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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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Ikram M, Rauf A, Rao MJ, Maqsood MFK, Bakhsh MZM, Ullah M, Batool M, Mehran M, Tahira M. CRISPR-Cas9 based molecular breeding in crop plants: a review. Mol Biol Rep 2024; 51:227. [PMID: 38281301 DOI: 10.1007/s11033-023-09086-w] [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: 09/04/2023] [Accepted: 11/30/2023] [Indexed: 01/30/2024]
Abstract
Traditional crop breeding techniques are not quickly boosting yields to fulfill the expanding population needs. Long crop lifespans hinder the ability of plant breeding to develop superior crop varieties. Due to the arduous crossing, selecting, and challenging processes, it can take decades to establish new varieties with desired agronomic traits. Develop new plant varieties instantly to reduce hunger and improve food security. As a result of the adoption of conventional agricultural techniques, crop genetic diversity has decreased over time. Several traditional and molecular techniques, such as genetic selection, mutant breeding, somaclonal variation, genome-wide association studies, and others, have improved agronomic traits associated with agricultural plant productivity, quality, and resistance to biotic and abiotic stresses. In addition, modern genome editing approaches based on programmable nucleases, CRISPR, and Cas9 proteins have escorted an exciting new era of plant breeding. Plant breeders and scientists worldwide rely on cutting-edge techniques like quick breeding, genome editing tools, and high-throughput phenotyping to boost crop breeding output. This review compiles discoveries in numerous areas of crop breeding, such as using genome editing tools to accelerate the breeding process and create yearly crop generations with the desired features, to describe the shift from conventional to modern plant breeding techniques.
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Affiliation(s)
- Muhammad Ikram
- MOA Key Laboratory of Crop Ecophysiology and Farming System in the Middle Reaches of the Yangtze River, College of Plant Science & Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Abdul Rauf
- National Key Laboratory of Horticultural Plant Biology, Ministry of Education, Wuhan, 430070, Hubei, China
| | - Muhammad Junaid Rao
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, 100 Daxue Rd., Nanning, 530004, China.
| | | | | | - Maaz Ullah
- MOA Key Laboratory of Crop Ecophysiology and Farming System in the Middle Reaches of the Yangtze River, College of Plant Science & Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Maria Batool
- MOA Key Laboratory of Crop Ecophysiology and Farming System in the Middle Reaches of the Yangtze River, College of Plant Science & Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Muhammad Mehran
- Key Laboratory of Arable Land Conservation, Huazhong Agricultural University, Ministry of Agriculture, Wuhan, 430070, China
| | - Maryam Tahira
- National Key Laboratory of Horticultural Plant Biology, Ministry of Education, Wuhan, 430070, Hubei, China
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Singer WM, Lee YC, Shea Z, Vieira CC, Lee D, Li X, Cunicelli M, Kadam SS, Khan MAW, Shannon G, Mian MAR, Nguyen HT, Zhang B. Soybean genetics, genomics, and breeding for improving nutritional value and reducing antinutritional traits in food and feed. THE PLANT GENOME 2023; 16:e20415. [PMID: 38084377 DOI: 10.1002/tpg2.20415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Revised: 10/25/2023] [Accepted: 10/27/2023] [Indexed: 12/22/2023]
Abstract
Soybean [Glycine max (L.) Merr.] is a globally important crop due to its valuable seed composition, versatile feed, food, and industrial end-uses, and consistent genetic gain. Successful genetic gain in soybean has led to widespread adaptation and increased value for producers, processors, and consumers. Specific focus on the nutritional quality of soybean seed composition for food and feed has further elucidated genetic knowledge and bolstered breeding progress. Seed components are historical and current targets for soybean breeders seeking to improve nutritional quality of soybean. This article reviews genetic and genomic foundations for improvement of nutritionally important traits, such as protein and amino acids, oil and fatty acids, carbohydrates, and specific food-grade considerations; discusses the application of advanced breeding technology such as CRISPR/Cas9 in creating seed composition variations; and provides future directions and breeding recommendations regarding soybean seed composition traits.
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Affiliation(s)
- William M Singer
- School of Plant and Environmental Sciences, Virginia Polytechnic Institute and State University, Blacksburg, Virginia, USA
| | - Yi-Chen Lee
- Department of Agriculture, Fort Hays State University, Hays, Kansas, USA
| | - Zachary Shea
- School of Plant and Environmental Sciences, Virginia Polytechnic Institute and State University, Blacksburg, Virginia, USA
| | - Caio Canella Vieira
- Department of Crop, Soil, and Environmental Sciences, University of Arkansas, Fayetteville, Arkansas, USA
| | - Dongho Lee
- Fisher Delta Research, Extension, and Education Center, University of Missouri, Portageville, Missouri, USA
| | - Xiaoying Li
- School of Plant and Environmental Sciences, Virginia Polytechnic Institute and State University, Blacksburg, Virginia, USA
| | - Mia Cunicelli
- Soybean and Nitrogen Fixation Research Unit, USDA-ARS, Raleigh, North Carolina, USA
| | - Shaila S Kadam
- Division of Plant Science and Technology, University of Missouri, Columbia, Missouri, USA
| | | | - Grover Shannon
- Fisher Delta Research, Extension, and Education Center, University of Missouri, Portageville, Missouri, USA
| | - M A Rouf Mian
- Soybean and Nitrogen Fixation Research Unit, USDA-ARS, Raleigh, North Carolina, USA
| | - Henry T Nguyen
- Division of Plant Science and Technology, University of Missouri, Columbia, Missouri, USA
| | - Bo Zhang
- School of Plant and Environmental Sciences, Virginia Polytechnic Institute and State University, Blacksburg, Virginia, USA
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Güngör B, Biró JB, Domonkos Á, Horváth B, Kaló P. Targeted mutagenesis of Medicago truncatula Nodule-specific Cysteine-Rich (NCR) genes using the Agrobacterium rhizogenes-mediated CRISPR/Cas9 system. Sci Rep 2023; 13:20676. [PMID: 38001333 PMCID: PMC10673856 DOI: 10.1038/s41598-023-47608-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Accepted: 11/16/2023] [Indexed: 11/26/2023] Open
Abstract
The host-produced nodule specific cysteine-rich (NCR) peptides control the terminal differentiation of endosymbiotic rhizobia in the nodules of IRLC legumes. Although the Medicago truncatula genome encodes about 700 NCR peptides, only few of them have been proven to be crucial for nitrogen-fixing symbiosis. In this study, we applied the CRISPR/Cas9 gene editing technology to generate knockout mutants of NCR genes for which no genetic or functional data were previously available. We have developed a workflow to analyse the mutation and the symbiotic phenotype of individual nodules formed on Agrobacterium rhizogenes-mediated transgenic hairy roots. The selected NCR genes were successfully edited by the CRISPR/Cas9 system and nodules formed on knockout hairy roots showed wild type phenotype indicating that peptides NCR068, NCR089, NCR128 and NCR161 are not essential for symbiosis between M. truncatula Jemalong and Sinorhizobium medicae WSM419. We regenerated stable mutants edited for the NCR068 from hairy roots obtained by A. rhizogenes-mediated transformation. The analysis of the symbiotic phenotype of stable ncr068 mutants showed that peptide NCR068 is not required for symbiosis with S. meliloti strains 2011 and FSM-MA either. Our study reports that gene editing can help to elicit the role of certain NCRs in symbiotic nitrogen fixation.
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Affiliation(s)
- Berivan Güngör
- Institute of Plant Biology, HUN-REN Biological Research Centre, Szeged, Hungary
- Institute of Genetics and Biotechnology, Hungarian University of Agriculture and Life Sciences, Gödöllő, Hungary
| | - János Barnabás Biró
- Institute of Plant Biology, HUN-REN Biological Research Centre, Szeged, Hungary
| | - Ágota Domonkos
- Institute of Genetics and Biotechnology, Hungarian University of Agriculture and Life Sciences, Gödöllő, Hungary
| | - Beatrix Horváth
- Institute of Genetics and Biotechnology, Hungarian University of Agriculture and Life Sciences, Gödöllő, Hungary
| | - Péter Kaló
- Institute of Plant Biology, HUN-REN Biological Research Centre, Szeged, Hungary.
- Institute of Genetics and Biotechnology, Hungarian University of Agriculture and Life Sciences, Gödöllő, Hungary.
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Bui TP, Le H, Ta DT, Nguyen CX, Le NT, Tran TT, Van Nguyen P, Stacey G, Stacey MG, Pham NB, Chu HH, Do PT. Enhancing powdery mildew resistance in soybean by targeted mutation of MLO genes using the CRISPR/Cas9 system. BMC PLANT BIOLOGY 2023; 23:533. [PMID: 37919649 PMCID: PMC10623788 DOI: 10.1186/s12870-023-04549-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Accepted: 10/19/2023] [Indexed: 11/04/2023]
Abstract
BACKGROUND Powdery mildew is a major disease that causes great losses in soybean yield and seed quality. Disease-resistant varieties, which are generated by reducing the impact of susceptibility genes through mutation in host plants, would be an effective approach to protect crops from this disease. The Mildew Locus O (MLO) genes are well-known susceptibility genes for powdery mildew in plant. In this study, we utilized the CRISPR/Cas9 system to induce targeted mutations in the soybean GmMLO genes to improve powdery mildew resistance. RESULTS A dual-sgRNA CRISPR/Cas9 construct was designed and successfully transferred into the Vietnamese soybean cultivar DT26 through Agrobacterium tumefaciens-mediated transformation. Various mutant forms of the GmMLO genes including biallelic, chimeric and homozygous were found at the T0 generation. The inheritance and segregation of CRISPR/Cas9-induced mutations were confirmed and validated at the T1 and T2 generations. Out of six GmMLO genes in the soybean genome, we obtained the Gmmlo02/Gmmlo19/Gmmlo23 triple and Gmmlo02/Gmmlo19/Gmmlo20/Gmmlo23 quadruple knockout mutants at the T2 generation. When challenged with Erysiphe diffusa, a fungus that causes soybean powdery mildew, all mutant plants showed enhanced resistance to the pathogen, especially the quadruple mutant. The powdery mildew severity in the mutant soybeans was reduced by up to 36.4% compared to wild-type plants. In addition, no pleiotropic effect on soybean growth and development under net-house conditions was observed in the CRISPR/Cas9 mutants. CONCLUSIONS Our results indicate the involvement of GmMLO02, GmMLO19, GmMLO20 and GmMLO23 genes in powdery mildew susceptibility in soybean. Further research should be conducted to investigate the roles of individual tested genes and the involvement of other GmMLO genes in this disease infection mechanism. Importantly, utilizing the CRISPR/Cas9 system successfully created the Gmmlo transgene-free homozygous mutant lines with enhanced resistance to powdery mildew, which could be potential materials for soybean breeding programs.
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Affiliation(s)
- Thao Phuong Bui
- Institute of Biotechnology, Vietnam Academy of Science and Technology, Hanoi, Vietnam
- University of Science and Technology of Hanoi, Vietnam Academy of Science and Technology, Hanoi, Vietnam
| | - Huy Le
- Institute of Biotechnology, Vietnam Academy of Science and Technology, Hanoi, Vietnam
- Present address: Department of Biology, Washington University in St. Louis, St. Louis, USA
| | - Dong Thi Ta
- Institute of Biotechnology, Vietnam Academy of Science and Technology, Hanoi, Vietnam
| | - Cuong Xuan Nguyen
- Institute of Biotechnology, Vietnam Academy of Science and Technology, Hanoi, Vietnam
- Division of Plant Sciences, University of Missouri, Columbia, MO, 65211, USA
| | - Ngoc Thu Le
- Institute of Biotechnology, Vietnam Academy of Science and Technology, Hanoi, Vietnam
| | - Truong Thi Tran
- Legumes Research and Development Center, Vietnam Academy of Agriculture Science, Hanoi, Vietnam
| | - Phuong Van Nguyen
- University of Science and Technology of Hanoi, Vietnam Academy of Science and Technology, Hanoi, Vietnam
| | - Gary Stacey
- Division of Plant Sciences, University of Missouri, Columbia, MO, 65211, USA
| | - Minviluz G Stacey
- Division of Plant Sciences, University of Missouri, Columbia, MO, 65211, USA
| | - Ngoc Bich Pham
- Institute of Biotechnology, Vietnam Academy of Science and Technology, Hanoi, Vietnam
- Graduate University of Science and Technology, Vietnam Academy of Science and Technology, Hanoi, Vietnam
| | - Ha Hoang Chu
- Institute of Biotechnology, Vietnam Academy of Science and Technology, Hanoi, Vietnam
- Graduate University of Science and Technology, Vietnam Academy of Science and Technology, Hanoi, Vietnam
| | - Phat Tien Do
- Institute of Biotechnology, Vietnam Academy of Science and Technology, Hanoi, Vietnam.
- Graduate University of Science and Technology, Vietnam Academy of Science and Technology, Hanoi, Vietnam.
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Lee D, Lara L, Moseley D, Vuong TD, Shannon G, Xu D, Nguyen HT. Novel genetic resources associated with sucrose and stachyose content through genome-wide association study in soybean ( Glycine max (L.) Merr.). FRONTIERS IN PLANT SCIENCE 2023; 14:1294659. [PMID: 38023839 PMCID: PMC10646508 DOI: 10.3389/fpls.2023.1294659] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Accepted: 10/19/2023] [Indexed: 12/01/2023]
Abstract
The nutritional value of soybean [Glycine max (L.) Merr.] for animals is influenced by soluble carbohydrates, such as sucrose and stachyose. Although sucrose is nutritionally desirable, stachyose is an antinutrient causing diarrhea and flatulence in non-ruminant animals. We conducted a genome-wide association study of 220 soybean accessions using 21,317 single nucleotide polymorphisms (SNPs) from the SoySNP50K iSelect Beadchip data to identify significant SNPs associated with sucrose and stachyose content. Seven significant SNPs were identified for sucrose content across chromosomes (Chrs.) 2, 8, 12, 17, and 20, while thirteen significant SNPs were identified for stachyose content across Chrs. 2, 5, 8, 9, 10, 13, 14, and 15. Among those significant SNPs, three sucrose-related SNPs on Chrs. 8 and 17 were novel, while twelve stachyose-related SNPs on Chrs. 2, 5, 8, 9, 10, 13, 14, and 15 were novel. Based on Phytozome, STRING, and GO annotation, 17 and 24 candidate genes for sucrose and stachyose content, respectively, were highly associated with the carbohydrate metabolic pathway. Among these, the publicly available RNA-seq Atlas database highlighted four candidate genes associated with sucrose (Glyma.08g361200 and Glyma.17g258100) and stachyose (Glyma.05g025300 and Glyma.13g077900) content, which had higher gene expression levels in developing seed and multiple parts of the soybean plant. The results of this study will extend knowledge of the molecular mechanism and genetic basis underlying sucrose and stachyose content in soybean seed. Furthermore, the novel candidate genes and SNPs can be valuable genetic resources that soybean breeders may utilize to modify carbohydrate profiles for animal and human usage.
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Affiliation(s)
- Dongho Lee
- Fisher Delta Research, Extension, and Education Center, Division of Plant Science and Technology, University of Missouri, Portageville, MO, United States
- Division of Plant Science and Technology, University of Missouri, Columbia, MO, United States
| | - Laura Lara
- Agrícola Los Alpes, Chimaltenango, Guatemala
| | - David Moseley
- Dean Lee Research and Extension Center, LSU AgCenter, Alexandria, LA, United States
| | - Tri D. Vuong
- Division of Plant Science and Technology, University of Missouri, Columbia, MO, United States
| | - Grover Shannon
- Fisher Delta Research, Extension, and Education Center, Division of Plant Science and Technology, University of Missouri, Portageville, MO, United States
| | - Dong Xu
- Department of Electrical Engineering and Computer Sciences, Christopher S. Bond Life Science Center, University of Missouri, Columbia, MO, United States
| | - Henry T. Nguyen
- Division of Plant Science and Technology, University of Missouri, Columbia, MO, United States
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Sim J, Kuwabara C, Sugano S, Adachi K, Yamada T. Recent advances in the improvement of soybean seed traits by genome editing. PLANT BIOTECHNOLOGY (TOKYO, JAPAN) 2023; 40:193-200. [PMID: 38293251 PMCID: PMC10824499 DOI: 10.5511/plantbiotechnology.23.0610a] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Accepted: 06/10/2023] [Indexed: 02/01/2024]
Abstract
Genetic improvement of soybean seed traits is important for developing new varieties that meet the demand for soybean as a food, forage crop, and industrial products. A large number of soybean genome sequences are currently publicly available. This genome sequence information provides a significant opportunity to design genomic approaches to improve soybean traits. Genome editing represents a major advancement in biotechnology. The production of soybean mutants through genome editing is commonly achieved with either an Agrobacterium-mediated or biolistic transformation platform, which have been optimized for various soybean genotypes. Currently, the clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated endonuclease 9 (Cas9) system, which represents a major advance in genome editing, is used to improve soybean traits, such as fatty acid composition, protein content and composition, flavor, digestibility, size, and seed-coat color. In this review, we summarize the recent advances in the improvement of soybean seed traits through genome editing. We also discuss the characteristics of genome editing using the CRISPR/Cas9 system with transformation platforms.
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Affiliation(s)
- Jaechol Sim
- Graduate School of Agriculture, Hokkaido University, Kita 9, Nishi 9, Kita-ku, Sapporo, Hokkaido 060-8589, Japan
| | - Chikako Kuwabara
- Graduate School of Agriculture, Hokkaido University, Kita 9, Nishi 9, Kita-ku, Sapporo, Hokkaido 060-8589, Japan
| | - Shota Sugano
- Graduate School of Agriculture, Hokkaido University, Kita 9, Nishi 9, Kita-ku, Sapporo, Hokkaido 060-8589, Japan
| | - Kohei Adachi
- Graduate School of Agriculture, Hokkaido University, Kita 9, Nishi 9, Kita-ku, Sapporo, Hokkaido 060-8589, Japan
| | - Tetsuya Yamada
- Graduate School of Agriculture, Hokkaido University, Kita 9, Nishi 9, Kita-ku, Sapporo, Hokkaido 060-8589, Japan
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Yao D, Zhou J, Zhang A, Wang J, Liu Y, Wang L, Pi W, Li Z, Yue W, Cai J, Liu H, Hao W, Qu X. Advances in CRISPR/Cas9-based research related to soybean [ Glycine max (Linn.) Merr] molecular breeding. FRONTIERS IN PLANT SCIENCE 2023; 14:1247707. [PMID: 37711287 PMCID: PMC10499359 DOI: 10.3389/fpls.2023.1247707] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Accepted: 07/28/2023] [Indexed: 09/16/2023]
Abstract
Soybean [Glycine max (Linn.) Merr] is a source of plant-based proteins and an essential oilseed crop and industrial raw material. The increase in the demand for soybeans due to societal changes has coincided with the increase in the breeding of soybean varieties with enhanced traits. Earlier gene editing technologies involved zinc finger nucleases and transcription activator-like effector nucleases, but the third-generation gene editing technology uses clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9). The rapid development of CRISPR/Cas9 technology has made it one of the most effective, straightforward, affordable, and user-friendly technologies for targeted gene editing. This review summarizes the application of CRISPR/Cas9 technology in soybean molecular breeding. More specifically, it provides an overview of the genes that have been targeted, the type of editing that occurs, the mechanism of action, and the efficiency of gene editing. Furthermore, suggestions for enhancing and accelerating the molecular breeding of novel soybean varieties with ideal traits (e.g., high yield, high quality, and durable disease resistance) are included.
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Affiliation(s)
- Dan Yao
- College of Life Science, Jilin Agricultural University, Changchun, Jilin, China
- Institute of Crop Resources, Jilin Provincial Academy of Agricultural Sciences, Gongzhuling, Jilin, China
| | - Junming Zhou
- College of Life Science, Jilin Agricultural University, Changchun, Jilin, China
| | - Aijing Zhang
- College of Agronomy, Jilin Agricultural University, Changchun, China
| | - Jiaxin Wang
- College of Life Science, Jilin Agricultural University, Changchun, Jilin, China
| | - Yixuan Liu
- College of Life Science, Jilin Agricultural University, Changchun, Jilin, China
| | - Lixue Wang
- College of Life Science, Jilin Agricultural University, Changchun, Jilin, China
| | - Wenxuan Pi
- College of Life Science, Jilin Agricultural University, Changchun, Jilin, China
| | - Zihao Li
- College of Life Science, Jilin Agricultural University, Changchun, Jilin, China
| | - Wenjun Yue
- College of Life Science, Jilin Agricultural University, Changchun, Jilin, China
| | - Jinliang Cai
- College of Life Science, Jilin Agricultural University, Changchun, Jilin, China
| | - Huijing Liu
- College of Life Science, Jilin Agricultural University, Changchun, Jilin, China
| | - Wenyuan Hao
- Jilin Provincial Academy of Agricultural Sciences, Changchun, Jilin, China
| | - Xiangchun Qu
- Institute of Crop Resources, Jilin Provincial Academy of Agricultural Sciences, Gongzhuling, Jilin, China
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Rao PJM, Pallavi M, Bharathi Y, Priya PB, Sujatha P, Prabhavathi K. Insights into mechanisms of seed longevity in soybean: a review. FRONTIERS IN PLANT SCIENCE 2023; 14:1206318. [PMID: 37546268 PMCID: PMC10400919 DOI: 10.3389/fpls.2023.1206318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/15/2023] [Accepted: 06/23/2023] [Indexed: 08/08/2023]
Abstract
Soybean, a crop of international importance, is challenged with the problem of seed longevity mainly due to its genetic composition and associated environmental cues. Soybean's fragile seed coat coupled with poor DNA integrity, ribosomal dysfunction, lipid peroxidation and poor antioxidant system constitute the rationale for fast deterioration. Variability among the genotypes for sensitivity to field weathering contributed to their differential seed longevity. Proportion and density of seed coat, glassy state of cells, calcium and lignin content, pore number, space between seed coat and cotyledon are some seed related traits that are strongly correlated to longevity. Further, efficient antioxidant system, surplus protective proteins, effective nucleotide and protein repair systems and free radical scavenging mechanisms also contributed to the storage potential of soybean seeds. Identification of molecular markers and QTLs associated with these mechanisms will pave way for enhanced selection efficiency for seed longevity in soybean breeding programs. This review reflects on the morphological, biochemical and molecular bases of seed longevity along with pointers on harvest, processing and storage strategies for extending vigour and viability in soybean.
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Guo Y, Zhao G, Gao X, Zhang L, Zhang Y, Cai X, Yuan X, Guo X. CRISPR/Cas9 gene editing technology: a precise and efficient tool for crop quality improvement. PLANTA 2023; 258:36. [PMID: 37395789 DOI: 10.1007/s00425-023-04187-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Accepted: 06/18/2023] [Indexed: 07/04/2023]
Abstract
MAIN CONCLUSION This review provides a direction for crop quality improvement and ideas for further research on the application of CRISPR/Cas9 gene editing technology for crop improvement. Various important crops, such as wheat, rice, soybean and tomato, are among the main sources of food and energy for humans. Breeders have long attempted to improve crop yield and quality through traditional breeding methods such as crossbreeding. However, crop breeding progress has been slow due to the limitations of traditional breeding methods. In recent years, clustered regularly spaced short palindromic repeat (CRISPR)/Cas9 gene editing technology has been continuously developed. And with the refinement of crop genome data, CRISPR/Cas9 technology has enabled significant breakthroughs in editing specific genes of crops due to its accuracy and efficiency. Precise editing of certain key genes in crops by means of CRISPR/Cas9 technology has improved crop quality and yield and has become a popular strategy for many breeders to focus on and adopt. In this paper, the present status and achievements of CRISPR/Cas9 gene technology as applied to the improvement of quality in several crops are reviewed. In addition, the shortcomings, challenges and development prospects of CRISPR/Cas9 gene editing technology are discussed.
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Affiliation(s)
- Yingxin Guo
- College of Biological and Chemical Engineering, Qilu Institute of Technology, Jinan, 250200, Shandong, People's Republic of China
| | - Guangdong Zhao
- College of Life Sciences, Linyi University, Linyi, 276000, Shandong, People's Republic of China
| | - Xing Gao
- College of Biological and Chemical Engineering, Qilu Institute of Technology, Jinan, 250200, Shandong, People's Republic of China
| | - Lin Zhang
- College of Biological and Chemical Engineering, Qilu Institute of Technology, Jinan, 250200, Shandong, People's Republic of China
| | - Yanan Zhang
- College of Biological and Chemical Engineering, Qilu Institute of Technology, Jinan, 250200, Shandong, People's Republic of China
| | - Xiaoming Cai
- College of Biological and Chemical Engineering, Qilu Institute of Technology, Jinan, 250200, Shandong, People's Republic of China
| | - Xuejiao Yuan
- College of Biological and Chemical Engineering, Qilu Institute of Technology, Jinan, 250200, Shandong, People's Republic of China.
| | - Xingqi Guo
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, 271018, Shandong, People's Republic of China.
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11
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Chen Z, Shen Y, Xu J. Efficient Degradation for Raffinose and Stachyose of a β-D-Fructofuranosidase and Its New Function to Improve Gel Properties of Coagulated Fermented-Soymilk. Gels 2023; 9:gels9040345. [PMID: 37102957 PMCID: PMC10137817 DOI: 10.3390/gels9040345] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 04/02/2023] [Accepted: 04/13/2023] [Indexed: 04/28/2023] Open
Abstract
A novel β-D-fructofuranosidase gene was identified via database mining from Leptothrix cholodnii. The gene was chemically synthesized and expressed in Escherichia coli, resulting in the production of a highly efficient enzyme known as LcFFase1s. The enzyme exhibited optimal activity at pH 6.5 and a temperature of 50 °C while maintaining stability at pH 5.5-8.0 and a temperature below 50 °C. Furthermore, LcFFase1s exhibited remarkable resistance to commercial proteases and various metal ions that could interfere with its activity. This study also revealed a new hydrolysis function of LcFFase1s, which could completely hydrolyze 2% raffinose and stachyose within 8 h and 24 h, respectively, effectively reducing the flatulence factor in legumes. This discovery expands the potential applications of LcFFase1s. Additionally, the incorporation of LcFFase1s significantly reduced the particle size of coagulated fermented-soymilk gel, resulting in a smoother texture while maintaining the gel hardness and viscosity formed during fermentation. This represents the first report of β-D-fructofuranosidase enhancing coagulated fermented-soymilk gel properties, highlighting promising possibilities for future applications of LcFFase1s. Overall, the exceptional enzymatic properties and unique functions of LcFFase1s render it a valuable tool for numerous applications.
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Affiliation(s)
- Zhou Chen
- School of Food and Health, Beijing Technology and Business University, Beijing 100048, China
| | - Yimei Shen
- School of Food and Health, Beijing Technology and Business University, Beijing 100048, China
| | - Jiangqi Xu
- School of Light Industry, Beijing Technology and Business University, Beijing 100048, China
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12
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Narayanan Z, Glick BR. Biotechnologically Engineered Plants. BIOLOGY 2023; 12:biology12040601. [PMID: 37106801 PMCID: PMC10135915 DOI: 10.3390/biology12040601] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 04/08/2023] [Accepted: 04/13/2023] [Indexed: 04/29/2023]
Abstract
The development of recombinant DNA technology during the past thirty years has enabled scientists to isolate, characterize, and manipulate a myriad of different animal, bacterial, and plant genes. This has, in turn, led to the commercialization of hundreds of useful products that have significantly improved human health and well-being. Commercially, these products have been mostly produced in bacterial, fungal, or animal cells grown in culture. More recently, scientists have begun to develop a wide range of transgenic plants that produce numerous useful compounds. The perceived advantage of producing foreign compounds in plants is that compared to other methods of producing these compounds, plants seemingly provide a much less expensive means of production. A few plant-produced compounds are already commercially available; however, many more are in the production pipeline.
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Affiliation(s)
- Zareen Narayanan
- Division of Biological Sciences, School of STEM, University of Washington, Bothell, WA 98011, USA
| | - Bernard R Glick
- Department of Biology, University of Waterloo, Waterloo, ON N2L3G1, Canada
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13
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Sanyal R, Kumar S, Pattanayak A, Kar A, Bishi SK. Optimizing raffinose family oligosaccharides content in plants: A tightrope walk. FRONTIERS IN PLANT SCIENCE 2023; 14:1134754. [PMID: 37056499 PMCID: PMC10088399 DOI: 10.3389/fpls.2023.1134754] [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: 12/30/2022] [Accepted: 03/08/2023] [Indexed: 06/19/2023]
Abstract
Plants synthesize various compounds for their growth, metabolism, and stress mitigation, and one such group of compounds is the raffinose family of oligosaccharides (RFOs). RFOs are non-reducing oligosaccharides having galactose residues attached to a sucrose moiety. They act as carbohydrate reserves in plants, assisting in seed germination, desiccation tolerance, and biotic/abiotic stress tolerance. Although legumes are among the richest sources of dietary proteins, the direct consumption of legumes is hindered by an excess of RFOs in the edible parts of the plant, which causes flatulence in humans and monogastric animals. These opposing characteristics make RFOs manipulation a complicated tradeoff. An in-depth knowledge of the chemical composition, distribution pattern, tissue mobilization, and metabolism is required to optimize the levels of RFOs. The most recent developments in our understanding of RFOs distribution, physiological function, genetic regulation of their biosynthesis, transport, and degradation in food crops have been covered in this review. Additionally, we have suggested a few strategies that can sustainably reduce RFOs in order to solve the flatulence issue in animals. The comprehensive information in this review can be a tool for researchers to precisely control the level of RFOs in crops and create low antinutrient, nutritious food with wider consumer acceptability.
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Affiliation(s)
- Rajarshi Sanyal
- School of Genomics and Molecular Breeding, ICAR-Indian Institute of Agricultural Biotechnology, Ranchi, Jharkhand, India
- Division of Biochemistry, ICAR-Indian Agricultural Research Institute, Pusa, New Delhi, India
| | - Sandeep Kumar
- Automation & Plant Engineering Division, ICAR-National Institute of Secondary Agriculture, Ranchi, Jharkhand, India
| | - Arunava Pattanayak
- School of Genomics and Molecular Breeding, ICAR-Indian Institute of Agricultural Biotechnology, Ranchi, Jharkhand, India
| | - Abhijit Kar
- Automation & Plant Engineering Division, ICAR-National Institute of Secondary Agriculture, Ranchi, Jharkhand, India
| | - Sujit K. Bishi
- School of Genomics and Molecular Breeding, ICAR-Indian Institute of Agricultural Biotechnology, Ranchi, Jharkhand, India
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14
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Nguyen NH, Bui TP, Le NT, Nguyen CX, Le MTT, Dao NT, Phan Q, Van Le T, To HMT, Pham NB, Chu HH, Do PT. Disrupting Sc-uORFs of a transcription factor bZIP1 using CRISPR/Cas9 enhances sugar and amino acid contents in tomato (Solanum lycopersicum). PLANTA 2023; 257:57. [PMID: 36795295 DOI: 10.1007/s00425-023-04089-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Accepted: 02/02/2023] [Indexed: 06/18/2023]
Abstract
Induced mutations in the SC-uORF of the tomato transcription factor gene SlbZIP1 by the CRISPR/Cas9 system led to the high accumulation of sugar and amino acid contents in tomato fruits. Tomato (Solanum lycopersicum) is one of the most popular and consumed vegetable crops in the world. Among important traits for tomato improvement such as yield, biotic and abiotic resistances, appearance, post-harvest shelf life and fruit quality, the last one seems to face more challenges because of its genetic and biochemical complexities. In this study, a dual-gRNAs CRISPR/Cas9 system was developed to induce targeted mutations in uORF regions of the SlbZIP1, a gene involved in the sucrose-induced repression of translation (SIRT) mechanism. Different induced mutations in the SlbZIP1-uORF region were identified at the T0 generation, stably transferred to the offspring, and no mutation was found at potential off-target sites. The induced mutations in the SlbZIP1-uORF region affected the transcription of SlbZIP1 and related genes in sugar and amino acid biosynthesis. Fruit component analysis showed significant increases in soluble solid, sugar and total amino acid contents in all SlbZIP1-uORF mutant lines. The accumulation of sour-tasting amino acids, including aspartic and glutamic acids, raised from 77 to 144%, while the accumulation of sweet-tasting amino acids such as alanine, glycine, proline, serine, and threonine increased from 14 to 107% in the mutant plants. Importantly, the potential SlbZIP1-uORF mutant lines with desirable fruit traits and no impaired effect on plant phenotype, growth and development were identified under the growth chamber condition. Our result indicates the potential utility of the CRISPR/Cas9 system for fruit quality improvement in tomato and other important crops.
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Affiliation(s)
- Nhung Hong Nguyen
- Laboratory of Plant Cell of Biotechnology, Institute of Biotechnology, Vietnam Academy of Science and Technology, Hanoi, Vietnam
- University of Science and Technology of Hanoi, Vietnam Academy of Science and Technology, Hanoi, Vietnam
| | - Thao Phuong Bui
- Laboratory of Plant Cell of Biotechnology, Institute of Biotechnology, Vietnam Academy of Science and Technology, Hanoi, Vietnam
| | - Ngoc Thu Le
- Laboratory of Plant Cell of Biotechnology, Institute of Biotechnology, Vietnam Academy of Science and Technology, Hanoi, Vietnam
| | - Cuong Xuan Nguyen
- Division of Plant Sciences, University of Missouri, Columbia, MO, USA
| | - My Tra Thi Le
- Laboratory of Plant Cell of Biotechnology, Institute of Biotechnology, Vietnam Academy of Science and Technology, Hanoi, Vietnam
| | - Nhan Trong Dao
- Laboratory of Plant Cell of Biotechnology, Institute of Biotechnology, Vietnam Academy of Science and Technology, Hanoi, Vietnam
| | - Quyen Phan
- Laboratory of Plant Cell of Biotechnology, Institute of Biotechnology, Vietnam Academy of Science and Technology, Hanoi, Vietnam
| | - Trong Van Le
- National Center for Food Analysis and Assessment, Food Industries Research Institute, Hanoi, Vietnam
| | - Huong Mai Thi To
- University of Science and Technology of Hanoi, Vietnam Academy of Science and Technology, Hanoi, Vietnam
| | - Ngoc Bich Pham
- Laboratory of Applied DNA Technology, Institute of Biotechnology, Vietnam Academy of Science and Technology, Hanoi, Vietnam
- Graduate University of Science and Technology, Vietnam Academy of Science and Technology, Hanoi, Vietnam
| | - Ha Hoang Chu
- Laboratory of Plant Cell of Biotechnology, Institute of Biotechnology, Vietnam Academy of Science and Technology, Hanoi, Vietnam.
- Graduate University of Science and Technology, Vietnam Academy of Science and Technology, Hanoi, Vietnam.
| | - Phat Tien Do
- Laboratory of Plant Cell of Biotechnology, Institute of Biotechnology, Vietnam Academy of Science and Technology, Hanoi, Vietnam.
- Graduate University of Science and Technology, Vietnam Academy of Science and Technology, Hanoi, Vietnam.
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15
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Duraiswamy A, Sneha A. NM, Jebakani K. S, Selvaraj S, Pramitha J. L, Selvaraj R, Petchiammal K. I, Kather Sheriff S, Thinakaran J, Rathinamoorthy S, Kumar P. R. Genetic manipulation of anti-nutritional factors in major crops for a sustainable diet in future. FRONTIERS IN PLANT SCIENCE 2023; 13:1070398. [PMID: 36874916 PMCID: PMC9976781 DOI: 10.3389/fpls.2022.1070398] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Accepted: 12/19/2022] [Indexed: 06/18/2023]
Abstract
The consumption of healthy food, in order to strengthen the immune system, is now a major focus of people worldwide and is essential to tackle the emerging pandemic concerns. Moreover, research in this area paves the way for diversification of human diets by incorporating underutilized crops which are highly nutritious and climate-resilient in nature. However, although the consumption of healthy foods increases nutritional uptake, the bioavailability of nutrients and their absorption from foods also play an essential role in curbing malnutrition in developing countries. This has led to a focus on anti-nutrients that interfere with the digestion and absorption of nutrients and proteins from foods. Anti-nutritional factors in crops, such as phytic acid, gossypol, goitrogens, glucosinolates, lectins, oxalic acid, saponins, raffinose, tannins, enzyme inhibitors, alkaloids, β-N-oxalyl amino alanine (BOAA), and hydrogen cyanide (HCN), are synthesized in crop metabolic pathways and are interconnected with other essential growth regulation factors. Hence, breeding with the aim of completely eliminating anti-nutrition factors tends to compromise desirable features such as yield and seed size. However, advanced techniques, such as integrated multi-omics, RNAi, gene editing, and genomics-assisted breeding, aim to breed crops in which negative traits are minimized and to provide new strategies to handle these traits in crop improvement programs. There is also a need to emphasize individual crop-based approaches in upcoming research programs to achieve smart foods with minimum constraints in future. This review focuses on progress in molecular breeding and prospects for additional approaches to improve nutrient bioavailability in major crops.
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Affiliation(s)
- Aishwarya Duraiswamy
- Genetics and Plant Breeding, School of Agricultural Sciences, Karunya Institute of Technology and Sciences, Coimbatore, India
| | - Nancy Mano Sneha A.
- Genetics and Plant Breeding, School of Agricultural Sciences, Karunya Institute of Technology and Sciences, Coimbatore, India
| | - Sherina Jebakani K.
- Genetics and Plant Breeding, School of Agricultural Sciences, Karunya Institute of Technology and Sciences, Coimbatore, India
| | - Sellakumar Selvaraj
- Genetics and Plant Breeding, School of Agricultural Sciences, Karunya Institute of Technology and Sciences, Coimbatore, India
| | - Lydia Pramitha J.
- Genetics and Plant Breeding, School of Agricultural Sciences, Karunya Institute of Technology and Sciences, Coimbatore, India
| | - Ramchander Selvaraj
- Genetics and Plant Breeding, School of Agricultural Sciences, Karunya Institute of Technology and Sciences, Coimbatore, India
| | - Indira Petchiammal K.
- Genetics and Plant Breeding, School of Agricultural Sciences, Karunya Institute of Technology and Sciences, Coimbatore, India
| | - Sharmili Kather Sheriff
- Agronomy, School of Agricultural Sciences, Karunya Institute of Technology and Sciences, Coimbatore, India
| | - Jenita Thinakaran
- Horticulture, School of Agricultural Sciences, Karunya Institute of Technology and Sciences, Coimbatore, India
| | - Samundeswari Rathinamoorthy
- Crop Physiology, School of Agricultural Sciences, Karunya Institute of Technology and Sciences, Coimbatore, India
| | - Ramesh Kumar P.
- Plant Biochemistry, School of Agricultural Sciences, Karunya Institute of Technology and Sciences, Coimbatore, India
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16
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Padalkar G, Mandlik R, Sudhakaran S, Vats S, Kumawat S, Kumar V, Kumar V, Rani A, Ratnaparkhe MB, Jadhav P, Bhat JA, Deshmukh R, Sharma TR, Sonah H. Necessity and challenges for exploration of nutritional potential of staple-food grade soybean. J Food Compost Anal 2022. [DOI: 10.1016/j.jfca.2022.105093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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17
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Shcherban AB. Plant genome modification: from induced mutagenesis to genome editing. Vavilovskii Zhurnal Genet Selektsii 2022; 26:684-696. [DOI: 10.18699/vjgb-22-83] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Revised: 09/20/2022] [Accepted: 09/20/2022] [Indexed: 12/03/2022] Open
Affiliation(s)
- A. B. Shcherban
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences; Kurchatov Genomic Center of ICG SB RAS
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18
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Cao L, Wang Z, Ma H, Liu T, Ji J, Duan K. Multiplex CRISPR/Cas9-mediated raffinose synthase gene editing reduces raffinose family oligosaccharides in soybean. FRONTIERS IN PLANT SCIENCE 2022; 13:1048967. [PMID: 36457532 PMCID: PMC9706108 DOI: 10.3389/fpls.2022.1048967] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Accepted: 10/18/2022] [Indexed: 06/17/2023]
Abstract
Soybean [Glycine max (L.) Merr.] is an important world economic crop. It is rich in oil, protein, and starch, and soluble carbohydrates in soybean seeds are also important for human and livestock consumption. The predominant soluble carbohydrate in soybean seed is composed of sucrose and raffinose family oligosaccharides (RFOs). Among these carbohydrates, only sucrose can be digested by humans and monogastric animals and is beneficial for metabolizable energy, while RFOs are anti-nutritional factors in diets, usually leading to flatulence and indigestion, ultimately reducing energy efficiency. Hence, breeding efforts to remove RFOs from soybean seeds can increase metabolizable energy and improve nutritional quality. The objective of this research is to use the multiplex Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)/Cas9-mediated gene editing system to induce the knockout of soybean raffinose synthase (RS) genes RS2 and RS3 simultaneously to reduce RFOs in mature seeds. First, we constructed five types of multiplex gene editing systems and compared their editing efficiency in soybean hairy roots. We confirmed that the two-component transcriptional unit (TCTU) and single transcriptional unit (STU) systems with transfer RNA (tRNA) as the cleavage site performed better than other systems. The average editing efficiency at the four targets with TCTU-tRNA and STU-tRNA was 50.5% and 46.7%, respectively. Then, we designed four single-guide RNA (sgRNA) targets to induce mutations at RS2 and RS3 by using the TCTU-tRNA system. After the soybean transformation, we obtained several RS2 and RS3 mutation plants, and a subset of alleles was successfully transferred to the progeny. We identified null single and double mutants at the T2 generation and analyzed the seed carbohydrate content of their progeny. The RS2 and RS3 double mutants and the RS2 single mutant exhibited dramatically reduced levels of raffinose and stachyose in mature seeds. Further analysis of the growth and development of these mutants showed that there were no penalties on these phenotypes. Our results indicate that knocking out RS genes by multiplex CRISPR/Cas9-mediated gene editing is an efficient way to reduce RFOs in soybean. This research demonstrates the potential of using elite soybean cultivars to improve the soybean meal trait by multiplex CRISPR(Clustered Regularly Interspaced Short Palindromic Repeats)/Cas9-mediated gene editing.
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Salvi P, Varshney V, Majee M. Raffinose family oligosaccharides (RFOs): role in seed vigor and longevity. Biosci Rep 2022; 42:BSR20220198. [PMID: 36149314 PMCID: PMC9547172 DOI: 10.1042/bsr20220198] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 09/22/2022] [Accepted: 09/23/2022] [Indexed: 11/17/2022] Open
Abstract
Seed vigor and longevity are important agronomic attributes, as they are essentially associated with crop yield and thus the global economy. Seed longevity is a measure of seed viability and the most essential property in gene bank management since it affects regeneration of seed recycling. Reduced seed life or storability is a serious issue in seed storage since germplasm conservation and agricultural enhancement initiatives rely on it. The irreversible and ongoing process of seed deterioration comprises a complex gene regulatory network and altered metabolism that results in membrane damage, DNA integrity loss, mitochondrial dysregulation, protein damage, and disrupted antioxidative machinery. Carbohydrates and/or sugars, primarily raffinose family oligosaccharides (RFOs), have emerged as feasible components for boosting or increasing seed vigor and longevity in recent years. RFOs are known to perform diverse functions in plants, including abiotic and biotic stress tolerance, besides being involved in regulating seed germination, desiccation tolerance, vigor, and longevity. We emphasized and analyzed the potential impact of RFOs on seed vigor and longevity in this review. Here, we comprehensively reviewed the molecular mechanisms involved in seed longevity, RFO metabolism, and how RFO content is critical and linked with seed vigor and longevity. Further molecular basis, biotechnological approaches, and CRISPR/Cas applications have been discussed briefly for the improvement of seed attributes and ultimately crop production. Likewise, we suggest advancements, challenges, and future possibilities in this area.
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Affiliation(s)
- Prafull Salvi
- National Agri-Food Biotechnology Institute, Punjab 140308, India
| | - Vishal Varshney
- Govt. Shaheed Gend Singh College, Charama, Chhattisgarh 494337, India
| | - Manoj Majee
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India
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20
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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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Ramtekey V, Cherukuri S, Kumar S, V. SK, Sheoran S, K. UB, K. BN, Kumar S, Singh AN, Singh HV. Seed Longevity in Legumes: Deeper Insights Into Mechanisms and Molecular Perspectives. FRONTIERS IN PLANT SCIENCE 2022; 13:918206. [PMID: 35968115 PMCID: PMC9364935 DOI: 10.3389/fpls.2022.918206] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 05/31/2022] [Indexed: 06/15/2023]
Abstract
Sustainable agricultural production largely depends upon the viability and longevity of high-quality seeds during storage. Legumes are considered as rich source of dietary protein that helps to ensure nutritional security, but associated with poor seed longevity that hinders their performance and productivity in farmer's fields. Seed longevity is the key determinant to assure proper seed plant value and crop yield. Thus, maintenance of seed longevity during storage is of prime concern and a pre-requisite for enhancing crop productivity of legumes. Seed longevity is significantly correlated with other seed quality parameters such as germination, vigor, viability and seed coat permeability that affect crop growth and development, consequently distressing crop yield. Therefore, information on genetic basis and regulatory networks associated with seed longevity, as well as molecular dissection of traits linked to longevity could help in developing crop varieties with good storability. Keeping this in view, the present review focuses towards highlighting the molecular basis of seed longevity, with special emphasis on candidate genes and proteins associated with seed longevity and their interplay with other quality parameters. Further, an attempt was made to provide information on 3D structures of various genetic loci (genes/proteins) associated to seed longevity that could facilitate in understanding the interactions taking place within the seed at molecular level. This review compiles and provides information on genetic and genomic approaches for the identification of molecular pathways and key players involved in the maintenance of seed longevity in legumes, in a holistic manner. Finally, a hypothetical fast-forward breeding pipeline has been provided, that could assist the breeders to successfully develop varieties with improved seed longevity in legumes.
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Affiliation(s)
| | | | - Sunil Kumar
- Indian Agricultural Statistics Research Institute-IASRI, New Delhi, India
| | | | - Seema Sheoran
- ICAR-Indian Agricultural Research Institute, Regional Station, Karnal, India
| | - Udaya Bhaskar K.
- ICAR-Indian Institute of Seed Science, Regional Station, Bengaluru, India
| | - Bhojaraja Naik K.
- ICAR-Indian Institute of Seed Science, Regional Station, Bengaluru, India
| | - Sanjay Kumar
- ICAR-Indian Institute of Seed Science, Mau, India
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22
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Melzer R, McCabe PF, Schilling S. Evolution, genetics and biochemistry of plant cannabinoid synthesis: a challenge for biotechnology in the years ahead. Curr Opin Biotechnol 2022; 75:102684. [DOI: 10.1016/j.copbio.2022.102684] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Revised: 12/14/2021] [Accepted: 01/03/2022] [Indexed: 12/14/2022]
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23
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Incorporation of engineered nanoparticles of biochar and fly ash against bacterial leaf spot of pepper. Sci Rep 2022; 12:8561. [PMID: 35595743 PMCID: PMC9123008 DOI: 10.1038/s41598-022-10795-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Accepted: 04/12/2022] [Indexed: 12/02/2022] Open
Abstract
In agriculture, the search for higher net profit is the main challenge in the economy of the producers and nano biochar attracts increasing interest in recent years due to its unique environmental behavior and increasing the productivity of plants by inducing resistance against phytopathogens. The effect of rice straw biochar and fly ash nanoparticles (RSBNPs and FNPs, respectively) in combination with compost soil on bacterial leaf spot of pepper caused by Xanthomonascampestris pv. vesicatoria was investigated both in vitro and in vivo. The application of nanoparticles as soil amendment significantly improved the chili pepper plant growth. However, RSBNPs were more effective in enhancing the above and belowground plant biomass production. Moreover, both RSBNPs and FNPs, significantly reduced (30.5 and 22.5%, respectively), while RSBNPs had shown in vitro growth inhibition of X.campestris pv. vesicatoria by more than 50%. The X-ray diffractometry of RSBNPs and FNPs highlighted the unique composition of nano forms which possibly contributed in enhancing the plant defence against invading X.campestris pv. vesicatoria. Based on our findings, it is suggested that biochar and fly ash nanoparticles can be used for reclaiming the problem soil and enhance crop productivity depending upon the nature of the soil and the pathosystem under investigation.
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24
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Wen D, Wu L, Wang M, Yang W, Wang X, Ma W, Sun W, Chen S, Xiang L, Shi Y. CRISPR/Cas9-Mediated Targeted Mutagenesis of FtMYB45 Promotes Flavonoid Biosynthesis in Tartary Buckwheat ( Fagopyrum tataricum). FRONTIERS IN PLANT SCIENCE 2022; 13:879390. [PMID: 35646007 PMCID: PMC9133938 DOI: 10.3389/fpls.2022.879390] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2022] [Accepted: 04/25/2022] [Indexed: 06/01/2023]
Abstract
The clustered regularly interspaced short palindromic repeat/CRISPR-associated protein 9 (CRISPR/Cas9) technology is an efficient genome editing tool used in multiple plant species. However, it has not been applied to Tartary buckwheat (Fagopyrum tataricum), which is an important edible and medicinal crop rich in rutin and other flavonoids. FtMYB45 is an R2R3-type MYB transcription factor that negatively regulates flavonoid biosynthesis in Tartary buckwheat. Here, the CRISPR/Cas9 system polycistronic tRNA-sgRNA (PTG)/Cas9 was employed to knock out the FtMYB45 gene in Tartary buckwheat. Two single-guide RNAs (sgRNAs) were designed to target the second exon of the FtMYB45 gene. Twelve transgenic hairy roots were obtained using Agrobacterium rhizogenes-mediated transformation. Sequencing data revealed that six lines containing six types of mutations at the predicted double-stranded break site were generated using sgRNA1. The mutation frequency reached 50%. A liquid chromatography coupled with triple quadrupole mass spectrometry (LC-QqQ-MS) based metabolomic analysis revealed that the content of rutin, catechin, and other flavonoids was increased in hairy root mutants compared with that of lines transformed with the empty vector. Thus, CRISPR/Cas9-mediated targeted mutagenesis of FtMYB45 effectively increased the flavonoids content of Tartary buckwheat. This finding demonstrated that the CRISPR/Cas9 system is an efficient tool for precise genome editing in Tartary buckwheat and lays the foundation for gene function research and quality improvement in Tartary buckwheat.
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Affiliation(s)
- Dong Wen
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Artemisinin Research Center, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Lan Wu
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Artemisinin Research Center, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Mengyue Wang
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Artemisinin Research Center, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Wei Yang
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Artemisinin Research Center, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Xingwen Wang
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Artemisinin Research Center, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Wei Ma
- College of Pharmaceutical Sciences, Heilongjiang University of Chinese Medicine, Harbin, China
| | - Wei Sun
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Artemisinin Research Center, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Shilin Chen
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Artemisinin Research Center, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Li Xiang
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Artemisinin Research Center, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Yuhua Shi
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Artemisinin Research Center, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
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25
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Aznar-Moreno JA, Mukherjee T, Morley SA, Duressa D, Kambhampati S, Chu KL, Koley S, Allen DK, Durrett TP. Suppression of SDP1 Improves Soybean Seed Composition by Increasing Oil and Reducing Undigestible Oligosaccharides. FRONTIERS IN PLANT SCIENCE 2022; 13:863254. [PMID: 35401590 PMCID: PMC8983916 DOI: 10.3389/fpls.2022.863254] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 02/22/2022] [Indexed: 06/01/2023]
Abstract
In developing soybean seeds, carbon is partitioned between oil, protein and carbohydrates. Here, we demonstrate that suppression of lipase-mediated turnover of triacylglycerols (TAG) during late seed development increases fatty acid content and decreases the presence of undigestible oligosaccharides. During late stages of embryo development, the fatty acid content of soybean seed decreases while the levels of the oligosaccharides raffinose and stachyose increase. Three soybean genes orthologous to the Arabidopsis lipase gene SUGAR-DEPENDENT1 (SDP1) are upregulated at this time. Suppression of these genes resulted in higher oil levels, with lipid levels in the best lines exceeding 24% of seed weight. In addition, lipase-suppressed lines produced larger seeds compared to wild-type plants, resulting in increases of over 20% in total lipid per seed. Levels of raffinose and stachyose were lower in the transgenic lines, with average reductions of 15% in total raffinose family oligosaccharides observed. Despite the increase in oil, protein content was not negatively impacted and trended higher in the transgenic lines. These results are consistent with a role for SDP1 in turning over TAG to supply carbon for other needs, including the synthesis of oligosaccharides, and offer new strategies to further improve the composition of soybean seeds.
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Affiliation(s)
- Jose A. Aznar-Moreno
- Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, KS, United States
| | - Thiya Mukherjee
- Donald Danforth Plant Science Center, St. Louis, MO, United States
| | - Stewart A. Morley
- Donald Danforth Plant Science Center, St. Louis, MO, United States
- United States Department of Agriculture, Agricultural Research Service, St. Louis, MO, United States
| | - Dechassa Duressa
- Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, KS, United States
| | | | - Kevin L. Chu
- Donald Danforth Plant Science Center, St. Louis, MO, United States
- United States Department of Agriculture, Agricultural Research Service, St. Louis, MO, United States
| | - Somnath Koley
- Donald Danforth Plant Science Center, St. Louis, MO, United States
| | - Doug K. Allen
- Donald Danforth Plant Science Center, St. Louis, MO, United States
- United States Department of Agriculture, Agricultural Research Service, St. Louis, MO, United States
| | - Timothy P. Durrett
- Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, KS, United States
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26
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Elango D, Rajendran K, Van der Laan L, Sebastiar S, Raigne J, Thaiparambil NA, El Haddad N, Raja B, Wang W, Ferela A, Chiteri KO, Thudi M, Varshney RK, Chopra S, Singh A, Singh AK. Raffinose Family Oligosaccharides: Friend or Foe for Human and Plant Health? FRONTIERS IN PLANT SCIENCE 2022; 13:829118. [PMID: 35251100 PMCID: PMC8891438 DOI: 10.3389/fpls.2022.829118] [Citation(s) in RCA: 37] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2021] [Accepted: 01/26/2022] [Indexed: 05/27/2023]
Abstract
Raffinose family oligosaccharides (RFOs) are widespread across the plant kingdom, and their concentrations are related to the environment, genotype, and harvest time. RFOs are known to carry out many functions in plants and humans. In this paper, we provide a comprehensive review of RFOs, including their beneficial and anti-nutritional properties. RFOs are considered anti-nutritional factors since they cause flatulence in humans and animals. Flatulence is the single most important factor that deters consumption and utilization of legumes in human and animal diets. In plants, RFOs have been reported to impart tolerance to heat, drought, cold, salinity, and disease resistance besides regulating seed germination, vigor, and longevity. In humans, RFOs have beneficial effects in the large intestine and have shown prebiotic potential by promoting the growth of beneficial bacteria reducing pathogens and putrefactive bacteria present in the colon. In addition to their prebiotic potential, RFOs have many other biological functions in humans and animals, such as anti-allergic, anti-obesity, anti-diabetic, prevention of non-alcoholic fatty liver disease, and cryoprotection. The wide-ranging applications of RFOs make them useful in food, feed, cosmetics, health, pharmaceuticals, and plant stress tolerance; therefore, we review the composition and diversity of RFOs, describe the metabolism and genetics of RFOs, evaluate their role in plant and human health, with a primary focus in grain legumes.
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Affiliation(s)
- Dinakaran Elango
- Department of Agronomy, Iowa State University, Ames, IA, United States
| | - Karthika Rajendran
- VIT School of Agricultural Innovations and Advanced Learning, Vellore Institute of Technology, Vellore, India
| | - Liza Van der Laan
- Department of Agronomy, Iowa State University, Ames, IA, United States
| | - Sheelamary Sebastiar
- Division of Crop Improvement, ICAR-Sugarcane Breeding Institute, Coimbatore, India
| | - Joscif Raigne
- Department of Agronomy, Iowa State University, Ames, IA, United States
| | | | - Noureddine El Haddad
- International Center for Agricultural Research in the Dry Areas, Rabat, Morocco
- Faculty of Sciences, Mohammed V University of Rabat, Rabat, Morocco
| | - Bharath Raja
- School of Biosciences and Technology, Vellore Institute of Technology, Vellore, India
| | - Wanyan Wang
- Ecosystem Science and Management, Penn State University, University Park, PA, United States
| | - Antonella Ferela
- Department of Agronomy, Iowa State University, Ames, IA, United States
| | - Kevin O. Chiteri
- Department of Agronomy, Iowa State University, Ames, IA, United States
| | - Mahendar Thudi
- Department of Agricultural Biotechnology and Molecular Biology, Dr. Rajendra Prasad Central Agricultural University, Pusa, India
- Centre for Crop Health, University of Southern Queensland, Toowoomba, QLD, Australia
| | - Rajeev K. Varshney
- International Crops Research Institute for the Semi-Arid Tropics, Patancheru, India
- State Agricultural Biotechnology Centre, Crop Research Innovation Centre, Food Futures Institute, Murdoch University, Murdoch, WA, Australia
| | - Surinder Chopra
- Department of Plant Science, Penn State University, University Park, PA, United States
| | - Arti Singh
- Department of Agronomy, Iowa State University, Ames, IA, United States
| | - Asheesh K. Singh
- Department of Agronomy, Iowa State University, Ames, IA, United States
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27
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Nguyen DV, Hoang TTH, Le NT, Tran HT, Nguyen CX, Moon YH, Chu HH, Do PT. An Efficient Hairy Root System for Validation of Plant Transformation Vector and CRISPR/Cas Construct Activities in Cucumber ( Cucumis sativus L.). FRONTIERS IN PLANT SCIENCE 2022; 12:770062. [PMID: 35222448 PMCID: PMC8874011 DOI: 10.3389/fpls.2021.770062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Accepted: 12/27/2021] [Indexed: 06/14/2023]
Abstract
Hairy root induction system has been applied in various plant species as an effective method to study gene expression and function due to its fast-growing and high genetic stability. Recently, these systems have shown to be an effective tool to evaluate activities of CRISPR/Cas9 systems for genome editing. In this study, Rhizobium rhizogenes mediated hairy root induction was optimized to provide an effective tool for validation of plant transformation vector, CRISPR/Cas9 construct activities as well as selection of targeted gRNAs for gene editing in cucumber (Cucumis sativus L.). Under the optimized conditions including OD650 at 0.4 for infection and 5 days of co-cultivation, the highest hairy root induction frequency reached 100% for the cucumber variety Choka F1. This procedure was successfully utilized to overexpress a reporter gene (gus) and induce mutations in two Lotus japonicus ROOTHAIRLESS1 homolog genes CsbHLH66 and CsbHLH82 using CRISPR/Cas9 system. For induced mutation, about 78% of transgenic hairy roots exhibited mutant phenotypes including sparse root hair and root hair-less. The targeted mutations were obtained in individual CsbHLH66, CsbHLH82, or both CsbHLH66 and CsbHLH82 genes by heteroduplex analysis and sequencing. The hairy root transformation system established in this study is sufficient and potential for further research in genome editing of cucumber as well as other cucumis plants.
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Affiliation(s)
- Doai Van Nguyen
- Laboratory of Plant Cell Biotechnology, Institute of Biotechnology, Vietnam Academy of Science and Technology, Hanoi, Vietnam
- Department of Integrated Biological Science, Pusan National University, Busan, South Korea
| | - Trang Thi-Huyen Hoang
- Laboratory of Plant Cell Biotechnology, Institute of Biotechnology, Vietnam Academy of Science and Technology, Hanoi, Vietnam
| | - Ngoc Thu Le
- Laboratory of Plant Cell Biotechnology, Institute of Biotechnology, Vietnam Academy of Science and Technology, Hanoi, Vietnam
| | - Huyen Thi Tran
- Laboratory of Plant Cell Biotechnology, Institute of Biotechnology, Vietnam Academy of Science and Technology, Hanoi, Vietnam
| | - Cuong Xuan Nguyen
- Division of Plant Sciences, University of Missouri, Columbia, MO, United States
| | - Yong-Hwan Moon
- Department of Integrated Biological Science, Pusan National University, Busan, South Korea
- Department of Molecular Biology, Pusan National University, Busan, South Korea
| | - Ha Hoang Chu
- Laboratory of Plant Cell Biotechnology, Institute of Biotechnology, Vietnam Academy of Science and Technology, Hanoi, Vietnam
- Graduate University of Science and Technology, Vietnam Academy of Science and Technology, Hanoi, Vietnam
| | - Phat Tien Do
- Laboratory of Plant Cell Biotechnology, Institute of Biotechnology, Vietnam Academy of Science and Technology, Hanoi, Vietnam
- Graduate University of Science and Technology, Vietnam Academy of Science and Technology, Hanoi, Vietnam
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28
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Subburaj S, Zanatta CB, Nunn JAL, Hoepers AM, Nodari RO, Agapito-Tenfen SZ. A DNA-Free Editing Platform for Genetic Screens in Soybean via CRISPR/Cas9 Ribonucleoprotein Delivery. FRONTIERS IN PLANT SCIENCE 2022; 13:939997. [PMID: 35903231 PMCID: PMC9315425 DOI: 10.3389/fpls.2022.939997] [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: 05/09/2022] [Accepted: 06/20/2022] [Indexed: 05/06/2023]
Abstract
CRISPR/Cas9-based ribonucleoprotein (RNP)-mediated system has the property of minimizing the effects related to the unwanted introduction of vector DNA and random integration of recombinant DNA. Here, we describe a platform based on the direct delivery of Cas9 RNPs to soybean protoplasts for genetic screens in knockout gene-edited soybean lines without the transfection of DNA vectors. The platform is based on the isolation of soybean protoplasts and delivery of Cas RNP complex. To empirically test our platform, we have chosen a model gene from the soybean genetic toolbox. We have used five different guide RNA (gRNA) sequences that targeted the constitutive pathogen response 5 (CPR5) gene associated with the growth of trichomes in soybean. In addition, efficient protoplast transformation, concentration, and ratio of Cas9 and gRNAs were optimized for soybean for the first time. Targeted mutagenesis insertion and deletion frequency and sequences were analyzed using both Sanger and targeted deep sequencing strategies. We were able to identify different mutation patterns within insertions and deletions (InDels) between + 5 nt and -30 bp and mutation frequency ranging from 4.2 to 18.1% in the GmCPR5 locus. Our results showed that DNA-free delivery of Cas9 complexes to protoplasts is a useful approach to perform early-stage genetic screens and anticipated analysis of Cas9 activity in soybeans.
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Affiliation(s)
- Saminathan Subburaj
- NORCE Norwegian Research Centre AS, Department of Climate & Environment, Tromsø, Norway
| | - Caroline Bedin Zanatta
- NORCE Norwegian Research Centre AS, Department of Climate & Environment, Tromsø, Norway
- Department of Crop Science, Federal University of Santa Catarina, Florianópolis, Brazil
| | - Jennifer A. L. Nunn
- NORCE Norwegian Research Centre AS, Department of Climate & Environment, Tromsø, Norway
| | - Aline Martins Hoepers
- Department of Crop Science, Federal University of Santa Catarina, Florianópolis, Brazil
| | - Rubens Onofre Nodari
- Department of Crop Science, Federal University of Santa Catarina, Florianópolis, Brazil
| | - Sarah Zanon Agapito-Tenfen
- NORCE Norwegian Research Centre AS, Department of Climate & Environment, Tromsø, Norway
- *Correspondence: Sarah Zanon Agapito-Tenfen,
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29
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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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30
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Liu LM, Zhang HQ, Cheng K, Zhang YM. Integrated Bioinformatics Analyses of PIN1, CKX, and Yield-Related Genes Reveals the Molecular Mechanisms for the Difference of Seed Number Per Pod Between Soybean and Cowpea. FRONTIERS IN PLANT SCIENCE 2021; 12:749902. [PMID: 34912354 PMCID: PMC8667476 DOI: 10.3389/fpls.2021.749902] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Accepted: 10/29/2021] [Indexed: 06/14/2023]
Abstract
There is limited advancement on seed number per pod (SNPP) in soybean breeding, resulting in low yield in China. To address this issue, we identified PIN1 and CKX gene families that regulate SNPP in Arabidopsis, analyzed the differences of auxin and cytokinin pathways, and constructed interaction networks on PIN1, CKX, and yield-related genes in soybean and cowpea. First, the relative expression level (REL) of PIN1 and the plasma membrane localization and phosphorylation levels of PIN1 protein were less in soybean than in cowpea, which make auxin transport efficiency lower in soybean, and its two interacted proteins might be involved in serine hydrolysis, so soybean has lower SNPP than cowpea. Then, the CKX gene family, along with its positive regulatory factor ROCK1, had higher REL and less miRNA regulation in soybean flowers than in cowpea ones. These lead to higher cytokinin degradation level, which further reduces the REL of PIN1 and decreases soybean SNPP. We found that VuACX4 had much higher REL than GmACX4, although the two genes essential in embryo development interact with the CKX gene family. Next, a tandem duplication experienced by legumes led to the differentiation of CKX3 into CKX3a and CKX3b, in which CKX3a is a key gene affecting ovule number. Finally, in the yield-related gene networks, three cowpea CBP genes had higher RELs than two soybean CBP genes, low RELs of three soybean-specific IPT genes might lead to a decrease in cytokinin synthesis, and some negative and positive SNPP regulation were found, respectively, in soybean and cowpea. These networks may explain the SNPP difference in the two crops. We deduced that ckx3a or ckx3a ckx6 ckx7 mutants, interfering CYP88A, and over-expressed DELLA increase SNPP in soybean. This study reveals the molecular mechanism for the SNPP difference in the two crops, and provides an important idea for increasing soybean yield.
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31
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de Koning R, Kiekens R, Toili MEM, Angenon G. Identification and Expression Analysis of the Genes Involved in the Raffinose Family Oligosaccharides Pathway of Phaseolus vulgaris and Glycine max. PLANTS (BASEL, SWITZERLAND) 2021; 10:1465. [PMID: 34371668 PMCID: PMC8309293 DOI: 10.3390/plants10071465] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Revised: 07/12/2021] [Accepted: 07/13/2021] [Indexed: 11/17/2022]
Abstract
Raffinose family oligosaccharides (RFO) play an important role in plants but are also considered to be antinutritional factors. A profound understanding of the galactinol and RFO biosynthetic gene families and the expression patterns of the individual genes is a prerequisite for the sustainable reduction of the RFO content in the seeds, without compromising normal plant development and functioning. In this paper, an overview of the annotation and genetic structure of all galactinol- and RFO biosynthesis genes is given for soybean and common bean. In common bean, three galactinol synthase genes, two raffinose synthase genes and one stachyose synthase gene were identified for the first time. To discover the expression patterns of these genes in different tissues, two expression atlases have been created through re-analysis of publicly available RNA-seq data. De novo expression analysis through an RNA-seq study during seed development of three varieties of common bean gave more insight into the expression patterns of these genes during the seed development. The results of the expression analysis suggest that different classes of galactinol- and RFO synthase genes have tissue-specific expression patterns in soybean and common bean. With the obtained knowledge, important galactinol- and RFO synthase genes that specifically play a key role in the accumulation of RFOs in the seeds are identified. These candidate genes may play a pivotal role in reducing the RFO content in the seeds of important legumes which could improve the nutritional quality of these beans and would solve the discomforts associated with their consumption.
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Affiliation(s)
- Ramon de Koning
- Research Group Plant Genetics, Vrije Universiteit Brussel, 1050 Brussels, Belgium; (R.d.K.); (R.K.); (M.E.M.T.)
| | - Raphaël Kiekens
- Research Group Plant Genetics, Vrije Universiteit Brussel, 1050 Brussels, Belgium; (R.d.K.); (R.K.); (M.E.M.T.)
| | - Mary Esther Muyoka Toili
- Research Group Plant Genetics, Vrije Universiteit Brussel, 1050 Brussels, Belgium; (R.d.K.); (R.K.); (M.E.M.T.)
- Department of Horticulture, Jomo Kenyatta University of Agriculture and Technology, Juja 01001, Kiambu County, Kenya
| | - Geert Angenon
- Research Group Plant Genetics, Vrije Universiteit Brussel, 1050 Brussels, Belgium; (R.d.K.); (R.K.); (M.E.M.T.)
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