement. This review shows the latest developments in CRISPR/Cas9 genome editing system variants, discussing their benefits and limitations for plant improvement. While this technology presents immense opportunities for plant breeding, it also raises serious biosafety concerns that require careful consideration, including potential off-target effects and the unintended transfer of modified genes to other organisms. This paper highlights strategies to mitigate biosafety risks and explores innovative plant gene editing detection methods. Our review investigates the international biosafety guidelines for gene-edited crops, analyzing their broad implications for agricultural and biotechnology research and advancement. We hope to provide illuminating and refined perspectives for industry practitioners and policymakers by evaluating CRISPR genome enhancement in plants.
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Affiliation(s)
- Ali Movahedi
- Department of Biology and the Environment, College of Life Sciences, Nanjing Forestry University, Nanjing 210037, China
| | - Soheila Aghaei-Dargiri
- Department of Biological Control Research, Iranian Research Institute of Plant Protection, Agricultural Research Education and Extension Organization (AREEO), Tehran 19858-13111, Iran
| | - Hongyan Li
- Department of Biology and the Environment, College of Life Sciences, Nanjing Forestry University, Nanjing 210037, China
| | - Qiang Zhuge
- Department of Biology and the Environment, College of Life Sciences, Nanjing Forestry University, Nanjing 210037, China
| | - Weibo Sun
- Department of Biology and the Environment, College of Life Sciences, Nanjing Forestry University, Nanjing 210037, China
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Nishihara M, Hirabuchi A, Goto F, Watanabe A, Yoshida C, Washiashi R, Odashima M, Nemoto K. Efficient double-flowered gentian plant production using the CRISPR/Cas9 system. PLANT BIOTECHNOLOGY (TOKYO, JAPAN) 2023; 40:229-236. [PMID: 38420567 PMCID: PMC10901158 DOI: 10.5511/plantbiotechnology.23.0424a] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Accepted: 04/24/2023] [Indexed: 03/02/2024]
Abstract
Japanese cultivated gentians are highly valued ornamental flowers in Japan, but the flower shape is mostly limited to the single-flower type, unlike other flowers such as roses and carnations. To overcome this limitation, we used the CRISPR/Cas9 genome editing system to increase double-flowered genetic resources in gentians. Our approach targeted an AGAMOUS (AG) floral homeotic gene (AG1), which is responsible for the natural mutation that causes double flowers in gentians. We designed two targets in exon 1 of AG1 for genome editing and found that 9 of 12 herbicide-resistant shoots had biallelic mutations in the target regions of AG1. These nine lines all produced double flowers, with stamens converted into petaloid organs, similar to the natural mutant. We also analyzed the off-target effects of AG2, which is homologous to AG1, and found that such effects occurred in gentian genome editing but with low frequency. Furthermore, we successfully produced transgene-free genome-edited plants (null segregants) by crossing with wild-type pollen. F1 seedlings were subjected to PCR analysis to determine whether foreign DNA sequences, two partial regions of the CaMV35S promoter and Cas9 gene, were present in the genome. As a result, foreign genes were segregated at a 1 : 1 ratio, indicating successful null segregant production. Using PCR analysis, we confirmed that four representative null segregants did not contain transfer DNA. In summary, our study demonstrates that the CRISPR/Cas9 system can efficiently produce double-flowered gentians, and null segregants can also be obtained. These genome-edited plants are valuable genetic resources for future gentian breeding programs.
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Affiliation(s)
- Masahiro Nishihara
- Iwate Biotechnology Research Center, 22-174-4 Narita, Kitakami, Iwate 024-0003, Japan
| | - Akiko Hirabuchi
- Iwate Biotechnology Research Center, 22-174-4 Narita, Kitakami, Iwate 024-0003, Japan
| | - Fumina Goto
- Iwate Biotechnology Research Center, 22-174-4 Narita, Kitakami, Iwate 024-0003, Japan
| | - Aiko Watanabe
- Iwate Biotechnology Research Center, 22-174-4 Narita, Kitakami, Iwate 024-0003, Japan
| | - Chiharu Yoshida
- Iwate Biotechnology Research Center, 22-174-4 Narita, Kitakami, Iwate 024-0003, Japan
| | - Rie Washiashi
- Iwate Biotechnology Research Center, 22-174-4 Narita, Kitakami, Iwate 024-0003, Japan
| | - Masashi Odashima
- Iwate Agricultural Research Center, 20-1 Narita, Kitakami, Iwate 024-0003, Japan
| | - Keiichirou Nemoto
- Iwate Biotechnology Research Center, 22-174-4 Narita, Kitakami, Iwate 024-0003, Japan
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Elsharawy H, Refat M. CRISPR/Cas9 genome editing in wheat: enhancing quality and productivity for global food security-a review. Funct Integr Genomics 2023; 23:265. [PMID: 37541970 DOI: 10.1007/s10142-023-01190-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 07/26/2023] [Accepted: 07/27/2023] [Indexed: 08/06/2023]
Abstract
Wheat (Triticum aestivum L.) is an important cereal crop that is grown all over the world for food and industrial purposes. Wheat is essential to the human diet due to its rich content of necessary amino acids, minerals, vitamins, and calories. Various wheat breeding techniques have been utilized to improve its quality, productivity, and resistance to biotic and abiotic stress impairing production. However, these techniques are expensive, demanding, and time-consuming. Additionally, these techniques need multiple generations to provide the desired results, and the improved traits could be lost over time. To overcome these challenges, researchers have developed various genome editing tools to improve the quality and quantity of cereal crops, including wheat. Genome editing technologies evolve quickly. Nowadays, single or multiple mutations can be enabled and targeted at specific loci in the plant genome, allowing controlled removal of undesirable features or insertion of advantageous ones. Clustered, regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated protein (Cas) is a powerful genome editing tool that can be effectively used for precise genome editing of wheat and other crops. This review aims to provide a comprehensive understanding of this technology's potential applications to enhance wheat's quality and productivity. It will first explore the function of CRISPR/Cas9 in preserving the adaptive immunity of prokaryotic organisms, followed by a discussion of its current applications in wheat breeding.
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Affiliation(s)
- Hany Elsharawy
- Department of Genetics, Faculty of Agriculture, Cairo University, Giza, Egypt.
| | - Moath Refat
- Department of Biochemistry and Molecular Biology, The Key Laboratory of Environment and Genes Related to Disease of Ministry of Education, Health Science Center, Xi'an Jiaotong, University, Xi'an, 710061, China
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Nishiguchi M, Futamura N, Endo M, Mikami M, Toki S, Katahata SI, Ohmiya Y, Konagaya KI, Nanasato Y, Taniguchi T, Maruyama TE. CRISPR/Cas9-mediated disruption of CjACOS5 confers no-pollen formation on sugi trees (Cryptomeria japonica D. Don). Sci Rep 2023; 13:11779. [PMID: 37479866 PMCID: PMC10361980 DOI: 10.1038/s41598-023-38339-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Accepted: 07/06/2023] [Indexed: 07/23/2023] Open
Abstract
Sugi (Cryptomeria japonica D. Don) is an economically important coniferous tree in Japan. However, abundant sugi pollen grains are dispersed and transported by the wind each spring and cause a severe pollen allergy syndrome (Japanese cedar pollinosis). The use of pollen-free sugi that cannot produce pollen has been thought as a countermeasure to Japanese cedar pollinosis. The sugi CjACOS5 gene is an ortholog of Arabidopsis ACOS5 and rice OsACOS12, which encode an acyl-CoA synthetase that is involved in the synthesis of sporopollenin in pollen walls. To generate pollen-free sugi, we mutated CjACOS5 using the CRISPR/Cas9 system. As a result of sugi transformation mediated by Agrobacterium tumefaciens harboring the CjACOS5-targeted CRISPR/Cas9 vector, 1 bp-deleted homo biallelic mutant lines were obtained. Chimeric mutant lines harboring both mutant and wild-type CjACOS5 genes were also generated. The homo biallelic mutant lines had no-pollen in male strobili, whereas chimeric mutant lines had male strobili with or without pollen grains. Our results suggest that CjACOS5 is essential for the production of pollen in sugi and that its disruption is useful for the generation of pollen-free sugi. In addition to conventional transgenic technology, genome editing technology, including CRISPR/Cas9, can confer new traits on sugi.
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Affiliation(s)
- Mitsuru Nishiguchi
- Department of Forest Molecular Genetics and Biotechnology, Forestry and Forest Products Research Institute (FFPRI), 1 Matsunosato, Tsukuba, Ibaraki, 305-8687, Japan.
| | - Norihiro Futamura
- Department of Forest Molecular Genetics and Biotechnology, Forestry and Forest Products Research Institute (FFPRI), 1 Matsunosato, Tsukuba, Ibaraki, 305-8687, Japan
| | - Masaki Endo
- Institute of Agrobiological Sciences, National Agriculture and Food Research Organization (NARO), 1-2 Owashi, Tsukuba, Ibaraki, 305-8634, Japan
- Graduate School of Nanobioscience, Yokohama City University, 22-2 Seto, Kanazawa-ku, Yokohama, Kanagawa, 236-0027, Japan
| | - Masafumi Mikami
- Institute of Agrobiological Sciences, National Agriculture and Food Research Organization (NARO), 1-2 Owashi, Tsukuba, Ibaraki, 305-8634, Japan
| | - Seiichi Toki
- Institute of Agrobiological Sciences, National Agriculture and Food Research Organization (NARO), 1-2 Owashi, Tsukuba, Ibaraki, 305-8634, Japan
- Graduate School of Nanobioscience, Yokohama City University, 22-2 Seto, Kanazawa-ku, Yokohama, Kanagawa, 236-0027, Japan
- Department of Plant Life Science, Faculty of Agriculture, Ryukoku University, 1-5 Yokotani, Seta Oe-cho, Otsu, Shiga, 520-2194, Japan
- Kihara Institute for Biological Research, Yokohama City University, 641-12 Maioka-cho, Totsuka-ku, Yokohama, Kanagawa, 244-0813, Japan
| | - Shin-Ichiro Katahata
- Faculty of Applied Biological Sciences, Gifu University, Yanagido 1-1, Gifu, 501-1193, Japan
| | - Yasunori Ohmiya
- Extension and International Cooperation Department, Forest Tree Breeding Center, Forestry and Forest Products Research Institute (FFPRI), 3809-1 Ishi, Juo, Hitachi, Ibaraki, 319-1301, Japan
| | - Ken-Ichi Konagaya
- Forest Bio-Research Center, Forestry and Forest Products Research Institute (FFPRI), 3809-1 Ishi, Juo, Hitachi, Ibaraki, 319-1301, Japan
| | - Yoshihiko Nanasato
- Forest Bio-Research Center, Forestry and Forest Products Research Institute (FFPRI), 3809-1 Ishi, Juo, Hitachi, Ibaraki, 319-1301, Japan
| | - Toru Taniguchi
- Forest Bio-Research Center, Forestry and Forest Products Research Institute (FFPRI), 3809-1 Ishi, Juo, Hitachi, Ibaraki, 319-1301, Japan
| | - Tsuyoshi Emilio Maruyama
- Department of Forest Molecular Genetics and Biotechnology, Forestry and Forest Products Research Institute (FFPRI), 1 Matsunosato, Tsukuba, Ibaraki, 305-8687, Japan
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Slaman E, Lammers M, Angenent GC, de Maagd RA. High-throughput sgRNA testing reveals rules for Cas9 specificity and DNA repair in tomato cells. Front Genome Ed 2023; 5:1196763. [PMID: 37346168 PMCID: PMC10279869 DOI: 10.3389/fgeed.2023.1196763] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Accepted: 05/22/2023] [Indexed: 06/23/2023] Open
Abstract
CRISPR/Cas9 technology has the potential to significantly enhance plant breeding. To determine the specificity and the mutagenic spectrum of SpCas9 in tomato, we designed 89 g(uide) RNAs targeting genes of the tomato MYB transcription factor family with varying predicted specificities. Plasmids encoding sgRNAs and Cas9 were introduced into tomato protoplasts, and target sites as well as 224 predicted off-target sites were screened for the occurrence of mutations using amplicon sequencing. Algorithms for the prediction of efficacy of the sgRNAs had little predictive power in this system. The analysis of mutations suggested predictable identity of single base insertions. Off-target mutations were found for 13 out of 89 sgRNAs and only occurred at positions with one or two mismatches (at 14 and 3 sites, respectively). We found that PAM-proximal mismatches do not preclude low frequency off-target mutations. Off-target mutations were not found at all 138 positions that had three or four mismatches. We compared off-target mutation frequencies obtained with plasmid encoding sgRNAs and Cas9 with those induced by ribonucleoprotein (RNP) transfections. The use of RNPs led to a significant decrease in relative off-target frequencies at 6 out of 17, no significant difference at 9, and an increase at 2 sites. Additionally, we show that off-target sequences with insertions or deletions relative to the sgRNA may be mutated, and should be considered during sgRNA design. Altogether, our data help sgRNA design by providing insight into the Cas9-induced double-strand break repair outcomes and the occurrence of off-target mutations.
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Affiliation(s)
- Ellen Slaman
- Laboratory of Molecular Biology, Wageningen University & Research, Wageningen, Netherlands
- Bioscience, Wageningen University & Research, Wageningen, Netherlands
| | - Michiel Lammers
- Bioscience, Wageningen University & Research, Wageningen, Netherlands
| | - Gerco C. Angenent
- Laboratory of Molecular Biology, Wageningen University & Research, Wageningen, Netherlands
- Bioscience, Wageningen University & Research, Wageningen, Netherlands
| | - Ruud A. de Maagd
- Bioscience, Wageningen University & Research, Wageningen, Netherlands
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Mackon E, Mackon GCJDE, Guo Y, Ma Y, Yao Y, Liu P. Development and Application of CRISPR/Cas9 to Improve Anthocyanin Pigmentation in Plants: Opportunities and Perspectives. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2023:111746. [PMID: 37230190 DOI: 10.1016/j.plantsci.2023.111746] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 04/22/2023] [Accepted: 05/21/2023] [Indexed: 05/27/2023]
Abstract
Since its discovery in 2012, the novel technology of clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated protein 9 (Cas9) has greatly contributed to revolutionizing molecular biology. It has been demonstrated to be an effective approach for identifying gene function and improving some important traits. Anthocyanins are secondary metabolites responsible for a wide spectrum of aesthetic coloration in various plant organs and are beneficial for health. As such, increasing anthocyanin content in plants, especially the edible tissue and organs, is always a main goal for plant breeding. Recently, CRISPR/Cas9 technology has been highly desired to enhance the amount of anthocyanin in vegetables, fruits, cereals, and other attractive plants with more precision. Here we reviewed the recent knowledge concerning CRISPR/Cas9-mediated anthocyanin enhancement in plants. In addition, we addressed the future avenues of promising potential target genes that could be helpful for achieving the same goal using CRISPR/Cas9 in several plants. Thus, molecular biologists, genetic engineers, agricultural scientists, plant geneticists, and physiologists may benefit from CRISPR technology to boost the biosynthesis and accumulation of anthocyanins in fresh fruits, vegetables, grains, roots, and ornamental plants.
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Affiliation(s)
- Enerand Mackon
- State Key Laboratory of Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Science and Technology, Guangxi University.
| | | | - Yongqiang Guo
- State Key Laboratory of Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning 530005, P.R. China.
| | - Yafei Ma
- State Key Laboratory of Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning 530005, P.R. China.
| | - Yuhang Yao
- State Key Laboratory of Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning 530005, P.R. China.
| | - Piqing Liu
- State Key Laboratory of Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning 530005, P.R. China.
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Brower-Toland B, Shyu C, Vega-Sanchez ME, Slewinski TL. Pedigree or identity? How genome editing can fundamentally change the path for crop development. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:2794-2798. [PMID: 36738269 PMCID: PMC10134896 DOI: 10.1093/jxb/erad033] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Accepted: 01/24/2023] [Indexed: 06/06/2023]
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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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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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Mateo-Bonmatí E. Massive effects on chromatin after ploidy rearrangement in doubled haploids. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:677-679. [PMID: 36739579 PMCID: PMC9899410 DOI: 10.1093/jxb/erac478] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
This article comments on:Piskorz EW, Xu L, Ma Y, Jiang H. 2023. Doubled-haploid induction generates extensive differential DNA methylation in Arabidopsis. Journal of Experimental Botany 74, 835–847
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Affiliation(s)
- Eduardo Mateo-Bonmatí
- Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Colney Ln, NR4 7UH, UK
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13
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Tamura K, Sakamoto M, Tanizawa Y, Mochizuki T, Matsushita S, Kato Y, Ishikawa T, Okuhara K, Nakamura Y, Bono H. A highly contiguous genome assembly of red perilla (Perilla frutescens) domesticated in Japan. DNA Res 2023; 30:dsac044. [PMID: 36383440 PMCID: PMC9835750 DOI: 10.1093/dnares/dsac044] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 11/09/2022] [Accepted: 11/11/2022] [Indexed: 11/17/2022] Open
Abstract
Perilla frutescens (Lamiaceae) is an important herbal plant with hundreds of bioactive chemicals, among which perillaldehyde and rosmarinic acid are the two major bioactive compounds in the plant. The leaves of red perilla are used as traditional Kampo medicine or food ingredients. However, the medicinal and nutritional uses of this plant could be improved by enhancing the production of valuable metabolites through the manipulation of key enzymes or regulatory genes using genome editing technology. Here, we generated a high-quality genome assembly of red perilla domesticated in Japan. A near-complete chromosome-level assembly of P. frutescens was generated contigs with N50 of 41.5 Mb from PacBio HiFi reads. 99.2% of the assembly was anchored into 20 pseudochromosomes, among which seven pseudochromosomes consisted of one contig, while the rest consisted of less than six contigs. Gene annotation and prediction of the sequences successfully predicted 86,258 gene models, including 76,825 protein-coding genes. Further analysis showed that potential targets of genome editing for the engineering of anthocyanin pathways in P. frutescens are located on the late-stage pathways. Overall, our genome assembly could serve as a valuable reference for selecting target genes for genome editing of P. frutescens.
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Affiliation(s)
- Keita Tamura
- Laboratory of Genome Informatics, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Hiroshima 739-0046, Japan
- Laboratory of BioDX, Genome Editing Innovation Center, Hiroshima University, Higashi-Hiroshima, Hiroshima 739-0046, Japan
| | - Mika Sakamoto
- Genome Informatics Laboratory, Department of Informatics, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| | - Yasuhiro Tanizawa
- Genome Informatics Laboratory, Department of Informatics, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| | - Takako Mochizuki
- Genome Informatics Laboratory, Department of Informatics, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| | - Shuji Matsushita
- Agricultural Technology Research Center, Hiroshima Prefectural Technology Research Institute, Higashi-Hiroshima, Hiroshima 739-0151, Japan
| | - Yoshihiro Kato
- Mishima Foods Co., Ltd., Hiroshima City, Hiroshima 733-0036, Japan
| | - Takeshi Ishikawa
- Mishima Foods Co., Ltd., Hiroshima City, Hiroshima 733-0036, Japan
| | - Keisuke Okuhara
- Laboratory of Genome Informatics, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Hiroshima 739-0046, Japan
- PtBio Inc., Higashi-Hiroshima, Hiroshima 739-0046, Japan
| | - Yasukazu Nakamura
- Genome Informatics Laboratory, Department of Informatics, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| | - Hidemasa Bono
- Laboratory of Genome Informatics, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Hiroshima 739-0046, Japan
- Laboratory of BioDX, Genome Editing Innovation Center, Hiroshima University, Higashi-Hiroshima, Hiroshima 739-0046, Japan
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14
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Barrero LS, Willmann MR, Craft EJ, Akther KM, Harrington SE, Garzon‐Martinez GA, Glahn RP, Piñeros MA, McCouch SR. Identifying genes associated with abiotic stress tolerance suitable for CRISPR/Cas9 editing in upland rice cultivars adapted to acid soils. PLANT DIRECT 2022; 6:e469. [PMID: 36514785 PMCID: PMC9737570 DOI: 10.1002/pld3.469] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 11/07/2022] [Accepted: 11/08/2022] [Indexed: 06/17/2023]
Abstract
Five genes of large phenotypic effect known to confer abiotic stress tolerance in rice were selected to characterize allelic variation in commercial Colombian tropical japonica upland rice cultivars adapted to drought-prone acid soil environments (cv. Llanura11 and Porvenir12). Allelic variants of the genes ART1, DRO1, SUB1A, PSTOL1, and SPDT were characterized by PCR and/or Sanger sequencing in the two upland cultivars and compared with the Nipponbare and other reference genomes. Two genes were identified as possible targets for gene editing: SUB1A (Submergence 1A), to improve tolerance to flooding, and SPDT (SULTR3;4) (SULTR-like Phosphorus Distribution Transporter), to improve phosphorus utilization efficiency and grain quality. Based on technical and regulatory considerations, SPDT was targeted for editing. The two upland cultivars were shown to carry the SPDT wild-type (nondesirable) allele based on sequencing, RNA expression, and phenotypic evaluations under hydroponic and greenhouse conditions. A gene deletion was designed using the CRISPR/Cas9 system, and specialized reagents were developed for SPDT editing, including vectors targeting the gene and a protoplast transfection transient assay. The desired edits were confirmed in protoplasts and serve as the basis for ongoing plant transformation experiments aiming to improve the P-use efficiency of upland rice grown in acidic soils.
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Affiliation(s)
- Luz S. Barrero
- Corporacion Colombiana de Investigacion AgropecuariaAGROSAVIAMosqueraColombia
- Plant Breeding & Genetics Section, School of Integrative Plant ScienceCornell UniversityIthacaNew YorkUSA
| | - Matthew R. Willmann
- Plant Transformation Facility, School of Integrative Plant ScienceCornell UniversityIthacaNew YorkUSA
- Present address:
USDA‐ARS, Robert W. Holley CenterIthacaNew YorkUSA
| | - Eric J. Craft
- Present address:
USDA‐ARS, Robert W. Holley CenterIthacaNew YorkUSA
| | - Kazi M. Akther
- Plant Breeding & Genetics Section, School of Integrative Plant ScienceCornell UniversityIthacaNew YorkUSA
| | - Sandra E. Harrington
- Plant Breeding & Genetics Section, School of Integrative Plant ScienceCornell UniversityIthacaNew YorkUSA
| | | | - Raymond P. Glahn
- Present address:
USDA‐ARS, Robert W. Holley CenterIthacaNew YorkUSA
| | | | - Susan R. McCouch
- Plant Breeding & Genetics Section, School of Integrative Plant ScienceCornell UniversityIthacaNew YorkUSA
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15
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Luo G, Najafi J, Correia PMP, Trinh MDL, Chapman EA, Østerberg JT, Thomsen HC, Pedas PR, Larson S, Gao C, Poland J, Knudsen S, DeHaan L, Palmgren M. Accelerated Domestication of New Crops: Yield is Key. PLANT & CELL PHYSIOLOGY 2022; 63:1624-1640. [PMID: 35583202 PMCID: PMC9680862 DOI: 10.1093/pcp/pcac065] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Revised: 04/17/2022] [Accepted: 05/17/2022] [Indexed: 05/05/2023]
Abstract
Sustainable agriculture in the future will depend on crops that are tolerant to biotic and abiotic stresses, require minimal input of water and nutrients and can be cultivated with a minimal carbon footprint. Wild plants that fulfill these requirements abound in nature but are typically low yielding. Thus, replacing current high-yielding crops with less productive but resilient species will require the intractable trade-off of increasing land area under cultivation to produce the same yield. Cultivating more land reduces natural resources, reduces biodiversity and increases our carbon footprint. Sustainable intensification can be achieved by increasing the yield of underutilized or wild plant species that are already resilient, but achieving this goal by conventional breeding programs may be a long-term prospect. De novo domestication of orphan or crop wild relatives using mutagenesis is an alternative and fast approach to achieve resilient crops with high yields. With new precise molecular techniques, it should be possible to reach economically sustainable yields in a much shorter period of time than ever before in the history of agriculture.
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Affiliation(s)
| | | | | | | | | | | | | | - Pai Rosager Pedas
- Carlsberg Research Laboratory, J.C. Jacobsens Gade 4, Copenhagen V DK-1799, Denmark
| | - Steve Larson
- US Department of Agriculture (USDA), USDA–ARS Forage & Range Research Lab, Utah State University Logan, Logan, UT 84322, USA
| | - Caixia Gao
- Center for Genome Editing, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Jesse Poland
- Center for Desert Agriculture, King Abdullah University of Science and Technology, Thuwal, Makkah 23955, Saudi Arabia
| | - Søren Knudsen
- Carlsberg Research Laboratory, J.C. Jacobsens Gade 4, Copenhagen V DK-1799, Denmark
| | - Lee DeHaan
- The Land Institute, Salina, KS 67401, USA
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16
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Abdul Aziz M, Brini F, Rouached H, Masmoudi K. Genetically engineered crops for sustainably enhanced food production systems. FRONTIERS IN PLANT SCIENCE 2022; 13:1027828. [PMID: 36426158 PMCID: PMC9680014 DOI: 10.3389/fpls.2022.1027828] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Accepted: 10/18/2022] [Indexed: 06/16/2023]
Abstract
Genetic modification of crops has substantially focused on improving traits for desirable outcomes. It has resulted in the development of crops with enhanced yields, quality, and tolerance to biotic and abiotic stresses. With the advent of introducing favorable traits into crops, biotechnology has created a path for the involvement of genetically modified (GM) crops into sustainable food production systems. Although these plants heralded a new era of crop production, their widespread adoption faces diverse challenges due to concerns about the environment, human health, and moral issues. Mitigating these concerns with scientific investigations is vital. Hence, the purpose of the present review is to discuss the deployment of GM crops and their effects on sustainable food production systems. It provides a comprehensive overview of the cultivation of GM crops and the issues preventing their widespread adoption, with appropriate strategies to overcome them. This review also presents recent tools for genome editing, with a special focus on the CRISPR/Cas9 platform. An outline of the role of crops developed through CRSIPR/Cas9 in achieving sustainable development goals (SDGs) by 2030 is discussed in detail. Some perspectives on the approval of GM crops are also laid out for the new age of sustainability. The advancement in molecular tools through plant genome editing addresses many of the GM crop issues and facilitates their development without incorporating transgenic modifications. It will allow for a higher acceptance rate of GM crops in sustainable agriculture with rapid approval for commercialization. The current genetic modification of crops forecasts to increase productivity and prosperity in sustainable agricultural practices. The right use of GM crops has the potential to offer more benefit than harm, with its ability to alleviate food crises around the world.
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Affiliation(s)
- Mughair Abdul Aziz
- Department of Integrative Agriculture, College of Agriculture and Veterinary Medicine, United Arab Emirates University, Al−Ain, Abu−Dhabi, United Arab Emirates
| | - Faical Brini
- Biotechnology and Plant Improvement Laboratory, Centre of Biotechnology of Sfax, University of Sfax, Sfax, Tunisia
| | - Hatem Rouached
- Michigan State University, Plant and Soil Science Building, East Lansing, MI, United States
| | - Khaled Masmoudi
- Department of Integrative Agriculture, College of Agriculture and Veterinary Medicine, United Arab Emirates University, Al−Ain, Abu−Dhabi, United Arab Emirates
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17
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Kalaitzandonakes N, Willig C, Zahringer K. The economics and policy of genome editing in crop improvement. THE PLANT GENOME 2022:e20248. [PMID: 36321718 DOI: 10.1002/tpg2.20248] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Accepted: 05/26/2022] [Indexed: 06/16/2023]
Abstract
In this review article we analyze the economics of genome editing and its potential long-term effect on crop improvement and agriculture. We describe the emergence of genome editing as a novel platform for crop improvement, distinct from the existing platforms of plant breeding and genetic engineering. We review key technical characteristics of genome editing and describe how it enables faster trait development, lower research and development costs, and the development of novel traits not possible through previous crop improvement methods. Given these fundamental technical and economic advantages, we describe how genome editing can greatly increase the productivity and broaden the scope of crop improvement with potential outsized economic effects. We further discuss how the global regulatory policy environment, which is still emerging, can shape the ultimate path of genome editing innovation, its effect on crop improvement, and its overall socioeconomic benefits to society.
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Affiliation(s)
| | | | - Kenneth Zahringer
- Division of Applied Social Sciences, Univ. of Missouri, Columbia, MO, 65211, USA
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18
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ABA-Dependent Regulation of Calcium-Dependent Protein Kinase Gene GmCDPK5 in Cultivated and Wild Soybeans. LIFE (BASEL, SWITZERLAND) 2022; 12:life12101576. [PMID: 36295011 PMCID: PMC9604703 DOI: 10.3390/life12101576] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 09/29/2022] [Accepted: 10/07/2022] [Indexed: 11/07/2022]
Abstract
Calcium-dependent protein kinases (CDPKs) regulate plant development and stress responses. However, the interaction of these protein kinases with the abscisic acid (ABA) stress hormone signalling system has not been studied in detail. In Arabidopsis, AtCPK1 plays an important role in the acclimation of plants to environmental stresses. Phylogenetic and molecular analyses showed that, among 50 isoforms of Glycine max (L.) Merrill CDPKs, the GmCDPK27/GmCDPK48, GmCDPK5/GmCDPK24, and GmCDPK10/GmCDPK46 paralogous pairs were the isoforms most related to AtCDPK1. We investigated the expression of the corresponding six GmCDPKs genes during treatment with cold, heat, and salt stress. Wild soybean was the most resistant to stresses, and among the three cultivars studied (Sfera, Hodgson, and Hefeng25), Sfera was close to the wild type in terms of resistance. GmCDPK5 and GmCDPK10 were the most responsive to stress treatments, especially in wild soybean, compared with cultivars. Among the studied GmCDPK isoforms, only GmCDPK5 expression increased after treatment with abscisic acid (ABA) in a dose- and time-dependent manner. Targeted LC-MS/MS analysis of endogenous ABA levels showed that wild soybean and Sfera had nearly twice the ABA content of Hodgson and Hefeng25. An analysis of the expression of marker genes involved in ABA biosynthesis showed that GmNCED1-gene-encoding 9-cis-epoxycarotenoid dioxygenase 1 is induced to the greatest extent in wild soybean and Sfera under salt, cold, and heat exposure. Our data established a correlation between the induction of GmCDPK5 and ABA biosynthesis genes. GmCDPK5 is an interesting target for genetic and bioengineering purposes and can be used for genetic editing, overexpression, or as a marker gene in soybean varieties growing under unfavourable conditions.
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19
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Jones MGK, Fosu-Nyarko J, Iqbal S, Adeel M, Romero-Aldemita R, Arujanan M, Kasai M, Wei X, Prasetya B, Nugroho S, Mewett O, Mansoor S, Awan MJA, Ordonio RL, Rao SR, Poddar A, Hundleby P, Iamsupasit N, Khoo K. Enabling Trade in Gene-Edited Produce in Asia and Australasia: The Developing Regulatory Landscape and Future Perspectives. PLANTS 2022; 11:plants11192538. [PMID: 36235403 PMCID: PMC9571430 DOI: 10.3390/plants11192538] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 09/12/2022] [Accepted: 09/13/2022] [Indexed: 11/24/2022]
Abstract
Genome- or gene-editing (abbreviated here as ‘GEd’) presents great opportunities for crop improvement. This is especially so for the countries in the Asia-Pacific region, which is home to more than half of the world’s growing population. A brief description of the science of gene-editing is provided with examples of GEd products. For the benefits of GEd technologies to be realized, international policy and regulatory environments must be clarified, otherwise non-tariff trade barriers will result. The status of regulations that relate to GEd crop products in Asian countries and Australasia are described, together with relevant definitions and responsible regulatory bodies. The regulatory landscape is changing rapidly: in some countries, the regulations are clear, in others they are developing, and some countries have yet to develop appropriate policies. There is clearly a need for the harmonization or alignment of GEd regulations in the region: this will promote the path-to-market and enable the benefits of GEd technologies to reach the end-users.
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Affiliation(s)
- Michael G. K. Jones
- Crop Biotechnology Research Group, Centre for Crop and Food Innovation, Food Futures Institute, Murdoch University, Perth, WA 6150, Australia
- Correspondence: ; Tel.: +61-(0)4-1423-9428
| | - John Fosu-Nyarko
- Crop Biotechnology Research Group, Centre for Crop and Food Innovation, Food Futures Institute, Murdoch University, Perth, WA 6150, Australia
| | - Sadia Iqbal
- Crop Biotechnology Research Group, Centre for Crop and Food Innovation, Food Futures Institute, Murdoch University, Perth, WA 6150, Australia
| | - Muhammad Adeel
- Crop Biotechnology Research Group, Centre for Crop and Food Innovation, Food Futures Institute, Murdoch University, Perth, WA 6150, Australia
| | - Rhodora Romero-Aldemita
- ISAAA—BioTrust Global Knowledge Center on Biotechnology, International Service for the Acquisition of Agri-Biotech Applications (ISAAA), IRRI, Los Banos 4031, Philippines
| | - Mahaletchumy Arujanan
- Malaysian Biotechnology Information Centre, Monash University Malaysia, Jalan Lagoon Selatan, Bandar Sunway 47500, Malaysia
| | - Mieko Kasai
- Japan Plant Factory Association, 6-2-1 Kashiwanoha Kashiwa, Chiba 277-0012, Japan
| | - Xun Wei
- Zhongzhi International Institute of Agricultural Biosciences, Research Center of Biology and Agriculture, Shunde Graduate School, University of Science and Technology Beijing, Beijing 100024, China
| | - Bambang Prasetya
- National Biosafety Committee of Genetically Engineered Products (KKH-PRG), Research Center for Testing Technology and Standards, National Research and Innovation Agency (BRIN), Central Jakarta 10340, Indonesia
| | - Satya Nugroho
- Research Center for Genetic Engineering, Research Organization for Life Sciences and Environment, National Research and Innovation Agency (BRIN), Central Jakarta 10340, Indonesia
| | - Osman Mewett
- Australian Seed Federation, 20 Napier Cl, Deakin, Canberra, ACT 2600, Australia
| | - Shahid Mansoor
- National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad 44000, Pakistan
| | - Muhammad J. A. Awan
- National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad 44000, Pakistan
| | - Reynante L. Ordonio
- Crop Biotech Center, Philippine Rice Research Institute, Munoz 3119, Philippines
| | - S. R. Rao
- Sri Balaji Vidyapeeth University, Pondicherry 607402, India
| | - Abhijit Poddar
- MGM Advanced Research Institute, Pondicherry 607402, India
| | - Penny Hundleby
- John Innes Centre, Norwich, Research Park, Norwich NR4 7UH, UK
| | | | - Kay Khoo
- Regulatory Affairs Manager, Seeds Asia-Pacific, BASF Australia Ltd., 12/28 Freshwater Pl, Southbank, VIC 3006, Australia
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20
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Targeted Mutagenesis of the Multicopy Myrosinase Gene Family in Allotetraploid Brassica juncea Reduces Pungency in Fresh Leaves across Environments. PLANTS 2022; 11:plants11192494. [PMID: 36235360 PMCID: PMC9572489 DOI: 10.3390/plants11192494] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Revised: 09/08/2022] [Accepted: 09/19/2022] [Indexed: 11/17/2022]
Abstract
Recent breeding efforts in Brassica have focused on the development of new oilseed feedstock crop for biofuels (e.g., ethanol, biodiesel, bio-jet fuel), bio-industrial uses (e.g., bio-plastics, lubricants), specialty fatty acids (e.g., erucic acid), and producing low glucosinolates levels for oilseed and feed meal production for animal consumption. We identified a novel opportunity to enhance the availability of nutritious, fresh leafy greens for human consumption. Here, we demonstrated the efficacy of disarming the ‘mustard bomb’ reaction in reducing pungency upon the mastication of fresh tissue—a major source of unpleasant flavor and/or odor in leafy Brassica. Using gene-specific mutagenesis via CRISPR-Cas12a, we created knockouts of all functional copies of the type-I myrosinase multigene family in tetraploid Brassica juncea. Our greenhouse and field trials demonstrate, via sensory and biochemical analyses, a stable reduction in pungency in edited plants across multiple environments. Collectively, these efforts provide a compelling path toward boosting the human consumption of nutrient-dense, fresh, leafy green vegetables.
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21
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de Lange J, Nalley LL, Yang W, Shew A, de Steur H. The future of CRISPR gene editing according to plant scientists. iScience 2022; 25:105012. [PMID: 36093047 PMCID: PMC9460836 DOI: 10.1016/j.isci.2022.105012] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Revised: 06/29/2022] [Accepted: 08/19/2022] [Indexed: 11/18/2022] Open
Abstract
This study surveyed 669 plant scientists globally to elicit how (which outcomes of gene editing), where (which continent) and what (which crops) are most likely to benefit from CRISPR research and if there is a consensus about specific barriers to commercial adoption in agriculture. Further, we disaggregated public and private plant scientists to see if there was heterogeneity in their views of the future of CRISPR research. Our findings suggest that maize and soybeans are anticipated to benefit the most from CRISPR technology with fungus and virus resistance the most common vehicle for its implementation. Across the board, plant scientists viewed consumer perception/knowledge gap to be the most impeding barrier of CRISPR adoption. Although CRISPR has been hailed as a technology that can help alleviate food insecurity and improve agricultural sustainability, our study has shown that plant scientists believe there are some large concerns about the consumer perceptions of CRISPR.
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Affiliation(s)
- Job de Lange
- Department of Agricultural Economics, University of Arkansas, Fayetteville, AR 72701, USA
| | - Lawton Lanier Nalley
- Department of Agricultural Economics, University of Arkansas, Fayetteville, AR 72701, USA
| | - Wei Yang
- Department of Agricultural Economics, University of Arkansas, Fayetteville, AR 72701, USA
| | - Aaron Shew
- Department of Agricultural Economics, University of Arkansas, Fayetteville, AR 72701, USA
| | - Hans de Steur
- Department of Agricultural Economics, University of Gent, Gent, Belgium
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22
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Chapman EA, Thomsen HC, Tulloch S, Correia PMP, Luo G, Najafi J, DeHaan LR, Crews TE, Olsson L, Lundquist PO, Westerbergh A, Pedas PR, Knudsen S, Palmgren M. Perennials as Future Grain Crops: Opportunities and Challenges. FRONTIERS IN PLANT SCIENCE 2022; 13:898769. [PMID: 35968139 PMCID: PMC9372509 DOI: 10.3389/fpls.2022.898769] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Accepted: 06/20/2022] [Indexed: 06/15/2023]
Abstract
Perennial grain crops could make a valuable addition to sustainable agriculture, potentially even as an alternative to their annual counterparts. The ability of perennials to grow year after year significantly reduces the number of agricultural inputs required, in terms of both planting and weed control, while reduced tillage improves soil health and on-farm biodiversity. Presently, perennial grain crops are not grown at large scale, mainly due to their early stages of domestication and current low yields. Narrowing the yield gap between perennial and annual grain crops will depend on characterizing differences in their life cycles, resource allocation, and reproductive strategies and understanding the trade-offs between annualism, perennialism, and yield. The genetic and biochemical pathways controlling plant growth, physiology, and senescence should be analyzed in perennial crop plants. This information could then be used to facilitate tailored genetic improvement of selected perennial grain crops to improve agronomic traits and enhance yield, while maintaining the benefits associated with perennialism.
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Affiliation(s)
| | | | - Sophia Tulloch
- Department of Raw Materials, Carlsberg Research Laboratory, Copenhagen, Denmark
| | - Pedro M. P. Correia
- Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Guangbin Luo
- Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Javad Najafi
- Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
| | | | | | - Lennart Olsson
- Lund University Centre for Sustainability Studies, Lund, Sweden
| | - Per-Olof Lundquist
- Department of Plant Biology, Uppsala BioCenter, Linnean Centre for Plant Biology in Uppsala, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Anna Westerbergh
- Department of Plant Biology, Uppsala BioCenter, Linnean Centre for Plant Biology in Uppsala, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Pai Rosager Pedas
- Department of Raw Materials, Carlsberg Research Laboratory, Copenhagen, Denmark
| | - Søren Knudsen
- Department of Raw Materials, Carlsberg Research Laboratory, Copenhagen, Denmark
| | - Michael Palmgren
- Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
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Garland S, Curry HA. Turning promise into practice: Crop biotechnology for increasing genetic diversity and climate resilience. PLoS Biol 2022; 20:e3001716. [PMID: 35881573 PMCID: PMC9321377 DOI: 10.1371/journal.pbio.3001716] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
As climate change increasingly threatens agricultural production, expanding genetic diversity in crops is an important strategy for climate resilience in many agricultural contexts. In this Essay, we explore the potential of crop biotechnology to contribute to this diversification, especially in industrialized systems, by using historical perspectives to frame the current dialogue surrounding recent innovations in gene editing. We unearth comments about the possibility of enhancing crop diversity made by ambitious scientists in the early days of recombinant DNA and follow the implementation of this technology, which has not generated the diversification some anticipated. We then turn to recent claims about the promise of gene editing tools with respect to this same goal. We encourage researchers and other stakeholders to engage in activities beyond the laboratory if they hope to see what is technologically possible translated into practice at this critical point in agricultural transformation. Will gene editing contribute to improved crop diversity and climate resilience? In this Essay, the authors look at lessons from past biotechnology efforts to inform action for the future.
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Affiliation(s)
- Sarah Garland
- The Earth Institute, Columbia University, New York, New York, United States of America
- * E-mail:
| | - Helen Anne Curry
- Department of History and Philosophy of Science, University of Cambridge, Cambridge, United Kingdom
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Egan LM, Stiller WN. The Past, Present, and Future of Host Plant Resistance in Cotton: An Australian Perspective. FRONTIERS IN PLANT SCIENCE 2022; 13:895877. [PMID: 35873986 PMCID: PMC9297922 DOI: 10.3389/fpls.2022.895877] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Accepted: 06/06/2022] [Indexed: 05/24/2023]
Abstract
Cotton is a key global fiber crop. However, yield potential is limited by the presence of endemic and introduced pests and diseases. The introduction of host plant resistance (HPR), defined as the purposeful use of resistant crop cultivars to reduce the impact of pests and diseases, has been a key breeding target for the Commonwealth Scientific and Industrial Research Organisation (CSIRO) cotton breeding program. The program has seen success in releasing cultivars resistant to Bacterial blight, Verticillium wilt, Fusarium wilt, and Cotton bunchy top. However, emerging biotic threats such as Black root rot and secondary pests, are becoming more frequent in Australian cotton production systems. The uptake of tools and breeding methods, such as genomic selection, high throughput phenomics, gene editing, and landscape genomics, paired with the continued utilization of sources of resistance from Gossypium germplasm, will be critical for the future of cotton breeding. This review celebrates the success of HPR breeding activities in the CSIRO cotton breeding program and maps a pathway for the future in developing resistant cultivars.
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Touzdjian Pinheiro Kohlrausch Távora F, de Assis dos Santos Diniz F, de Moraes Rêgo-Machado C, Chagas Freitas N, Barbosa Monteiro Arraes F, Chumbinho de Andrade E, Furtado LL, Osiro KO, Lima de Sousa N, Cardoso TB, Márcia Mertz Henning L, Abrão de Oliveira Molinari P, Feingold SE, Hunter WB, Fátima Grossi de Sá M, Kobayashi AK, Lima Nepomuceno A, Santiago TR, Correa Molinari HB. CRISPR/Cas- and Topical RNAi-Based Technologies for Crop Management and Improvement: Reviewing the Risk Assessment and Challenges Towards a More Sustainable Agriculture. Front Bioeng Biotechnol 2022; 10:913728. [PMID: 35837551 PMCID: PMC9274005 DOI: 10.3389/fbioe.2022.913728] [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: 04/06/2022] [Accepted: 06/06/2022] [Indexed: 11/13/2022] Open
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated gene (Cas) system and RNA interference (RNAi)-based non-transgenic approaches are powerful technologies capable of revolutionizing plant research and breeding. In recent years, the use of these modern technologies has been explored in various sectors of agriculture, introducing or improving important agronomic traits in plant crops, such as increased yield, nutritional quality, abiotic- and, mostly, biotic-stress resistance. However, the limitations of each technique, public perception, and regulatory aspects are hindering its wide adoption for the development of new crop varieties or products. In an attempt to reverse these mishaps, scientists have been researching alternatives to increase the specificity, uptake, and stability of the CRISPR and RNAi system components in the target organism, as well as to reduce the chance of toxicity in nontarget organisms to minimize environmental risk, health problems, and regulatory issues. In this review, we discuss several aspects related to risk assessment, toxicity, and advances in the use of CRISPR/Cas and topical RNAi-based technologies in crop management and breeding. The present study also highlights the advantages and possible drawbacks of each technology, provides a brief overview of how to circumvent the off-target occurrence, the strategies to increase on-target specificity, the harm/benefits of association with nanotechnology, the public perception of the available techniques, worldwide regulatory frameworks regarding topical RNAi and CRISPR technologies, and, lastly, presents successful case studies of biotechnological solutions derived from both technologies, raising potential challenges to reach the market and being social and environmentally safe.
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Affiliation(s)
| | | | | | | | | | | | | | - Karen Ofuji Osiro
- Department of Phytopathology, University of Brasília, Brasília, Brazil
- Embrapa Agroenergy, Brasília, Brazil
| | | | | | | | | | | | - Wayne B. Hunter
- USDA-ARS, U.S. Horticultural Research Laboratory, Fort Pierce, FL, United States
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Genome-wide specificity of plant genome editing by both CRISPR-Cas9 and TALEN. Sci Rep 2022; 12:9330. [PMID: 35665758 PMCID: PMC9167288 DOI: 10.1038/s41598-022-13034-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 05/19/2022] [Indexed: 12/25/2022] Open
Abstract
CRISPR and TALENs are efficient systems for gene editing in many organisms including plants. In many cases the CRISPR–Cas or TALEN modules are expressed in the plant cell only transiently. Theoretically, transient expression of the editing modules should limit unexpected effects compared to stable transformation. However, very few studies have measured the off-target and unpredicted effects of editing strategies on the plant genome, and none of them have compared these two major editing systems. We conducted, in Physcomitrium patens, a comprehensive genome-wide investigation of off-target mutations using either a CRISPR–Cas9 or a TALEN strategy. We observed a similar number of differences for the two editing strategies compared to control non-transfected plants, with an average of 8.25 SNVs and 19.5 InDels for the CRISPR-edited plants, and an average of 17.5 SNVs and 32 InDels for the TALEN-edited plants. Interestingly, a comparable number of SNVs and InDels could be detected in the PEG-treated control plants. This shows that except for the on-target modifications, the gene editing tools used in this study did not show a significant off-target activity nor unpredicted effects on the genome, and did not lead to transgene integration. The PEG treatment, a well-established biotechnological method, in itself, was the main source of mutations found in the edited plants.
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Mohd Saad NS, Neik TX, Thomas WJW, Amas JC, Cantila AY, Craig RJ, Edwards D, Batley J. Advancing designer crops for climate resilience through an integrated genomics approach. CURRENT OPINION IN PLANT BIOLOGY 2022; 67:102220. [PMID: 35489163 DOI: 10.1016/j.pbi.2022.102220] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Revised: 03/15/2022] [Accepted: 03/25/2022] [Indexed: 06/14/2023]
Abstract
Climate change and exponential population growth are exposing an immediate need for developing future crops that are highly resilient and adaptable to changing environments to maintain global food security in the next decade. Rigorous selection from long domestication history has rendered cultivated crops genetically disadvantaged, raising concerns in their ability to adapt to these new challenges and limiting their usefulness in breeding programmes. As a result, future crop improvement efforts must rely on integrating various genomic strategies ranging from high-throughput sequencing to machine learning, in order to exploit germplasm diversity and overcome bottlenecks created by domestication, expansive multi-dimensional phenotypes, arduous breeding processes, complex traits and big data.
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Affiliation(s)
- Nur Shuhadah Mohd Saad
- UWA School of Biological Sciences and the UWA Institute of Agriculture, University of Western Australia, Crawley, WA, Australia
| | - Ting Xiang Neik
- Sunway College Kuala Lumpur, Bandar Sunway, 47500, Selangor, Malaysia
| | - William J W Thomas
- UWA School of Biological Sciences and the UWA Institute of Agriculture, University of Western Australia, Crawley, WA, Australia
| | - Junrey C Amas
- UWA School of Biological Sciences and the UWA Institute of Agriculture, University of Western Australia, Crawley, WA, Australia
| | - Aldrin Y Cantila
- UWA School of Biological Sciences and the UWA Institute of Agriculture, University of Western Australia, Crawley, WA, Australia
| | - Ryan J Craig
- UWA School of Biological Sciences and the UWA Institute of Agriculture, University of Western Australia, Crawley, WA, Australia
| | - David Edwards
- UWA School of Biological Sciences and the UWA Institute of Agriculture, University of Western Australia, Crawley, WA, Australia
| | - Jacqueline Batley
- UWA School of Biological Sciences and the UWA Institute of Agriculture, University of Western Australia, Crawley, WA, Australia.
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Sturme MHJ, van der Berg JP, Bouwman LMS, De Schrijver A, de Maagd RA, Kleter GA, Battaglia-de Wilde E. Occurrence and Nature of Off-Target Modifications by CRISPR-Cas Genome Editing in Plants. ACS AGRICULTURAL SCIENCE & TECHNOLOGY 2022; 2:192-201. [PMID: 35548699 PMCID: PMC9075866 DOI: 10.1021/acsagscitech.1c00270] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 02/18/2022] [Accepted: 02/18/2022] [Indexed: 12/26/2022]
Abstract
![]()
CRISPR-Cas-based
genome editing allows for precise and targeted
genetic modification of plants. Nevertheless, unintended off-target
edits can arise that might confer risks when present in gene-edited
food crops. Through an extensive literature review we gathered information
on CRISPR-Cas off-target edits in plants. Most observed off-target
changes were small insertions or deletions (1–22 bp) or nucleotide
substitutions, and large deletions (>100 bp) were rare. One study
detected the insertion of vector-derived DNA sequences, which is important
considering the risk assessment of gene-edited plants. Off-target
sites had few mismatches (1–3 nt) with the target sequence
and were mainly located in protein-coding regions, often in target
gene homologues. Off-targets edits were predominantly detected via
biased analysis of predicted off-target sites instead of unbiased
genome-wide analysis. CRISPR-Cas-edited plants showed lower off-target
mutation frequencies than conventionally bred plants. This Review
can aid discussions on the relevance of evaluating off-target modifications
for risk assessment of CRISPR-Cas-edited plants.
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Affiliation(s)
- Mark H J Sturme
- Wageningen Food Safety Research, Wageningen University and Research, P.O. Box 230, 6700 AE Wageningen, The Netherlands
| | - Jan Pieter van der Berg
- Wageningen Food Safety Research, Wageningen University and Research, P.O. Box 230, 6700 AE Wageningen, The Netherlands
| | - Lianne M S Bouwman
- Wageningen Food Safety Research, Wageningen University and Research, P.O. Box 230, 6700 AE Wageningen, The Netherlands
| | | | - Ruud A de Maagd
- Wageningen Plant Research, Wageningen University and Research, P.O. Box 16, 6700 AA Wageningen, The Netherlands
| | - Gijs A Kleter
- Wageningen Food Safety Research, Wageningen University and Research, P.O. Box 230, 6700 AE Wageningen, The Netherlands
| | - Evy Battaglia-de Wilde
- Wageningen Food Safety Research, Wageningen University and Research, P.O. Box 230, 6700 AE Wageningen, The Netherlands
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30
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Wyant SR, Rodriguez MF, Carter CK, Parrott WA, Jackson SA, Stupar RM, Morrell PL. Fast neutron mutagenesis in soybean enriches for small indels and creates frameshift mutations. G3 (BETHESDA, MD.) 2022; 12:jkab431. [PMID: 35100358 PMCID: PMC9335934 DOI: 10.1093/g3journal/jkab431] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Accepted: 11/14/2021] [Indexed: 11/13/2022]
Abstract
The mutagenic effects of ionizing radiation have been used for decades to create novel variants in experimental populations. Fast neutron (FN) bombardment as a mutagen has been especially widespread in plants, with extensive reports describing the induction of large structural variants, i.e., deletions, insertions, inversions, and translocations. However, the full spectrum of FN-induced mutations is poorly understood. We contrast small insertions and deletions (indels) observed in 27 soybean lines subject to FN irradiation with the standing indels identified in 107 diverse soybean lines. We use the same populations to contrast the nature and context (bases flanking a nucleotide change) of single-nucleotide variants. The accumulation of new single-nucleotide changes in FN lines is marginally higher than expected based on spontaneous mutation. In FN-treated lines and in standing variation, C→T transitions and the corresponding reverse complement G→A transitions are the most abundant and occur most frequently in a CpG local context. These data indicate that most SNPs identified in FN lines are likely derived from spontaneous de novo processes in generations following mutagenesis rather than from the FN irradiation mutagen. However, small indels in FN lines differ from standing variants. Short insertions, from 1 to 6 bp, are less abundant than in standing variation. Short deletions are more abundant and prone to induce frameshift mutations that should disrupt the structure and function of encoded proteins. These findings indicate that FN irradiation generates numerous small indels, increasing the abundance of loss-of-function mutations that impact single genes.
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Affiliation(s)
- Skylar R Wyant
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA 92697, USA
| | - M Fernanda Rodriguez
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN 55108, USA
| | - Corey K Carter
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN 55108, USA
| | - Wayne A Parrott
- Department of Crop and Soil Sciences, University of Georgia, Athens, GA 30602, USA
| | - Scott A Jackson
- Department of Crop and Soil Sciences, University of Georgia, Athens, GA 30602, USA
| | - Robert M Stupar
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN 55108, USA
| | - Peter L Morrell
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN 55108, USA
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31
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Cao HX, Vu GTH, Gailing O. From Genome Sequencing to CRISPR-Based Genome Editing for Climate-Resilient Forest Trees. Int J Mol Sci 2022; 23:966. [PMID: 35055150 PMCID: PMC8780650 DOI: 10.3390/ijms23020966] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 01/13/2022] [Accepted: 01/13/2022] [Indexed: 12/11/2022] Open
Abstract
Due to the economic and ecological importance of forest trees, modern breeding and genetic manipulation of forest trees have become increasingly prevalent. The CRISPR-based technology provides a versatile, powerful, and widely accepted tool for analyzing gene function and precise genetic modification in virtually any species but remains largely unexplored in forest species. Rapidly accumulating genetic and genomic resources for forest trees enabled the identification of numerous genes and biological processes that are associated with important traits such as wood quality, drought, or pest resistance, facilitating the selection of suitable gene editing targets. Here, we introduce and discuss the latest progress, opportunities, and challenges of genome sequencing and editing for improving forest sustainability.
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Affiliation(s)
- Hieu Xuan Cao
- Forest Genetics and Forest Tree Breeding, Georg-August University of Göttingen, Büsgenweg 2, 37077 Gottingen, Germany;
| | - Giang Thi Ha Vu
- Forest Genetics and Forest Tree Breeding, Georg-August University of Göttingen, Büsgenweg 2, 37077 Gottingen, Germany;
| | - Oliver Gailing
- Forest Genetics and Forest Tree Breeding, Georg-August University of Göttingen, Büsgenweg 2, 37077 Gottingen, Germany;
- Center for Integrated Breeding Research (CiBreed), Georg-August University of Göttingen, 37073 Gottingen, Germany
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32
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Patil GB, Stupar RM, Zhang F. Protoplast Isolation, Transfection, and Gene Editing for Soybean (Glycine max ). Methods Mol Biol 2022; 2464:173-186. [PMID: 35258833 DOI: 10.1007/978-1-0716-2164-6_13] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Protoplast is a versatile system for conducting cell-based assays, analyzing diverse signaling pathways, studying functions of cellular machineries, and functional genomics screening. Protoplast engineering has become an important tool for basic plant molecular biology research and developing genome-edited crops. This system allows the direct delivery of DNA, RNA, or proteins into plant cells and provides a high-throughput system to validate gene-editing reagents. It also facilitates the delivery of homology-directed repair templates (donor molecules) into plant cells, enabling precise DNA edits in the genome. There is a great deal of interest in the plant community to develop these precise edits, as they may expand the potential for developing value-added traits which may be difficult to achieve by other gene-editing applications and/or traditional breeding alone. This chapter provides improved working protocols for isolating and transforming protoplast from immature soybean seeds with 44% of transfection efficiency validated by the green fluorescent protein reporter. We also describe a method for gene editing in soybean protoplasts using single guide RNA molecules.
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Affiliation(s)
- Gunvant B Patil
- Institute of Genomics for Crop Abiotic Stress Tolerance, Department of Plant and Soil Science, Texas Tech University, Lubbock, TX, USA.
| | - Robert M Stupar
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN, USA
| | - Feng Zhang
- Department of Plant and Microbial Biology, University of Minnesota, Saint Paul, MN, USA
- Center for Precision Plant Genomics, University of Minnesota, Saint Paul, MN, USA
- Center for Genome Engineering, University of Minnesota, Saint Paul, MN, USA
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Yassitepe JEDCT, da Silva VCH, Hernandes-Lopes J, Dante RA, Gerhardt IR, Fernandes FR, da Silva PA, Vieira LR, Bonatti V, Arruda P. Maize Transformation: From Plant Material to the Release of Genetically Modified and Edited Varieties. FRONTIERS IN PLANT SCIENCE 2021; 12:766702. [PMID: 34721493 PMCID: PMC8553389 DOI: 10.3389/fpls.2021.766702] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2021] [Accepted: 09/15/2021] [Indexed: 05/17/2023]
Abstract
Over the past decades, advances in plant biotechnology have allowed the development of genetically modified maize varieties that have significantly impacted agricultural management and improved the grain yield worldwide. To date, genetically modified varieties represent 30% of the world's maize cultivated area and incorporate traits such as herbicide, insect and disease resistance, abiotic stress tolerance, high yield, and improved nutritional quality. Maize transformation, which is a prerequisite for genetically modified maize development, is no longer a major bottleneck. Protocols using morphogenic regulators have evolved significantly towards increasing transformation frequency and genotype independence. Emerging technologies using either stable or transient expression and tissue culture-independent methods, such as direct genome editing using RNA-guided endonuclease system as an in vivo desired-target mutator, simultaneous double haploid production and editing/haploid-inducer-mediated genome editing, and pollen transformation, are expected to lead significant progress in maize biotechnology. This review summarises the significant advances in maize transformation protocols, technologies, and applications and discusses the current status, including a pipeline for trait development and regulatory issues related to current and future genetically modified and genetically edited maize varieties.
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Affiliation(s)
- Juliana Erika de Carvalho Teixeira Yassitepe
- Embrapa Informática Agropecuária, Campinas, Brazil
- Genomics for Climate Change Research Center (GCCRC), Universidade Estadual de Campinas, Campinas, Brazil
- Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas, Campinas, Brazil
| | - Viviane Cristina Heinzen da Silva
- Genomics for Climate Change Research Center (GCCRC), Universidade Estadual de Campinas, Campinas, Brazil
- Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas, Campinas, Brazil
| | - José Hernandes-Lopes
- Embrapa Informática Agropecuária, Campinas, Brazil
- Genomics for Climate Change Research Center (GCCRC), Universidade Estadual de Campinas, Campinas, Brazil
- Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas, Campinas, Brazil
| | - Ricardo Augusto Dante
- Embrapa Informática Agropecuária, Campinas, Brazil
- Genomics for Climate Change Research Center (GCCRC), Universidade Estadual de Campinas, Campinas, Brazil
- Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas, Campinas, Brazil
| | - Isabel Rodrigues Gerhardt
- Embrapa Informática Agropecuária, Campinas, Brazil
- Genomics for Climate Change Research Center (GCCRC), Universidade Estadual de Campinas, Campinas, Brazil
- Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas, Campinas, Brazil
| | - Fernanda Rausch Fernandes
- Embrapa Informática Agropecuária, Campinas, Brazil
- Genomics for Climate Change Research Center (GCCRC), Universidade Estadual de Campinas, Campinas, Brazil
- Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas, Campinas, Brazil
| | - Priscila Alves da Silva
- Genomics for Climate Change Research Center (GCCRC), Universidade Estadual de Campinas, Campinas, Brazil
- Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas, Campinas, Brazil
| | - Leticia Rios Vieira
- Genomics for Climate Change Research Center (GCCRC), Universidade Estadual de Campinas, Campinas, Brazil
- Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas, Campinas, Brazil
| | - Vanessa Bonatti
- Genomics for Climate Change Research Center (GCCRC), Universidade Estadual de Campinas, Campinas, Brazil
- Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas, Campinas, Brazil
| | - Paulo Arruda
- Genomics for Climate Change Research Center (GCCRC), Universidade Estadual de Campinas, Campinas, Brazil
- Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas, Campinas, Brazil
- Departamento de Genética, Evolução, Microbiologia e Imunologia, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, Brazil
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Jenkins D, Dobert R, Atanassova A, Pavely C. Impacts of the regulatory environment for gene editing on delivering beneficial products. IN VITRO CELLULAR & DEVELOPMENTAL BIOLOGY. PLANT : JOURNAL OF THE TISSUE CULTURE ASSOCIATION 2021; 57:609-626. [PMID: 34429575 PMCID: PMC8376113 DOI: 10.1007/s11627-021-10201-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Accepted: 05/20/2021] [Indexed: 05/12/2023]
Abstract
Various genome-editing technologies have been embraced by plant breeders across the world as promising tools for the improvement of different crops to deliver consumer benefits, improve agronomic performance, and increase sustainability. The uptake of genome-editing technologies in plant breeding greatly depends on how governments regulate its use. Some major agricultural production countries have already developed regulatory approaches that enable the application of genome editing for crop improvement, while other governments are in the early stages of formulating policy. Central to the discussion is the principle of "like products should be treated in like ways" and the subsequent utilization of exclusions and exemptions from the scope of GMO regulations for these products. In some countries, the outcomes of genome editing that could also have been achieved through conventional breeding have been defined as not needing GMO regulatory oversight. In this paper, we provide a short overview of plant breeding and the history of plant biotechnology policy development, the different classes of current regulatory systems and their use of exemptions and exclusions for genome-edited plants, and the potential benefits of such approaches as it relates to achieving societal goals.
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Affiliation(s)
- Daniel Jenkins
- Pairwise Plants Services, Inc., 807 East Main Street, Suite 4-100, Durham, NC 27701 USA
| | - Raymond Dobert
- Bayer Crop Science, 700 Chesterfield Parkway West, St. Louis, MO 63017 USA
| | - Ana Atanassova
- BASF Business Coordination Centre – Innovation Center Gent, Technologiepark 101, 9052 Gent, Belgium
| | - Chloe Pavely
- Calyxt, Inc., 2800 Mount Ridge Road, Roseville, MN 55113 USA
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35
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Buzdin AV, Patrushev MV, Sverdlov ED. Will Plant Genome Editing Play a Decisive Role in "Quantum-Leap" Improvements in Crop Yield to Feed an Increasing Global Human Population? PLANTS (BASEL, SWITZERLAND) 2021; 10:1667. [PMID: 34451712 PMCID: PMC8398637 DOI: 10.3390/plants10081667] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 08/04/2021] [Accepted: 08/07/2021] [Indexed: 02/08/2023]
Abstract
Growing scientific evidence demonstrates unprecedented planetary-scale human impacts on the Earth's system with a predicted threat to the existence of the terrestrial biosphere due to population increase, resource depletion, and pollution. Food systems account for 21-34% of global carbon dioxide (CO2) emissions. Over the past half-century, water and land-use changes have significantly impacted ecosystems, biogeochemical cycles, biodiversity, and climate. At the same time, food production is falling behind consumption, and global grain reserves are shrinking. Some predictions suggest that crop yields must approximately double by 2050 to adequately feed an increasing global population without a large expansion of crop area. To achieve this, "quantum-leap" improvements in crop cultivar productivity are needed within very narrow planetary boundaries of permissible environmental perturbations. Strategies for such a "quantum-leap" include mutation breeding and genetic engineering of known crop genome sequences. Synthetic biology makes it possible to synthesize DNA fragments of any desired sequence, and modern bioinformatics tools may hopefully provide an efficient way to identify targets for directed modification of selected genes responsible for known important agronomic traits. CRISPR/Cas9 is a new technology for incorporating seamless directed modifications into genomes; it is being widely investigated for its potential to enhance the efficiency of crop production. We consider the optimism associated with the new genetic technologies in terms of the complexity of most agronomic traits, especially crop yield potential (Yp) limits. We also discuss the possible directions of overcoming these limits and alternative ways of providing humanity with food without transgressing planetary boundaries. In conclusion, we support the long-debated idea that new technologies are unlikely to provide a rapidly growing population with significantly increased crop yield. Instead, we suggest that delicately balanced humane measures to limit its growth and the amount of food consumed per capita are highly desirable for the foreseeable future.
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Affiliation(s)
- Anton V Buzdin
- The Laboratory of Clinical and Genomic Bioinformatics, I.M. Sechenov First Moscow State Medical University, 119991 Moscow, Russia
- Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, 141701 Moscow, Russia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
| | - Maxim V Patrushev
- Kurchatov Center for Genome Research, National Research Center Kurchatov Institute, 123182 Moscow, Russia
| | - Eugene D Sverdlov
- Kurchatov Center for Genome Research, National Research Center Kurchatov Institute, 123182 Moscow, Russia
- Institute of Molecular Genetics, National Research Center Kurchatov Institute, 123182 Moscow, Russia
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Ahmad S, Tang L, Shahzad R, Mawia AM, Rao GS, Jamil S, Wei C, Sheng Z, Shao G, Wei X, Hu P, Mahfouz MM, Hu S, Tang S. CRISPR-Based Crop Improvements: A Way Forward to Achieve Zero Hunger. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:8307-8323. [PMID: 34288688 DOI: 10.1021/acs.jafc.1c02653] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
Zero hunger is one of the sustainable development goals set by the United Nations in 2015 to achieve global food security by 2030. The current harvest of crops is insufficient; feeding the world's population and meeting the goal of zero hunger by 2030 will require larger and more consistent crop production. Clustered regularly interspaced short palindromic repeats-associated protein (CRISPR-Cas) technology is widely used for the plant genome editing. In this review, we consider this technology as a potential tool for achieving zero hunger. We provide a comprehensive overview of CRISPR-Cas technology and its most important applications for food crops' improvement. We also conferred current and potential technological breakthroughs that will help in breeding future crops to end global hunger. The regulatory aspects of deploying this technology in commercial sectors, bioethics, and the production of transgene-free plants are also discussed. We hope that the CRISPR-Cas system will accelerate the breeding of improved crop cultivars compared with conventional breeding and pave the way toward the zero hunger goal.
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Affiliation(s)
- Shakeel Ahmad
- State Key Laboratory of Rice Biology, China National Center for Rice Improvement, China National Rice Research Institute, Hangzhou 310006, China
- Maize Research Station, Ayub Agricultural Research Institute, Faisalabad 38000, Pakistan
| | - Liqun Tang
- State Key Laboratory of Rice Biology, China National Center for Rice Improvement, China National Rice Research Institute, Hangzhou 310006, China
| | - Rahil Shahzad
- Agricultural Biotechnology Research Institute, Ayub Agricultural Research Institute, Faisalabad 38000, Pakistan
| | - Amos Musyoki Mawia
- State Key Laboratory of Rice Biology, China National Center for Rice Improvement, China National Rice Research Institute, Hangzhou 310006, China
| | - Gundra Sivakrishna Rao
- Laboratory for Genome Engineering and Synthetic Biology, Division of Biological Sciences, 4700 King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
| | - Shakra Jamil
- Agricultural Biotechnology Research Institute, Ayub Agricultural Research Institute, Faisalabad 38000, Pakistan
| | - Chen Wei
- State Key Laboratory of Rice Biology, China National Center for Rice Improvement, China National Rice Research Institute, Hangzhou 310006, China
| | - Zhonghua Sheng
- State Key Laboratory of Rice Biology, China National Center for Rice Improvement, China National Rice Research Institute, Hangzhou 310006, China
| | - Gaoneng Shao
- State Key Laboratory of Rice Biology, China National Center for Rice Improvement, China National Rice Research Institute, Hangzhou 310006, China
| | - Xiangjin Wei
- State Key Laboratory of Rice Biology, China National Center for Rice Improvement, China National Rice Research Institute, Hangzhou 310006, China
| | - Peisong Hu
- State Key Laboratory of Rice Biology, China National Center for Rice Improvement, China National Rice Research Institute, Hangzhou 310006, China
| | - Magdy M Mahfouz
- Laboratory for Genome Engineering and Synthetic Biology, Division of Biological Sciences, 4700 King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
| | - Shikai Hu
- State Key Laboratory of Rice Biology, China National Center for Rice Improvement, China National Rice Research Institute, Hangzhou 310006, China
| | - Shaoqing Tang
- State Key Laboratory of Rice Biology, China National Center for Rice Improvement, China National Rice Research Institute, Hangzhou 310006, China
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Lassoued R, Phillips PW, Macall DM, Hesseln H, Smyth SJ. Expert opinions on the regulation of plant genome editing. PLANT BIOTECHNOLOGY JOURNAL 2021; 19:1104-1109. [PMID: 33834596 PMCID: PMC8196660 DOI: 10.1111/pbi.13597] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Revised: 03/09/2021] [Accepted: 04/03/2021] [Indexed: 05/06/2023]
Abstract
Global food security is largely affected by factors such as environmental (e.g. drought, flooding), social (e.g. gender inequality), socio-economic (e.g. overpopulation, poverty) and health (e.g. diseases). In response, extensive public and private investment in agricultural research has focused on increasing yields of staple food crops and developing new traits for crop improvement. New breeding techniques pioneered by genome editing have gained substantial traction within the last decade, revolutionizing the plant breeding field. Both industry and academia have been investing and working to optimize the potentials of gene editing and to bring derived crops to market. The spectrum of cutting-edge genome editing tools along with their technical differences has led to a growing international regulatory, ethical and societal divide. This article is a summary of a multi-year survey project exploring how experts view the risks of new breeding techniques, including genome editing and their related regulatory requirements. Surveyed experts opine that emerging biotechnologies offer great promise to address social and climate challenges, yet they admit that the market growth of genome-edited crops will be limited by an ambiguous regulatory environment shaped by societal uncertainty.
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Affiliation(s)
- Rim Lassoued
- Department of Agricultural and Resource EconomicsUniversity of SaskatchewanSaskatoonSKCanada
| | - Peter W.B. Phillips
- The Johnson Shoyama Graduate School of Public PolicyUniversity of SaskatchewanSaskatoonSKCanada
| | | | - Hayley Hesseln
- Department of Agricultural and Resource EconomicsUniversity of SaskatchewanSaskatoonSKCanada
| | - Stuart J. Smyth
- Department of Agricultural and Resource EconomicsUniversity of SaskatchewanSaskatoonSKCanada
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Technologies enabling rapid crop improvements for sustainable agriculture: example pennycress (Thlaspi arvense L.). Emerg Top Life Sci 2021; 5:325-335. [DOI: 10.1042/etls20200330] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 02/17/2021] [Accepted: 03/04/2021] [Indexed: 11/17/2022]
Abstract
Growing concerns over food insecurity and ecosystems health related to population growth and climate change have challenged scientists to develop new crops, employing revolutionary technologies in combination with traditional methods. In this review, we discuss the domestication of the oilseed-producing cover crop pennycress, which along with the development of other new crops and improvements to farming practices can provide sustainable solutions to address malnutrition and environmental impacts of production agriculture. We highlight some of the new technologies such as bioinformatics-enabled next-generation sequencing and CRISPR genome editing in combination with traditional mutation breeding that has accelerated pennycress development as a new crop and a potential model system. Furthermore, we provide a brief overview of the technologies that can be integrated for improving pennycress and other crops and the status of pennycress development using these technologies.
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Bandyopadhyay A, Kancharla N, Javalkote VS, Dasgupta S, Brutnell TP. CRISPR-Cas12a (Cpf1): A Versatile Tool in the Plant Genome Editing Tool Box for Agricultural Advancement. FRONTIERS IN PLANT SCIENCE 2020; 11:584151. [PMID: 33214794 PMCID: PMC7668199 DOI: 10.3389/fpls.2020.584151] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Accepted: 09/28/2020] [Indexed: 05/08/2023]
Abstract
Global population is predicted to approach 10 billion by 2050, an increase of over 2 billion from today. To meet the demands of growing, geographically and socio-economically diversified nations, we need to diversity and expand agricultural production. This expansion of agricultural productivity will need to occur under increasing biotic, and environmental constraints driven by climate change. Clustered regularly interspaced short palindromic repeats-site directed nucleases (CRISPR-SDN) and similar genome editing technologies will likely be key enablers to meet future agricultural needs. While the application of CRISPR-Cas9 mediated genome editing has led the way, the use of CRISPR-Cas12a is also increasing significantly for genome engineering of plants. The popularity of the CRISPR-Cas12a, the type V (class-II) system, is gaining momentum because of its versatility and simplified features. These include the use of a small guide RNA devoid of trans-activating crispr RNA, targeting of T-rich regions of the genome where Cas9 is not suitable for use, RNA processing capability facilitating simpler multiplexing, and its ability to generate double strand breaks (DSB) with staggered ends. Many monocot and dicot species have been successfully edited using this Cas12a system and further research is ongoing to improve its efficiency in plants, including improving the temperature stability of the Cas12a enzyme, identifying new variants of Cas12a or synthetically producing Cas12a with flexible PAM sequences. In this review we provide a comparative survey of CRISPR-Cas12a and Cas9, and provide a perspective on applications of CRISPR-Cas12 in agriculture.
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Affiliation(s)
| | - Nagesh Kancharla
- Reliance Industries Ltd., R&D-Synthetic Biology, Navi Mumbai, India
| | | | - Santanu Dasgupta
- Reliance Industries Ltd., R&D-Synthetic Biology, Navi Mumbai, India
| | - Thomas P. Brutnell
- Chinese Academy of Agricultural Sciences, Biotechnology Research Institute, Beijing China
- Gateway Biotechnology, Inc., St. Louis, MO, United States
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Fedorova M, Herman RA. Obligatory metabolomic profiling of gene-edited crops is risk disproportionate. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 103:1985-1988. [PMID: 32593232 PMCID: PMC7540486 DOI: 10.1111/tpj.14896] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Revised: 05/21/2020] [Accepted: 05/27/2020] [Indexed: 05/06/2023]
Abstract
It has been argued that the application of metabolomics to gene-edited crops would present value in three areas: (i) the detection of gene-edited crops; (ii) the characterization of unexpected changes that might affect safety; and (iii) building on the track record of rigorous government regulation in supporting consumer acceptance of genetically modified organisms (GMOs). Here, we offer a different perspective, relative to each of these areas: (i) metabolomics is unable to differentiate whether a mutation has resulted from gene editing or from traditional breeding techniques; (ii) it is risk-disproportionate to apply metabolomics for regulatory purposes to search for possible compositional differences within crops developed using the least likely technique to generate unexpected compositional changes; and (iii) onerous regulations for genetically engineered crops have only contributed to unwarranted public fears, and repeating this approach for gene-edited crops is unlikely to result in a different outcome. It is also suggested that article proposing the utility of specific analytical techniques to support risk assessment would benefit from the input of scientists with subject matter expertise in risk assessment.
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Affiliation(s)
- Maria Fedorova
- Corteva Agriscience7100 NW 62 AvePO Box 1000JohnstonIA50131USA
| | - Rod A. Herman
- Corteva Agriscience9330 Zionsville RoadIndianapolisIN46268USA
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