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Zheng Y, Guo T, Xia T, Guo S, Chen M, Ye S, Pan T, Xu X, Gan Y, Zhan Y, Zheng T, Zheng Z. Utility of Arabidopsis KASII Promoter in Development of an Effective CRISPR/Cas9 System for Soybean Genome Editing and Its Application in Engineering of Soybean Seeds Producing Super-High Oleic and Low Saturated Oils. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:21720-21730. [PMID: 39288439 DOI: 10.1021/acs.jafc.4c05840] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/19/2024]
Abstract
This study reports the use of the Arabidopsis KASII promoter (AtKASII) to develop an efficient CRISPR/Cas9 system for soybean genome editing. When this promoter was paired with Arabidopsis U6 promoters to drive Cas9 and single guide RNA expression, respectively, simultaneous editing of the three fatty acid desaturase genes GmFAD2-1A, GmFAD2-1B, and GmFAD3A occurred in more than 60% of transgenic soybean lines at T2 generation, and all the triple mutants possessed desirable high-oleic traits. In sharp contrast, not a single line underwent simultaneous editing of the three target genes when AtKASII was replaced by the widely used AtEC1.2 promoter. Furthermore, our study showed that the stable and inheritable mutations in the high-oleic lines did not alter the overall contents of oil and protein or amino acid composition while increasing the oleic acid content up to 87.6% from approximately 23.8% for wild-type seeds, concomitant with 34.4- and 3.7-fold reductions in linoleic and linolenic acid, respectively. Collectively, this study demonstrates that the AtKASII promoter is highly promising for optimization of the CRISPR/Cas9 system for genome editing in soybean and possibly beyond.
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Affiliation(s)
- Yueping Zheng
- Institute for Oilseed Crop Germplasm Innovation and Utilization, Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, College of Advanced Agricultural Sciences, Zhejiang A&F University, Hangzhou 311300, China
| | - Tian Guo
- Institute for Oilseed Crop Germplasm Innovation and Utilization, Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, College of Advanced Agricultural Sciences, Zhejiang A&F University, Hangzhou 311300, China
| | - Ting Xia
- Institute for Oilseed Crop Germplasm Innovation and Utilization, Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, College of Advanced Agricultural Sciences, Zhejiang A&F University, Hangzhou 311300, China
| | - Shixian Guo
- Institute for Oilseed Crop Germplasm Innovation and Utilization, Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, College of Advanced Agricultural Sciences, Zhejiang A&F University, Hangzhou 311300, China
| | - Mengyao Chen
- Institute for Oilseed Crop Germplasm Innovation and Utilization, Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, College of Advanced Agricultural Sciences, Zhejiang A&F University, Hangzhou 311300, China
| | - Shenhua Ye
- Institute for Oilseed Crop Germplasm Innovation and Utilization, Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, College of Advanced Agricultural Sciences, Zhejiang A&F University, Hangzhou 311300, China
| | - Tian Pan
- Institute for Oilseed Crop Germplasm Innovation and Utilization, Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, College of Advanced Agricultural Sciences, Zhejiang A&F University, Hangzhou 311300, China
| | - Xuezhen Xu
- Institute for Oilseed Crop Germplasm Innovation and Utilization, Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, College of Advanced Agricultural Sciences, Zhejiang A&F University, Hangzhou 311300, China
| | - Yi Gan
- Institute for Oilseed Crop Germplasm Innovation and Utilization, Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, College of Advanced Agricultural Sciences, Zhejiang A&F University, Hangzhou 311300, China
| | - Yihua Zhan
- Institute for Oilseed Crop Germplasm Innovation and Utilization, Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, College of Advanced Agricultural Sciences, Zhejiang A&F University, Hangzhou 311300, China
| | - Ting Zheng
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
- Zhejiang University Zhongyuan Institute, Zhengzhou 450000, China
| | - Zhifu Zheng
- Institute for Oilseed Crop Germplasm Innovation and Utilization, Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, College of Advanced Agricultural Sciences, Zhejiang A&F University, Hangzhou 311300, China
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Freitas-Alves NS, Moreira-Pinto CE, Távora FTPK, Paes-de-Melo B, Arraes FBM, Lourenço-Tessutti IT, Moura SM, Oliveira AC, Morgante CV, Qi Y, Fatima Grossi-de-Sa M. CRISPR/Cas genome editing in soybean: challenges and new insights to overcome existing bottlenecks. J Adv Res 2024:S2090-1232(24)00367-9. [PMID: 39163906 DOI: 10.1016/j.jare.2024.08.024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2024] [Revised: 07/23/2024] [Accepted: 08/16/2024] [Indexed: 08/22/2024] Open
Abstract
BACKGROUND Soybean is a worldwide-cultivated crop due to its applications in the food, feed, and biodiesel industries. Genome editing in soybean began with ZFN and TALEN technologies; however, CRISPR/Cas has emerged and shortly became the preferable approach for soybean genome manipulation since it is more precise, easy to handle, and cost-effective. Recent reports have focused on the conventional Cas9 nuclease, Cas9 nickase (nCas9) derived base editors, and Cas12a (formally Cpf1) as the most commonly used genome editors in soybean. Nonetheless, several challenges in the complex plant genetic engineering pipeline need to be overcome to effectively edit the genome of an elite soybean cultivar. These challenges include (1) optimizing CRISPR cassette design (i.e., gRNA and Cas promoters, gRNA design and testing, number of gRNAs, and binary vector), (2) improving transformation frequency, (3) increasing the editing efficiency ratio of targeted plant cells, and (4) improving soybean crop production. AIM OF REVIEW This review provides an overview of soybean genome editing using CRISPR/Cas technology, discusses current challenges, and highlights theoretical (insights) and practical suggestions to overcome the existing bottlenecks. KEY SCIENTIFIC CONCEPTS OF REVIEW The CRISPR/Cas system was discovered as part of the bacterial innate immune system. It has been used as a biotechnological tool for genome editing and efficiently applied in soybean to unveil gene function, improve agronomic traits such as yield and nutritional grain quality, and enhance biotic and abiotic stress tolerance. To date, the efficiency of gRNAs has been validated using protoplasts and hairy root assays, while stable plant transformation relies on Agrobacterium-mediated and particle bombardment methods. Nevertheless, most steps of the CRISPR/Cas workflow require optimizations to achieve a more effective genome editing in soybean plants.
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Affiliation(s)
- Nayara Sabrina Freitas-Alves
- Embrapa Genetic Resources and Biotechnology, Brasília, DF, Brazil; Bioprocess Engineering and Biotechnology Graduate Program, Federal University of Paraná (UFPR), Curitiba, PR, Brazil
| | - Clidia E Moreira-Pinto
- Embrapa Genetic Resources and Biotechnology, Brasília, DF, Brazil; National Institute of Science and Technology, INCT PlantStress Biotech, EMBRAPA, Brasília, DF, Brazil
| | - Fabiano T P K Távora
- Embrapa Genetic Resources and Biotechnology, Brasília, DF, Brazil; National Institute of Science and Technology, INCT PlantStress Biotech, EMBRAPA, Brasília, DF, Brazil
| | - Bruno Paes-de-Melo
- Embrapa Genetic Resources and Biotechnology, Brasília, DF, Brazil; National Institute of Science and Technology, INCT PlantStress Biotech, EMBRAPA, Brasília, DF, Brazil
| | - Fabricio B M Arraes
- Embrapa Genetic Resources and Biotechnology, Brasília, DF, Brazil; National Institute of Science and Technology, INCT PlantStress Biotech, EMBRAPA, Brasília, DF, Brazil
| | - Isabela T Lourenço-Tessutti
- Embrapa Genetic Resources and Biotechnology, Brasília, DF, Brazil; National Institute of Science and Technology, INCT PlantStress Biotech, EMBRAPA, Brasília, DF, Brazil
| | - Stéfanie M Moura
- Embrapa Genetic Resources and Biotechnology, Brasília, DF, Brazil; National Institute of Science and Technology, INCT PlantStress Biotech, EMBRAPA, Brasília, DF, Brazil
| | - Antonio C Oliveira
- National Institute of Science and Technology, INCT PlantStress Biotech, EMBRAPA, Brasília, DF, Brazil; Federal University of Pelotas (UFPEL), Pelotas, RS, Brazil
| | - Carolina V Morgante
- Embrapa Genetic Resources and Biotechnology, Brasília, DF, Brazil; National Institute of Science and Technology, INCT PlantStress Biotech, EMBRAPA, Brasília, DF, Brazil; Embrapa Semi-Arid, Petrolina, PE, Brazil
| | - Yiping Qi
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD, USA
| | - Maria Fatima Grossi-de-Sa
- Embrapa Genetic Resources and Biotechnology, Brasília, DF, Brazil; Bioprocess Engineering and Biotechnology Graduate Program, Federal University of Paraná (UFPR), Curitiba, PR, Brazil; National Institute of Science and Technology, INCT PlantStress Biotech, EMBRAPA, Brasília, DF, Brazil; Catholic University of Brasília, Graduate Program in Genomic Sciences and Biotechnology, Brasília, DF, Brazil; Catholic University Dom Bosco, Graduate Program in Biotechnology, Campo Grande, MS, Brazil.
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Develtere W, Decaestecker W, Rombaut D, Anders C, Clicque E, Vuylsteke M, Jacobs TB. Continual improvement of CRISPR-induced multiplex mutagenesis in Arabidopsis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 119:1158-1172. [PMID: 38713824 DOI: 10.1111/tpj.16785] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Revised: 04/08/2024] [Accepted: 04/16/2024] [Indexed: 05/09/2024]
Abstract
CRISPR/Cas9 is currently the most powerful tool to generate mutations in plant genomes and more efficient tools are needed as the scale of experiments increases. In the model plant Arabidopsis, the choice of the promoter driving Cas9 expression is critical to generate germline mutations. Several optimal promoters have been reported. However, it is unclear which promoter is ideal as they have not been thoroughly tested side by side. Furthermore, most plant vectors still use one of the two Cas9 nuclear localization sequence (NLS) configurations initially reported. We genotyped more than 6000 Arabidopsis T2 plants to test seven promoters and six types of NLSs across 14 targets to systematically improve the generation of single and multiplex inheritable mutations. We found that the RPS5A promoter and bipartite NLS were individually the most efficient components. When combined, 99% of T2 plants contained at least one knockout (KO) mutation and 84% contained 4- to 7-plex KOs, the highest multiplexing KO rate in Arabidopsis to date. These optimizations will be useful to generate higher-order KOs in the germline of Arabidopsis and will likely be applicable to other CRISPR systems as well.
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Affiliation(s)
- Ward Develtere
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052, Ghent, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 71, 9052, Ghent, Belgium
| | - Ward Decaestecker
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052, Ghent, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 71, 9052, Ghent, Belgium
| | - Debbie Rombaut
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052, Ghent, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 71, 9052, Ghent, Belgium
| | - Chantal Anders
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052, Ghent, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 71, 9052, Ghent, Belgium
| | - Elke Clicque
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052, Ghent, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 71, 9052, Ghent, Belgium
| | | | - Thomas B Jacobs
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052, Ghent, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 71, 9052, Ghent, Belgium
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Shi Y, Wang J, Yu T, Song R, Qi W. Callus-specific CRISPR/Cas9 system to increase heritable gene mutations in maize. PLANTA 2024; 260:16. [PMID: 38833022 DOI: 10.1007/s00425-024-04451-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Accepted: 05/28/2024] [Indexed: 06/06/2024]
Abstract
MAIN CONCLUSION A callus-specific CRISPR/Cas9 (CSC) system with Cas9 gene driven by the promoters of ZmCTA1 and ZmPLTP reduces somatic mutations and improves the production of heritable mutations in maize. The CRISPR/Cas9 system, due to its editing accuracy, provides an excellent tool for crop genetic breeding. Nevertheless, the traditional design utilizing CRISPR/Cas9 with ubiquitous expression leads to an abundance of somatic mutations, thereby complicating the detection of heritable mutations. We constructed a callus-specific CRISPR/Cas9 (CSC) system using callus-specific promoters of maize Chitinase A1 and Phospholipid transferase protein (pZmCTA1 and pZmPLTP) to drive Cas9 expression, and the target gene chosen for this study was the bZIP transcription factor Opaque2 (O2). The CRISPR/Cas9 system driven by the maize Ubiquitin promoter (pZmUbi) was employed as a comparative control. Editing efficiency analysis based on high-throughput tracking of mutations (Hi-TOM) showed that the CSC systems generated more target gene mutations than the ubiquitously expressed CRISPR/Cas9 (UC) system in calli. Transgenic plants were generated for the CSC and UC systems. We found that the CSC systems generated fewer target gene mutations than the UC system in the T0 seedlings but reduced the influence of somatic mutations. Nearly 100% of mutations in the T1 generation generated by the CSC systems were derived from the T0 plants. Only 6.3-16.7% of T1 mutations generated by the UC system were from the T0 generation. Our results demonstrated that the CSC system consistently produced more stable, heritable mutants in the subsequent generation, suggesting its potential application across various crops to facilitate the genetic breeding of desired mutations.
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Affiliation(s)
- Yuan Shi
- Shanghai Key Laboratory of Bio-Energy Crops, School of Life Sciences, Shanghai University, Shanghai, 200444, China
| | - Jing Wang
- Shanghai Key Laboratory of Bio-Energy Crops, School of Life Sciences, Shanghai University, Shanghai, 200444, China
| | - Tante Yu
- Shanghai Key Laboratory of Bio-Energy Crops, School of Life Sciences, Shanghai University, Shanghai, 200444, China
| | - Rentao Song
- State Key Laboratory of Maize Bio-Breeding, Frontiers Science Center for Molecular Design Breeding, Joint International Research Laboratory of Crop Molecular Breeding, National Maize Improvement Center, College of Agronomy and Biotechnology, China Agricultural University, Beijing, People's Republic of China.
- Sanya Institute of China Agricultural University, Sanya, People's Republic of China.
- Hainan Yazhou Bay Seed Laboratory, Sanya, People's Republic of China.
| | - Weiwei Qi
- Shanghai Key Laboratory of Bio-Energy Crops, School of Life Sciences, Shanghai University, Shanghai, 200444, China.
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Su J, Xu X, Cseke LJ, Whittier S, Zhou R, Zhang Z, Dietz Z, Singh K, Yang B, Chen SY, Picking W, Zou X, Gassmann W. Cell-specific polymerization-driven biomolecular condensate formation fine-tunes root tissue morphogenesis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.02.587845. [PMID: 38617336 PMCID: PMC11014531 DOI: 10.1101/2024.04.02.587845] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/16/2024]
Abstract
Formation of biomolecular condensates can be driven by weak multivalent interactions and emergent polymerization. However, the mechanism of polymerization-mediated condensate formation is less studied. We found lateral root cap cell (LRC)-specific SUPPRESSOR OF RPS4-RLD1 (SRFR1) condensates fine-tune primary root development. Polymerization of the SRFR1 N-terminal domain is required for both LRC condensate formation and optimal root growth. Surprisingly, the first intrinsically disordered region (IDR1) of SRFR1 can be functionally substituted by a specific group of intrinsically disordered proteins known as dehydrins. This finding facilitated the identification of functional segments in the IDR1 of SRFR1, a generalizable strategy to decode unknown IDRs. With this functional information we further improved root growth by modifying the SRFR1 condensation module, providing a strategy to improve plant growth and resilience.
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Niazian M, Belzile F, Curtin SJ, de Ronne M, Torkamaneh D. Optimization of in vitro and ex vitro Agrobacterium rhizogenes-mediated hairy root transformation of soybean for visual screening of transformants using RUBY. FRONTIERS IN PLANT SCIENCE 2023; 14:1207762. [PMID: 37484469 PMCID: PMC10361064 DOI: 10.3389/fpls.2023.1207762] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Accepted: 06/22/2023] [Indexed: 07/25/2023]
Abstract
In vitro and ex vitro Agrobacterium rhizogenes-mediated hairy root transformation (HRT) assays are key components of the plant biotechnology and functional genomics toolkit. In this report, both in vitro and ex vitro HRT were optimized in soybean using the RUBY reporter. Different parameters including A. rhizogenes strain, optical density of the bacterial cell culture (OD600), co-cultivation media, soybean genotype, explant age, and acetosyringone addition and concentration were evaluated. Overall, the in vitro assay was more efficient than the ex vitro assay in terms of the percentage of induction of hairy roots and transformed roots (expressing RUBY). Nonetheless, the ex vitro technique was deemed faster and a less complicated approach. The highest transformation of RUBY was observed on 7-d-old cotyledons of cv. Bert inoculated for 30 minutes with the R1000 resuspended in ¼ B5 medium to OD600 (0.3) and 150 µM of acetosyringone. The parameters of this assay also led to the highest percentage of RUBY through two-step ex vitro hairy root transformation. Finally, using machine learning-based modeling, optimal protocols for both assays were further defined. This study establishes efficient and reliable hairy root transformation protocols applicable for functional studies in soybean.
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Affiliation(s)
- Mohsen Niazian
- Département de Phytologie, Université Laval, Québec City, QC, Canada
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec City, QC, Canada
- Centre de recherche et d’innovation sur les végétaux (CRIV), Université Laval, Québec City, QC, Canada
| | - François Belzile
- Département de Phytologie, Université Laval, Québec City, QC, Canada
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec City, QC, Canada
- Centre de recherche et d’innovation sur les végétaux (CRIV), Université Laval, Québec City, QC, Canada
| | - Shaun J. Curtin
- Plant Science Research Unit, United States Department of Agriculture (USDA), St Paul, MN, United States
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN, United States
- Center for Plant Precision Genomics, University of Minnesota, St. Paul, MN, United States
- Center for Genome Engineering, University of Minnesota, St. Paul, MN, United States
| | - Maxime de Ronne
- Département de Phytologie, Université Laval, Québec City, QC, Canada
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec City, QC, Canada
- Centre de recherche et d’innovation sur les végétaux (CRIV), Université Laval, Québec City, QC, Canada
| | - Davoud Torkamaneh
- Département de Phytologie, Université Laval, Québec City, QC, Canada
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec City, QC, Canada
- Centre de recherche et d’innovation sur les végétaux (CRIV), Université Laval, Québec City, QC, Canada
- Institute Intelligence and Data (IID), Université Laval, Québec City, QC, Canada
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Khan A, Chen S, Fatima S, Ahamad L, Siddiqui MA. Biotechnological Tools to Elucidate the Mechanism of Plant and Nematode Interactions. PLANTS (BASEL, SWITZERLAND) 2023; 12:2387. [PMID: 37376010 DOI: 10.3390/plants12122387] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 06/16/2023] [Accepted: 06/17/2023] [Indexed: 06/29/2023]
Abstract
Plant-parasitic nematodes (PPNs) pose a threat to global food security in both the developed and developing worlds. PPNs cause crop losses worth a total of more than USD 150 billion worldwide. The sedentary root-knot nematodes (RKNs) also cause severe damage to various agricultural crops and establish compatible relationships with a broad range of host plants. This review aims to provide a broad overview of the strategies used to identify the morpho-physiological and molecular events that occur during RKN parasitism. It describes the most current developments in the transcriptomic, proteomic, and metabolomic strategies of nematodes, which are important for understanding compatible interactions of plants and nematodes, and several strategies for enhancing plant resistance against RKNs. We will highlight recent rapid advances in molecular strategies, such as gene-silencing technologies, RNA interference (RNAi), and small interfering RNA (siRNA) effector proteins, that are leading to considerable progress in understanding the mechanism of plant-nematode interactions. We also take into account genetic engineering strategies, such as targeted genome editing techniques, the clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR associated protein 9 (Cas9) (CRISPR/Cas-9) system, and quantitative trait loci (QTL), to enhance the resistance of plants against nematodes.
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Affiliation(s)
- Arshad Khan
- Department of Botany, Aligarh Muslim University, Aligarh 202002, India
| | - Shaohua Chen
- National Key Laboratory of Green Pesticide, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou 510642, China
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou 510642, China
| | - Saba Fatima
- Department of Botany, Aligarh Muslim University, Aligarh 202002, India
| | - Lukman Ahamad
- Department of Botany, Aligarh Muslim University, Aligarh 202002, India
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Villao-Uzho L, Chávez-Navarrete T, Pacheco-Coello R, Sánchez-Timm E, Santos-Ordóñez E. Plant Promoters: Their Identification, Characterization, and Role in Gene Regulation. Genes (Basel) 2023; 14:1226. [PMID: 37372407 DOI: 10.3390/genes14061226] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 05/17/2023] [Accepted: 05/30/2023] [Indexed: 06/29/2023] Open
Abstract
One of the strategies to overcome diseases or abiotic stress in crops is the use of improved varieties. Genetic improvement could be accomplished through different methods, including conventional breeding, induced mutation, genetic transformation, or gene editing. The gene function and regulated expression through promoters are necessary for transgenic crops to improve specific traits. The variety of promoter sequences has increased in the generation of genetically modified crops because they could lead to the expression of the gene responsible for the improved trait in a specific manner. Therefore, the characterization of the promoter activity is necessary for the generation of biotechnological crops. That is why several analyses have focused on identifying and isolating promoters using techniques such as reverse transcriptase-polymerase chain reaction (RT-PCR), genetic libraries, cloning, and sequencing. Promoter analysis involves the plant genetic transformation method, a potent tool for determining the promoter activity and function of genes in plants, contributing to understanding gene regulation and plant development. Furthermore, the study of promoters that play a fundamental role in gene regulation is highly relevant. The study of regulation and development in transgenic organisms has made it possible to understand the benefits of directing gene expression in a temporal, spatial, and even controlled manner, confirming the great diversity of promoters discovered and developed. Therefore, promoters are a crucial tool in biotechnological processes to ensure the correct expression of a gene. This review highlights various types of promoters and their functionality in the generation of genetically modified crops.
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Affiliation(s)
- Liliana Villao-Uzho
- Biotechnological Research Center of Ecuador, ESPOL Polytechnic University, Escuela Superior Politécnica del Litoral, ESPOL, Gustavo Galindo Campus Km. 30.5 Vía Perimetral, Guayaquil 090902, Ecuador
| | - Tatiana Chávez-Navarrete
- Biotechnological Research Center of Ecuador, ESPOL Polytechnic University, Escuela Superior Politécnica del Litoral, ESPOL, Gustavo Galindo Campus Km. 30.5 Vía Perimetral, Guayaquil 090902, Ecuador
| | - Ricardo Pacheco-Coello
- Biotechnological Research Center of Ecuador, ESPOL Polytechnic University, Escuela Superior Politécnica del Litoral, ESPOL, Gustavo Galindo Campus Km. 30.5 Vía Perimetral, Guayaquil 090902, Ecuador
| | - Eduardo Sánchez-Timm
- Biotechnological Research Center of Ecuador, ESPOL Polytechnic University, Escuela Superior Politécnica del Litoral, ESPOL, Gustavo Galindo Campus Km. 30.5 Vía Perimetral, Guayaquil 090902, Ecuador
- Faculty of Life Sciences, ESPOL Polytechnic University, Escuela Superior Politécnica del Litoral, ESPOL, Gustavo Galindo Campus Km. 30.5 Vía Perimetral, Guayaquil 090902, Ecuador
| | - Efrén Santos-Ordóñez
- Biotechnological Research Center of Ecuador, ESPOL Polytechnic University, Escuela Superior Politécnica del Litoral, ESPOL, Gustavo Galindo Campus Km. 30.5 Vía Perimetral, Guayaquil 090902, Ecuador
- Faculty of Life Sciences, ESPOL Polytechnic University, Escuela Superior Politécnica del Litoral, ESPOL, Gustavo Galindo Campus Km. 30.5 Vía Perimetral, Guayaquil 090902, Ecuador
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Zhou J, Luan X, Liu Y, Wang L, Wang J, Yang S, Liu S, Zhang J, Liu H, Yao D. Strategies and Methods for Improving the Efficiency of CRISPR/Cas9 Gene Editing in Plant Molecular Breeding. PLANTS (BASEL, SWITZERLAND) 2023; 12:1478. [PMID: 37050104 PMCID: PMC10097296 DOI: 10.3390/plants12071478] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 03/21/2023] [Accepted: 03/22/2023] [Indexed: 06/19/2023]
Abstract
Following recent developments and refinement, CRISPR-Cas9 gene-editing technology has become increasingly mature and is being widely used for crop improvement. The application of CRISPR/Cas9 enables the generation of transgene-free genome-edited plants in a short period and has the advantages of simplicity, high efficiency, high specificity, and low production costs, which greatly facilitate the study of gene functions. In plant molecular breeding, the gene-editing efficiency of the CRISPR-Cas9 system has proven to be a key step in influencing the effectiveness of molecular breeding, with improvements in gene-editing efficiency recently becoming a focus of reported scientific research. This review details strategies and methods for improving the efficiency of CRISPR/Cas9 gene editing in plant molecular breeding, including Cas9 variant enzyme engineering, the effect of multiple promoter driven Cas9, and gRNA efficient optimization and expression strategies. It also briefly introduces the optimization strategies of the CRISPR/Cas12a system and the application of BE and PE precision editing. These strategies are beneficial for the further development and optimization of gene editing systems in the field of plant molecular breeding.
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Affiliation(s)
- Junming Zhou
- College of Life Sciences, Jilin Agricultural University, Changchun 130118, China; (J.Z.); (X.L.); (Y.L.); (L.W.); (J.W.); (S.L.)
| | - Xinchao Luan
- College of Life Sciences, Jilin Agricultural University, Changchun 130118, China; (J.Z.); (X.L.); (Y.L.); (L.W.); (J.W.); (S.L.)
| | - Yixuan Liu
- College of Life Sciences, Jilin Agricultural University, Changchun 130118, China; (J.Z.); (X.L.); (Y.L.); (L.W.); (J.W.); (S.L.)
| | - Lixue Wang
- College of Life Sciences, Jilin Agricultural University, Changchun 130118, China; (J.Z.); (X.L.); (Y.L.); (L.W.); (J.W.); (S.L.)
| | - Jiaxin Wang
- College of Life Sciences, Jilin Agricultural University, Changchun 130118, China; (J.Z.); (X.L.); (Y.L.); (L.W.); (J.W.); (S.L.)
| | - Songnan Yang
- College of Agronomy, Jilin Agricultural University, Changchun 130118, China; (S.Y.); (J.Z.)
| | - Shuying Liu
- College of Life Sciences, Jilin Agricultural University, Changchun 130118, China; (J.Z.); (X.L.); (Y.L.); (L.W.); (J.W.); (S.L.)
| | - Jun Zhang
- College of Agronomy, Jilin Agricultural University, Changchun 130118, China; (S.Y.); (J.Z.)
| | - Huijing Liu
- College of Life Sciences, Jilin Agricultural University, Changchun 130118, China; (J.Z.); (X.L.); (Y.L.); (L.W.); (J.W.); (S.L.)
| | - Dan Yao
- College of Life Sciences, Jilin Agricultural University, Changchun 130118, China; (J.Z.); (X.L.); (Y.L.); (L.W.); (J.W.); (S.L.)
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10
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Seedlessness Trait and Genome Editing—A Review. Int J Mol Sci 2023; 24:ijms24065660. [PMID: 36982733 PMCID: PMC10057249 DOI: 10.3390/ijms24065660] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 03/13/2023] [Accepted: 03/14/2023] [Indexed: 03/18/2023] Open
Abstract
Parthenocarpy and stenospermocarpy are the two mechanisms underlying the seedless fruit set program. Seedless fruit occurs naturally and can be produced using hormone application, crossbreeding, or ploidy breeding. However, the two types of breeding are time-consuming and sometimes ineffective due to interspecies hybridization barriers or the absence of appropriate parental genotypes to use in the breeding process. The genetic engineering approach provides a better prospect, which can be explored based on an understanding of the genetic causes underlying the seedlessness trait. For instance, CRISPR/Cas is a comprehensive and precise technology. The prerequisite for using the strategy to induce seedlessness is identifying the crucial master gene or transcription factor liable for seed formation/development. In this review, we primarily explored the seedlessness mechanisms and identified the potential candidate genes underlying seed development. We also discussed the CRISPR/Cas-mediated genome editing approaches and their improvements.
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11
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Rahman SU, McCoy E, Raza G, Ali Z, Mansoor S, Amin I. Improvement of Soybean; A Way Forward Transition from Genetic Engineering to New Plant Breeding Technologies. Mol Biotechnol 2023; 65:162-180. [PMID: 35119645 DOI: 10.1007/s12033-022-00456-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Accepted: 01/21/2022] [Indexed: 01/18/2023]
Abstract
Soybean is considered one of the important crops among legumes. Due to high nutritional contents in seed (proteins, sugars, oil, fatty acids, and amino acids), soybean is used globally for food, feed, and fuel. The primary consumption of soybean is vegetable oil and feed for chickens and livestock. Apart from this, soybean benefits soil fertility by fixing atmospheric nitrogen through root nodular bacteria. While conventional breeding is practiced for soybean improvement, with the advent of new biotechnological methods scientists have also engineered soybean to improve different traits (herbicide, insect, and disease resistance) to fulfill consumer requirements and to meet the global food deficiency. Genetic engineering (GE) techniques such as transgenesis and gene silencing help to minimize the risks and increase the adaptability of soybean. Recently, new plant breeding technologies (NPBTs) emerged such as zinc-finger nucleases, transcription activator-like effector nucleases, and Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR/Cas9), which paved the way for enhanced genetic modification of soybean. These NPBTs have the potential to improve soybean via gene functional characterization precision genome engineering for trait improvement. Importantly, these NPBTs address the ethical and public acceptance issues related to genetic modifications and transgenesis in soybean. In the present review, we summarized the improvement of soybean through GE and NPBTs. The valuable traits that have been improved through GE for different constraints have been discussed. Moreover, the traits that have been improved through NPBTs and potential targets for soybean improvements via NPBTs and solutions for ethical and public acceptance are also presented.
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Affiliation(s)
- Saleem Ur Rahman
- National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad, Pakistan
- Constituent College Pakistan Institute of Engineering and Applied Sciences, Nilore, Islamabad, Pakistan
| | - Evan McCoy
- Center for Applied Genetic Technologies (CAGT), University of Georgia, Athens, USA
| | - Ghulam Raza
- National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad, Pakistan
- Constituent College Pakistan Institute of Engineering and Applied Sciences, Nilore, Islamabad, Pakistan
| | - Zahir Ali
- Laboratory for Genome Engineering, Center for Desert Agriculture and Division of Biological Sciences, 4700 King Abdullah University of Science and Technology, Thuwal, 23955-6900, Saudi Arabia
| | - Shahid Mansoor
- National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad, Pakistan
- Constituent College Pakistan Institute of Engineering and Applied Sciences, Nilore, Islamabad, Pakistan
| | - Imran Amin
- National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad, Pakistan.
- Constituent College Pakistan Institute of Engineering and Applied Sciences, Nilore, Islamabad, Pakistan.
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12
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Toda E, Kato N, Higashiyama T, Okamoto T. Genome editing approaches using reproductive cells/tissues in flowering plants. Front Genome Ed 2023; 4:1085023. [PMID: 36714390 PMCID: PMC9873966 DOI: 10.3389/fgeed.2022.1085023] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 12/30/2022] [Indexed: 01/13/2023] Open
Abstract
Targeted mutagenesis via programmable nucleases including the clustered regulatory interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9) (CRISPR/Cas9) system has been broadly utilized to generate genome-edited organisms including flowering plants. To date, specific expression of Cas9 protein and guide RNA (gRNA) in reproductive cells or tissues is considered one of the most effective genome-editing approaches for heritable targeted mutagenesis. In this report, we review recent advances in genome editing methods for reproductive cells or tissues, which have roles in transmitting genetic material to the next-generation, such as egg cells, pollen grains, zygotes, immature zygotic embryos, and shoot apical meristems (SAMs). Specific expression of Cas9 proteins in initiating cells efficiently induces targeted mutagenesis via Agrobacterium-mediated in planta transformation. In addition, genome editing by direct delivery of CRISPR/Cas9 components into pollen grains, zygotes, cells of embryos and SAMs has been successfully established to generate genome-edited plant lines. Notably, DNA-free genome editing by the delivery of Cas9-gRNA ribonucleoproteins (RNPs) is not associated with any legislative concerns about genetically modified organisms. In summary, the genome editing methods for reproductive cells or tissues have enormous potential for not only basic studies for plant reproduction but also applied sciences toward molecular plant breeding.
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Affiliation(s)
- Erika Toda
- Department of Biological Sciences, The University of Tokyo, Tokyo, Japan,Department of Biological Sciences, Tokyo Metropolitan University, Tokyo, Japan,*Correspondence: Erika Toda,
| | - Norio Kato
- Department of Biological Sciences, Tokyo Metropolitan University, Tokyo, Japan
| | | | - Takashi Okamoto
- Department of Biological Sciences, Tokyo Metropolitan University, Tokyo, Japan
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13
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Hassan MM, Yuan G, Liu Y, Alam M, Eckert CA, Tuskan GA, Golz JF, Yang X. Precision genome editing in plants using gene targeting and prime editing: existing and emerging strategies. Biotechnol J 2022; 17:e2100673. [PMID: 35766313 DOI: 10.1002/biot.202100673] [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: 12/15/2021] [Revised: 06/16/2022] [Accepted: 06/22/2022] [Indexed: 11/08/2022]
Abstract
Precise modification of plant genomes, such as seamless insertion, deletion, or replacement of DNA sequences at a predefined site, is a challenging task. Gene targeting (GT) and prime editing are currently the best approaches for this purpose. However, these techniques are inefficient in plants, which limits their applications for crop breeding programs. Recently, substantial developments have been made to improve the efficiency of these techniques in plants. Several strategies, such as RNA donor templating, chemically modified donor DNA template, and tandem-repeat homology-directed repair, are aimed at improving GT. Additionally, improved prime editing gRNA design, use of engineered reverse transcriptase enzymes, and splitting prime editing components have improved the efficacy of prime editing in plants. These emerging strategies and existing technologies are reviewed along with various perspectives on their future improvement and the development of robust precision genome editing technologies for plants.
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Affiliation(s)
- Md Mahmudul Hassan
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, 37831, USA
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, Tennessee, 37831, USA
- Department of Genetics and Plant Breeding, Patuakhali Science and Technology University, Dumki, Patuakhali, 8602, Bangladesh
| | - Guoliang Yuan
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, 37831, USA
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, Tennessee, 37831, USA
| | - Yang Liu
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, 37831, USA
| | - Mobashwer Alam
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Nambour, Queensland, Australia
| | - Carrie A Eckert
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, 37831, USA
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, Tennessee, 37831, USA
| | - Gerald A Tuskan
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, 37831, USA
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, Tennessee, 37831, USA
| | - John F Golz
- School of Biosciences, University of Melbourne, Royal Parade, Parkville, Victoria, 3010, Australia
| | - Xiaohan Yang
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, 37831, USA
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, Tennessee, 37831, USA
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14
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Trinh DD, Le NT, Bui TP, Le TNT, Nguyen CX, Chu HH, Do PT. A sequential transformation method for validating soybean genome editing by CRISPR/Cas9 system. Saudi J Biol Sci 2022; 29:103420. [PMID: 36060110 PMCID: PMC9434168 DOI: 10.1016/j.sjbs.2022.103420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Revised: 07/13/2022] [Accepted: 08/12/2022] [Indexed: 12/05/2022] Open
Abstract
This study was performed to evaluate the sequential transformation for soybean genome editing using the CRISPR/Cas9 system as well as to show a strategy for examining the activity of CRISPR/Cas9 constructs, especially the designed guide RNAs (gRNAs). The gRNAs for targeted mutations of an exogenous gene and multiple endogenous genes were constructed and transferred into a stably-overexpressed-Cas9 soybean line using Agrobacterium rhizogenes-mediated hairy root induction system. The targeted mutations were identified and characterized by the poly-acrylamide gel electrophoresis (PAGE) heteroduplex method and by sequencing. Induced mutations of the exogenous gene (gus) were observed in 57% of tested transgenic hairy roots, while 100% of the transgenic root lines showed targeted mutations of the endogenous (SACPD-C) gene. Multiple gRNAs targeting two endogenous genes (SACPD-C and SMT) induced mutation rates of 75% and 67%, respectively. Various indels including small and large deletions as well as insertions were found in target sites of the tested genes. This sequential transformation method could present the targeting efficacy of different gRNAs of each tested gene. Additionally, in this study differences in gRNA ratings were found between bioinformatics predictions and actual experimental results. This is the first successful application of the sequential transformation method for genome editing in soybean using the hairy root system. This method could be potentially useful for validating CRISPR/Cas9 constructs, evaluating gRNA targeting efficiencies, and could be applied for other research directions.
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Affiliation(s)
- Duy Dinh Trinh
- Institute of Biotechnology, Vietnam Academy of Science and Technology, Hoang Quoc Viet, Cau Giay, Hanoi, Viet Nam
| | - Ngoc Thu Le
- Institute of Biotechnology, Vietnam Academy of Science and Technology, Hoang Quoc Viet, Cau Giay, Hanoi, Viet Nam
| | - Thao Phuong Bui
- Institute of Biotechnology, Vietnam Academy of Science and Technology, Hoang Quoc Viet, Cau Giay, Hanoi, Viet Nam
- University of Science and Technology of Hanoi, Vietnam Academy of Science and Technology, Hoang Quoc Viet, Cau Giay, Hanoi, Viet Nam
| | - Thao Nhu Thi Le
- Institute of Biotechnology, Vietnam Academy of Science and Technology, Hoang Quoc Viet, Cau Giay, Hanoi, Viet Nam
| | - Cuong Xuan Nguyen
- Division of Plant Sciences, University of Missouri, Columbia, MO, United States
| | - Ha Hoang Chu
- Institute of Biotechnology, Vietnam Academy of Science and Technology, Hoang Quoc Viet, Cau Giay, Hanoi, Viet Nam
- Graduate University of Science and Technology, Vietnam Academy of Science and Technology, Hoang Quoc Viet, Cau Giay, Hanoi, Viet Nam
| | - Phat Tien Do
- Institute of Biotechnology, Vietnam Academy of Science and Technology, Hoang Quoc Viet, Cau Giay, Hanoi, Viet Nam
- Graduate University of Science and Technology, Vietnam Academy of Science and Technology, Hoang Quoc Viet, Cau Giay, Hanoi, Viet Nam
- Corresponding author at: Institute of Biotechnology, Vietnam Academy of Science and Technology, Hoang Quoc Viet, Cau Giay, Hanoi, Viet Nam.
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15
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Baloglu MC, Celik Altunoglu Y, Baloglu P, Yildiz AB, Türkölmez N, Özden Çiftçi Y. Gene-Editing Technologies and Applications in Legumes: Progress, Evolution, and Future Prospects. Front Genet 2022; 13:859437. [PMID: 35836569 PMCID: PMC9275826 DOI: 10.3389/fgene.2022.859437] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 05/13/2022] [Indexed: 12/22/2022] Open
Abstract
Legumes are rich in protein and phytochemicals and have provided a healthy diet for human beings for thousands of years. In recognition of the important role they play in human nutrition and agricultural production, the researchers have made great efforts to gain new genetic traits in legumes such as yield, stress tolerance, and nutritional quality. In recent years, the significant increase in genomic resources for legume plants has prepared the groundwork for applying cutting-edge breeding technologies, such as transgenic technologies, genome editing, and genomic selection for crop improvement. In addition to the different genome editing technologies including the CRISPR/Cas9-based genome editing system, this review article discusses the recent advances in plant-specific gene-editing methods, as well as problems and potential benefits associated with the improvement of legume crops with important agronomic properties. The genome editing technologies have been effectively used in different legume plants including model legumes like alfalfa and lotus, as well as crops like soybean, cowpea, and chickpea. We also discussed gene-editing methods used in legumes and the improvements of agronomic traits in model and recalcitrant legumes. Despite the immense opportunities genome editing can offer to the breeding of legumes, governmental regulatory restrictions present a major concern. In this context, the comparison of the regulatory framework of genome editing strategies in the European Union and the United States of America was also discussed. Gene-editing technologies have opened up new possibilities for the improvement of significant agronomic traits in legume breeding.
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Affiliation(s)
- Mehmet Cengiz Baloglu
- Department of Genetics and Bioengineering, Faculty of Engineering and Architecture, Kastamonu University, Kastamonu, Turkey
| | - Yasemin Celik Altunoglu
- Department of Genetics and Bioengineering, Faculty of Engineering and Architecture, Kastamonu University, Kastamonu, Turkey
| | - Pinar Baloglu
- Research and Application Center, Kastamonu University, Kastamonu, Turkey
| | - Ali Burak Yildiz
- Department of Molecular Biology and Genetics, Gebze Technical University, Kocaeli, Turkey
| | - Nil Türkölmez
- Department of Molecular Biology and Genetics, Gebze Technical University, Kocaeli, Turkey
| | - Yelda Özden Çiftçi
- Department of Molecular Biology and Genetics, Gebze Technical University, Kocaeli, Turkey
- Smart Agriculture Research and Application Center, Gebze Technical University, Kocaeli, Turkey
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16
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Kumar S, Liu ZB, Sanyour-Doyel N, Lenderts B, Worden A, Anand A, Cho HJ, Bolar J, Harris C, Huang L, Xing A, Richardson A. Efficient gene targeting in soybean using Ochrobactrum haywardense-mediated delivery of a marker-free donor template. PLANT PHYSIOLOGY 2022; 189:585-594. [PMID: 35191500 PMCID: PMC9157123 DOI: 10.1093/plphys/kiac075] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Accepted: 01/24/2022] [Indexed: 05/24/2023]
Abstract
Gene targeting (GT) for precise gene insertion or swap into pre-defined genomic location has been a bottleneck for expedited soybean precision breeding. We report a robust selectable marker-free GT system in soybean, one of the most economically important crops. An efficient Oh H1-8 (Ochrobactrum haywardense H1-8)-mediated embryonic axis transformation method was used for the delivery of CRISPR-Cas9 components and donor template to regenerate T0 plants 6-8 weeks after transformation. This approach generated up to 3.4% targeted insertion of the donor sequence into the target locus in T0 plants, with ∼ 90% mutation rate observed at the genomic target site. The GT was demonstrated in two genomic sites using two different donor DNA templates without the need for a selectable marker within the template. High-resolution Southern-by-Sequencing analysis identified T1 plants with precise targeted insertion and without unintended plasmid DNA. Unlike previous low-frequency GT reports in soybean that involved particle bombardment-mediated delivery and extensive selection, the method described here is fast, efficient, reproducible, does not require a selectable marker within the donor DNA, and generates nonchimeric plants with heritable GT.
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Affiliation(s)
| | | | | | | | | | - Ajith Anand
- Corteva Agriscience, Johnston, Iowa 50131, USA
| | | | - Joy Bolar
- Corteva Agriscience, Johnston, Iowa 50131, USA
| | | | | | - Aiqiu Xing
- Corteva Agriscience, Johnston, Iowa 50131, USA
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17
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Rasheed A, Barqawi AA, Mahmood A, Nawaz M, Shah AN, Bay DH, Alahdal MA, Hassan MU, Qari SH. CRISPR/Cas9 is a powerful tool for precise genome editing of legume crops: a review. Mol Biol Rep 2022; 49:5595-5609. [PMID: 35585381 DOI: 10.1007/s11033-022-07529-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 04/15/2022] [Accepted: 04/26/2022] [Indexed: 10/18/2022]
Abstract
Legumes are an imperative source of food and proteins across the globe. They also improve soil fertility through symbiotic nitrogen fixation (SNF). Genome editing (GE) is now a novel way of developing desirable traits in legume crops. Genome editing tools like clustered regularly interspaced short palindromic repeats (CRISPR) system permits a defined genome alteration to improve crop performance. This genome editing tool is reliable, cost-effective, and versatile, and it has to deepen in terms of use compared to other tools. Recently, many novel variations have drawn the attention of plant geneticists, and efforts are being made to develop trans-gene-free cultivars for ensuring biosafety measures. This review critically elaborates on the recent development in genome editing of major legumes crops. We hope this updated review will provide essential informations for the researchers working on legumes genome editing. In general, the CRISPR/Cas9 novel GE technique can be integrated with other techniques like omics approaches and next-generation tools to broaden the range of gene editing and develop any desired legumes traits. Regulatory ethics of CRISPR/Cas9 are also discussed.
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Affiliation(s)
- Adnan Rasheed
- Key Laboratory of Crops Physiology, Ecology and Genetic Breeding, Ministry of Education/College of Agronomy, Jiangxi Agricultural University, 330045, Nanchang, China
| | - Aminah A Barqawi
- Department of Chemistry, Al-Leith University College, Umm Al Qura University, Makkah, Saudi Arabia
| | - Athar Mahmood
- Department of Agronomy, University of Agriculture Faisalabad, 38040, Faisalabad, Pakistan
| | - Muhammad Nawaz
- Department of Agricultural Engineering, Khwaja Fareed University of Engineering and Information Technology, Rahim Yar Khan, 64200, Punjab, Pakistan
| | - Adnan Noor Shah
- Department of Agricultural Engineering, Khwaja Fareed University of Engineering and Information Technology, Rahim Yar Khan, 64200, Punjab, Pakistan.
| | - Daniyah H Bay
- Department of Biology, Faculty of Applied Sciences, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Maryam A Alahdal
- Biology Department Faculty of Applied Science, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Muhammad Umair Hassan
- Research Center on Ecological Sciences, Jiangxi Agricultural University, 330045, Nanchang, China
| | - Sameer H Qari
- Department of Biology, Al-Jumum University College, Umm Al-Qura University, 21955, Makkah, Saudi Arabia.
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18
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Rahman F, Mishra A, Gupta A, Sharma R. Spatiotemporal Regulation of CRISPR/Cas9 Enables Efficient, Precise, and Heritable Edits in Plant Genomes. Front Genome Ed 2022; 4:870108. [PMID: 35558825 PMCID: PMC9087570 DOI: 10.3389/fgeed.2022.870108] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2022] [Accepted: 03/24/2022] [Indexed: 12/04/2022] Open
Abstract
CRISPR/Cas-mediated editing has revolutionized crop engineering. Due to the broad scope and potential of this technology, many studies have been carried out in the past decade towards optimizing genome editing constructs. Clearly, the choice of the promoter used to drive gRNA and Cas9 expression is critical to achieving high editing efficiency, precision, and heritability. While some important considerations for choosing a promoter include the number and nature of targets, host organism, mode of transformation and goal of the experiment, spatiotemporal regulation of Cas9 expression using tissue-specific or inducible promoters enables higher heritability and efficiency of targeted mutagenesis with reduced off-target effects. In this review, we discuss specific studies that highlight the prospects and trade-offs associated with the choice of promoters on genome editing and emphasize the need for inductive exploration and discovery to further advance this area of research in crop plants.
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Affiliation(s)
- Farhanur Rahman
- Department of Biological Sciences, Birla Institute of Technology and Science (BITS), Pilani, India
| | - Apurva Mishra
- Department of Molecular and Cellular Biology, University of California, Davis, Davis, CA, United States
| | - Archit Gupta
- Department of Biological Sciences, Birla Institute of Technology and Science (BITS), Pilani, India
| | - Rita Sharma
- Department of Biological Sciences, Birla Institute of Technology and Science (BITS), Pilani, India
- *Correspondence: Rita Sharma, ,
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19
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Niazian M, Belzile F, Torkamaneh D. CRISPR/Cas9 in Planta Hairy Root Transformation: A Powerful Platform for Functional Analysis of Root Traits in Soybean. PLANTS (BASEL, SWITZERLAND) 2022; 11:1044. [PMID: 35448772 PMCID: PMC9027312 DOI: 10.3390/plants11081044] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 04/07/2022] [Accepted: 04/08/2022] [Indexed: 12/22/2022]
Abstract
Sequence and expression data obtained by next-generation sequencing (NGS)-based forward genetics methods often allow the identification of candidate causal genes. To provide true experimental evidence of a gene's function, reverse genetics techniques are highly valuable. Site-directed mutagenesis through transfer DNA (T-DNA) delivery is an efficient reverse screen method in plant functional analysis. Precise modification of targeted crop genome sequences is possible through the stable and/or transient delivery of clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated protein (CRISPR/Cas) reagents. Currently, CRISPR/Cas9 is the most powerful reverse genetics approach for fast and precise functional analysis of candidate genes/mutations of interest. Rapid and large-scale analyses of CRISPR/Cas-induced mutagenesis is achievable through Agrobacterium rhizogenes-mediated hairy root transformation. The combination of A. rhizogenes hairy root-CRISPR/Cas provides an extraordinary platform for rapid, precise, easy, and cost-effective "in root" functional analysis of genes of interest in legume plants, including soybean. Both hairy root transformation and CRISPR/Cas9 techniques have their own complexities and considerations. Here, we discuss recent advancements in soybean hairy root transformation and CRISPR/Cas9 techniques. We highlight the critical factors required to enhance mutation induction and hairy root transformation, including the new generation of reporter genes, methods of Agrobacterium infection, accurate gRNA design strategies, Cas9 variants, gene regulatory elements of gRNAs and Cas9 nuclease cassettes and their configuration in the final binary vector to study genes involved in root-related traits in soybean.
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Affiliation(s)
- Mohsen Niazian
- Département de Phytologie, Université Laval, Québec City, QC G1V 0A6, Canada; (M.N.); (F.B.)
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec City, QC G1V 0A6, Canada
- Field and Horticultural Crops Research Department, Kurdistan Agricultural and Natural Resources Research and Education Center, Agricultural Research, Education and Extension Organization (AREEO), Sanandaj 6616936311, Iran
| | - François Belzile
- Département de Phytologie, Université Laval, Québec City, QC G1V 0A6, Canada; (M.N.); (F.B.)
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec City, QC G1V 0A6, Canada
| | - Davoud Torkamaneh
- Département de Phytologie, Université Laval, Québec City, QC G1V 0A6, Canada; (M.N.); (F.B.)
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec City, QC G1V 0A6, Canada
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20
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Lin CS, Hsu CT, Yuan YH, Zheng PX, Wu FH, Cheng QW, Wu YL, Wu TL, Lin S, Yue JJ, Cheng YH, Lin SI, Shih MC, Sheen J, Lin YC. DNA-free CRISPR-Cas9 gene editing of wild tetraploid tomato Solanum peruvianum using protoplast regeneration. PLANT PHYSIOLOGY 2022; 188:1917-1930. [PMID: 35088855 PMCID: PMC8968427 DOI: 10.1093/plphys/kiac022] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 12/10/2021] [Indexed: 05/24/2023]
Abstract
Wild tomatoes (Solanum peruvianum) are important genomic resources for tomato research and breeding. Development of a foreign DNA-free clustered regularly interspaced short palindromic repeat (CRISPR)-Cas delivery system has potential to mitigate public concern about genetically modified organisms. Here, we established a DNA-free CRISPR-Cas9 genome editing system based on an optimized protoplast regeneration protocol of S. peruvianum, an important resource for tomato introgression breeding. We generated mutants for genes involved in small interfering RNAs biogenesis, RNA-DEPENDENT RNA POLYMERASE 6 (SpRDR6), and SUPPRESSOR OF GENE SILENCING 3 (SpSGS3); pathogen-related peptide precursors, PATHOGENESIS-RELATED PROTEIN-1 (SpPR-1) and PROSYSTEMIN (SpProSys); and fungal resistance (MILDEW RESISTANT LOCUS O, SpMlo1) using diploid or tetraploid protoplasts derived from in vitro-grown shoots. The ploidy level of these regenerants was not affected by PEG-Ca2+-mediated transfection, CRISPR reagents, or the target genes. By karyotyping and whole genome sequencing analysis, we confirmed that CRISPR-Cas9 editing did not introduce chromosomal changes or unintended genome editing sites. All mutated genes in both diploid and tetraploid regenerants were heritable in the next generation. spsgs3 null T0 regenerants and sprdr6 null T1 progeny had wiry, sterile phenotypes in both diploid and tetraploid lines. The sterility of the spsgs3 null mutant was partially rescued, and fruits were obtained by grafting to wild-type (WT) stock and pollination with WT pollen. The resulting seeds contained the mutated alleles. Tomato yellow leaf curl virus proliferated at higher levels in spsgs3 and sprdr6 mutants than in the WT. Therefore, this protoplast regeneration technique should greatly facilitate tomato polyploidization and enable the use of CRISPR-Cas for S. peruvianum domestication and tomato breeding.
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Affiliation(s)
| | - Chen-Tran Hsu
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Yu-Hsuan Yuan
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Po-Xing Zheng
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei 115, Taiwan
- Biotechnology Research Center in Southern Taiwan, Academia Sinica, Tainan 711, Taiwan
| | - Fu-Hui Wu
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Qiao-Wei Cheng
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Yu-Lin Wu
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei 115, Taiwan
- Biotechnology Research Center in Southern Taiwan, Academia Sinica, Tainan 711, Taiwan
| | - Ting-Li Wu
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei 115, Taiwan
- Biotechnology Research Center in Southern Taiwan, Academia Sinica, Tainan 711, Taiwan
| | - Steven Lin
- Institute of Biochemistry, Academia Sinica, Taipei 115, Taiwan
| | - Jin-Jun Yue
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou 311, China
| | - Ying-Huey Cheng
- Plant Pathology Division, Taiwan Agricultural Research Institute, Taichung 413, Taiwan
| | - Shu-I Lin
- Department of Horticulture and Landscape Architecture, National Taiwan University, Taipei 106, Taiwan
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Li JW, Zeng T, Xu ZZ, Li JJ, Hu H, Yu Q, Zhou L, Zheng RR, Luo J, Wang CY. Ribozyme-mediated CRISPR/Cas9 gene editing in pyrethrum (Tanacetum cinerariifolium) hairy roots using a RNA polymerase II-dependent promoter. PLANT METHODS 2022; 18:32. [PMID: 35292048 PMCID: PMC8925089 DOI: 10.1186/s13007-022-00863-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Accepted: 02/24/2022] [Indexed: 05/14/2023]
Abstract
BACKGROUND Traditional CRISPR/Cas9 systems that rely on U6 or U3 snRNA promoters (RNA polymerase III-dependent promoters) can only achieve constitutive gene editing in plants, hampering the functional analysis of specifically expressed genes. Ribozyme-mediated CRISPR/Cas9 systems increase the types of promoters which can be used to transcribe sgRNA. Therefore, such systems allow specific gene editing; for example, transcription of the artificial gene Ribozyme-sgRNA-Ribozyme (RGR) is initiated by an RNA polymerase II-dependent promoter. Genetic transformation is indispensable for editing plant genes. In certain plant species, including pyrethrum, genetic transformation remains challenging to do, limiting the functional verification of novel CRISPR/Cas9 systems. Thus, this study's aim was to develop a simple Agrobacterium rhizogenes-mediated hairy root transformation system to analyze the function of a ribozyme-mediated CRISPR/Cas9 system in pyrethrum. RESULTS A hairy root transformation system for pyrethrum is described, with a mean transformation frequency of 7%. Transgenic hairy roots transformed with the pBI121 vector exhibited significantly increased beta-glucuronidase staining as a visual marker of transgene expression. Further, a ribozyme-based CRISPR/Cas9 vector was constructed to edit the TcEbFS gene, which catalyzes synthesis of the defense-related compound (E)-β-farnesene in pyrethrum. The vector was transferred into the hairy roots of pyrethrum and two stably transformed hairy root transgenic lines obtained. Editing of the TcEbFS gene in the hairy roots was evaluated by gene sequencing, demonstrating that both hairy root transgenic lines had DNA base loss at the editing target site. Gas chromatography-mass spectrometry showed that the (E)-β-farnesene content was significantly decreased in both hairy root transgenic lines compared with the empty vector control group. Altogether, these results show that RGR can be driven by the CaMV35S promoter to realize TcEbFS gene editing in pyrethrum hairy roots. CONCLUSION An A. rhizogenes-mediated hairy root transformation and ribozyme-mediated CRISPR/Cas9 gene editing system in pyrethrum was established, thereby facilitating gene editing in specific organs or at a particular developmental stage in future pyrethrum research.
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Affiliation(s)
- Jia-Wen Li
- Key Laboratory for Biology of Horticultural Plants, Ministry of Education, Huazhong Agricultural University, Wuhan, 430070, China
| | - Tuo Zeng
- Key Laboratory for Biology of Horticultural Plants, Ministry of Education, Huazhong Agricultural University, Wuhan, 430070, China
- School of Life Sciences, Guizhou Normal University, Guiyang, 550025, China
| | - Zhi-Zhuo Xu
- Key Laboratory for Biology of Horticultural Plants, Ministry of Education, Huazhong Agricultural University, Wuhan, 430070, China
| | - Jin-Jin Li
- Key Laboratory for Biology of Horticultural Plants, Ministry of Education, Huazhong Agricultural University, Wuhan, 430070, China
| | - Hao Hu
- Key Laboratory for Biology of Horticultural Plants, Ministry of Education, Huazhong Agricultural University, Wuhan, 430070, China
| | - Qin Yu
- Key Laboratory for Biology of Horticultural Plants, Ministry of Education, Huazhong Agricultural University, Wuhan, 430070, China
| | - Li Zhou
- Key Laboratory for Biology of Horticultural Plants, Ministry of Education, Huazhong Agricultural University, Wuhan, 430070, China
| | - Ri-Ru Zheng
- Key Laboratory for Biology of Horticultural Plants, Ministry of Education, Huazhong Agricultural University, Wuhan, 430070, China
| | - Jing Luo
- Key Laboratory for Biology of Horticultural Plants, Ministry of Education, Huazhong Agricultural University, Wuhan, 430070, China.
| | - Cai-Yun Wang
- Key Laboratory for Biology of Horticultural Plants, Ministry of Education, Huazhong Agricultural University, Wuhan, 430070, China.
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22
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Lu QSM, Tian L. An efficient and specific CRISPR-Cas9 genome editing system targeting soybean phytoene desaturase genes. BMC Biotechnol 2022; 22:7. [PMID: 35168613 PMCID: PMC8845245 DOI: 10.1186/s12896-022-00737-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Accepted: 02/08/2022] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Genome editing by CRISPR/Cas9 has become a popular approach to induce targeted mutations for crop trait improvement. Soybean (Glycine max L. Merr.) is an economically important crop worldwide. Although gene editing has been demonstrated in soybean, its utilization in stably transformed plants through whole plant regeneration is still not widespread, largely due to difficulties with transformation or low mutation efficiencies. RESULTS We sought to establish a simple, efficient, and specific CRISPR/Cas9 system to induce heritable mutations in soybean through stable transformation. We targeted phytoene desaturase (PDS) genes due to the distinctive dwarf and albino phenotypes of the loss of function mutant. To evaluate gene editing efficiency and specificity, three constructs targeting each of the two homologous soybean PDS genes specifically, as well as two constructs targeting both simultaneously with one guide RNA were created. Instead of using cotyledonary nodes from germinated seedlings, we used 'half-seed' explants derived from imbibed seeds for Agrobacterium-mediated transformation of cultivar Williams 82. Transformed plants for all five constructs were recovered. Dwarf and albino phenotypes were observed in transgenic plants harboring the constructs targeting both PDS genes. Gene editing at the desired loci was detected in the majority of T0 transgenic plants, with 75-100% mutation efficiencies. Indel frequencies varied widely among plants (3-100%), with those exhibiting visible mutant phenotypes showing higher frequencies (27-100%). Deletion was the predominant mutation type, although 1-nucleotide insertion was also observed. Constructs designed to target only one PDS gene did not induce mutation in the other homologous counterpart; and no mutation at several potential off-target loci was detected, indicating high editing specificity. Modifications in both PDS genes were transmitted to T1 progenies, including plants that were negative for transgene detection. Strong mutant phenotypes were also observed in T1 plants. CONCLUSIONS Using simple constructs containing one guide RNA, we demonstrated efficient and specific CRISPR/Cas9-mediated mutagenesis in stably transformed soybean plants, and showed that the mutations could be inherited in progenies, even in plants that lost transgenes through segregation. The established system can be employed to edit other genes for soybean trait improvement.
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Affiliation(s)
- Qing Shi Mimmie Lu
- Agriculture and Agri-Food Canada, London Research and Development Center, 1391 Sandford Street, London, ON N5V 4T3 Canada
| | - Lining Tian
- Agriculture and Agri-Food Canada, London Research and Development Center, 1391 Sandford Street, London, ON N5V 4T3 Canada
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23
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Impens L, Jacobs TB, Nelissen H, Inzé D, Pauwels L. Mini-Review: Transgenerational CRISPR/Cas9 Gene Editing in Plants. Front Genome Ed 2022; 4:825042. [PMID: 35187531 PMCID: PMC8854858 DOI: 10.3389/fgeed.2022.825042] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 01/12/2022] [Indexed: 11/13/2022] Open
Abstract
CRISPR/Cas9 genome editing has been used extensively in a wide variety of plant species. Creation of loss-of-function alleles, promoter variants and mutant collections are a few of the many uses of genome editing. In a typical workflow for sexually reproducing species, plants are generated that contain an integrated CRISPR/Cas9 transgene. After editing of the gene of interest, T-DNA null segregants can be identified in the next generation that contain only the desired edit. However, maintained presence of the CRISPR/Cas9 transgene and continued editing in the subsequent generations offer a range of applications for model plants and crops. In this review, we define transgenerational gene editing (TGE) as the continued editing of CRISPR/Cas9 after a genetic cross. We discuss the concept of TGE, summarize the current main applications, and highlight special cases to illustrate the importance of TGE for plant genome editing research and breeding.
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Affiliation(s)
- Lennert Impens
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Thomas B. Jacobs
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Hilde Nelissen
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Dirk Inzé
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Laurens Pauwels
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
- *Correspondence: Laurens Pauwels,
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24
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Nissan N, Mimee B, Cober ER, Golshani A, Smith M, Samanfar B. A Broad Review of Soybean Research on the Ongoing Race to Overcome Soybean Cyst Nematode. BIOLOGY 2022; 11:211. [PMID: 35205078 PMCID: PMC8869295 DOI: 10.3390/biology11020211] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Revised: 01/24/2022] [Accepted: 01/26/2022] [Indexed: 12/12/2022]
Abstract
Plant pathogens greatly impact food security of the ever-growing human population. Breeding resistant crops is one of the most sustainable strategies to overcome the negative effects of these biotic stressors. In order to efficiently breed for resistant plants, the specific plant-pathogen interactions should be understood. Soybean is a short-day legume that is a staple in human food and animal feed due to its high nutritional content. Soybean cyst nematode (SCN) is a major soybean stressor infecting soybean worldwide including in China, Brazil, Argentina, USA and Canada. There are many Quantitative Trait Loci (QTLs) conferring resistance to SCN that have been identified; however, only two are widely used: rhg1 and Rhg4. Overuse of cultivars containing these QTLs/genes can lead to SCN resistance breakdown, necessitating the use of additional strategies. In this manuscript, a literature review is conducted on research related to soybean resistance to SCN. The main goal is to provide a current understanding of the mechanisms of SCN resistance and list the areas of research that could be further explored.
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Affiliation(s)
- Nour Nissan
- Agriculture and Agri-Food Canada, Ottawa Research and Development Centre, Ottawa, ON K1Y 4X2, Canada; (N.N.); (E.R.C.)
- Ottawa Institute of Systems Biology and Department of Biology, Carleton University, Ottawa, ON K1S 5B6, Canada; (A.G.); (M.S.)
| | - Benjamin Mimee
- Agriculture and Agri-Food Canada, Saint-Jean-sur-Richelieu Research and Development Centre, Saint-Jean-sur-Richelieu, QC J3B 7B5, Canada;
| | - Elroy R. Cober
- Agriculture and Agri-Food Canada, Ottawa Research and Development Centre, Ottawa, ON K1Y 4X2, Canada; (N.N.); (E.R.C.)
| | - Ashkan Golshani
- Ottawa Institute of Systems Biology and Department of Biology, Carleton University, Ottawa, ON K1S 5B6, Canada; (A.G.); (M.S.)
| | - Myron Smith
- Ottawa Institute of Systems Biology and Department of Biology, Carleton University, Ottawa, ON K1S 5B6, Canada; (A.G.); (M.S.)
| | - Bahram Samanfar
- Agriculture and Agri-Food Canada, Ottawa Research and Development Centre, Ottawa, ON K1Y 4X2, Canada; (N.N.); (E.R.C.)
- Ottawa Institute of Systems Biology and Department of Biology, Carleton University, Ottawa, ON K1S 5B6, Canada; (A.G.); (M.S.)
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25
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Popoola JO, Aworunse OS, Ojuederie OB, Adewale BD, Ajani OC, Oyatomi OA, Eruemulor DI, Adegboyega TT, Obembe OO. The Exploitation of Orphan Legumes for Food, Income, and Nutrition Security in Sub-Saharan Africa. FRONTIERS IN PLANT SCIENCE 2022; 13:782140. [PMID: 35665143 PMCID: PMC9156806 DOI: 10.3389/fpls.2022.782140] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Accepted: 04/19/2022] [Indexed: 05/17/2023]
Abstract
Poverty, food, and nutrition insecurity in sub-Saharan Africa (SSA) have become major concerns in recent times. The effects of climate change, drought, and unpredictable rainfall patterns threaten food production and sustainable agriculture. More so, insurgency, youth restiveness, and politico-economic instability amidst a burgeoning population requiring a sufficient and healthy diet remain front-burner issues in the region. Overdependence on only a few major staple crops is increasingly promoting the near extinction of many crops, especially orphan legumes, which possess immense potentials as protein and nutritional security crops. The major staple crops are declining in yield partly to their inability to adapt to the continuously changing climatic conditions. Remarkably, the orphan legumes are climate-smart crops with enormous agronomic features which foster sustainable livelihood. Research efforts on these crops have not attained a reasonable comparative status with most commercial crops. Though many research organizations and scientists have made efforts to promote the improvement and utilization of these orphan legumes, there is still more to be done. These legumes' vast genetic resources and economic utility are grossly under-exploited, but their values and promising impacts are immeasurable. Given the United Nations sustainable development goals (SDGs) of zero hunger, improved nutrition, health, and sustainable agriculture, the need to introduce these crops into food systems in SSA and other poverty-prone regions of the world is now more compelling than ever. This review unveils inherent values in orphan legumes needing focus for exploitation viz-a-viz cultivation, commercialization, and social acceptance. More so, this article discusses some of the nutraceutical potentials of the orphan legumes, their global adaptability, and modern plant breeding strategies that could be deployed to develop superior phenotypes to enrich the landraces. Advanced omics technologies, speed breeding, as well as the application of genome editing techniques, could significantly enhance the genetic improvement of these useful but underutilized legumes. Efforts made in this regard and the challenges of these approaches were also discussed.
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Affiliation(s)
- Jacob Olagbenro Popoola
- Department of Biological Sciences, Covenant University, Ota, Nigeria
- *Correspondence: Jacob Olagbenro Popoola, , orcid.org/0000-0001-5302-4856
| | | | - Omena Bernard Ojuederie
- Department of Biological Sciences, Biotechnology Unit, Kings University, Ode-Omu, Nigeria
- Food Security and Safety Niche Area, Faculty of Natural and Agricultural Sciences, North-West University, Mmabatho, South Africa
| | - Babasola Daniel Adewale
- Department of Crop Science and Horticulture, Federal University Oye-Ekiti, Ikole-Ekiti, Nigeria
| | | | - Olaniyi Ajewole Oyatomi
- Genetic Resources Center, International Institute of Tropical Agriculture (IITA), Ibadan, Nigeria
| | | | - Taofeek Tope Adegboyega
- Biology Unit, Faculty of Science, Air Force Institute of Technology, Nigerian Air Force Base, Rafin Kura, Kaduna, Nigeria
| | - Olawole Odun Obembe
- Department of Biological Sciences, Covenant University, Ota, Nigeria
- UNESCO Chair on Plant Biotechnology, Plant Science Research Cluster, Department of Biological Sciences, Covenant University, PMB, Ota, Nigeria
- Olawole Odun Obembe, , orcid.org/0000-0001-9050-8198
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26
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Xu H, Guo Y, Qiu L, Ran Y. Progress in Soybean Genetic Transformation Over the Last Decade. FRONTIERS IN PLANT SCIENCE 2022; 13:900318. [PMID: 35755694 PMCID: PMC9231586 DOI: 10.3389/fpls.2022.900318] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2022] [Accepted: 05/11/2022] [Indexed: 05/13/2023]
Abstract
Soybean is one of the important food, feed, and biofuel crops in the world. Soybean genome modification by genetic transformation has been carried out for trait improvement for more than 4 decades. However, compared to other major crops such as rice, soybean is still recalcitrant to genetic transformation, and transgenic soybean production has been hampered by limitations such as low transformation efficiency and genotype specificity, and prolonged and tedious protocols. The primary goal in soybean transformation over the last decade is to achieve high efficiency and genotype flexibility. Soybean transformation has been improved by modifying tissue culture conditions such as selection of explant types, adjustment of culture medium components and choice of selection reagents, as well as better understanding the transformation mechanisms of specific approaches such as Agrobacterium infection. Transgenesis-based breeding of soybean varieties with new traits is now possible by development of improved protocols. In this review, we summarize the developments in soybean genetic transformation to date, especially focusing on the progress made using Agrobacterium-mediated methods and biolistic methods over the past decade. We also discuss current challenges and future directions.
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Affiliation(s)
- Hu Xu
- Tianjin Genovo Biotechnology Co., Ltd., Tianjin, China
| | - Yong Guo
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Lijuan Qiu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
- *Correspondence: Lijuan Qiu,
| | - Yidong Ran
- Tianjin Genovo Biotechnology Co., Ltd., Tianjin, China
- Yidong Ran,
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27
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Kurokawa S, Rahman H, Yamanaka N, Ishizaki C, Islam S, Aiso T, Hirata S, Yamamoto M, Kobayashi K, Kaya H. A Simple Heat Treatment Increases SpCas9-Mediated Mutation Efficiency in Arabidopsis. PLANT & CELL PHYSIOLOGY 2021; 62:1676-1686. [PMID: 34347875 DOI: 10.1093/pcp/pcab123] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 07/15/2021] [Accepted: 08/04/2021] [Indexed: 06/13/2023]
Abstract
The CRISPR/Cas9 system is now commonly employed for genome editing in various plants such as Arabidopsis, rice and tobacco. In general, in genome editing of the Arabidopsis genome, the SpCas9 and guide RNA genes are introduced into the genome by the floral dip method. Mutations induced in the target sequence by SpCas9 are confirmed after selecting transformants by screening the T1 seed population. The advantage of this method is that genome-edited plants can be isolated easily. However, mutation efficiency in Arabidopsis using SpCas9 is not as high as that achieved in rice and tobacco, which are subjected to a tissue culture step. In this study, we compared four promoters and found that the parsley UBIQITIN promoter is highly active in Arabidopsis meristem tissue. Furthermore, we examined whether a simple heat treatment could improve mutation efficiency in Arabidopsis. Just one heat treatment at 37°C for 24 h increased the mutation efficiency at all four target sites from 3 to 42%, 43 to 62%, 54 to 75% and 89 to 91%, without detectable off-target mutations. We recommend heat treatment of plate-grown plants at 37°C for 24 h as a simple method to increase the efficiency of CRISPR/Cas9-mediated mutagenesis in Arabidopsis.
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Affiliation(s)
- Shuta Kurokawa
- Faculty of Agriculture, Ehime University, Matsuyama, Ehime, 790-8566 Japan
| | - Hafizur Rahman
- The United Graduate School of Agricultural Sciences, Ehime University, Matsuyama, Ehime, 790-8566 Japan
| | - Naoshi Yamanaka
- Graduate School of Agriculture, Ehime University, Matsuyama, Ehime, 790-8566 Japan
| | - Chisato Ishizaki
- Faculty of Agriculture, Ehime University, Matsuyama, Ehime, 790-8566 Japan
| | - Shaikhul Islam
- The United Graduate School of Agricultural Sciences, Ehime University, Matsuyama, Ehime, 790-8566 Japan
| | - Tsuyoshi Aiso
- Faculty of Agriculture, Ehime University, Matsuyama, Ehime, 790-8566 Japan
| | - Shunya Hirata
- Faculty of Agriculture, Ehime University, Matsuyama, Ehime, 790-8566 Japan
| | - Mayuka Yamamoto
- Faculty of Agriculture, Ehime University, Matsuyama, Ehime, 790-8566 Japan
| | - Kappei Kobayashi
- Faculty of Agriculture, Ehime University, Matsuyama, Ehime, 790-8566 Japan
- The United Graduate School of Agricultural Sciences, Ehime University, Matsuyama, Ehime, 790-8566 Japan
- Graduate School of Agriculture, Ehime University, Matsuyama, Ehime, 790-8566 Japan
- Research Unit for Citromics, Ehime University, Matsuyama, Ehime, 790-8566 Japan
| | - Hidetaka Kaya
- Faculty of Agriculture, Ehime University, Matsuyama, Ehime, 790-8566 Japan
- The United Graduate School of Agricultural Sciences, Ehime University, Matsuyama, Ehime, 790-8566 Japan
- Graduate School of Agriculture, Ehime University, Matsuyama, Ehime, 790-8566 Japan
- Research Unit for Citromics, Ehime University, Matsuyama, Ehime, 790-8566 Japan
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28
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Hassan MM, Zhang Y, Yuan G, De K, Chen JG, Muchero W, Tuskan GA, Qi Y, Yang X. Construct design for CRISPR/Cas-based genome editing in plants. TRENDS IN PLANT SCIENCE 2021; 26:1133-1152. [PMID: 34340931 DOI: 10.1016/j.tplants.2021.06.015] [Citation(s) in RCA: 53] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Revised: 06/21/2021] [Accepted: 06/24/2021] [Indexed: 05/06/2023]
Abstract
CRISPR construct design is a key step in the practice of genome editing, which includes identification of appropriate Cas proteins, design and selection of guide RNAs (gRNAs), and selection of regulatory elements to express gRNAs and Cas proteins. Here, we review the choices of CRISPR-based genome editors suited for different needs in plant genome editing applications. We consider the technical aspects of gRNA design and the associated computational tools. We also discuss strategies for the design of multiplex CRISPR constructs for high-throughput manipulation of complex biological processes or polygenic traits. We provide recommendations for different elements of CRISPR constructs and discuss the remaining challenges of CRISPR construct optimization in plant genome editing.
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Affiliation(s)
- Md Mahmudul Hassan
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA; The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA; Department of Genetics and Plant Breeding, Patuakhali Science and Technology University, Dumki, Patuakhali-8602, Bangladesh
| | - Yingxiao Zhang
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD 20742, USA
| | - Guoliang Yuan
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA; The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Kuntal De
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Jin-Gui Chen
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA; The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Wellington Muchero
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA; The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Gerald A Tuskan
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA; The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Yiping Qi
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD 20742, USA; Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, MD 20850, USA.
| | - Xiaohan Yang
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA; The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA.
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29
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da Silva ÉDB, Xavier A, Faria MV. Impact of Genomic Prediction Model, Selection Intensity, and Breeding Strategy on the Long-Term Genetic Gain and Genetic Erosion in Soybean Breeding. Front Genet 2021; 12:637133. [PMID: 34539725 PMCID: PMC8440908 DOI: 10.3389/fgene.2021.637133] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Accepted: 08/05/2021] [Indexed: 11/21/2022] Open
Abstract
Genomic-assisted breeding has become an important tool in soybean breeding. However, the impact of different genomic selection (GS) approaches on short- and long-term gains is not well understood. Such gains are conditional on the breeding design and may vary with a combination of the prediction model, family size, selection strategies, and selection intensity. To address these open questions, we evaluated various scenarios through a simulated closed soybean breeding program over 200 breeding cycles. Genomic prediction was performed using genomic best linear unbiased prediction (GBLUP), Bayesian methods, and random forest, benchmarked against selection on phenotypic values, true breeding values (TBV), and random selection. Breeding strategies included selections within family (WF), across family (AF), and within pre-selected families (WPSF), with selection intensities of 2.5, 5.0, 7.5, and 10.0%. Selections were performed at the F4 generation, where individuals were phenotyped and genotyped with a 6K single nucleotide polymorphism (SNP) array. Initial genetic parameters for the simulation were estimated from the SoyNAM population. WF selections provided the most significant long-term genetic gains. GBLUP and Bayesian methods outperformed random forest and provided most of the genetic gains within the first 100 generations, being outperformed by phenotypic selection after generation 100. All methods provided similar performances under WPSF selections. A faster decay in genetic variance was observed when individuals were selected AF and WPSF, as 80% of the genetic variance was depleted within 28-58 cycles, whereas WF selections preserved the variance up to cycle 184. Surprisingly, the selection intensity had less impact on long-term gains than did the breeding strategies. The study supports that genetic gains can be optimized in the long term with specific combinations of prediction models, family size, selection strategies, and selection intensity. A combination of strategies may be necessary for balancing the short-, medium-, and long-term genetic gains in breeding programs while preserving the genetic variance.
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Affiliation(s)
| | - Alencar Xavier
- Department of Biostatistics, Corteva Agriscience, Johnston, IA, United States
- Department of Agronomy, Purdue University, West Lafayette, IN, United States
| | - Marcos Ventura Faria
- Department of Agronomy, Universidade Estadual do Centro-Oeste, Guarapuava, Brazil
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30
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Xu H, Zhang L, Zhang K, Ran Y. Progresses, Challenges, and Prospects of Genome Editing in Soybean ( Glycine max). FRONTIERS IN PLANT SCIENCE 2020; 11:571138. [PMID: 33193504 PMCID: PMC7642200 DOI: 10.3389/fpls.2020.571138] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Accepted: 09/28/2020] [Indexed: 05/17/2023]
Abstract
Soybean is grown worldwide for oil and protein source as food, feed and industrial raw material for biofuel. Steady increase in soybean production in the past century mainly attributes to genetic mediation including hybridization, mutagenesis and transgenesis. However, genetic resource limitation and intricate social issues in use of transgenic technology impede soybean improvement to meet rapid increases in global demand for soybean products. New approaches in genomics and development of site-specific nucleases (SSNs) based genome editing technologies have expanded soybean genetic variations in its germplasm and have potential to make precise modification of genes controlling the important agronomic traits in an elite background. ZFNs, TALENS and CRISPR/Cas9 have been adapted in soybean improvement for targeted deletions, additions, replacements and corrections in the genome. The availability of reference genome assembly and genomic resources increases feasibility in using current genome editing technologies and their new development. This review summarizes the status of genome editing in soybean improvement and future directions in this field.
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Affiliation(s)
| | | | | | - Yidong Ran
- Tianjin Genovo Biotechnology Co., Ltd., Tianjin, China
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Maioli A, Gianoglio S, Moglia A, Acquadro A, Valentino D, Milani AM, Prohens J, Orzaez D, Granell A, Lanteri S, Comino C. Simultaneous CRISPR/Cas9 Editing of Three PPO Genes Reduces Fruit Flesh Browning in Solanum melongena L. FRONTIERS IN PLANT SCIENCE 2020; 11:607161. [PMID: 33343607 PMCID: PMC7744776 DOI: 10.3389/fpls.2020.607161] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Accepted: 11/06/2020] [Indexed: 05/04/2023]
Abstract
Polyphenol oxidases (PPOs) catalyze the oxidization of polyphenols, which in turn causes the browning of the eggplant berry flesh after cutting. This has a negative impact on fruit quality for both industrial transformation and fresh consumption. Ten PPO genes (named SmelPPO1-10) were identified in eggplant thanks to the recent availability of a high-quality genome sequence. A CRISPR/Cas9-based mutagenesis approach was applied to knock-out three target PPO genes (SmelPPO4, SmelPPO5, and SmelPPO6), which showed high transcript levels in the fruit after cutting. An optimized transformation protocol for eggplant cotyledons was used to obtain plants in which Cas9 is directed to a conserved region shared by the three PPO genes. The successful editing of the SmelPPO4, SmelPPO5, and SmelPPO6 loci of in vitro regenerated plantlets was confirmed by Illumina deep sequencing of amplicons of the target sites. Besides, deep sequencing of amplicons of the potential off-target loci identified in silico proved the absence of detectable non-specific mutations. The induced mutations were stably inherited in the T1 and T2 progeny and were associated with a reduced PPO activity and browning of the berry flesh after cutting. Our results provide the first example of the use of the CRISPR/Cas9 system in eggplant for biotechnological applications and open the way to the development of eggplant genotypes with low flesh browning which maintain a high polyphenol content in the berries.
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Affiliation(s)
- Alex Maioli
- DISAFA, Plant Genetics and Breeding, University of Torino, Grugliasco, Italy
| | - Silvia Gianoglio
- Crop Biotechnology Department, Instituto de Biología Molecular y Celular de Plantas (IBMCP), CSIC-UPV, Valencia, Spain
| | - Andrea Moglia
- DISAFA, Plant Genetics and Breeding, University of Torino, Grugliasco, Italy
- *Correspondence: Andrea Moglia
| | - Alberto Acquadro
- DISAFA, Plant Genetics and Breeding, University of Torino, Grugliasco, Italy
| | - Danila Valentino
- DISAFA, Plant Genetics and Breeding, University of Torino, Grugliasco, Italy
| | - Anna Maria Milani
- DISAFA, Plant Genetics and Breeding, University of Torino, Grugliasco, Italy
| | - Jaime Prohens
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de València, Valencia, Spain
| | - Diego Orzaez
- Crop Biotechnology Department, Instituto de Biología Molecular y Celular de Plantas (IBMCP), CSIC-UPV, Valencia, Spain
| | - Antonio Granell
- Crop Biotechnology Department, Instituto de Biología Molecular y Celular de Plantas (IBMCP), CSIC-UPV, Valencia, Spain
| | - Sergio Lanteri
- DISAFA, Plant Genetics and Breeding, University of Torino, Grugliasco, Italy
| | - Cinzia Comino
- DISAFA, Plant Genetics and Breeding, University of Torino, Grugliasco, Italy
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