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Zhao S, Zhang C, Jiao J, Zhang Y, Jiang T, Wu P, Feng K, Li L. The transcription factor NnNAC100 positively regulates amylopectin biosynthesis by activating NnSBEII in the rhizome of Nelumbo nucifera Gaertn. PLANT CELL REPORTS 2025; 44:21. [PMID: 39751893 DOI: 10.1007/s00299-024-03408-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2024] [Accepted: 12/17/2024] [Indexed: 01/04/2025]
Abstract
KEY MESSAGE NnNAC100-NnSBEII modules enhance starch content of the rhizome in Nelumbo nucifera Gaertn. Nelumbo nucifera Gaertn. is a popular aquatic vegetable and traditional Chinese medicine whose quality and taste are mainly determined by the starch. Although starch-related genes have been functionally characterized, the regulated mechanism of enzyme (SBE) remains unclear. In this study, we identified and functionally elucidated the functions of NnSBEII and NnNAC100 using transient overexpression of NnSBEII and NnNAC100 in rhizomes of lotus, and it significantly increased the amylopectin content and total starch content. Accordingly, functional complementation assay in defective Arabidopsis also showed that NnSBEII compensated for the low content of starch in the mutant sbe2.2. In addition, overexpression of NnSBEII and NnNAC100 significantly increased the content of starch in transgenic lines. Consistently, opposite results were observed under the background of repressed NnSBEII and NnNAC100 in rhizomes of lotus. Furthermore, yeast one-hybrid and dual-luciferase assays revealed that NnNAC100 could directly bind to the NnSBEII promoter and promote the expression of NnSBEII. Transient overexpression of NnNAC100 upregulated NnSBEII expression significantly, while the expression level of AtSBE2.2 in transgenic Arabidopsis overexpressing NnNAC100 was higher than that of WT, which indicated that NnNAC100 promoted the synthesis of amylopectin by enhancing the expression of NnSBEII. In addition, we found that NnSBEII could form a complex protein by interacting with soluble starch synthase (NnSS2) to increase the activity of the SBEII enzyme. These results reveal a novel mechanism that the NnNAC100-NnSBEII-NnSBEII/NnSS2 module regulates amylopectin biosynthesis and these will provide insights into the broader implications of the regulation mechanism of starch biosynthesis.
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Affiliation(s)
- Shuping Zhao
- School of Horticulture and Gardens, Yangzhou University, Yangzhou, 225009, China
| | - Chuyan Zhang
- School of Horticulture and Gardens, Yangzhou University, Yangzhou, 225009, China
| | - Jiao Jiao
- School of Horticulture and Gardens, Yangzhou University, Yangzhou, 225009, China
| | - Yao Zhang
- School of Horticulture and Gardens, Yangzhou University, Yangzhou, 225009, China
| | - Tao Jiang
- School of Horticulture and Gardens, Yangzhou University, Yangzhou, 225009, China
| | - Peng Wu
- School of Horticulture and Gardens, Yangzhou University, Yangzhou, 225009, China
| | - Kai Feng
- School of Horticulture and Gardens, Yangzhou University, Yangzhou, 225009, China
| | - Liangjun Li
- School of Horticulture and Gardens, Yangzhou University, Yangzhou, 225009, China.
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou, 225009, China.
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Ahmad D, Ying Y, Bao J. Understanding starch biosynthesis in potatoes for metabolic engineering to improve starch quality: A detailed review. Carbohydr Polym 2024; 346:122592. [PMID: 39245484 DOI: 10.1016/j.carbpol.2024.122592] [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: 06/22/2024] [Revised: 07/27/2024] [Accepted: 08/06/2024] [Indexed: 09/10/2024]
Abstract
Potato tubers accumulate substantial quantities of starch, which serves as their primary energy reserve. As the predominant component of potato tubers, starch strongly influences tuber yield, processing quality, and nutritional attributes. Potato starch is distinguished from other food starches by its unique granule morphology and compositional attributes. It possesses large, oval granules with amylose content ranging from 20 to 33 % and high phosphorus levels, which collectively determine the unique physicochemical characteristics. These physicochemical properties direct the utility of potato starch across diverse food and industrial applications. This review synthesizes current knowledge on the molecular factors controlling potato starch biosynthesis and structure-function relationships. Key topics covered are starch granule morphology, the roles and regulation of major biosynthetic enzymes, transcriptional and hormonal control, genetic engineering strategies, and opportunities to tailor starch functionality. Elucidating the contributions of different enzymes in starch biosynthesis has enabled targeted modification of potato starch composition and properties. However, realizing the full potential of this knowledge faces challenges in optimizing starch quality without compromising plant vigor and yield. Overall, integrating multi-omics datasets with advanced genetic and metabolic engineering tools can facilitate the development of elite cultivars with enhanced starch yield and tailored functionalities.
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Affiliation(s)
- Daraz Ahmad
- Institute of Nuclear Agricultural Sciences, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Yining Ying
- Institute of Nuclear Agricultural Sciences, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Jinsong Bao
- Institute of Nuclear Agricultural Sciences, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China; Hainan Institute, Zhejiang University, Yazhou Bay Science and Technology City, Yazhou District, Sanya 572025, China.
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Hochmuth A, Carswell M, Rowland A, Scarbrough D, Esch L, Kamble NU, Habig JW, Seung D. Distinct effects of PTST2b and MRC on starch granule morphogenesis in potato tubers. PLANT BIOTECHNOLOGY JOURNAL 2024. [PMID: 39659019 DOI: 10.1111/pbi.14505] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Revised: 10/17/2024] [Accepted: 10/18/2024] [Indexed: 12/12/2024]
Abstract
The molecular mechanisms underpinning the formation of the large, ellipsoidal starch granules of potato tuber are poorly understood. Here, we demonstrate the distinct effects of PROTEIN TARGETING TO STARCH2b (PTST2b) and MYOSIN RESEMBLING CHLOROPLAST PROTEIN (MRC) on tuber starch granule morphology. A gene duplication event in the Solanaceae resulted in two PTST2 paralogs (PTST2a and PTST2b). PTST2b is expressed in potato tubers, and unlike PTST2a, it had no detectable interaction with STARCH SYNTHASE 4. MRC expression was detectable in leaves, but not in tubers. Using transgenic potato lines in the variety Clearwater Russet, we demonstrate that MRC overexpression leads to the formation of granules with aberrant shapes, many of which arise from multiple initiation points. Silencing PTST2b led to the production of striking near-spherical granules, each arising from a single, central initiation point. Contrary to all reported PTST2 mutants in other species, we observed no change in the number of granules per cell in these lines, suggesting PTST2b is specifically involved in the control of starch granule shape. Starch content and tuber yield per plant were not affected by PTST2b silencing, but MRC overexpression led to strong decreases in both parameters. Notably, the spherical granules in PTST2b silencing lines had a distinctively altered pasting profile, with higher peak and final viscosity than the wild type. Thus, PTST2b and MRC are promising target genes for altering starch granule size and shape in potato tubers, and can be used to create novel starches with altered physicochemical and/or functional properties.
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Affiliation(s)
- Anton Hochmuth
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Matthew Carswell
- Simplot Plant Sciences, J. R. Simplot Company, Boise, Idaho, 83707, USA
| | - Aaron Rowland
- Simplot Plant Sciences, J. R. Simplot Company, Boise, Idaho, 83707, USA
| | | | - Lara Esch
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | | | - Jeffrey W Habig
- Simplot Plant Sciences, J. R. Simplot Company, Boise, Idaho, 83707, USA
| | - David Seung
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
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4
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Harris HC, Warren FJ. The impact of Cas9-mediated mutagenesis of genes encoding potato starch-branching enzymes on starch structural properties and in vitro digestibility. Carbohydr Polym 2024; 345:122561. [PMID: 39227100 DOI: 10.1016/j.carbpol.2024.122561] [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: 02/26/2024] [Revised: 07/25/2024] [Accepted: 07/30/2024] [Indexed: 09/05/2024]
Abstract
The digestibility of starch is affected by amylose content, and increasing amylopectin chain length which can be manipulated by alterations to genes encoding starch-branching enzymes (SBEs). We investigated the impact of Cas9-mediated mutagenesis of SBEs in potato on starch structural properties and digestibility. Four potato starches with edited SBE genes were tested. One lacked SBE1 and SBE2, two lacked SBE2 and had reduced SBE1, and one had reduced SBE2 only. Starch structure and thermal properties were characterised by DSC and XRD. The impact of different thermal treatments on digestibility was studied using an in vitro digestion protocol. All native potato starches were resistant to digestion, and all gelatinised starches were highly digestible. SBE modified starches had higher gelatinisation temperatures than wild type potatoes and retrograded more rapidly. Gelatinisation and 18 h of retrogradation, increased gelatinisation enthalpy, but this did not translate to differences in digestion. Following 7 days of retrogradation, starch from three modified SBE starch lines was less digestible than starch from wild-type potatoes, likely due to the recrystallisation of the long amylopectin chains. Our results indicate that reductions in SBE in potato may be beneficial to health by increasing the amount of fibre reaching the colon after retrogradation.
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Affiliation(s)
- Hannah C Harris
- Quadram Institute Biosciences, Norwich Research Park, Norwich NR4 7UQ, UK.
| | - Frederick J Warren
- Quadram Institute Biosciences, Norwich Research Park, Norwich NR4 7UQ, UK.
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5
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Li L, Zhu T, Wen L, Zhang T, Ren M. Biofortification of potato nutrition. J Adv Res 2024:S2090-1232(24)00487-9. [PMID: 39486784 DOI: 10.1016/j.jare.2024.10.033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2024] [Accepted: 10/27/2024] [Indexed: 11/04/2024] Open
Abstract
BACKGROUND Potato (Solanum tuberosum L.) is the fourth most important food crop after rice, wheat and maize in the world with the potential to feed the world's population, and potato is a major staple food in many countries. Currently, potato is grown in more than 100 countries and is consumed by more than 1 billion people worldwide, and the global annual output exceeds 300 million tons. With the rapid increase in the global population, potato will play a key role in food supply. These aspects have driven scientists to genetically engineer potato for yield and nutrition improvement. AIM OF REVIEW Potato is an excellent source of carbohydrates, rich in vitamins, phenols and minerals. At present, the nutritional fortification of potato has made remarkable progress, and the biomass and nutrient compositions of potato have been significantly improved through agronomic operation and genetic improvement. This review aims to summarize recent advances in the nutritional fortification of potato protein, lipid and vitamin, and provides new insights for future potato research. KEY SCIENTIFIC CONCEPTS OF REVIEW This review comprehensively summarizes the biofortification of potato five nutrients from protein, lipid, starch, vitamin to mineral. Meanwhile, we also discuss the multilayered insights in the prospects of edible potato fruit, vaccines and high-value products synthesis, and diploid potato seeds reproduction.
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Affiliation(s)
- Linxuan Li
- Institute of Urban Agriculture, Chinese Academy of Agricultural Sciences, Chengdu National Agricultural Science and Technology Center, Chengdu 610213, China
| | - Tingting Zhu
- Institute of Urban Agriculture, Chinese Academy of Agricultural Sciences, Chengdu National Agricultural Science and Technology Center, Chengdu 610213, China
| | - Lina Wen
- School of Agricultural Science, Zhengzhou University, Zhengzhou 450001, China
| | - Tanran Zhang
- Institute of Urban Agriculture, Chinese Academy of Agricultural Sciences, Chengdu National Agricultural Science and Technology Center, Chengdu 610213, China
| | - Maozhi Ren
- Institute of Urban Agriculture, Chinese Academy of Agricultural Sciences, Chengdu National Agricultural Science and Technology Center, Chengdu 610213, China; School of Agricultural Science, Zhengzhou University, Zhengzhou 450001, China.
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Jayarathna S, Péter-Szabó Z, Nestor G, Andersson M, Vilaplana F, Andersson R. Impact of mutations in starch synthesis genes on morphological, compositional, molecular structure, and functional properties of potato starch. PLoS One 2024; 19:e0310990. [PMID: 39325801 PMCID: PMC11426511 DOI: 10.1371/journal.pone.0310990] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2024] [Accepted: 09/10/2024] [Indexed: 09/28/2024] Open
Abstract
Morphology, composition and molecular structure of starch directly affect the functional properties. This study investigated the morphological, compositional, and molecular structure properties of starch from starch branching enzyme gene (SBE) and granule-bound starch synthase gene (GBSS) mutated potato, and their associations with thermal, pasting, and film-making properties. SBE mutations were induced in native variety Desiree while GBSS mutations were herestacked to a selected SBE mutated parental line. Mutations in SBE resulted in smaller starch granules and higher amylose content, while GBSS mutations in the SBE background reduced amylose content. Mutations in SBE, particularly with GBSS mutations, significantly increased total phosphorus content. 31P NMR spectroscopy revealed higher proportions of C6-bound phosphate than of C3-bound phosphate in all studied lines. Amylopectin unit chain and internal chain distributions showed higher proportions of long chains in mutated lines compared with Desiree. These amylopectin long-chains were positively correlated with gelatinizationand, pasting temperatures, and temperature at peak viscosity. Short amylopectin chains showed positive correlations with breakdown viscosity, but negative correlations with the crystal melting temperature of retrograded starch. Total phosphorus content was positively correlated with the crystal melting temperature of retrograded starch. Starch from different lines was used to produce a series of potato starch films that differed in morphology and functional properties. A negative correlation was observed between Young's modulus of films and the long amylopectin-chain fraction. Thermal gravimetric analysis revealed highest thermal stability of Desiree starch films, followed by films from SBE-mutated high-amylose lines. Oxygen transmission rate and oxygen permeability analyses showed that films made with starch from selected GBSS and SBEs mutated line maintained comparable oxygen barrier properties to Desiree film. These insights on the impact of genetic mutations on starch properties indicate potential applications of in-planta starch modification for specific end-uses including packaging.
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Affiliation(s)
- Shishanthi Jayarathna
- Department of Molecular Sciences, BioCenter, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Zsuzsanna Péter-Szabó
- Division of Glycoscience, Department of Chemistry, KTH-Royal Institute of Technology, AlbaNova University Centre, Stockholm, Sweden
| | - Gustav Nestor
- Department of Molecular Sciences, BioCenter, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Mariette Andersson
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Lomma, Sweden
| | - Francisco Vilaplana
- Division of Glycoscience, Department of Chemistry, KTH-Royal Institute of Technology, AlbaNova University Centre, Stockholm, Sweden
| | - Roger Andersson
- Department of Molecular Sciences, BioCenter, Swedish University of Agricultural Sciences, Uppsala, Sweden
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7
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Bekele-Alemu A, Girma-Tola D, Ligaba-Osena A. The Potential of CRISPR/Cas9 to Circumvent the Risk Factor Neurotoxin β-N-oxalyl-L-α, β-diaminopropionic acid Limiting Wide Acceptance of the Underutilized Grass Pea ( Lathyrus sativus L.). Curr Issues Mol Biol 2024; 46:10570-10589. [PMID: 39329978 PMCID: PMC11430654 DOI: 10.3390/cimb46090626] [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: 07/07/2024] [Revised: 09/11/2024] [Accepted: 09/18/2024] [Indexed: 09/28/2024] Open
Abstract
Grass pea (Lathyrus sativus L.) is a protein-rich crop that is resilient to various abiotic stresses, including drought. However, it is not cultivated widely for human consumption due to the neurotoxin β-N-oxalyl-L-α, β-diaminopropionic acid (β-ODAP) and its association with neurolathyrism. Though some varieties with low β-ODAP have been developed through classical breeding, the β-ODAP content is increasing due to genotype x environment interactions. This review covers grass pea nutritional quality, β-ODAP biosynthesis, mechanism of paralysis, traditional ways to reduce β-ODAP, candidate genes for boosting sulfur-containing amino acids, and the potential and targets of gene editing to reduce β-ODAP content. Recently, two key enzymes (β-ODAP synthase and β-cyanoalanine synthase) have been identified in the biosynthetic pathway of β-ODAP. We proposed four strategies through which the genes encoding these enzymes can be targeted and suppressed using CRISPR/Cas9 gene editing. Compared to its homology in Medicago truncatula, the grass pea β-ODAP synthase gene sequence and β-cyanoalanine synthase showed 62.9% and 95% similarity, respectively. The β-ODAP synthase converts the final intermediate L-DAPA into toxic β-ODAP, whist β-cyanoalanine synthase converts O-Acetylserine into β-isoxazolin-5-on-2-yl-alanine. Since grass pea is low in methionine and cysteine amino acids, improvement of these amino acids is also needed to boost its protein content. This review contains useful resources for grass pea improvement while also offering potential gene editing strategies to lower β-ODAP levels.
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Affiliation(s)
- Abreham Bekele-Alemu
- Laboratory of Plant Molecular Biology and Biotechnology, Department of Biology, University of North Carolina Greensboro, Greensboro, NC 27412, USA
| | - Deribew Girma-Tola
- Department of Biology, College of Natural Sciences, Salale University, Fitche P.O. Box 245, Ethiopia
| | - Ayalew Ligaba-Osena
- Laboratory of Plant Molecular Biology and Biotechnology, Department of Biology, University of North Carolina Greensboro, Greensboro, NC 27412, USA
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Qu L, Huang X, Su X, Zhu G, Zheng L, Lin J, Wang J, Xue H. Potato: from functional genomics to genetic improvement. MOLECULAR HORTICULTURE 2024; 4:34. [PMID: 39160633 PMCID: PMC11331666 DOI: 10.1186/s43897-024-00105-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2024] [Accepted: 07/17/2024] [Indexed: 08/21/2024]
Abstract
Potato is the most widely grown non-grain crop and ranks as the third most significant global food crop following rice and wheat. Despite its long history of cultivation over vast areas, slow breeding progress and environmental stress have led to a scarcity of high-yielding potato varieties. Enhancing the quality and yield of potato tubers remains the ultimate objective of potato breeding. However, conventional breeding has faced challenges due to tetrasomic inheritance, high genomic heterozygosity, and inbreeding depression. Recent advancements in molecular biology and functional genomic studies of potato have provided valuable insights into the regulatory network of physiological processes and facilitated trait improvement. In this review, we present a summary of identified factors and genes governing potato growth and development, along with progress in potato genomics and the adoption of new breeding technologies for improvement. Additionally, we explore the opportunities and challenges in potato improvement, offering insights into future avenues for potato research.
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Affiliation(s)
- Li Qu
- Shanghai Collaborative Innovation Center of Agri-Seeds, Joint Center for Single Cell Biology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Xueqing Huang
- Shanghai Collaborative Innovation Center of Agri-Seeds, Joint Center for Single Cell Biology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Xin Su
- Shanghai Collaborative Innovation Center of Agri-Seeds, Joint Center for Single Cell Biology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Guoqing Zhu
- Shanghai Collaborative Innovation Center of Agri-Seeds, Joint Center for Single Cell Biology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Lingli Zheng
- Shanghai Collaborative Innovation Center of Agri-Seeds, Joint Center for Single Cell Biology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Jing Lin
- Shanghai Collaborative Innovation Center of Agri-Seeds, Joint Center for Single Cell Biology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Jiawen Wang
- Shanghai Collaborative Innovation Center of Agri-Seeds, Joint Center for Single Cell Biology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Hongwei Xue
- Shanghai Collaborative Innovation Center of Agri-Seeds, Joint Center for Single Cell Biology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China.
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Agriculture, South China Agricultural University, Guangzhou, 510642, China.
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9
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Nie H, Yang X, Zheng S, Hou L. Gene-Based Developments in Improving Quality of Tomato: Focus on Firmness, Shelf Life, and Pre- and Post-Harvest Stress Adaptations. HORTICULTURAE 2024; 10:641. [DOI: 10.3390/horticulturae10060641] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2025]
Abstract
Tomato (Solanum lycopersicum) is a widely consumed vegetable crop with significant economic and nutritional importance. This review paper discusses the recent advancements in gene-based approaches to enhance the quality of tomatoes, particularly focusing on firmness, shelf life, and adaptations to pre- and post-harvest stresses. Utilizing genetic engineering techniques, such as Clustered Regularly Interspaced Short Palindromic Repeats/CRISPR-associated proteins 9 (CRISPR/Cas9) and Transcription Activator-like Effector Nucleases (TALENs), researchers have made remarkable progress in developing tomatoes with improved traits that address key challenges faced during cultivation, storage, and transportation. We further highlighted the potential of genetic modifications in enhancing tomato firmness, thereby reducing post-harvest losses and improving consumer satisfaction. Furthermore, strategies to extend tomato shelf life through genetic interventions are discussed, emphasizing the importance of maintaining quality and freshness for sustainable food supply chains. Furthermore, the review delves into the ways in which gene-based adaptations can bolster tomatoes against environmental stresses, pests, and diseases, thereby enhancing crop resilience and ensuring stable yields. Emphasizing these crucial facets, this review highlights the essential contribution of genetic advancements in transforming tomato production, elevating quality standards, and promoting the sustainability of tomato cultivation practices.
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Affiliation(s)
- Hongmei Nie
- College of Horticulture, Shanxi Agricultural University, Taigu, Jinzhong 030801, China
| | - Xiu Yang
- College of Horticulture, Shanxi Agricultural University, Taigu, Jinzhong 030801, China
| | - Shaowen Zheng
- College of Horticulture, Shanxi Agricultural University, Taigu, Jinzhong 030801, China
| | - Leiping Hou
- College of Horticulture, Shanxi Agricultural University, Taigu, Jinzhong 030801, China
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10
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Akanmu AO, Asemoloye MD, Marchisio MA, Babalola OO. Adoption of CRISPR-Cas for crop production: present status and future prospects. PeerJ 2024; 12:e17402. [PMID: 38860212 PMCID: PMC11164064 DOI: 10.7717/peerj.17402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Accepted: 04/25/2024] [Indexed: 06/12/2024] Open
Abstract
Background Global food systems in recent years have been impacted by some harsh environmental challenges and excessive anthropogenic activities. The increasing levels of both biotic and abiotic stressors have led to a decline in food production, safety, and quality. This has also contributed to a low crop production rate and difficulty in meeting the requirements of the ever-growing population. Several biotic stresses have developed above natural resistance in crops coupled with alarming contamination rates. In particular, the multiple antibiotic resistance in bacteria and some other plant pathogens has been a hot topic over recent years since the food system is often exposed to contamination at each of the farm-to-fork stages. Therefore, a system that prioritizes the safety, quality, and availability of foods is needed to meet the health and dietary preferences of everyone at every time. Methods This review collected scattered information on food systems and proposes methods for plant disease management. Multiple databases were searched for relevant specialized literature in the field. Particular attention was placed on the genetic methods with special interest in the potentials of the Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) and Cas (CRISPR associated) proteins technology in food systems and security. Results The review reveals the approaches that have been developed to salvage the problem of food insecurity in an attempt to achieve sustainable agriculture. On crop plants, some systems tend towards either enhancing the systemic resistance or engineering resistant varieties against known pathogens. The CRISPR-Cas technology has become a popular tool for engineering desired genes in living organisms. This review discusses its impact and why it should be considered in the sustainable management, availability, and quality of food systems. Some important roles of CRISPR-Cas have been established concerning conventional and earlier genome editing methods for simultaneous modification of different agronomic traits in crops. Conclusion Despite the controversies over the safety of the CRISPR-Cas system, its importance has been evident in the engineering of disease- and drought-resistant crop varieties, the improvement of crop yield, and enhancement of food quality.
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Affiliation(s)
- Akinlolu Olalekan Akanmu
- Food Security and Safety Focus Area, Faculty of Natural and Agricultural Sciences, University of North-West, Mmabatho, South Africa
| | - Michael Dare Asemoloye
- Food Security and Safety Focus Area, Faculty of Natural and Agricultural Sciences, University of North-West, Mmabatho, South Africa
| | | | - Olubukola Oluranti Babalola
- Food Security and Safety Focus Area, Faculty of Natural and Agricultural Sciences, University of North-West, Mmabatho, South Africa
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11
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Gaur VS, Sood S, Guzmán C, Olsen KM. Molecular insights on the origin and development of waxy genotypes in major crop plants. Brief Funct Genomics 2024; 23:193-213. [PMID: 38751352 DOI: 10.1093/bfgp/elad035] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2023] [Revised: 07/21/2023] [Accepted: 07/25/2023] [Indexed: 06/14/2024] Open
Abstract
Starch is a significant ingredient of the seed endosperm with commercial importance in food and industry. Crop varieties with glutinous (waxy) grain characteristics, i.e. starch with high amylopectin and low amylose, hold longstanding cultural importance in some world regions and unique properties for industrial manufacture. The waxy character in many crop species is regulated by a single gene known as GBSSI (or waxy), which encodes the enzyme Granule Bound Starch Synthase1 with null or reduced activity. Several allelic variants of the waxy gene that contribute to varying levels of amylose content have been reported in different crop plants. Phylogenetic analysis of protein sequences and the genomic DNA encoding GBSSI of major cereals and recently sequenced millets and pseudo-cereals have shown that GBSSI orthologs form distinct clusters, each representing a separate crop lineage. With the rapidly increasing demand for waxy starch in food and non-food applications, conventional crop breeding techniques and modern crop improvement technologies such as gene silencing and genome editing have been deployed to develop new waxy crop cultivars. The advances in research on waxy alleles across different crops have unveiled new possibilities for modifying the synthesis of amylose and amylopectin starch, leading to the potential creation of customized crops in the future. This article presents molecular lines of evidence on the emergence of waxy genes in various crops, including their genesis and evolution, molecular structure, comparative analysis and breeding innovations.
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Affiliation(s)
- Vikram S Gaur
- Raja Bhoj College of Agriculture, Balaghat, JNKVV, Jabalpur, Madhya Pradesh, India
| | - Salej Sood
- ICAR-Central Potato Research Institute, Shimla- 171001, Himachal Pradesh, India
| | - Carlos Guzmán
- Departamento de Genética, Escuela Técnica Superior de Ingeniería Agronómica y de Montes, Edificio Gregor Mendel, Campus de Rabanales, Universidad de Córdoba, CeiA3, ES-14071, Córdoba, Spain
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12
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Jayarathna S, Hofvander P, Péter-Szabó Z, Andersson M, Andersson R. GBSS mutations in an SBE mutated background restore the potato starch granule morphology and produce ordered granules despite differences to native molecular structure. Carbohydr Polym 2024; 331:121860. [PMID: 38388056 DOI: 10.1016/j.carbpol.2024.121860] [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: 10/08/2023] [Revised: 01/10/2024] [Accepted: 01/22/2024] [Indexed: 02/24/2024]
Abstract
Potato starch with mutations in starch branching enzyme genes (SBEI, SBEII) and granule-bound starch synthase gene (GBSS) was characterized for molecular and thermal properties. Mutations in GBSS were here stacked to a previously developed SBEI and SBEII mutation line. Additionally, mutations in the GBSS gene alone were induced in the wild-type variety for comparison. The parental line with mutations in the SBE genes showed a ∼ 40 % increase in amylose content compared with the wild-type. Mutations in GBSS-SBEI-SBEII produced non-waxy, low-amylose lines compared with the wild-type. An exception was a line with one remaining GBSS wild-type allele, which displayed ∼80 % higher amylose content than wild-type. Stacked mutations in GBSS in the SBEI-SBEII parental line caused alterations in amylopectin chain length distribution and building block size categories of whole starch. Correlations between size categories of building blocks and unit chains of amylopectin were observed. Starch in GBSS-SBEI-SBEII mutational lines had elevated peak temperature of gelatinization, which was positively correlated with large building blocks.
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Affiliation(s)
- Shishanthi Jayarathna
- Department of Molecular Sciences, BioCenter, Swedish University of Agricultural Sciences, P.O. Box 7015, SE-750 07 Uppsala, Sweden.
| | - Per Hofvander
- Department of Plant Breeding, Swedish University of Agricultural Sciences, P.O. Box 190, SE-23422 Lomma, Sweden
| | - Zsuzsanna Péter-Szabó
- Division of Glycoscience, Department of Chemistry, KTH-Royal Institute of Technology, SE-10621 Stockholm, Sweden
| | - Mariette Andersson
- Department of Plant Breeding, Swedish University of Agricultural Sciences, P.O. Box 190, SE-23422 Lomma, Sweden
| | - Roger Andersson
- Department of Molecular Sciences, BioCenter, Swedish University of Agricultural Sciences, P.O. Box 7015, SE-750 07 Uppsala, Sweden
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13
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Shirani-Bidabadi M, Nazarian-Firouzabadi F, Sorkheh K, Ismaili A. Transcriptomic analysis of potato (Solanum tuberosum L.) tuber development reveals new insights into starch biosynthesis. PLoS One 2024; 19:e0297334. [PMID: 38574179 PMCID: PMC10994339 DOI: 10.1371/journal.pone.0297334] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Accepted: 01/03/2024] [Indexed: 04/06/2024] Open
Abstract
Potato tubers are rich sources of various nutrients and unique sources of starch. Many genes play major roles in different pathways, including carbohydrate metabolism during the potato tuber's life cycle. Despite substantial scientific evidence about the physiological and morphological development of potato tubers, the molecular genetic aspects of mechanisms underlying tuber formation have not yet been fully understood. In this study, for the first time, RNA-seq analysis was performed to shed light on the expression of genes involved in starch biosynthesis during potato tuber development. To this end, samples were collected at the hook-like stolon (Stage I), swollen tips stolon (Stage II), and tuber initiation (Stage III) stages of tuber formation. Overall, 23 GB of raw data were generated and assembled. There were more than 20000 differentially expressed genes (DEGs); the expression of 73 genes involved in starch metabolism was further studied. Moreover, qRT-PCR analysis revealed that the expression profile of the starch biosynthesis DEGs was consistent with that of the RNA-seq data, which further supported the role of the DEGs in starch biosynthesis. This study provides substantial resources on potato tuber development and several starch synthesis isoforms associated with starch biosynthesis.
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Affiliation(s)
- Maryam Shirani-Bidabadi
- Production Engineering and Plant Genetics Department, Faculty of Agriculture, Lorestan University, Khorramabad, Iran
| | - Farhad Nazarian-Firouzabadi
- Production Engineering and Plant Genetics Department, Faculty of Agriculture, Lorestan University, Khorramabad, Iran
| | - Karim Sorkheh
- Production Engineering and Plant Genetics Department, Faculty of Agriculture, Shahid Chamran University of Ahvaz, Ahvaz, Iran
| | - Ahmad Ismaili
- Production Engineering and Plant Genetics Department, Faculty of Agriculture, Lorestan University, Khorramabad, Iran
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14
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Mishra A, Pandey VP. CRISPR/Cas system: A revolutionary tool for crop improvement. Biotechnol J 2024; 19:e2300298. [PMID: 38403466 DOI: 10.1002/biot.202300298] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Revised: 12/01/2023] [Accepted: 12/22/2023] [Indexed: 02/27/2024]
Abstract
World's population is elevating at an alarming rate thus, the rising demands of producing crops with better adaptability to biotic and abiotic stresses, superior nutritional as well as morphological qualities, and generation of high-yielding varieties have led to encourage the development of new plant breeding technologies. The availability and easy accessibility of genome sequences for a number of crop plants as well as the development of various genome editing technologies such as zinc finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs) has opened up possibilities to develop new varieties of crop plants with superior desirable traits. However, these approaches has limitation of being more expensive as well as having complex steps and time-consuming. The CRISPR/Cas genome editing system has been intensively studied for allowing versatile target-specific modifications of crop genome that fruitfully aid in the generation of novel varieties. It is an advanced and promising technology with the potential to meet hunger needs and contribute to food production for the ever-growing human population. This review summarizes the usage of novel CRISPR/Cas genome editing tool for targeted crop improvement in stress resistance, yield, quality and nutritional traits in the desired crop plants.
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Affiliation(s)
- Ayushi Mishra
- Department of Biochemistry, University of Lucknow, Lucknow, India
| | - Veda P Pandey
- Department of Biochemistry, University of Lucknow, Lucknow, India
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15
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Kusano H, Takeuchi A, Shimada H. Efficiency of potato genome editing: Targeted mutation on the genes involved in starch biosynthesis using the CRISPR/dMac3-Cas9 system. PLANT BIOTECHNOLOGY (TOKYO, JAPAN) 2023; 40:201-209. [PMID: 38420566 PMCID: PMC10901159 DOI: 10.5511/plantbiotechnology.23.0611a] [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: 03/29/2023] [Accepted: 06/11/2023] [Indexed: 03/02/2024]
Abstract
Potato (Solanum tuberosum L.) has a tetraploid genome. To make a mutant lacking a specific gene function, it is necessary to introduce mutations into all four gene alleles. To achieve this goal, we developed a powerful genome editing tool, CRISPR/dMac3-Cas9, which installed the translation enhancer dMac3 that greatly increased the translation of the downstream open reading frame. The CRISPR/dMac3-Cas9 system employing three guide RNAs (gRNAs) greatly elevated the frequency of the generation rate of mutation. This system enabled to create the 4-allele mutants of granule-bound starch synthase (GBSS) and starch branching enzyme (SBE). These mutants indicated functionally defective features, suggesting that we succeeded in efficient genome editing of the potato tetraploid genome. Here, we show the effect of the number of gRNAs for efficient mutagenesis of the target gene using the mutants of the GBSS1 gene. CRISPR/dMac3-Cas9 employing three gRNA genes achieved a higher mutation efficiency than the CRISPR/dMac3-Cas9 with two gRNAs, suggesting being influenced by the dose effect of the number of gRNAs at the target region. The alleles of the SBE3 gene contained SNPs that caused sequence differences in the gRNAs but these gRNAs functioned efficiently. However, many rearrangement events and large deletions were induced. These results support the importance of accurate binding of gRNA to the target sequence, which may lead to a hint to avoid the unexpected mutation on the off-target sites.
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Affiliation(s)
- Hiroaki Kusano
- Laboratory of Plant Gene Expression, Research Institute for Sustainable Humanosphere, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Ami Takeuchi
- Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba 277-8562, Japan
| | - Hiroaki Shimada
- Department of Biological Science and Technology, Tokyo University of Science,Tokyo 125-8585, Japan
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16
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Zhang H, Li X, Yu D, Guan J, Ding H, Wu H, Wang Q, Wan Y. A vector-free gene interference system using delaminated Mg-Al-lactate layered double hydroxide nanosheets as molecular carriers to intact plant cells. PLANT METHODS 2023; 19:44. [PMID: 37158914 PMCID: PMC10165820 DOI: 10.1186/s13007-023-01021-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Accepted: 05/01/2023] [Indexed: 05/10/2023]
Abstract
BACKGROUND The Mg-Al-lactate layered double hydroxide nanosheet (LDH-NS) has shown great potential as an optimal nanocarrier for extensive use in plants. However, previous studies in plant sciences have not provided a clear description of the application for the LDH-NSs-based double-stranded RNA (dsRNA) delivery (LDH-dsRNA) system in different tissues of both model and non-model species. RESULTS LDH-NSs were synthesized by using the co-precipitation method, while the dsRNAs targeting genes of interest were prepared in vitro using T7 RNA polymerase. The LDH-dsRNA bioconjugates with a neutral charge were produced by incubating with the mass ratio of LDH-NSs to dsRNA at 3:1, which were then introduced into intact plant cells using three different approaches, including injection, spray, and soak. The LDH-dsRNA delivery method was optimized by inhibiting the expression of the Arabidopsis thaliana ACTIN2 gene. As a result, soaking A. thaliana seedlings in a medium containing LDH-dsRNA for 30 min led to the silencing of 80% of the target genes. The stability and effectiveness of the LDH-dsRNA system were further confirmed by the high-efficiency knockdown of plant tissue-specific genes, including that encoding phytoene desaturase (PDS), WUSCHEL (WUS), WUSCHEL-related homeobox 5 (WOX5), and ROOT HAIR DEFECTIVE 6 (RHD6). In addition, the LDH-dsRNA system was employed in cassava, where it was found that the expression of the gene encoding nucleotide-binding site and leucine-rich repeat (NBS-LRR) was significantly reduced. As a result, the resistance of cassava leaves to pathogens was weakened. Noteworthy, the injection of LDH-dsRNA into leaves resulted in a significant downregulation of target genes in both stems and flowers, indicating the successful transport of LDH-dsRNA from leaves to other parts of plants. CONCLUSIONS LDH-NSs have proven to be a highly effective molecular tool for delivering dsRNA into intact plant cells, enabling accurate control of target gene expression.
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Affiliation(s)
- He Zhang
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Tropical Crops, Hainan University, Haikou, 570228, China
- Key Laboratory of Integrated Pest Management On Tropical Crops, Ministry of Agriculture and Rural Affairs, Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, China
| | - Xinyu Li
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Tropical Crops, Hainan University, Haikou, 570228, China
| | - Dong Yu
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Tropical Crops, Hainan University, Haikou, 570228, China
| | - Junqi Guan
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Tropical Crops, Hainan University, Haikou, 570228, China
| | - Hao Ding
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Tropical Crops, Hainan University, Haikou, 570228, China
| | - Hongyang Wu
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Qiang Wang
- College of Environmental Science and Engineering, Beijing Forestry University, 35 Qinghua East Road, Haidian District, Beijing, 100083, China
| | - Yinglang Wan
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Tropical Crops, Hainan University, Haikou, 570228, China.
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17
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Pfotenhauer AC, Occhialini A, Harbison SA, Li L, Piatek AA, Luckett CR, Yang Y, Stewart CN, Lenaghan SC. Genome-Editing of FtsZ1 for Alteration of Starch Granule Size in Potato Tubers. PLANTS (BASEL, SWITZERLAND) 2023; 12:plants12091878. [PMID: 37176936 PMCID: PMC10180631 DOI: 10.3390/plants12091878] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 04/06/2023] [Accepted: 04/25/2023] [Indexed: 05/15/2023]
Abstract
Genome-editing has enabled rapid improvement for staple food crops, such as potato, a key beneficiary of the technology. In potato, starch contained within tubers represents the primary product for use in food and non-food industries. Starch granules are produced in the plastids of tubers with plastid size correlated with the size of starch grana. The division of plastids is controlled by proteins, including the tubulin-like GTPase FtsZ1. The altered expression of FtsZ1 has been shown to disrupt plastid division, leading to the production of "macro-plastid"-containing plants. These macro-chloroplast plants are characterized by cells containing fewer and enlarged plastids. In this work, we utilize CRISPR/Cas9 to generate FtsZ1 edited potato lines to demonstrate that genome-editing can be used to increase the size of starch granules in tubers. Altered plastid morphology was comparable to the overexpression of FtsZ1 in previous work in potato and other crops. Several lines were generated with up to a 1.98-fold increase in starch granule size that was otherwise phenotypically indistinguishable from wild-type plants. Further, starch paste from one of the most promising lines showed a 2.07-fold increase in final viscosity. The advantages of enlarged starch granules and the potential of CRISPR/Cas9-based technologies for food crop improvement are further discussed.
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Affiliation(s)
- Alexander C Pfotenhauer
- Center for Agricultural Synthetic Biology (CASB), University of Tennessee, Knoxville, TN 37996, USA
| | - Alessandro Occhialini
- Center for Agricultural Synthetic Biology (CASB), University of Tennessee, Knoxville, TN 37996, USA
- Department of Plant Sciences, University of Tennessee, Knoxville, TN 37920, USA
| | - Stacee A Harbison
- Center for Agricultural Synthetic Biology (CASB), University of Tennessee, Knoxville, TN 37996, USA
| | - Li Li
- Center for Agricultural Synthetic Biology (CASB), University of Tennessee, Knoxville, TN 37996, USA
| | - Agnieszka A Piatek
- Department of Food Science, University of Tennessee, Knoxville, TN 37920, USA
| | - Curtis R Luckett
- Department of Plant Sciences, University of Tennessee, Knoxville, TN 37920, USA
| | - Yongil Yang
- Center for Agricultural Synthetic Biology (CASB), University of Tennessee, Knoxville, TN 37996, USA
| | - C Neal Stewart
- Center for Agricultural Synthetic Biology (CASB), University of Tennessee, Knoxville, TN 37996, USA
- Department of Plant Sciences, University of Tennessee, Knoxville, TN 37920, USA
| | - Scott C Lenaghan
- Center for Agricultural Synthetic Biology (CASB), University of Tennessee, Knoxville, TN 37996, USA
- Department of Food Science, University of Tennessee, Knoxville, TN 37920, USA
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18
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Ahn-Jarvis JH, Sosh D, Lombardo E, Lesinski GB, Conwell DL, Hart PA, Vodovotz Y. Short-Term Soy Bread Intervention Leads to a Dose-Response Increase in Urinary Isoflavone Metabolites and Satiety in Chronic Pancreatitis. Foods 2023; 12:foods12091762. [PMID: 37174299 PMCID: PMC10178207 DOI: 10.3390/foods12091762] [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: 03/01/2023] [Revised: 04/19/2023] [Accepted: 04/22/2023] [Indexed: 05/15/2023] Open
Abstract
Patients with chronic pancreatitis (CP) are particularly vulnerable to nutrient malabsorption and undernutrition caused by the underlying pathology of their disease. Dietary intervention trials involving soy isoflavones in patients with CP are limited and isoflavone metabolites have not yet been reported. We hypothesized soy bread containing plant-based protein, dietary fiber, and isoflavones would be well-tolerated and restore gut functional capacity which would lead to isoflavone metabolites profiles like those of healthy populations. Participants (n = 9) received 1 week of soy bread in a dose-escalation design (1 to 3 slices/day) or a 4-week maximally tolerated dose (n = 1). Dietary adherence, satiety, and palatability were measured. Isoflavone metabolites from 24 h urine collections were quantified using high-performance liquid chromatography. A maximum dose of three slices (99 mg of isoflavones) of soy bread per day was achieved. Short-term exposure to soy bread showed a significant dose-response increase (p = 0.007) of total isoflavones and their metabolites in urine. With increasing slices of soy bread, dietary animal protein intake (p = 0.009) and perceived thirst (p < 0.001) significantly decreased with prolonged satiety (p < 0.001). In this study, adherence to short-term intervention with soy bread in CP patients was excellent. Soy isoflavones were reliably delivered. These findings provide the foundation for evaluating a well-characterized soy bread in supporting healthy nutrition and gut function in CP.
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Affiliation(s)
- Jennifer H Ahn-Jarvis
- College of Food, Agricultural, and Environmental Sciences, Department of Food Science and Technology, The Ohio State University, Columbus, OH 43210, USA
| | - Daniel Sosh
- College of Food, Agricultural, and Environmental Sciences, Department of Food Science and Technology, The Ohio State University, Columbus, OH 43210, USA
| | - Erin Lombardo
- College of Public Health, The Ohio State University, Columbus, OH 43210, USA
| | - Gregory B Lesinski
- Division of Gastroenterology, Hepatology and Nutrition, The Ohio State University Wexner Medical Center, Columbus, OH 43210, USA
| | - Darwin L Conwell
- Division of Gastroenterology, Hepatology and Nutrition, The Ohio State University Wexner Medical Center, Columbus, OH 43210, USA
| | - Phil A Hart
- Division of Gastroenterology, Hepatology and Nutrition, The Ohio State University Wexner Medical Center, Columbus, OH 43210, USA
| | - Yael Vodovotz
- College of Food, Agricultural, and Environmental Sciences, Department of Food Science and Technology, The Ohio State University, Columbus, OH 43210, USA
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19
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Hemalatha P, Abda EM, Shah S, Venkatesa Prabhu S, Jayakumar M, Karmegam N, Kim W, Govarthanan M. Multi-faceted CRISPR-Cas9 strategy to reduce plant based food loss and waste for sustainable bio-economy - A review. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2023; 332:117382. [PMID: 36753844 DOI: 10.1016/j.jenvman.2023.117382] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 01/14/2023] [Accepted: 01/25/2023] [Indexed: 06/18/2023]
Abstract
Currently, international development requires innovative solutions to address imminent challenges like climate change, unsustainable food system, food waste, energy crisis, and environmental degradation. All the same, addressing these concerns with conventional technologies is time-consuming, causes harmful environmental impacts, and is not cost-effective. Thus, biotechnological tools become imperative for enhancing food and energy resilience through eco-friendly bio-based products by valorisation of plant and food waste to meet the goals of circular bioeconomy in conjunction with Sustainable Developmental Goals (SDGs). Genome editing can be accomplished using a revolutionary DNA modification tool, CRISPR-Cas9, through its uncomplicated guided mechanism, with great efficiency in various organisms targeting different traits. This review's main objective is to examine how the CRISPR-Cas system, which has positive features, could improve the bioeconomy by reducing food loss and waste with all-inclusive food supply chain both at on-farm and off-farm level; utilising food loss and waste by genome edited microorganisms through food valorisation; efficient microbial conversion of low-cost substrates as biofuel; valorisation of agro-industrial wastes; mitigating greenhouse gas emissions through forestry plantation crops; and protecting the ecosystem and environment. Finally, the ethical implications and regulatory issues that are related to CRISPR-Cas edited products in the international markets have also been taken into consideration.
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Affiliation(s)
- Palanivel Hemalatha
- Department of Biotechnology, Center of Excellence for Biotechnology and Bioprocess, College of Biological and Chemical Engineering, Addis Ababa Science and Technology University, PO Box 16417, Addis Ababa, Ethiopia
| | - Ebrahim M Abda
- Department of Biotechnology, Center of Excellence for Biotechnology and Bioprocess, College of Biological and Chemical Engineering, Addis Ababa Science and Technology University, PO Box 16417, Addis Ababa, Ethiopia
| | - Shipra Shah
- Department of Forestry, College of Agriculture, Fisheries and Forestry, Fiji National University, Kings Road, Koronivia, P. O. Box 1544, Nausori, Republic of Fiji
| | - S Venkatesa Prabhu
- Department of Chemical Engineering, Center of Excellence for Biotechnology and Bioprocess, College of Biological and Chemical Engineering, Addis Ababa Science and Technology University, PO Box 16417, Addis Ababa, Ethiopia
| | - M Jayakumar
- Department of Chemical Engineering, Haramaya Institute of Technology, Haramaya University, P.O. Box 138, Dire Dawa, Ethiopia.
| | - N Karmegam
- PG and Research Department of Botany, Government Arts College (Autonomous), Salem, 636 007, Tamil Nadu, India
| | - Woong Kim
- Department of Environmental Engineering, Kyungpook National University, Daegu, 41566, Republic of Korea
| | - M Govarthanan
- Department of Environmental Engineering, Kyungpook National University, Daegu, 41566, Republic of Korea; Department of Biomaterials, Saveetha Dental College and Hospital, Saveetha Institute of Medical and Technical Sciences, Chennai, 600 077, India.
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20
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Tong C, Ma Z, Chen H, Gao H. Toward an understanding of potato starch structure, function, biosynthesis, and applications. FOOD FRONTIERS 2023. [DOI: 10.1002/fft2.223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/29/2023] Open
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21
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Ravikiran KT, Thribhuvan R, Sheoran S, Kumar S, Kushwaha AK, Vineeth TV, Saini M. Tailoring crops with superior product quality through genome editing: an update. PLANTA 2023; 257:86. [PMID: 36949234 DOI: 10.1007/s00425-023-04112-4] [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: 09/06/2022] [Accepted: 02/28/2023] [Indexed: 06/18/2023]
Abstract
In this review, using genome editing, the quality trait alterations in important crops have been discussed, along with the challenges encountered to maintain the crop products' quality. The delivery of economic produce with superior quality is as important as high yield since it dictates consumer's acceptance and end use. Improving product quality of various agricultural and horticultural crops is one of the important targets of plant breeders across the globe. Significant achievements have been made in various crops using conventional plant breeding approaches, albeit, at a slower rate. To keep pace with ever-changing consumer tastes and preferences and industry demands, such efforts must be supplemented with biotechnological tools. Fortunately, many of the quality attributes are resultant of well-understood biochemical pathways with characterized genes encoding enzymes at each step. Targeted mutagenesis and transgene transfer have been instrumental in bringing out desired qualitative changes in crops but have suffered from various pitfalls. Genome editing, a technique for methodical and site-specific modification of genes, has revolutionized trait manipulation. With the evolution of versatile and cost effective CRISPR/Cas9 system, genome editing has gained significant traction and is being applied in several crops. The availability of whole genome sequences with the advent of next generation sequencing (NGS) technologies further enhanced the precision of these techniques. CRISPR/Cas9 system has also been utilized for desirable modifications in quality attributes of various crops such as rice, wheat, maize, barley, potato, tomato, etc. The present review summarizes salient findings and achievements of application of genome editing for improving product quality in various crops coupled with pointers for future research endeavors.
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Affiliation(s)
- K T Ravikiran
- ICAR-Central Soil Salinity Research Institute, Regional Research Station, Lucknow, Uttar Pradesh, India
| | - R Thribhuvan
- ICAR-Central Research Institute for Jute and Allied Fibres, Barrackpore, West Bengal, India
| | - Seema Sheoran
- ICAR-Indian Agricultural Research Institute, Regional Station, Karnal, Haryana, India.
| | - Sandeep Kumar
- ICAR-Indian Institute of Natural Resins and Gums, Ranchi, Jharkhand, India
| | - Amar Kant Kushwaha
- ICAR-Central Institute for Subtropical Horticulture, Lucknow, Uttar Pradesh, India
| | - T V Vineeth
- ICAR-Central Soil Salinity Research Institute, Regional Research Station, Bharuch, Gujarat, India
- Department of Plant Physiology, College of Agriculture, Kerala Agricultural University, Vellanikkara, Thrissur, Kerala, India
| | - Manisha Saini
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, India
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22
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Hou X, Guo X, Zhang Y, Zhang Q. CRISPR/Cas genome editing system and its application in potato. Front Genet 2023; 14:1017388. [PMID: 36861125 PMCID: PMC9968925 DOI: 10.3389/fgene.2023.1017388] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Accepted: 01/23/2023] [Indexed: 02/17/2023] Open
Abstract
Potato is the largest non-cereal food crop worldwide and a vital substitute for cereal crops, considering its high yield and great nutritive value. It plays an important role in food security. The CRISPR/Cas (clustered regularly interspaced short palindromic repeats/CRISPR-associated) system has the advantages of easy operation, high efficiency, and low cost, which shows a potential in potato breeding. In this paper, the action mechanism and derivative types of the CRISPR/Cas system and the application of the CRISPR/Cas system in improving the quality and resistance of potatoes, as well as overcoming the self-incompatibility of potatoes, are reviewed in detail. At the same time, the application of the CRISPR/Cas system in the future development of the potato industry was analyzed and prospected.
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Affiliation(s)
- Xin Hou
- College of Plant Protection, Shandong Agricultural University, Tai’an, China
| | - Xiaomeng Guo
- College of Plant Protection, Shandong Agricultural University, Tai’an, China
| | - Yan Zhang
- *Correspondence: Yan Zhang, ; Qiang Zhang,
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23
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Verma V, Kumar A, Partap M, Thakur M, Bhargava B. CRISPR-Cas: A robust technology for enhancing consumer-preferred commercial traits in crops. FRONTIERS IN PLANT SCIENCE 2023; 14:1122940. [PMID: 36824195 PMCID: PMC9941649 DOI: 10.3389/fpls.2023.1122940] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Accepted: 01/16/2023] [Indexed: 06/18/2023]
Abstract
The acceptance of new crop varieties by consumers is contingent on the presence of consumer-preferred traits, which include sensory attributes, nutritional value, industrial products and bioactive compounds production. Recent developments in genome editing technologies provide novel insight to identify gene functions and improve the various qualitative and quantitative traits of commercial importance in plants. Various conventional as well as advanced gene-mutagenesis techniques such as physical and chemical mutagenesis, CRISPR-Cas9, Cas12 and base editors are used for the trait improvement in crops. To meet consumer demand, breakthrough biotechnologies, especially CRISPR-Cas have received a fair share of scientific and industrial interest, particularly in plant genome editing. CRISPR-Cas is a versatile tool that can be used to knock out, replace and knock-in the desired gene fragments at targeted locations in the genome, resulting in heritable mutations of interest. This review highlights the existing literature and recent developments in CRISPR-Cas technologies (base editing, prime editing, multiplex gene editing, epigenome editing, gene delivery methods) for reliable and precise gene editing in plants. This review also discusses the potential of gene editing exhibited in crops for the improvement of consumer-demanded traits such as higher nutritional value, colour, texture, aroma/flavour, and production of industrial products such as biofuel, fibre, rubber and pharmaceuticals. In addition, the bottlenecks and challenges associated with gene editing system, such as off targeting, ploidy level and the ability to edit organelle genome have also been discussed.
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Affiliation(s)
- Vipasha Verma
- Floriculture Laboratory, Agrotechnology Division, Council of Scientific and Industrial Research (CSIR) –Institute of Himalayan Bioresource Technology (IHBT), Palampur, India
| | - Akhil Kumar
- Floriculture Laboratory, Agrotechnology Division, Council of Scientific and Industrial Research (CSIR) –Institute of Himalayan Bioresource Technology (IHBT), Palampur, India
| | - Mahinder Partap
- Floriculture Laboratory, Agrotechnology Division, Council of Scientific and Industrial Research (CSIR) –Institute of Himalayan Bioresource Technology (IHBT), Palampur, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, India
| | - Meenakshi Thakur
- Floriculture Laboratory, Agrotechnology Division, Council of Scientific and Industrial Research (CSIR) –Institute of Himalayan Bioresource Technology (IHBT), Palampur, India
| | - Bhavya Bhargava
- Floriculture Laboratory, Agrotechnology Division, Council of Scientific and Industrial Research (CSIR) –Institute of Himalayan Bioresource Technology (IHBT), Palampur, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, India
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Ly DNP, Iqbal S, Fosu-Nyarko J, Milroy S, Jones MGK. Multiplex CRISPR-Cas9 Gene-Editing Can Deliver Potato Cultivars with Reduced Browning and Acrylamide. PLANTS (BASEL, SWITZERLAND) 2023; 12:plants12020379. [PMID: 36679094 PMCID: PMC9864857 DOI: 10.3390/plants12020379] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 12/19/2022] [Accepted: 01/10/2023] [Indexed: 05/14/2023]
Abstract
Storing potato tubers at cold temperatures, either for transport or continuity of supply, is associated with the conversion of sucrose to reducing sugars. When cold-stored cut tubers are processed at high temperatures, with endogenous asparagine, acrylamide is formed. Acrylamide is classified as a carcinogen. Potato processors prefer cultivars which accumulate fewer reducing sugars and thus less acrylamide on processing, and suitable processing cultivars may not be available. We used CRISPR-Cas9 to disrupt the genes encoding vacuolar invertase (VInv) and asparagine synthetase 1 (AS1) of cultivars Atlantic and Desiree to reduce the accumulation of reducing sugars and the production of asparagine after cold storage. Three of the four guide RNAs employed induced mutation frequencies of 17-98%, which resulted in deletions, insertions and substitutions at the targeted gene sites. Eight of ten edited events had mutations in at least one allele of both genes; for two, only the VInv was edited. No wild-type allele was detected in both genes of events DSpco7, DSpFN4 and DSpco12, suggesting full allelic mutations. Tubers of two Atlantic and two Desiree events had reduced fructose and glucose concentrations after cold storage. Crisps from these and four other Desiree events were lighter in colour and included those with 85% less acrylamide. These results demonstrate that multiplex CRISPR-Cas9 technology can generate improved potato cultivars for healthier processed potato products.
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Affiliation(s)
- Diem Nguyen Phuoc Ly
- Crop Biotechnology Research Group, School of Agricultural Sciences, College of Environmental and Life Sciences, Murdoch University, Perth, WA 6150, Australia
- State Agricultural Biotechnology Centre, Centre for Crop and Food Innovation, Food Futures Institute, Murdoch University, Perth, WA 6150, Australia
| | - Sadia Iqbal
- Crop Biotechnology Research Group, School of Agricultural Sciences, College of Environmental and Life Sciences, Murdoch University, Perth, WA 6150, Australia
- State Agricultural Biotechnology Centre, Centre for Crop and Food Innovation, Food Futures Institute, Murdoch University, Perth, WA 6150, Australia
- Correspondence: (S.I.); (J.F.-N.); (M.G.K.J.)
| | - John Fosu-Nyarko
- Crop Biotechnology Research Group, School of Agricultural Sciences, College of Environmental and Life Sciences, Murdoch University, Perth, WA 6150, Australia
- State Agricultural Biotechnology Centre, Centre for Crop and Food Innovation, Food Futures Institute, Murdoch University, Perth, WA 6150, Australia
- Correspondence: (S.I.); (J.F.-N.); (M.G.K.J.)
| | - Stephen Milroy
- Crop Biotechnology Research Group, School of Agricultural Sciences, College of Environmental and Life Sciences, Murdoch University, Perth, WA 6150, Australia
- Potato Research Western Australia, Murdoch University, Perth, WA 6150, Australia
| | - Michael G. K. Jones
- Crop Biotechnology Research Group, School of Agricultural Sciences, College of Environmental and Life Sciences, Murdoch University, Perth, WA 6150, Australia
- State Agricultural Biotechnology Centre, Centre for Crop and Food Innovation, Food Futures Institute, Murdoch University, Perth, WA 6150, Australia
- Potato Research Western Australia, Murdoch University, Perth, WA 6150, Australia
- Correspondence: (S.I.); (J.F.-N.); (M.G.K.J.)
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González MN, Massa GA, Andersson M, Storani L, Olsson N, Décima Oneto CA, Hofvander P, Feingold SE. CRISPR/Cas9 Technology for Potato Functional Genomics and Breeding. Methods Mol Biol 2023; 2653:333-361. [PMID: 36995636 DOI: 10.1007/978-1-0716-3131-7_21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/31/2023]
Abstract
Cultivated potato (Solanum tuberosum L.) is one of the most important staple food crops worldwide. Its tetraploid and highly heterozygous nature poses a great challenge to its basic research and trait improvement through traditional mutagenesis and/or crossbreeding. The establishment of the clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated protein 9 (Cas9) as a gene editing tool has allowed the alteration of specific gene sequences and their concomitant gene function, providing powerful technology for potato gene functional analysis and improvement of elite cultivars. This technology relies on a short RNA molecule called single guide RNA (sgRNA) that directs the Cas9 nuclease to induce a site-specific double-stranded break (DSB). Further, repair of the DSB by the error-prone non-homologous end joining (NHEJ) mechanism leads to the introduction of targeted mutations, which can be used to produce the loss of function of specific gene(s). In this chapter, we describe experimental procedures to apply the CRISPR/Cas9 technology for potato genome editing. First, we provide strategies for target selection and sgRNA design and describe a Golden Gate-based cloning system to obtain a sgRNA/Cas9-encoding binary vector. We also describe an optimized protocol for ribonucleoprotein (RNP) complex assembly. The binary vector can be used for both Agrobacterium-mediated transformation and transient expression in potato protoplasts, while the RNP complexes are intended to obtain edited potato lines through protoplast transfection and plant regeneration. Finally, we describe procedures to identify the gene-edited potato lines. The methods described here are suitable for potato gene functional analysis and breeding.
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Affiliation(s)
- Matías Nicolás González
- Laboratorio de Agrobiotecnología, IPADS (INTA - CONICET), Balcarce, Argentina.
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina.
| | - Gabriela Alejandra Massa
- Laboratorio de Agrobiotecnología, IPADS (INTA - CONICET), Balcarce, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
- Facultad de Ciencias Agrarias, Universidad Nacional de Mar del Plata, Balcarce, Argentina
| | - Mariette Andersson
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Lomma, Sweden
| | - Leonardo Storani
- Laboratorio de Agrobiotecnología, IPADS (INTA - CONICET), Balcarce, Argentina
- Agencia Nacional de Promoción Científica y Tecnológica, Buenos Aires, Argentina
| | - Niklas Olsson
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Lomma, Sweden
| | - Cecilia Andrea Décima Oneto
- Laboratorio de Agrobiotecnología, IPADS (INTA - CONICET), Balcarce, Argentina
- Facultad de Ciencias Agrarias, Universidad Nacional de Mar del Plata, Balcarce, Argentina
| | - Per Hofvander
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Lomma, Sweden
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Chincinska IA, Miklaszewska M, Sołtys-Kalina D. Recent advances and challenges in potato improvement using CRISPR/Cas genome editing. PLANTA 2022; 257:25. [PMID: 36562862 PMCID: PMC9789015 DOI: 10.1007/s00425-022-04054-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/10/2022] [Accepted: 12/11/2022] [Indexed: 06/17/2023]
Abstract
MAIN CONCLUSION Genome editing using CRISPR/Cas technology improves the quality of potato as a food crop and enables its use as both a model plant in fundamental research and as a potential biofactory for producing valuable compounds for industrial applications. Potato (Solanum tuberosum L.) plays a significant role in ensuring global food and nutritional security. Tuber yield is negatively affected by biotic and abiotic stresses, and enzymatic browning and cold-induced sweetening significantly contribute to post-harvest quality losses. With the dual challenges of a growing population and a changing climate, potato enhancement is essential for its sustainable production. However, due to several characteristics of potato, including high levels of heterozygosity, tetrasomic inheritance, inbreeding depression, and self-incompatibility of diploid potato, conventional breeding practices are insufficient to achieve substantial trait improvement in tetraploid potato cultivars within a relatively short time. CRISPR/Cas-mediated genome editing has opened new possibilities to develop novel potato varieties with high commercialization potential. In this review, we summarize recent developments in optimizing CRISPR/Cas-based methods for potato genome editing, focusing on approaches addressing the challenging biology of this species. We also discuss the feasibility of obtaining transgene-free genome-edited potato varieties and explore different strategies to improve potato stress resistance, nutritional value, starch composition, and storage and processing characteristics. Altogether, this review provides insight into recent advances, possible bottlenecks, and future research directions in potato genome editing using CRISPR/Cas technology.
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Affiliation(s)
- Izabela Anna Chincinska
- Department of Plant Physiology and Biotechnology, University of Gdańsk, Wita Stwosza 59, 80-308, Gdańsk, Poland.
| | - Magdalena Miklaszewska
- Department of Functional and Evolutionary Ecology, Division of Molecular Systems Biology (MOSYS), Faculty of Life Sciences, University of Vienna, Djerassiplatz 1, 1030, Vienna, Austria
| | - Dorota Sołtys-Kalina
- Plant Breeding and Acclimatization Institute-National Research Institute, Platanowa 19, 05-831, Młochów, Poland
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27
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Tuncel A, Qi Y. CRISPR/Cas mediated genome editing in potato: Past achievements and future directions. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2022; 325:111474. [PMID: 36174801 DOI: 10.1016/j.plantsci.2022.111474] [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: 06/20/2022] [Revised: 08/29/2022] [Accepted: 09/22/2022] [Indexed: 06/16/2023]
Abstract
Genome engineering has been re-shaping plant biotechnology and agriculture. Crop improvement using the recently developed gene editing techniques is now easier, faster, and more precise than ever. Although considered to be a global food security crop, potato has not benefitted enough from diverse collection of these techniques. Unique genetic features of cultivated potatoes such as tetrasomic inheritance, high genomic heterozygosity, and inbreeding depression hamper conventional breeding of this important crop. Therefore, genome editing provides an excellent arsenal of tools for trait improvement in potato. Moreover, using specific transformation protocols, it is possible to engineer transgene free commercial varieties. In this review we first describe the past achievements in potato genome editing and highlight some of the missing aspects of these efforts. Then, we discuss about technical challenges of genome editing in potato and present approaches to overcome these difficulties. Finally, we talk about genome editing applications that have not been explored in potato and point out some of the missing venues in literature.
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Affiliation(s)
- Aytug Tuncel
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD, USA.
| | - Yiping Qi
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD, USA; Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, MD, USA.
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28
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Abdul Aziz M, Brini F, Rouached H, Masmoudi K. Genetically engineered crops for sustainably enhanced food production systems. FRONTIERS IN PLANT SCIENCE 2022; 13:1027828. [PMID: 36426158 PMCID: PMC9680014 DOI: 10.3389/fpls.2022.1027828] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Accepted: 10/18/2022] [Indexed: 06/16/2023]
Abstract
Genetic modification of crops has substantially focused on improving traits for desirable outcomes. It has resulted in the development of crops with enhanced yields, quality, and tolerance to biotic and abiotic stresses. With the advent of introducing favorable traits into crops, biotechnology has created a path for the involvement of genetically modified (GM) crops into sustainable food production systems. Although these plants heralded a new era of crop production, their widespread adoption faces diverse challenges due to concerns about the environment, human health, and moral issues. Mitigating these concerns with scientific investigations is vital. Hence, the purpose of the present review is to discuss the deployment of GM crops and their effects on sustainable food production systems. It provides a comprehensive overview of the cultivation of GM crops and the issues preventing their widespread adoption, with appropriate strategies to overcome them. This review also presents recent tools for genome editing, with a special focus on the CRISPR/Cas9 platform. An outline of the role of crops developed through CRSIPR/Cas9 in achieving sustainable development goals (SDGs) by 2030 is discussed in detail. Some perspectives on the approval of GM crops are also laid out for the new age of sustainability. The advancement in molecular tools through plant genome editing addresses many of the GM crop issues and facilitates their development without incorporating transgenic modifications. It will allow for a higher acceptance rate of GM crops in sustainable agriculture with rapid approval for commercialization. The current genetic modification of crops forecasts to increase productivity and prosperity in sustainable agricultural practices. The right use of GM crops has the potential to offer more benefit than harm, with its ability to alleviate food crises around the world.
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Affiliation(s)
- Mughair Abdul Aziz
- Department of Integrative Agriculture, College of Agriculture and Veterinary Medicine, United Arab Emirates University, Al−Ain, Abu−Dhabi, United Arab Emirates
| | - Faical Brini
- Biotechnology and Plant Improvement Laboratory, Centre of Biotechnology of Sfax, University of Sfax, Sfax, Tunisia
| | - Hatem Rouached
- Michigan State University, Plant and Soil Science Building, East Lansing, MI, United States
| | - Khaled Masmoudi
- Department of Integrative Agriculture, College of Agriculture and Veterinary Medicine, United Arab Emirates University, Al−Ain, Abu−Dhabi, United Arab Emirates
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29
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Nerkar G, Devarumath S, Purankar M, Kumar A, Valarmathi R, Devarumath R, Appunu C. Advances in Crop Breeding Through Precision Genome Editing. Front Genet 2022; 13:880195. [PMID: 35910205 PMCID: PMC9329802 DOI: 10.3389/fgene.2022.880195] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Accepted: 05/02/2022] [Indexed: 11/13/2022] Open
Abstract
The global climate change and unfavourable abiotic and biotic factors are limiting agricultural productivity and therefore intensifying the challenges for crop scientists to meet the rising demand for global food supply. The introduction of applied genetics to agriculture through plant breeding facilitated the development of hybrid varieties with improved crop productivity. However, the development of new varieties with the existing gene pools poses a challenge for crop breeders. Genetic engineering holds the potential to broaden genetic diversity by the introduction of new genes into crops. But the random insertion of foreign DNA into the plant's nuclear genome often leads to transgene silencing. Recent advances in the field of plant breeding include the development of a new breeding technique called genome editing. Genome editing technologies have emerged as powerful tools to precisely modify the crop genomes at specific sites in the genome, which has been the longstanding goal of plant breeders. The precise modification of the target genome, the absence of foreign DNA in the genome-edited plants, and the faster and cheaper method of genome modification are the remarkable features of the genome-editing technology that have resulted in its widespread application in crop breeding in less than a decade. This review focuses on the advances in crop breeding through precision genome editing. This review includes: an overview of the different breeding approaches for crop improvement; genome editing tools and their mechanism of action and application of the most widely used genome editing technology, CRISPR/Cas9, for crop improvement especially for agronomic traits such as disease resistance, abiotic stress tolerance, herbicide tolerance, yield and quality improvement, reduction of anti-nutrients, and improved shelf life; and an update on the regulatory approval of the genome-edited crops. This review also throws a light on development of high-yielding climate-resilient crops through precision genome editing.
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Affiliation(s)
- Gauri Nerkar
- Molecular Biology and Genetic Engineering Laboratory, Vasantdada Sugar Institute, Pune, India
| | - Suman Devarumath
- Vidya Pratishthan's College of Agricultural Biotechnology, Baramati, India
| | - Madhavi Purankar
- Molecular Biology and Genetic Engineering Laboratory, Vasantdada Sugar Institute, Pune, India
| | - Atul Kumar
- Molecular Biology and Genetic Engineering Laboratory, Vasantdada Sugar Institute, Pune, India
| | - R Valarmathi
- ICAR-Sugarcane Breeding Institute, Coimbatore, India
| | - Rachayya Devarumath
- Molecular Biology and Genetic Engineering Laboratory, Vasantdada Sugar Institute, Pune, India
| | - C Appunu
- ICAR-Sugarcane Breeding Institute, Coimbatore, India
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30
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Biswas S, Ibarra O, Shaphek M, Molina-Risco M, Faion-Molina M, Bellinatti-Della Gracia M, Thomson MJ, Septiningsih EM. Increasing the level of resistant starch in 'Presidio' rice through multiplex CRISPR-Cas9 gene editing of starch branching enzyme genes. THE PLANT GENOME 2022:e20225. [PMID: 35713092 DOI: 10.1002/tpg2.20225] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Accepted: 04/15/2022] [Indexed: 06/15/2023]
Abstract
Rice (Oryza sativa L.) is an excellent source of starch, which is composed of amylopectin and amylose. Resistant starch (RS) is a starch product that is not easily digestible and absorbed in the stomach or small intestine and instead is passed on directly to the large intestine. Cereals high in RS may be beneficial to improve human health and reduce the risk of diet-related chronic diseases. It has been reported through chemical mutagenesis and RNA interference studies that starch branching enzymes (SBEs) play a major role in contributing to higher levels of RS in cereal crops. In this study, we used multiplex clustered regularly interspaced short palindromic repeat (CRISPR)-CRISPR associated protein 9 (Cas9) genome editing to simultaneously target all four SBE genes in rice using the endogenous transfer RNA (tRNA)-processing system for expressing the single-guide RNAs (sgRNAs) targeting these genes. The CRISPR-Cas9 vector construct with four SBE gene sgRNAs was transformed into the U.S. rice cultivar Presidio using Agrobacterium-mediated transformation. Knockout mutations were identified at all four SBE genes across eight transgene-positive T0 plants. Transgene-free T1 lines with different combinations of disrupted SBE genes were identified, with several SBE-edited lines showing significantly increased RS content up to 15% higher than the wild-type (WT) cultivar Presidio. Although further efforts are needed to fix all of the mutant alleles as homozygous, our study demonstrated the potential of multiplex genome editing to develop high-RS lines.
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Affiliation(s)
- Sudip Biswas
- Dep. of Soil and Crop Sciences, Texas A&M Univ., College Station, TX, 77843, USA
| | - Oneida Ibarra
- Dep. of Soil and Crop Sciences, Texas A&M Univ., College Station, TX, 77843, USA
- Avance Biosciences Inc., Houston, TX, 77040, USA
| | - Mariam Shaphek
- Dep. of Soil and Crop Sciences, Texas A&M Univ., College Station, TX, 77843, USA
- Dep. of Biochemistry and Biophysics, Texas A&M Univ., College Station, TX, 77843, USA
| | - Marco Molina-Risco
- Dep. of Soil and Crop Sciences, Texas A&M Univ., College Station, TX, 77843, USA
| | - Mayra Faion-Molina
- Dep. of Soil and Crop Sciences, Texas A&M Univ., College Station, TX, 77843, USA
| | | | - Michael J Thomson
- Dep. of Soil and Crop Sciences, Texas A&M Univ., College Station, TX, 77843, USA
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31
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Sergeeva EM, Larichev KT, Salina EA, Kochetov AV. Starch metabolism in potato <i>Solanum tuberosum</i> L. Vavilovskii Zhurnal Genet Selektsii 2022; 26:250-263. [PMID: 35774362 PMCID: PMC9168746 DOI: 10.18699/vjgb-22-32] [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: 10/13/2021] [Revised: 12/20/2021] [Accepted: 12/20/2021] [Indexed: 11/19/2022] Open
Abstract
Starch is a major storage carbohydrate in plants. It is an important source of calories in the human and animal diet. Also, it is widely used in various industries. Native starch consists of water-insoluble semicrystalline granules formed by natural glucose polymers amylose and amylopectin. The physicochemical properties of starch are determined by the amylose:amylopectin ratio in the granule and degrees of their polymerization and phosphorylation. Potato Solanum tuberosum L. is one of the main starch-producing crops. Growing industrial needs necessitate the breeding of plant varieties with increased starch content and specified starch properties. This task demands detailed information on starch metabolism in the producing plant. It is a complex process, requiring the orchestrated work of many enzymes, transporter and targeting proteins, transcription factors, and other regulators. Two types of starch are recognized with regard to their biological functions. Transitory starch is synthesized in chloroplasts of photosynthetic organs and degraded in the absence of light, providing carbohydrates for cell needs. Storage starch is synthesized and stored in amyloplasts of storage organs: grains and tubers. The main enzymatic reactions of starch biosynthesis and degradation, as well as carbohydrate transport and metabolism, are well known in the case of transitory starch of the model plant Arabidopsis thaliana. Less is known about features of starch metabolism in storage organs, in particular, potato tubers. Several issues remain obscure: the roles of enzyme isoforms and different regulatory factors in tissues at various plant developmental stages and under different environmental conditions; alternative enzymatic processes; targeting and transport proteins. In this review, the key enzymatic reactions of plant carbohydrate metabolism, transitory and storage starch biosynthesis,
and starch degradation are discussed, and features specific for potato are outlined. Attention is also paid to the
known regulatory factors affecting starch metabolism
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Affiliation(s)
- E. M. Sergeeva
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences
| | - K. T. Larichev
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences
| | - E. A. Salina
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences
| | - A. V. Kochetov
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences
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32
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The biological feasibility and social context of gene-edited, caffeine-free coffee. Food Sci Biotechnol 2022; 31:635-655. [PMID: 35646415 PMCID: PMC9133285 DOI: 10.1007/s10068-022-01082-3] [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: 08/23/2021] [Revised: 03/23/2022] [Accepted: 04/04/2022] [Indexed: 11/16/2022] Open
Abstract
Coffee, especially the species Coffea arabica and Coffea canephora, is one of the world’s most consumed beverages. The consumer demand for caffeine-free coffee is currently being met through chemical decaffeination processes. However, this method leads to loss of beverage quality. In this review, the feasibility of using gene editing to produce caffeine-free coffee plants is reviewed. The genes XMT (7-methylxanthosine methyltransferase) and DXMT (3,7-dimethylxanthine methyltransferase) were identified as candidate target genes for knocking out caffeine production in coffee plants. The possible effect of the knock-out of the candidate genes was assessed. Using Agrobacterium tumefaciens-mediated introduction of the CRISPR-Cas system to Knock out XMT or DXMT would lead to blocking caffeine biosynthesis. The use of CRISPR-Cas to genetically edit consumer products is not yet widely accepted, which may lead to societal hurdles for introducing gene-edited caffeine-free coffee cultivars onto the market. However, increased acceptance of CRISPR-Cas/gene editing on products with a clear benefit for consumers offers better prospects for gene editing efforts for caffeine-free coffee.
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Mir TUG, Wani AK, Akhtar N, Shukla S. CRISPR/Cas9: Regulations and challenges for law enforcement to combat its dual-use. Forensic Sci Int 2022; 334:111274. [DOI: 10.1016/j.forsciint.2022.111274] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 02/19/2022] [Accepted: 03/13/2022] [Indexed: 12/15/2022]
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Kumari C, Sharma M, Kumar V, Sharma R, Kumar V, Sharma P, Kumar P, Irfan M. Genome Editing Technology for Genetic Amelioration of Fruits and Vegetables for Alleviating Post-Harvest Loss. Bioengineering (Basel) 2022; 9:bioengineering9040176. [PMID: 35447736 PMCID: PMC9028506 DOI: 10.3390/bioengineering9040176] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Revised: 02/02/2022] [Accepted: 04/15/2022] [Indexed: 01/13/2023] Open
Abstract
Food security and crop production are challenged worldwide due to overpopulation, changing environmental conditions, crop establishment failure, and various kinds of post-harvest losses. The demand for high-quality foods with improved nutritional quality is also growing day by day. Therefore, production of high-quality produce and reducing post-harvest losses of produce, particularly of perishable fruits and vegetables, are vital. For many decades, attempts have been made to improve the post-harvest quality traits of horticultural crops. Recently, modern genetic tools such as genome editing emerged as a new approach to manage and overcome post-harvest effectively and efficiently. The different genome editing tools including ZFNs, TALENs, and CRISPR/Cas9 system effectively introduce mutations (In Dels) in many horticultural crops to address and resolve the issues associated with post-harvest storage quality. Henceforth, we provide a broad review of genome editing applications in horticulture crops to improve post-harvest stability traits such as shelf life, texture, and resistance to pathogens without compromising nutritional value. Moreover, major roadblocks, challenges, and their possible solutions for employing genome editing tools are also discussed.
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Affiliation(s)
- Chanchal Kumari
- Department of Biotechnology, Dr. Yashwant Singh Parmar University of Horticulture and Forestry, Solan, Himachal Pradesh 173230, India; (C.K.); (M.S.); (V.K.); (R.S.); (P.K.)
| | - Megha Sharma
- Department of Biotechnology, Dr. Yashwant Singh Parmar University of Horticulture and Forestry, Solan, Himachal Pradesh 173230, India; (C.K.); (M.S.); (V.K.); (R.S.); (P.K.)
| | - Vinay Kumar
- Department of Biotechnology, Dr. Yashwant Singh Parmar University of Horticulture and Forestry, Solan, Himachal Pradesh 173230, India; (C.K.); (M.S.); (V.K.); (R.S.); (P.K.)
| | - Rajnish Sharma
- Department of Biotechnology, Dr. Yashwant Singh Parmar University of Horticulture and Forestry, Solan, Himachal Pradesh 173230, India; (C.K.); (M.S.); (V.K.); (R.S.); (P.K.)
| | - Vinay Kumar
- Department of Physiology and Cell Biology, Department of Internal Medicine, The Ohio State University Wexner Medical Center, Columbus, OH 43210, USA;
| | - Parul Sharma
- Department of Biotechnology, Dr. Yashwant Singh Parmar University of Horticulture and Forestry, Solan, Himachal Pradesh 173230, India; (C.K.); (M.S.); (V.K.); (R.S.); (P.K.)
- Correspondence: (P.S.); (M.I.)
| | - Pankaj Kumar
- Department of Biotechnology, Dr. Yashwant Singh Parmar University of Horticulture and Forestry, Solan, Himachal Pradesh 173230, India; (C.K.); (M.S.); (V.K.); (R.S.); (P.K.)
| | - Mohammad Irfan
- Plant Biology Section, School of Integrative Plant Sciences, Cornell University, Ithaca, NY 14853, USA
- Correspondence: (P.S.); (M.I.)
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35
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Naik BJ, Shimoga G, Kim SC, Manjulatha M, Subramanyam Reddy C, Palem RR, Kumar M, Kim SY, Lee SH. CRISPR/Cas9 and Nanotechnology Pertinence in Agricultural Crop Refinement. FRONTIERS IN PLANT SCIENCE 2022; 13:843575. [PMID: 35463432 PMCID: PMC9024397 DOI: 10.3389/fpls.2022.843575] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/26/2021] [Accepted: 02/07/2022] [Indexed: 05/08/2023]
Abstract
The CRISPR/Cas9 (Clustered Regularly Interspaced Short Palindromic Repeats/CRISPR-associated protein 9) method is a versatile technique that can be applied in crop refinement. Currently, the main reasons for declining agricultural yield are global warming, low rainfall, biotic and abiotic stresses, in addition to soil fertility issues caused by the use of harmful chemicals as fertilizers/additives. The declining yields can lead to inadequate supply of nutritional food as per global demand. Grains and horticultural crops including fruits, vegetables, and ornamental plants are crucial in sustaining human life. Genomic editing using CRISPR/Cas9 and nanotechnology has numerous advantages in crop development. Improving crop production using transgenic-free CRISPR/Cas9 technology and produced fertilizers, pesticides, and boosters for plants by adopting nanotechnology-based protocols can essentially overcome the universal food scarcity. This review briefly gives an overview on the potential applications of CRISPR/Cas9 and nanotechnology-based methods in developing the cultivation of major agricultural crops. In addition, the limitations and major challenges of genome editing in grains, vegetables, and fruits have been discussed in detail by emphasizing its applications in crop refinement strategy.
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Affiliation(s)
- Banavath Jayanna Naik
- Research Institute of Climate Change and Agriculture, National Institute of Horticultural and Herbal Science, Rural Development Administration (RDA), Jeju, South Korea
| | - Ganesh Shimoga
- Interaction Laboratory, Future Convergence Engineering, Advanced Technology Research Center, Korea University of Technology and Education, Cheonan-si, South Korea
| | - Seong-Cheol Kim
- Research Institute of Climate Change and Agriculture, National Institute of Horticultural and Herbal Science, Rural Development Administration (RDA), Jeju, South Korea
| | | | | | | | - Manu Kumar
- Department of Life Science, College of Life Science and Biotechnology, Dongguk University, Seoul, South Korea
| | - Sang-Youn Kim
- Interaction Laboratory, Future Convergence Engineering, Advanced Technology Research Center, Korea University of Technology and Education, Cheonan-si, South Korea
| | - Soo-Hong Lee
- Department of Medical Biotechnology, Dongguk University, Seoul, South Korea
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Wang L, Wang Y, Makhmoudova A, Nitschke F, Tetlow IJ, Emes MJ. CRISPR-Cas9-mediated editing of starch branching enzymes results in altered starch structure in Brassica napus. PLANT PHYSIOLOGY 2022; 188:1866-1886. [PMID: 34850950 PMCID: PMC8968267 DOI: 10.1093/plphys/kiab535] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Accepted: 10/20/2021] [Indexed: 05/24/2023]
Abstract
Starch branching enzymes (SBEs) are one of the major classes of enzymes that catalyze starch biosynthesis in plants. Here, we utilized the clustered regularly interspaced short palindromic repeats-CRISPR associated protein 9 (CRISPR-Cas9)-mediated gene editing system to investigate the effects of SBE mutation on starch structure and turnover in the oilseed crop Brassica napus. Multiple single-guide RNA (sgRNA) expression cassettes were assembled into a binary vector and two rounds of transformation were employed to edit all six BnaSBE genes. All mutations were heterozygous monoallelic or biallelic, and no chimeric mutations were detected from a total of 216 editing events. Previously unannotated gene duplication events associated with two BnaSBE genes were characterized through analysis of DNA sequencing chromatograms, reflecting the complexity of genetic information in B. napus. Five Cas9-free homozygous mutant lines carrying two to six mutations of BnaSBE were obtained, allowing us to compare the effect of editing different BnaSBE isoforms. We also found that in the sextuple sbe mutant, although indels were introduced at the genomic DNA level, an alternate transcript of one BnaSBE2.1 gene bypassed the indel-induced frame shift and was translated to a modified full-length protein. Subsequent analyses showed that the sextuple mutant possesses much lower SBE enzyme activity and starch branching frequency, higher starch-bound phosphate content, and altered pattern of amylopectin chain length distribution relative to wild-type (WT) plants. In the sextuple mutant, irregular starch granules and a slower rate of starch degradation during darkness were observed in rosette leaves. At the pod-filling stage, the sextuple mutant was distinguishable from WT plants by its thick main stem. This work demonstrates the applicability of the CRISPR-Cas9 system for the study of multi-gene families and for investigation of gene-dosage effects in the oil crop B. napus. It also highlights the need for rigorous analysis of CRISPR-Cas9-mutated plants, particularly with higher levels of ploidy, to ensure detection of gene duplications.
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Affiliation(s)
- Liping Wang
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - You Wang
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - Amina Makhmoudova
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - Felix Nitschke
- Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Ian J Tetlow
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - Michael J Emes
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON N1G 2W1, Canada
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Utsumi Y, Utsumi C, Tanaka M, Takahashi S, Okamoto Y, Ono M, Nakamura Y, Seki M. Suppressed expression of starch branching enzyme 1 and 2 increases resistant starch and amylose content and modifies amylopectin structure in cassava. PLANT MOLECULAR BIOLOGY 2022; 108:413-427. [PMID: 34767147 DOI: 10.1007/s11103-021-01209-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Accepted: 10/23/2021] [Indexed: 06/13/2023]
Abstract
Suppression of starch branching enzymes 1 and 2 in cassava leads to increased resistant starch content through the production of high-amylose and modification of the amylopectin structure. Cassava (Manihot esculenta Crantz) is a starchy root crop used for human consumption as a staple food and industrial applications. Starch is synthesized by various isoforms of several enzymes. However, the function of starch branching enzymes (SBEs) in starch biosynthesis and mechanisms of starch regulation in cassava have not been understood well. In this study, we aimed to suppress the expression of SBEs in cassava to generate starches with a range of distinct properties, in addition to verifying the functional characteristics of the SBEs. One SBE1, two SBE2, and one SBE3 genes were classified by phylogenetic analysis and amino acid alignment. Quantitative real-time RT-PCR revealed tissue-specific expression of SBE genes in the tuberous roots and leaves of cassava. We introduced RNAi constructs containing fragments of SBE1, SBE2, or both genes into cassava by Agrobacterium-mediated transformation, and assessed enzymatic activity of SBE using tuberous roots and leaves from these transgenic plants. Simultaneous suppression of SBE1 and SBE2 rendered an extreme starch phenotype compared to suppression of SBE2 alone. Degree of polymerization of 6-13 chains in amylopectin was markedly reduced by suppression of both SBE1 and SBE2 in comparison to the SBE2 suppression; however, no change in chain-length profiles was observed in the SBE1 suppression alone. The role of SBE1 and SBE2 may have functional overlap in the storage tissue of cassava. Simultaneous suppression of SBE1 and SBE2 resulted in highly resistant starch with increased apparent amylose content compared to suppression of SBE2 alone. This study provides valuable information for understanding starch biosynthesis and suggests targets for altering starch quality.
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Affiliation(s)
- Yoshinori Utsumi
- Plant Genomic Network Research Team, RIKEN Center for Sustainable Resource Science, 1-7- 22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan.
| | - Chikako Utsumi
- Plant Genomic Network Research Team, RIKEN Center for Sustainable Resource Science, 1-7- 22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
| | - Maho Tanaka
- Plant Genomic Network Research Team, RIKEN Center for Sustainable Resource Science, 1-7- 22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
- Plant Epigenome Regulation Laboratory, RIKEN Cluster for Pioneering Research, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
| | - Satoshi Takahashi
- Plant Genomic Network Research Team, RIKEN Center for Sustainable Resource Science, 1-7- 22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
| | - Yoshie Okamoto
- Plant Genomic Network Research Team, RIKEN Center for Sustainable Resource Science, 1-7- 22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
| | - Masami Ono
- Faculty of Bioresource Sciences, Akita Prefectural University, 241-438 Kaidobata-nishi, Shimoshinjo-Nakano, Akita, 010-0195, Japan
- Akita Natural Science Laboratory, 25-44 Oiwake-Nishi, Tennoh, Katagami, Akita, 010-0101, Japan
| | - Yasunori Nakamura
- Faculty of Bioresource Sciences, Akita Prefectural University, 241-438 Kaidobata-nishi, Shimoshinjo-Nakano, Akita, 010-0195, Japan
- Akita Natural Science Laboratory, 25-44 Oiwake-Nishi, Tennoh, Katagami, Akita, 010-0101, Japan
| | - Motoaki Seki
- Plant Genomic Network Research Team, RIKEN Center for Sustainable Resource Science, 1-7- 22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan.
- Plant Epigenome Regulation Laboratory, RIKEN Cluster for Pioneering Research, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan.
- Kihara Institute for Biological Research, Yokohama City University, 641-12 Maioka-cho, Totsuka-ku, Yokohama, Kanagawa, 244-0813, Japan.
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Luo S, Ma Q, Zhong Y, Jing J, Wei Z, Zhou W, Lu X, Tian Y, Zhang P. Editing of the starch branching enzyme gene SBE2 generates high-amylose storage roots in cassava. PLANT MOLECULAR BIOLOGY 2022; 106:67-84. [PMID: 34792751 DOI: 10.1007/s11103-021-01130-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Accepted: 02/09/2021] [Indexed: 05/25/2023]
Abstract
The production of high-amylose cassava through CRISPR/Cas9-mediated mutagenesis of the starch branching enzyme gene SBE2 was firstly achieved. High-amylose cassava (Manihot esculenta Crantz) is desirable for starch industrial applications and production of healthier processed food for human consumption. In this study, we report the production of high-amylose cassava through CRISPR/Cas9-mediated mutagenesis of the starch branching enzyme 2 (SBE2). Mutations in two targeted exons of SBE2 were identified in all regenerated plants; these mutations, which included nucleotide insertions, and short or long deletions in the SBE2 gene, were classified into eight mutant lines. Three mutants, M6, M7 and M8, with long fragment deletions in the second exon of SBE2 showed no accumulation of SBE2 protein. After harvest from the field, significantly higher amylose (up to 56% in apparent amylose content) and resistant starch (up to 35%) was observed in these mutants compared with the wild type, leading to darker blue coloration of starch granules after quick iodine staining and altered starch viscosity with a higher pasting temperature and peak time. Further 1H-NMR analysis revealed a significant reduction in the degree of starch branching, together with fewer short chains (degree of polymerization [DP] 15-25) and more long chains (DP>25 and especially DP>40) of amylopectin, which indicates that cassava SBE2 catalyzes short chain formation during amylopectin biosynthesis. Transition from A- to B-type crystallinity was also detected in the starches. Our study showed that CRISPR/Cas9-mediated mutagenesis of starch biosynthetic genes in cassava is an effective approach for generating novel varieties with valuable starch properties for food and industrial applications.
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Affiliation(s)
- Shu Luo
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Qiuxiang Ma
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032, China.
| | - Yingying Zhong
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
- Shanghai Sanshu Biotechnology Co., LTD, Shanghai, 201210, China
| | - Jianling Jing
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Zusheng Wei
- Guangxi Subtropical Crops Research Institute, Nanning, 530001, China
| | - Wenzhi Zhou
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
- Shanghai Sanshu Biotechnology Co., LTD, Shanghai, 201210, China
| | - Xinlu Lu
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Yinong Tian
- Guangxi Subtropical Crops Research Institute, Nanning, 530001, China
| | - Peng Zhang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032, China.
- University of Chinese Academy of Sciences, Beijing, China.
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Luo S, Ma Q, Zhong Y, Jing J, Wei Z, Zhou W, Lu X, Tian Y, Zhang P. Editing of the starch branching enzyme gene SBE2 generates high-amylose storage roots in cassava. PLANT MOLECULAR BIOLOGY 2022; 108:429-442. [PMID: 34792751 DOI: 10.1007/s11103-021-01215-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2021] [Accepted: 11/03/2021] [Indexed: 06/13/2023]
Abstract
The production of high-amylose cassava through CRISPR/Cas9-mediated mutagenesis of the starch branching enzyme gene SBE2 was firstly achieved. High-amylose cassava (Manihot esculenta Crantz) is desirable for starch industrial applications and production of healthier processed food for human consumption. In this study, we report the production of high-amylose cassava through CRISPR/Cas9-mediated mutagenesis of the starch branching enzyme 2 (SBE2). Mutations in two targeted exons of SBE2 were identified in all regenerated plants; these mutations, which included nucleotide insertions, and short or long deletions in the SBE2 gene, were classified into eight mutant lines. Three mutants, M6, M7 and M8, with long fragment deletions in the second exon of SBE2 showed no accumulation of SBE2 protein. After harvest from the field, significantly higher amylose (up to 56% in apparent amylose content) and resistant starch (up to 35%) was observed in these mutants compared with the wild type, leading to darker blue coloration of starch granules after quick iodine staining and altered starch viscosity with a higher pasting temperature and peak time. Further 1H-NMR analysis revealed a significant reduction in the degree of starch branching, together with fewer short chains (degree of polymerization [DP] 15-25) and more long chains (DP>25 and especially DP>40) of amylopectin, which indicates that cassava SBE2 catalyzes short chain formation during amylopectin biosynthesis. Transition from A- to B-type crystallinity was also detected in the starches. Our study showed that CRISPR/Cas9-mediated mutagenesis of starch biosynthetic genes in cassava is an effective approach for generating novel varieties with valuable starch properties for food and industrial applications.
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Affiliation(s)
- Shu Luo
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Qiuxiang Ma
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032, China.
| | - Yingying Zhong
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
- Shanghai Sanshu Biotechnology Co., LTD, Shanghai, 201210, China
| | - Jianling Jing
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Zusheng Wei
- Guangxi Subtropical Crops Research Institute, Nanning, 530001, China
| | - Wenzhi Zhou
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
- Shanghai Sanshu Biotechnology Co., LTD, Shanghai, 201210, China
| | - Xinlu Lu
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Yinong Tian
- Guangxi Subtropical Crops Research Institute, Nanning, 530001, China
| | - Peng Zhang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032, China.
- University of Chinese Academy of Sciences, Beijing, China.
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40
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Tiwari JK, Buckseth T, Challam C, Zinta R, Bhatia N, Dalamu D, Naik S, Poonia AK, Singh RK, Luthra SK, Kumar V, Kumar M. CRISPR/Cas Genome Editing in Potato: Current Status and Future Perspectives. Front Genet 2022; 13:827808. [PMID: 35186041 PMCID: PMC8849127 DOI: 10.3389/fgene.2022.827808] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Accepted: 01/11/2022] [Indexed: 11/13/2022] Open
Affiliation(s)
| | | | | | - Rasna Zinta
- ICAR-Central Potato Research Institute, Shimla, India.,School of Bioengineering and Biosciences, Lovely Professional University, Phagwara, India
| | - Nisha Bhatia
- ICAR-Central Potato Research Institute, Shimla, India.,School of Biotechnology, Shoolini University, Solan, India
| | - Dalamu Dalamu
- ICAR-Central Potato Research Institute, Shimla, India
| | - Sharmistha Naik
- ICAR-Central Potato Research Institute, Shimla, India.,ICAR-National Research Centre for Grapes, Pune, India
| | - Anuj K Poonia
- School of Biotechnology, Shoolini University, Solan, India
| | | | | | - Vinod Kumar
- ICAR-Central Potato Research Institute, Shimla, India
| | - Manoj Kumar
- ICAR-Central Potato Research Institute, Meerut, India
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41
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Nahirñak V, Almasia NI, González MN, Massa GA, Décima Oneto CA, Feingold SE, Hopp HE, Vazquez Rovere C. State of the Art of Genetic Engineering in Potato: From the First Report to Its Future Potential. FRONTIERS IN PLANT SCIENCE 2022; 12:768233. [PMID: 35082806 PMCID: PMC8784693 DOI: 10.3389/fpls.2021.768233] [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: 08/31/2021] [Accepted: 12/09/2021] [Indexed: 06/14/2023]
Abstract
Potato (Solanum tuberosum L.) is a crop of world importance that produces tubers of high nutritional quality. It is considered one of the promising crops to overcome the challenges of poverty and hunger worldwide. However, it is exposed to different biotic and abiotic stresses that can cause significant losses in production. Thus, potato is a candidate of special relevance for improvements through conventional breeding and biotechnology. Since conventional breeding is time-consuming and challenging, genetic engineering provides the opportunity to introduce/switch-off genes of interest without altering the allelic combination that characterize successful commercial cultivars or to induce targeted sequence modifications by New Breeding Techniques. There is a variety of methods for potato improvement via genetic transformation. Most of them incorporate genes of interest into the nuclear genome; nevertheless, the development of plastid transformation protocols broadened the available approaches for potato breeding. Although all methods have their advantages and disadvantages, Agrobacterium-mediated transformation is the most used approach. Alternative methods such as particle bombardment, protoplast transfection with polyethylene glycol and microinjection are also effective. Independently of the DNA delivery approach, critical steps for a successful transformation are a rapid and efficient regeneration protocol and a selection system. Several critical factors affect the transformation efficiency: vector type, insert size, Agrobacterium strain, explant type, composition of the subculture media, selective agent, among others. Moreover, transient or stable transformation, constitutive or inducible promoters, antibiotic/herbicide resistance or marker-free strategies can be considered. Although great efforts have been made to optimize all the parameters, potato transformation protocols are highly genotype-dependent. Genome editing technologies provide promising tools in genetic engineering allowing precise modification of targeted sequences. Interestingly, transient expression of genome editing components in potato protoplasts was reported to generate edited plants without the integration of any foreign DNA, which is a valuable aspect from both a scientific and a regulatory perspective. In this review, current challenges and opportunities concerning potato genetic engineering strategies developed to date are discussed. We describe their critical parameters and constrains, and the potential application of the available tools for functional analyses or biotechnological purposes. Public concerns and safety issues are also addressed.
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Affiliation(s)
- Vanesa Nahirñak
- Instituto de Agrobiotecnología y Biología Molecular, UEDD INTA-CONICET, Hurlingham, Argentina
| | - Natalia I. Almasia
- Instituto de Agrobiotecnología y Biología Molecular, UEDD INTA-CONICET, Hurlingham, Argentina
| | - Matías N. González
- Laboratorio de Agrobiotecnología, IPADS (INTA – CONICET), Balcarce, Argentina
| | - Gabriela A. Massa
- Laboratorio de Agrobiotecnología, IPADS (INTA – CONICET), Balcarce, Argentina
- Facultad de Ciencias Agrarias, Universidad Nacional de Mar del Plata, Balcarce, Argentina
| | - Cecilia A. Décima Oneto
- Laboratorio de Agrobiotecnología, IPADS (INTA – CONICET), Balcarce, Argentina
- Facultad de Ciencias Agrarias, Universidad Nacional de Mar del Plata, Balcarce, Argentina
| | - Sergio E. Feingold
- Laboratorio de Agrobiotecnología, IPADS (INTA – CONICET), Balcarce, Argentina
| | - Horacio E. Hopp
- Instituto de Agrobiotecnología y Biología Molecular, UEDD INTA-CONICET, Hurlingham, Argentina
- Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Cecilia Vazquez Rovere
- Instituto de Agrobiotecnología y Biología Molecular, UEDD INTA-CONICET, Hurlingham, Argentina
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Yadav CB, Srivastava RK, Beynon S, Englyst K, Gangashetty PI, Yadav RS. Genetic variability and genome‐wide marker association studies for starch traits contributing to low glycaemic index in pearl millet. Food Energy Secur 2021. [DOI: 10.1002/fes3.341] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Affiliation(s)
- Chandra Bhan Yadav
- Institute of Biological Environmental and Rural Sciences (IBERS) Aberystwyth University Aberystwyth UK
| | - Rakesh K. Srivastava
- International Crops Research Institute for the Semi‐Arid Tropics Patancheru India
| | - Sarah Beynon
- Institute of Biological Environmental and Rural Sciences (IBERS) Aberystwyth University Aberystwyth UK
| | | | - Prakash I. Gangashetty
- International Crops Research Institute for the Semi‐Arid Tropics Patancheru India
- International Crops Research Institute for the Semi‐Arid Tropics Niamey Niger
| | - Rattan S. Yadav
- Institute of Biological Environmental and Rural Sciences (IBERS) Aberystwyth University Aberystwyth UK
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43
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Shah P, Magar ND, Barbadikar KM. Current technological interventions and applications of CRISPR/Cas for crop improvement. Mol Biol Rep 2021; 49:5751-5770. [PMID: 34807378 DOI: 10.1007/s11033-021-06926-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2021] [Accepted: 11/01/2021] [Indexed: 10/19/2022]
Abstract
Efficient and innovative breeding strategies are immensely required to meet the global food demand, nutritional security and sustainable agriculture. Genome editing tools have emerged as an effective technology for site-directed genome modification causing the change in gene expression and protein function for the improvement of various important traits in particular the CRISPR/Cas (Clustered Regularly Interspaced Short Palindromic Repeats/CRISPR-associated protein). As the technology evolved with time, advances have been observed like prime editing, base editing, PAMless editing, Drosha based editing with multiple targets having the potential to fulfill the regulatory processes around the world. These recent interventions are highly proficient, cost-efficient, user-friendly, and holds promise for a major revolution in basic and applied plant biology research in the ever-evolving climatic conditions. In the review, we have discussed the most recent technologies and advances for CRISPR/Cas editing in plants.
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Affiliation(s)
- Priya Shah
- Tamil Nadu Agricultural University, Tamil Nadu, India
| | - Nakul D Magar
- ICAR-Indian Institute of Rice Research, Rajendranagar, Hyderabad, Telangana State, 500030, India
| | - Kalyani M Barbadikar
- ICAR-Indian Institute of Rice Research, Rajendranagar, Hyderabad, Telangana State, 500030, India.
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Abstract
Nature has developed starch granules varying in size from less than 1 μm to more than 100 μm. The granule size is an important factor affecting the functional properties and the applicability of starch for food and non-food applications. Within the same botanical species, the range of starch granule size can be up to sevenfold. This review critically evaluated the biological and environmental factors affecting the size of starch granules, the methods for the separation of starch granules and the measurement of size distribution. Further, the structure at different length scales and properties of starch-based on the granule size is elucidated by specifying the typical applications of granules with varying sizes. An amylopectin cluster model showing the arrangement of amylopectin from inside toward the granule surface is proposed with the hypothesis that the steric hindrance for the growth of lamellar structure may limit the size of starch granules.
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Affiliation(s)
- Ming Li
- Laboratory of Cereal Processing and Quality Control, Institute of Food Science and Technology, CAAS/Key Laboratory of Agro-Products Processing, Ministry of Agriculture and Rural Affairs, Beijing, China
| | - Venea Dara Daygon
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, St Lucia, Queensland, Australia
| | - Vicky Solah
- College of Science, Health, Engineering and Education, Murdoch University, Murdoch, Western Australia, Australia
| | - Sushil Dhital
- Department of Chemical and Biological Engineering, Monash University, Clayton, Victoria, Australia
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45
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Hofvander P, Andreasson E, Andersson M. Potato trait development going fast-forward with genome editing. Trends Genet 2021; 38:218-221. [PMID: 34702578 DOI: 10.1016/j.tig.2021.10.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 10/04/2021] [Accepted: 10/04/2021] [Indexed: 11/28/2022]
Abstract
Implementations and improvements of genome editing techniques used in plant science have increased exponentially. For some crops, such as potato, the use of transcription activator-like effector nucleases (TALEN) and clustered regularly interspaced short palindromic repeats (CRISPR) has moved to the next step of trait development and field trials, and should soon be applied to commercial cultivation.
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Affiliation(s)
- Per Hofvander
- Department of Plant Breeding, Swedish University of Agricultural Sciences, SLU Alnarp, Box 190, 234 22 Lomma, Sweden
| | - Erik Andreasson
- Department of Plant Protection Biology, Swedish University of Agricultural Sciences, SLU Alnarp, Box 190, 234 22 Lomma, Sweden
| | - Mariette Andersson
- Department of Plant Breeding, Swedish University of Agricultural Sciences, SLU Alnarp, Box 190, 234 22 Lomma, Sweden.
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Yu J, Wang K, Beckles DM. Starch branching enzymes as putative determinants of postharvest quality in horticultural crops. BMC PLANT BIOLOGY 2021; 21:479. [PMID: 34674662 PMCID: PMC8529802 DOI: 10.1186/s12870-021-03253-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Accepted: 10/08/2021] [Indexed: 06/13/2023]
Abstract
Starch branching enzymes (SBEs) are key determinants of the structure and amount of the starch in plant organs, and as such, they have the capacity to influence plant growth, developmental, and fitness processes, and in addition, the industrial end-use of starch. However, little is known about the role of SBEs in determining starch structure-function relations in economically important horticultural crops such as fruit and leafy greens, many of which accumulate starch transiently. Further, a full understanding of the biological function of these types of starches is lacking. Because of this gap in knowledge, this minireview aims to provide an overview of SBEs in horticultural crops, to investigate the potential role of starch in determining postharvest quality. A systematic examination of SBE sequences in 43 diverse horticultural species, identified SBE1, 2 and 3 isoforms in all species examined except apple, olive, and Brassicaceae, which lacked SBE1, but had a duplicated SBE2. Among our findings after a comprehensive and critical review of published data, was that as apple, banana, and tomato fruits ripens, the ratio of the highly digestible amylopectin component of starch increases relative to the more digestion-resistant amylose fraction, with parallel increases in SBE2 transcription, fruit sugar content, and decreases in starch. It is tempting to speculate that during the ripening of these fruit when starch degradation occurs, there are rearrangements made to the structure of starch possibly via branching enzymes to increase starch digestibility to sugars. We propose that based on the known action of SBEs, and these observations, SBEs may affect produce quality, and shelf-life directly through starch accumulation, and indirectly, by altering sugar availability. Further studies where SBE activity is fine-tuned in these crops, can enrich our understanding of the role of starch across species and may improve horticulture postharvest quality.
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Affiliation(s)
- Jingwei Yu
- Department of Plant Sciences, University of California, One Shields Avenue, Davis, CA, 95616, USA
- Graduate Group of Horticulture & Agronomy, University of California, Davis, CA, 95616, USA
- Present Address: Institute of Plant and Food Science, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055, PR China
| | - Keyun Wang
- Department of Plant Sciences, University of California, One Shields Avenue, Davis, CA, 95616, USA
| | - Diane M Beckles
- Department of Plant Sciences, University of California, One Shields Avenue, Davis, CA, 95616, USA.
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Takeuchi A, Ohnuma M, Teramura H, Asano K, Noda T, Kusano H, Tamura K, Shimada H. Creation of a potato mutant lacking the starch branching enzyme gene StSBE3 that was generated by genome editing using the CRISPR/dMac3-Cas9 system. PLANT BIOTECHNOLOGY (TOKYO, JAPAN) 2021; 38:345-353. [PMID: 34782822 PMCID: PMC8562579 DOI: 10.5511/plantbiotechnology.21.0727a] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Accepted: 07/27/2021] [Indexed: 06/13/2023]
Abstract
The potato tuber starch trait is changed depending on the composition of amylose and amylopectin. The amount of amylopectin is determined by the activity of the starch branching enzymes SBE1, SBE2, and SBE3 in potato. SBE3, a homolog of rice BEI, is a major gene that is abundant in tubers. In this study, we created mutants of the potato SBE3 gene using CRISPR/Cas9 attached to the translation enhancer dMac3. Potato has a tetraploid genome, and a four-allele mutant of the SBE3 gene is desired. Mutations in the SBE3 gene were found in 89 of 126 transformants of potato plants. Among these mutants, 10 lines contained four mutant SBE3 genes, indicating that 8% efficiency of target mutagenesis was achieved. These mutants grew normally, similar to the wild-type plant, and yielded sufficient amounts of tubers. The potato starch in these tubers was similar to that of the rice BEI mutant. Western blot analysis revealed the defective production of SBE3 in the mutant tubers, suggesting that these transformants were loss-of-function mutants of SBE3.
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Affiliation(s)
- Ami Takeuchi
- Department of Biological Science and Technology, Tokyo University of Science, Katsushika, Tokyo 125-8585, Japan
| | - Mariko Ohnuma
- Department of Biological Science and Technology, Tokyo University of Science, Katsushika, Tokyo 125-8585, Japan
| | - Hiroshi Teramura
- Department of Biological Science and Technology, Tokyo University of Science, Katsushika, Tokyo 125-8585, Japan
| | - Kenji Asano
- Division of Northern Field Crop Research, Field Crop Breeding Group, NARO, 9-4 Shinsei-minami, Memuro, Kasai, Hokkaido 082-0081, Japan
| | - Takahiro Noda
- Division of Northern Field Crop Research, Field Crop Breeding Group, NARO, 9-4 Shinsei-minami, Memuro, Kasai, Hokkaido 082-0081, Japan
| | - Hiroaki Kusano
- Department of Biological Science and Technology, Tokyo University of Science, Katsushika, Tokyo 125-8585, Japan
| | - Koji Tamura
- Department of Biological Science and Technology, Tokyo University of Science, Katsushika, Tokyo 125-8585, Japan
| | - Hiroaki Shimada
- Department of Biological Science and Technology, Tokyo University of Science, Katsushika, Tokyo 125-8585, Japan
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Yue JJ, Yuan JL, Wu FH, Yuan YH, Cheng QW, Hsu CT, Lin CS. Protoplasts: From Isolation to CRISPR/Cas Genome Editing Application. Front Genome Ed 2021; 3:717017. [PMID: 34713263 PMCID: PMC8525356 DOI: 10.3389/fgeed.2021.717017] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2021] [Accepted: 07/30/2021] [Indexed: 12/26/2022] Open
Abstract
In the clustered regulatory interspaced short palindromic repeats (CRISPR)/CRISPR associated protein (Cas) system, protoplasts are not only useful for rapidly validating the mutagenesis efficiency of various RNA-guided endonucleases, promoters, sgRNA designs, or Cas proteins, but can also be a platform for DNA-free gene editing. To date, the latter approach has been applied to numerous crops, particularly those with complex genomes, a long juvenile period, a tendency for heterosis, and/or self-incompatibility. Protoplast regeneration is thus a key step in DNA-free gene editing. In this report, we review the history and some future prospects for protoplast technology, including protoplast transfection, transformation, fusion, regeneration, and current protoplast applications in CRISPR/Cas-based breeding.
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Affiliation(s)
- Jin-Jun Yue
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, China
| | - Jin-Ling Yuan
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, China
| | - Fu-Hui Wu
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan
| | - Yu-Hsuan Yuan
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan
| | - Qiao-Wei Cheng
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan
| | - Chen-Tran Hsu
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan
| | - Choun-Sea Lin
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan
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Li J, Seng S, Li D, Zhang F, Liu Y, Yao T, Liang J, Yi M, Wu J. Antagonism between abscisic acid and gibberellin regulates starch synthesis and corm development in Gladiolus hybridus. HORTICULTURE RESEARCH 2021; 8:155. [PMID: 34193854 PMCID: PMC8245626 DOI: 10.1038/s41438-021-00589-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2020] [Revised: 03/22/2021] [Accepted: 05/04/2021] [Indexed: 05/20/2023]
Abstract
Understanding corm development in flower bulbs is of importance for securing the quality of cut flowers and propagation of commercial stocks. Gladiolus is one of the most popular bulb plants worldwide. Its corm development is characterized by starch accumulation. Previous research has shown that phytohormones (especially gibberellin (GA)) are involved in tuber development. However, the relationship between abscisic acid (ABA)/GA and starch during corm development remains unclear. To gain deeper insights into the biological process of corm development, we performed a detailed anatomical characterization of different stages of corm development and analyzed phytohormone levels. Our study showed that corm development is linked to hormones (ABA and GA) and carbohydrates (sucrose and starch). Exogenous hormone treatment and silencing of endogenous hormone biosynthesis genes indicated that ABA positively regulates corm development, while GA acts as an antagonist of ABA function. A sucrose synthase gene (GhSUS2) was shown to be involved in the antagonism between ABA and GA. GhSUS2 was upregulated by ABA and downregulated by GA. The increase in the transcript level of GhSUS2 coincided with the development of corm/cormels. Silencing of GhSUS2 repressed corm development and starch accumulation. In conclusion, we propose that GhSUS2, an essential enzyme in sucrose degradation, is differentially regulated by ABA and GA and controls corm development in Gladiolus.
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Affiliation(s)
- Jingru Li
- Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture and Landscape Architecture, China Agricultural University, Beijing, China
| | - Shanshan Seng
- Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture and Landscape Architecture, China Agricultural University, Beijing, China
| | - Donglei Li
- Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture and Landscape Architecture, China Agricultural University, Beijing, China
| | - Fengqin Zhang
- Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture and Landscape Architecture, China Agricultural University, Beijing, China
| | - Yixuan Liu
- Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture and Landscape Architecture, China Agricultural University, Beijing, China
| | - Ting Yao
- Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture and Landscape Architecture, China Agricultural University, Beijing, China
| | - Jiahui Liang
- Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture and Landscape Architecture, China Agricultural University, Beijing, China
| | - Mingfang Yi
- Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture and Landscape Architecture, China Agricultural University, Beijing, China
| | - Jian Wu
- Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture and Landscape Architecture, China Agricultural University, Beijing, China.
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Hawkins E, Chen J, Watson-Lazowski A, Ahn-Jarvis J, Barclay JE, Fahy B, Hartley M, Warren FJ, Seung D. STARCH SYNTHASE 4 is required for normal starch granule initiation in amyloplasts of wheat endosperm. THE NEW PHYTOLOGIST 2021; 230:2371-2386. [PMID: 33714222 DOI: 10.1111/nph.17342] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Accepted: 03/05/2021] [Indexed: 05/26/2023]
Abstract
Starch granule initiation is poorly understood at the molecular level. The glucosyltransferase, STARCH SYNTHASE 4 (SS4), plays a central role in granule initiation in Arabidopsis leaves, but its function in cereal endosperms is unknown. We investigated the role of SS4 in wheat, which has a distinct spatiotemporal pattern of granule initiation during grain development. We generated TILLING mutants in tetraploid wheat (Triticum turgidum) that are defective in both SS4 homoeologs. The morphology of endosperm starch was examined in developing and mature grains. SS4 deficiency led to severe alterations in endosperm starch granule morphology. During early grain development, while the wild-type initiated single 'A-type' granules per amyloplast, most amyloplasts in the mutant formed compound granules due to multiple initiations. This phenotype was similar to mutants deficient in B-GRANULE CONTENT 1 (BGC1). SS4 deficiency also reduced starch content in leaves and pollen grains. We propose that SS4 and BGC1 are required for the proper control of granule initiation during early grain development that leads to a single A-type granule per amyloplast. The absence of either protein results in a variable number of initiations per amyloplast and compound granule formation.
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Affiliation(s)
- Erica Hawkins
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Jiawen Chen
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | | | | | | | - Brendan Fahy
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Matthew Hartley
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | | | - David Seung
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
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