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Gawande ND, Bhalla H, Watts A, Shelake RM, Sankaranarayanan S. Application of genome editing in plant reproductive biology: recent advances and challenges. PLANT REPRODUCTION 2024:10.1007/s00497-024-00506-w. [PMID: 38954018 DOI: 10.1007/s00497-024-00506-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2024] [Accepted: 06/21/2024] [Indexed: 07/04/2024]
Abstract
KEY MESSAGE This comprehensive review underscores the application of genome editing in plant reproductive biology, including recent advances and challenges associated with it. Genome editing (GE) is a powerful technology that has the potential to accelerate crop improvement by enabling efficient, precise, and rapid engineering of plant genomes. Over the last decade, this technology has rapidly evolved from the use of meganucleases (homing endonucleases), zinc-finger nucleases, transcription activator-like effector nucleases to the use of clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein (CRISPR/Cas), which has emerged as a popular GE tool in recent times and has been extensively used in several organisms, including plants. GE has been successfully employed in several crops to improve plant reproductive traits. Improving crop reproductive traits is essential for crop yields and securing the world's food supplies. In this review, we discuss the application of GE in various aspects of plant reproductive biology, including its potential application in haploid induction, apomixis, parthenocarpy, development of male sterile lines, and the regulation of self-incompatibility. We also discuss current challenges and future prospects of this technology for crop improvement, focusing on plant reproduction.
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Affiliation(s)
- Nilesh D Gawande
- Department of Biological Sciences and Engineering, Indian Institute of Technology Gandhinagar, Palaj, Gujarat, 382355, India
| | - Hemal Bhalla
- Department of Biological Sciences and Engineering, Indian Institute of Technology Gandhinagar, Palaj, Gujarat, 382355, India
| | - Anshul Watts
- ICAR-National Institute for Plant Biotechnology, New Delhi, India
| | - Rahul Mahadev Shelake
- Division of Applied Life Science (BK21 Four Program), Plant Molecular and Biotechnology Research Center, Gyeongsang National University, Jinju, 52828, Korea
| | - Subramanian Sankaranarayanan
- Department of Biological Sciences and Engineering, Indian Institute of Technology Gandhinagar, Palaj, Gujarat, 382355, India.
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2
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Zhang X, Heng S, Xiao C, Liu C, Song L, Tang L, He C, Wang B, Wang A, Gao C. Effective strategies for creating self-compatible B. rapa by introgression of mutated SRK and SCR/SP11 genes from B. napus. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2024; 44:48. [PMID: 38974420 PMCID: PMC11226566 DOI: 10.1007/s11032-024-01487-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2024] [Accepted: 06/26/2024] [Indexed: 07/09/2024]
Affiliation(s)
- Xueli Zhang
- Wuhan Vegetable Research Institute, Wuhan Academy of Agricultural Sciences, Wuhan, 430345 China
| | - Shuangping Heng
- College of Life Science, Xinyang Normal University, Xinyang, 464000 P. R. China
| | - Chunxiu Xiao
- Wuhan Vegetable Research Institute, Wuhan Academy of Agricultural Sciences, Wuhan, 430345 China
| | - Cong Liu
- Wuhan Vegetable Research Institute, Wuhan Academy of Agricultural Sciences, Wuhan, 430345 China
| | - Liping Song
- Wuhan Vegetable Research Institute, Wuhan Academy of Agricultural Sciences, Wuhan, 430345 China
| | - Liguang Tang
- Wuhan Vegetable Research Institute, Wuhan Academy of Agricultural Sciences, Wuhan, 430345 China
| | - Congan He
- Wuhan Vegetable Research Institute, Wuhan Academy of Agricultural Sciences, Wuhan, 430345 China
| | - Bincai Wang
- Wuhan Vegetable Research Institute, Wuhan Academy of Agricultural Sciences, Wuhan, 430345 China
| | - Aihua Wang
- Wuhan Vegetable Research Institute, Wuhan Academy of Agricultural Sciences, Wuhan, 430345 China
| | - Changbin Gao
- Wuhan Vegetable Research Institute, Wuhan Academy of Agricultural Sciences, Wuhan, 430345 China
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3
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Tang X, Ren Q, Yan X, Zhang R, Liu L, Han Q, Zheng X, Qi Y, Song H, Zhang Y. Boosting genome editing in plants with single transcript unit surrogate reporter systems. PLANT COMMUNICATIONS 2024; 5:100921. [PMID: 38616491 PMCID: PMC11211634 DOI: 10.1016/j.xplc.2024.100921] [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: 01/02/2024] [Revised: 03/20/2024] [Accepted: 04/11/2024] [Indexed: 04/16/2024]
Abstract
CRISPR-Cas-based genome editing holds immense promise for advancing plant genomics and crop enhancement. However, the challenge of low editing activity complicates the identification of editing events. In this study, we introduce multiple single transcript unit surrogate reporter (STU-SR) systems to enhance the selection of genome-edited plants. These systems use the same single guide RNAs designed for endogenous genes to edit reporter genes, establishing a direct link between reporter gene editing activity and that of endogenous genes. Various strategies are used to restore functional reporter genes after genome editing, including efficient single-strand annealing (SSA) for homologous recombination in STU-SR-SSA systems. STU-SR-base editor systems leverage base editing to reinstate the start codon, enriching C-to-T and A-to-G base editing events. Our results showcase the effectiveness of these STU-SR systems in enhancing genome editing events in the monocot rice, encompassing Cas9 nuclease-based targeted mutagenesis, cytosine base editing, and adenine base editing. The systems exhibit compatibility with Cas9 variants, such as the PAM-less SpRY, and are shown to boost genome editing in Brassica oleracea, a dicot vegetable crop. In summary, we have developed highly efficient and versatile STU-SR systems for enrichment of genome-edited plants.
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Affiliation(s)
- Xu Tang
- Chongqing Key Laboratory of Plant Resource Conservation and Germplasm Innovation, Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science City, School of Life Sciences, Southwest University, Chongqing 400715, China; Key Laboratory of Agricultural Biosafety and Green Production of Upper Yangtze River, Ministry of Education, Chongqing 400715, China; College of Horticulture and Landscape Architecture, Southwest University, Chongqing 400715, China; Department of Biotechnology, School of Life Sciences and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu 610054, China
| | - Qiurong Ren
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing 400715, China; School of Synbiology, School of Life Science, Shanxi University, Taiyuan 030006, China
| | - Xiaodan Yan
- Key Laboratory of Agricultural Biosafety and Green Production of Upper Yangtze River, Ministry of Education, Chongqing 400715, China; College of Horticulture and Landscape Architecture, Southwest University, Chongqing 400715, China
| | - Rui Zhang
- Department of Biotechnology, School of Life Sciences and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu 610054, China
| | - Li Liu
- Department of Biotechnology, School of Life Sciences and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu 610054, China
| | - Qinqin Han
- Department of Biotechnology, School of Life Sciences and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu 610054, China
| | - Xuelian Zheng
- Chongqing Key Laboratory of Plant Resource Conservation and Germplasm Innovation, Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science City, School of Life Sciences, Southwest University, Chongqing 400715, China; Department of Biotechnology, School of Life Sciences and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu 610054, China
| | - Yiping Qi
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD 20742, USA; Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, MD 20850, USA.
| | - Hongyuan Song
- Key Laboratory of Agricultural Biosafety and Green Production of Upper Yangtze River, Ministry of Education, Chongqing 400715, China; College of Horticulture and Landscape Architecture, Southwest University, Chongqing 400715, China.
| | - Yong Zhang
- Chongqing Key Laboratory of Plant Resource Conservation and Germplasm Innovation, Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science City, School of Life Sciences, Southwest University, Chongqing 400715, China; Key Laboratory of Agricultural Biosafety and Green Production of Upper Yangtze River, Ministry of Education, Chongqing 400715, China; College of Horticulture and Landscape Architecture, Southwest University, Chongqing 400715, China; Department of Biotechnology, School of Life Sciences and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu 610054, China.
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4
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Masani MYA, Norfaezah J, Bahariah B, Fizree MDPMAA, Sulaiman WNSW, Shaharuddin NA, Rasid OA, Parveez GKA. Towards DNA-free CRISPR/Cas9 genome editing for sustainable oil palm improvement. 3 Biotech 2024; 14:166. [PMID: 38817736 PMCID: PMC11133284 DOI: 10.1007/s13205-024-04010-w] [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: 01/04/2024] [Accepted: 05/18/2024] [Indexed: 06/01/2024] Open
Abstract
The CRISPR/Cas9 genome editing system has been in the spotlight compared to programmable nucleases such as ZFNs and TALENs due to its simplicity, versatility, and high efficiency. CRISPR/Cas9 has revolutionized plant genetic engineering and is broadly used to edit various plants' genomes, including those transformation-recalcitrant species such as oil palm. This review will comprehensively present the CRISPR-Cas9 system's brief history and underlying mechanisms. We then highlighted the establishment of the CRISPR/Cas9 system in plants with an emphasis on the strategies of highly efficient guide RNA design, the establishment of various CRISPR/Cas9 vector systems, approaches of multiplex editing, methods of transformation for stable and transient techniques, available methods for detecting and analyzing mutations, which have been applied and could be adopted for CRISPR/Cas9 genome editing in oil palm. In addition, we also provide insight into the strategy of DNA-free genome editing and its potential application in oil palm.
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Affiliation(s)
- Mat Yunus Abdul Masani
- Malaysian Palm Oil Board (MPOB), 6, Persiaran Institusi, Bandar Baru Bangi, 43000 Kajang, Selangor Malaysia
| | - Jamaludin Norfaezah
- Malaysian Palm Oil Board (MPOB), 6, Persiaran Institusi, Bandar Baru Bangi, 43000 Kajang, Selangor Malaysia
| | - Bohari Bahariah
- Malaysian Palm Oil Board (MPOB), 6, Persiaran Institusi, Bandar Baru Bangi, 43000 Kajang, Selangor Malaysia
| | | | | | - Noor Azmi Shaharuddin
- Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, UPM, 43400 Serdang, Malaysia
| | - Omar Abdul Rasid
- Malaysian Palm Oil Board (MPOB), 6, Persiaran Institusi, Bandar Baru Bangi, 43000 Kajang, Selangor Malaysia
| | - Ghulam Kadir Ahmad Parveez
- Malaysian Palm Oil Board (MPOB), 6, Persiaran Institusi, Bandar Baru Bangi, 43000 Kajang, Selangor Malaysia
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Li B, Sun C, Li J, Gao C. Targeted genome-modification tools and their advanced applications in crop breeding. Nat Rev Genet 2024:10.1038/s41576-024-00720-2. [PMID: 38658741 DOI: 10.1038/s41576-024-00720-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/01/2024] [Indexed: 04/26/2024]
Abstract
Crop improvement by genome editing involves the targeted alteration of genes to improve plant traits, such as stress tolerance, disease resistance or nutritional content. Techniques for the targeted modification of genomes have evolved from generating random mutations to precise base substitutions, followed by insertions, substitutions and deletions of small DNA fragments, and are finally starting to achieve precision manipulation of large DNA segments. Recent developments in base editing, prime editing and other CRISPR-associated systems have laid a solid technological foundation to enable plant basic research and precise molecular breeding. In this Review, we systematically outline the technological principles underlying precise and targeted genome-modification methods. We also review methods for the delivery of genome-editing reagents in plants and outline emerging crop-breeding strategies based on targeted genome modification. Finally, we consider potential future developments in precise genome-editing technologies, delivery methods and crop-breeding approaches, as well as regulatory policies for genome-editing products.
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Affiliation(s)
- Boshu Li
- New Cornerstone Science Laboratory, Center for Genome Editing, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Chao Sun
- New Cornerstone Science Laboratory, Center for Genome Editing, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Jiayang Li
- Hainan Yazhou Bay Seed Laboratory, Sanya, China
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Caixia Gao
- New Cornerstone Science Laboratory, Center for Genome Editing, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China.
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China.
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6
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He J, Zeng C, Li M. Plant Functional Genomics Based on High-Throughput CRISPR Library Knockout Screening: A Perspective. ADVANCED GENETICS (HOBOKEN, N.J.) 2024; 5:2300203. [PMID: 38465224 PMCID: PMC10919289 DOI: 10.1002/ggn2.202300203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 10/19/2023] [Indexed: 03/12/2024]
Abstract
Plant biology studies in the post-genome era have been focused on annotating genome sequences' functions. The established plant mutant collections have greatly accelerated functional genomics research in the past few decades. However, most plant genome sequences' roles and the underlying regulatory networks remain substantially unknown. Clustered, regularly interspaced short palindromic repeat (CRISPR)-associated systems are robust, versatile tools for manipulating plant genomes with various targeted DNA perturbations, providing an excellent opportunity for high-throughput interrogation of DNA elements' roles. This study compares methods frequently used for plant functional genomics and then discusses different DNA multi-targeted strategies to overcome gene redundancy using the CRISPR-Cas9 system. Next, this work summarizes recent reports using CRISPR libraries for high-throughput gene knockout and function discoveries in plants. Finally, this work envisions the future perspective of optimizing and leveraging CRISPR library screening in plant genomes' other uncharacterized DNA sequences.
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Affiliation(s)
- Jianjie He
- Department of BiotechnologyCollege of Life Science and TechnologyHuazhong University of Science and TechnologyWuhan430074China
- Key Laboratory of Molecular Biophysics of the Ministry of EducationWuhan430074China
| | - Can Zeng
- Department of BiotechnologyCollege of Life Science and TechnologyHuazhong University of Science and TechnologyWuhan430074China
- Key Laboratory of Molecular Biophysics of the Ministry of EducationWuhan430074China
| | - Maoteng Li
- Department of BiotechnologyCollege of Life Science and TechnologyHuazhong University of Science and TechnologyWuhan430074China
- Key Laboratory of Molecular Biophysics of the Ministry of EducationWuhan430074China
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7
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Zhang D, Li YY, Zhao X, Zhang C, Liu DK, Lan S, Yin W, Liu ZJ. Molecular insights into self-incompatibility systems: From evolution to breeding. PLANT COMMUNICATIONS 2024; 5:100719. [PMID: 37718509 PMCID: PMC10873884 DOI: 10.1016/j.xplc.2023.100719] [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: 03/29/2023] [Revised: 08/18/2023] [Accepted: 09/13/2023] [Indexed: 09/19/2023]
Abstract
Plants have evolved diverse self-incompatibility (SI) systems for outcrossing. Since Darwin's time, considerable progress has been made toward elucidating this unrivaled reproductive innovation. Recent advances in interdisciplinary studies and applications of biotechnology have given rise to major breakthroughs in understanding the molecular pathways that lead to SI, particularly the strikingly different SI mechanisms that operate in Solanaceae, Papaveraceae, Brassicaceae, and Primulaceae. These best-understood SI systems, together with discoveries in other "nonmodel" SI taxa such as Poaceae, suggest a complex evolutionary trajectory of SI, with multiple independent origins and frequent and irreversible losses. Extensive exploration of self-/nonself-discrimination signaling cascades has revealed a comprehensive catalog of male and female identity genes and modifier factors that control SI. These findings also enable the characterization, validation, and manipulation of SI-related factors for crop improvement, helping to address the challenges associated with development of inbred lines. Here, we review current knowledge about the evolution of SI systems, summarize key achievements in the molecular basis of pollen‒pistil interactions, discuss potential prospects for breeding of SI crops, and raise several unresolved questions that require further investigation.
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Affiliation(s)
- Diyang Zhang
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yuan-Yuan Li
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Xuewei Zhao
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, Fujian Agriculture and Forestry University, Fuzhou 350002, China; College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Cuili Zhang
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Ding-Kun Liu
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, Fujian Agriculture and Forestry University, Fuzhou 350002, China; College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Siren Lan
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
| | - Weilun Yin
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, Fujian Agriculture and Forestry University, Fuzhou 350002, China; College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China.
| | - Zhong-Jian Liu
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
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Stajič E, Kunej U. Optimization of cabbage ( Brassica oleracea var. capitata L.) protoplast transformation for genome editing using CRISPR/Cas9. FRONTIERS IN PLANT SCIENCE 2023; 14:1245433. [PMID: 37849838 PMCID: PMC10577288 DOI: 10.3389/fpls.2023.1245433] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Accepted: 09/13/2023] [Indexed: 10/19/2023]
Abstract
Genome editing techniques, such as Clustered Regularly Interspaced Short Palindromic Repeats/CRISPR-associated systems (CRISPR/Cas9) are undoubtedly becoming an indispensable tool for improving food crops and tackling agricultural challenges. In the present study, key factors affecting transformation efficiency, such as PEG4000 concentration, incubation time, and plasmid amount were evaluated to achieve efficient delivery of CRISPR/Cas9 vector into cabbage protoplasts. Using amplicon sequencing, we confirmed a significant effect of PEG4000 concentration and incubation time on the induced target mutations. By optimizing the transformation protocol, editing efficiency of 26.4% was achieved with 40 µg of plasmid and 15 minutes incubation with 50% PEG4000. While these factors strongly affected the mutation rate, the viability of the transformed protoplasts remained high. Our findings would be useful for successful genome editing in cabbage and other brassicas, as well as in research areas such as gene function analysis and subcellular localization that rely on transient transformation methods in protoplasts.
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Affiliation(s)
- Ester Stajič
- Department of Agronomy, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
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Wang Y, Song S, Hao Y, Chen C, Ou X, He B, Zhang J, Jiang Z, Li C, Zhang S, Su W, Chen R. Role of BraRGL1 in regulation of Brassica rapa bolting and flowering. HORTICULTURE RESEARCH 2023; 10:uhad119. [PMID: 37547730 PMCID: PMC10402658 DOI: 10.1093/hr/uhad119] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 05/25/2023] [Indexed: 08/08/2023]
Abstract
Gibberellin (GA) plays a major role in controlling Brassica rapa stalk development. As an essential negative regulator of GA signal transduction, DELLA proteins may exert significant effects on stalk development. However, the regulatory mechanisms underlying this regulation remain unclear. In this study, we report highly efficient and inheritable mutagenesis using the CRISPR/Cas9 gene editing system in BraPDS (phytoene desaturase) and BraRGL1 (key DELLA protein) genes. We observed a loss-of-function mutation in BraRGL1 due to two amino acids in GRAS domain. The flower bud differentiation and bolting time of BraRGL1 mutants were significantly advanced. The expression of GA-regulatory protein (BraGASA6), flowering related genes (BraSOC1, BraLFY), expansion protein (BraEXPA11) and xyloglucan endotransferase (BraXTH3) genes was also significantly upregulated in these mutants. BraRGL1-overexpressing plants displayed the contrasting phenotypes. BraRGL1 mutants were more sensitive to GA signaling. BraRGL1 interacted with BraSOC1, and the interaction intensity decreased after GA3 treatment. In addition, BraRGL1 inhibited the transcription-activation ability of BraSOC1 for BraXTH3 and BraLFY genes, but the presence of GA3 enhanced the activation ability of BraSOC1, suggesting that the BraRGL1-BraSOC1 module regulates bolting and flowering of B. rapa through GA signal transduction. Thus, we hypothesized that BraRGL1 is degraded, and BraSOC1 is released in the presence of GA3, which promotes the expression of BraXTH3 and BraLFY, thereby inducing stalk development in B. rapa. Further, the BraRGL1-M mutant promoted the flower bud differentiation without affecting the stalk quality. Thus, BraRGL1 can serve as a valuable target for the molecular breeding of early maturing varieties.
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Affiliation(s)
- Yudan Wang
- Key Laboratory of Horticultural Crop Biology and Germplasm Innovation in South China, Ministry of Agriculture, College of Horticulture, South China Agricultural University, Guangzhou 510642, China
| | | | - Yanwei Hao
- Key Laboratory of Horticultural Crop Biology and Germplasm Innovation in South China, Ministry of Agriculture, College of Horticulture, South China Agricultural University, Guangzhou 510642, China
| | - Changming Chen
- Key Laboratory of Horticultural Crop Biology and Germplasm Innovation in South China, Ministry of Agriculture, College of Horticulture, South China Agricultural University, Guangzhou 510642, China
| | - Xi Ou
- Key Laboratory of Horticultural Crop Biology and Germplasm Innovation in South China, Ministry of Agriculture, College of Horticulture, South China Agricultural University, Guangzhou 510642, China
| | - Bin He
- Key Laboratory of Horticultural Crop Biology and Germplasm Innovation in South China, Ministry of Agriculture, College of Horticulture, South China Agricultural University, Guangzhou 510642, China
| | - Jiewen Zhang
- Key Laboratory of Horticultural Crop Biology and Germplasm Innovation in South China, Ministry of Agriculture, College of Horticulture, South China Agricultural University, Guangzhou 510642, China
| | - Zhehao Jiang
- Key Laboratory of Horticultural Crop Biology and Germplasm Innovation in South China, Ministry of Agriculture, College of Horticulture, South China Agricultural University, Guangzhou 510642, China
| | - Chengming Li
- Key Laboratory of Horticultural Crop Biology and Germplasm Innovation in South China, Ministry of Agriculture, College of Horticulture, South China Agricultural University, Guangzhou 510642, China
| | - Shuaiwei Zhang
- Key Laboratory of Horticultural Crop Biology and Germplasm Innovation in South China, Ministry of Agriculture, College of Horticulture, South China Agricultural University, Guangzhou 510642, China
| | - Wei Su
- Corresponding authors. E-mails: ; ;
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Ahmad N, Fatima S, Mehmood MA, Zaman QU, Atif RM, Zhou W, Rahman MU, Gill RA. Targeted genome editing in polyploids: lessons from Brassica. FRONTIERS IN PLANT SCIENCE 2023; 14:1152468. [PMID: 37409308 PMCID: PMC10318174 DOI: 10.3389/fpls.2023.1152468] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Accepted: 04/11/2023] [Indexed: 07/07/2023]
Abstract
CRISPR-mediated genome editing has emerged as a powerful tool for creating targeted mutations in the genome for various applications, including studying gene functions, engineering resilience against biotic and abiotic stresses, and increasing yield and quality. However, its utilization is limited to model crops for which well-annotated genome sequences are available. Many crops of dietary and economic importance, such as wheat, cotton, rapeseed-mustard, and potato, are polyploids with complex genomes. Therefore, progress in these crops has been hampered due to genome complexity. Excellent work has been conducted on some species of Brassica for its improvement through genome editing. Although excellent work has been conducted on some species of Brassica for genome improvement through editing, work on polyploid crops, including U's triangle species, holds numerous implications for improving other polyploid crops. In this review, we summarize key examples from genome editing work done on Brassica and discuss important considerations for deploying CRISPR-mediated genome editing more efficiently in other polyploid crops for improvement.
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Affiliation(s)
- Niaz Ahmad
- National Institute for Biotechnology and Genetic Engineering College, Pakistan Institute of Engineering and Applied Sciences (PIEAS), Faisalabad, Pakistan
| | - Samia Fatima
- National Institute for Biotechnology and Genetic Engineering College, Pakistan Institute of Engineering and Applied Sciences (PIEAS), Faisalabad, Pakistan
| | - Muhammad Aamer Mehmood
- Department of Bioinformatics & Biotechnology, Government College University Faisalabad, Faisalabad, Pakistan
| | - Qamar U. Zaman
- Hainan Yazhou Bay Seed Laboratory, Sanya Nanfan Research Institute of Hainan University, Sanya, China
- College of Tropical Crops, Hainan University, Haikou, China
| | - Rana Muhammad Atif
- National Center of Genome Editing, Center of Advanced Studies, Agriculture and Food Security, University of Agriculture, Faisalabad, Pakistan
- Department of Plant Breeding and Genetics, University of Agriculture Faisalabad, Faisalabad, Pakistan
| | - Weijun Zhou
- Ministry of Agriculture and Rural Affairs Key Lab of Spectroscopy Sensing, Institute of Crop Science, Zhejiang University, Hangzhou, China
| | - Mehboob-ur Rahman
- National Institute for Biotechnology and Genetic Engineering College, Pakistan Institute of Engineering and Applied Sciences (PIEAS), Faisalabad, Pakistan
| | - Rafaqat Ali Gill
- Key Laboratory for Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, China
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Zhang F, Neik TX, Thomas WJW, Batley J. CRISPR-Based Genome Editing Tools: An Accelerator in Crop Breeding for a Changing Future. Int J Mol Sci 2023; 24:ijms24108623. [PMID: 37239967 DOI: 10.3390/ijms24108623] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 05/03/2023] [Accepted: 05/04/2023] [Indexed: 05/28/2023] Open
Abstract
Genome editing is an important strategy to maintain global food security and achieve sustainable agricultural development. Among all genome editing tools, CRISPR-Cas is currently the most prevalent and offers the most promise. In this review, we summarize the development of CRISPR-Cas systems, outline their classification and distinctive features, delineate their natural mechanisms in plant genome editing and exemplify the applications in plant research. Both classical and recently discovered CRISPR-Cas systems are included, detailing the class, type, structures and functions of each. We conclude by highlighting the challenges that come with CRISPR-Cas and offer suggestions on how to tackle them. We believe the gene editing toolbox will be greatly enriched, providing new avenues for a more efficient and precise breeding of climate-resilient crops.
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Affiliation(s)
- Fangning Zhang
- College of Life Sciences, Shandong Normal University, Jinan 250014, China
| | - Ting Xiang Neik
- School of Biosciences, University of Nottingham Malaysia, Semenyih 43500, Malaysia
| | - William J W Thomas
- School of Biological Sciences, University of Western Australia, Perth, WA 6009, Australia
| | - Jacqueline Batley
- School of Biological Sciences, Institute of Agriculture, University of Western Australia, Perth, WA 6009, Australia
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12
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Resistance strategies for defense against Albugo candida causing white rust disease. Microbiol Res 2023; 270:127317. [PMID: 36805163 DOI: 10.1016/j.micres.2023.127317] [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: 05/26/2022] [Revised: 12/12/2022] [Accepted: 02/01/2023] [Indexed: 02/11/2023]
Abstract
Albugo candida, the causal organism of white rust, is an oomycete obligate pathogen infecting crops of Brassicaceae family occurred on aerial part, including vegetable and oilseed crops at all growth stages. The disease expression is characterized by local infection appearing on the abaxial region developing white or creamy yellow blister (sori) on leaves and systemic infections cause hypertrophy and hyperplasia leading to stag-head of reproductive organ. To overcome this problem, several disease management strategies like fungicide treatments were used in the field and disease-resistant varieties have also been developed using conventional and molecular breeding. Due to high variability among A. candida isolates, there is no single approach available to understand the diverse spectrum of disease symptoms. In absence of resistance sources against pathogen, repetitive cultivation of genetically-similar varieties locally tends to attract oomycete pathogen causing heavy yield losses. In the present review, a deep insight into the underlying role of the non-host resistance (NHR) defence mechanism available in plants, and the strategies to exploit available gene pools from plant species that are non-host to A. candida could serve as novel sources of resistance. This work summaries the current knowledge pertaining to the resistance sources available in non-host germ plasm, the understanding of defence mechanisms and the advance strategies covers molecular, biochemical and nature-based solutions in protecting Brassica crops from white rust disease.
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13
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Mourou M, Raimondo ML, Lops F, Carlucci A. Brassicaceae Fungi and Chromista Diseases: Molecular Detection and Host–Plant Interaction. PLANTS (BASEL, SWITZERLAND) 2023; 12:1033. [PMID: 36903895 PMCID: PMC10005080 DOI: 10.3390/plants12051033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 02/20/2023] [Accepted: 02/21/2023] [Indexed: 06/18/2023]
Abstract
Brassicaceae plants cover a large number of species with great economic and nutritional importance around the world. The production of Brassica spp. is limited due to phytopathogenic fungal species causing enormous yield losses. In this scenario, precise and rapid detection and identification of plant-infecting fungi are essential to facilitate the effective management of diseases. DNA-based molecular methods have become popular methods for accurate plant disease diagnostics and have been used to detect Brassicaceae fungal pathogens. Polymerase chain reaction (PCR) assays including nested, multiplex, quantitative post, and isothermal amplification methods represent a powerful weapon for early detection of fungal pathogens and preventively counteract diseases on brassicas with the aim to drastically reduce the fungicides as inputs. It is noteworthy also that Brassicaceae plants can establish a wide variety of relationships with fungi, ranging from harmful interactions with pathogens to beneficial associations with endophytic fungi. Thus, understanding host and pathogen interaction in brassica crops prompts better disease management. The present review reports the main fungal diseases of Brassicaceae, molecular methods used for their detection, review studies on the interaction between fungi and brassicas plants, and the various mechanisms involved including the application of omics technologies.
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Affiliation(s)
- Marwa Mourou
- Department of Agricultural Sciences, Food, Natural Resources and Engineering, University of Foggia, Via Napoli 25, 71122 Foggia, Italy
| | | | | | - Antonia Carlucci
- Department of Agricultural Sciences, Food, Natural Resources and Engineering, University of Foggia, Via Napoli 25, 71122 Foggia, Italy
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14
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Lawrenson T, Youles M, Chhetry M, Clarke M, Harwood W, Hundleby P. Efficient Targeted Mutagenesis in Brassica Crops Using CRISPR/Cas Systems. Methods Mol Biol 2023; 2653:253-271. [PMID: 36995631 DOI: 10.1007/978-1-0716-3131-7_16] [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
CRISPR/Cas has been established for targeted mutagenesis in many plant species since 2013, including Brassica napus and Brassica oleracea. Since that time, improvements have been made in terms of efficiency and choice of CRISPR systems. This protocol encompasses improved Cas9 efficiency and an alternative Cas12a system, allowing more challenging and diverse editing outcomes to be achieved.
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15
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Hoffman NE. USDA's revised biotechnology regulation's contribution to increasing agricultural sustainability and responding to climate change. FRONTIERS IN PLANT SCIENCE 2022; 13:1055529. [PMID: 36507369 PMCID: PMC9726801 DOI: 10.3389/fpls.2022.1055529] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Accepted: 10/28/2022] [Indexed: 06/17/2023]
Abstract
Biotechnology can provide a valuable tool to meet UN Sustainable Development Goals and U.S. initiatives to find climate solutions and improve agricultural sustainability. The literature contains hundreds of examples of crops that may serve this purpose, yet most remain un-launched due to high regulatory barriers. Recently the USDA revised its biotechnology regulations to make them more risk-proportionate, science-based, and streamlined. Here, we review some of the promising leads that may enable agriculture to contribute to UN sustainability goals. We further describe and discuss how the revised biotechnology regulation would hypothetically apply to these cases.
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16
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Dong S, Zou J, Fang B, Zhao Y, Shi F, Song G, Huang S, Feng H. Defect in BrMS1, a PHD-finger transcription factor, induces male sterility in ethyl methane sulfonate-mutagenized Chinese cabbage ( Brassica rapa L. ssp. pekinensis). FRONTIERS IN PLANT SCIENCE 2022; 13:992391. [PMID: 36061794 PMCID: PMC9433997 DOI: 10.3389/fpls.2022.992391] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Accepted: 08/01/2022] [Indexed: 05/30/2023]
Abstract
Male sterility is an ideal character for the female parent in commercial hybrid seed production in Chinese cabbages. We identified three allele male sterile mutants msm2-1/2/3 in progenies of ethyl methane sulfonate mutagenized Chinese cabbage. It was proved that their male sterilities were controlled by a same recessive nuclear gene. Cytological observation showed that the delayed tapetal programmed cell death (PCD) as well as the abnormal pollen exine and intine led to pollen abortion in these mutants. MutMap combined with KASP analyses showed that BraA10g019050.3C, a homologous gene of AtMS1 encoding a PHD-finger transcription factor and regulated pollen development, was the causal gene. A single-nucleotide mutation from G to A occurred at the 2443th base of BrMS1 in msm2-1 which results in premature termination of the PHD-finger protein translation; a single-nucleotide mutation from G to A existed at 1372th base in msm2-2 that makes for frameshift mutation; a single-nucleotide mutation from G to A distributed at 1887th base in msm2-3 which issues in the amino acid changed from Asp to Asn. The three allelic mutations in BrMS1 all led to the male sterile phenotype, which revealed its function in stamen development. Quantitative reverse transcription polymerase chain reaction analysis indicated that BrMS1 specially expressed in the anther at the early stage of pollen development and its expression level was higher in msm2-1/2/3 than that in the wild-type "FT." BrMS1 was located at the nucleus and a length of 12 amino acid residues at the C-terminus had transcriptional activation activity. RNA-seq indicated that the mutation in BrMS1 affected the transcript level of genes related to the tapetum PCD and pollen wall formation, which brought out the pollen abortion. These male sterile mutants we developed provided a novel gene resource for hybrid breeding in Chinese cabbage.
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17
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Kim NS, Yu J, Bae S, Kim HS, Park S, Lee K, Lee SI, Kim JA. Identification and Characterization of PSEUDO-RESPONSE REGULATOR (PRR) 1a and 1b Genes by CRISPR/Cas9-Targeted Mutagenesis in Chinese Cabbage (Brassica rapa L.). Int J Mol Sci 2022; 23:ijms23136963. [PMID: 35806003 PMCID: PMC9266808 DOI: 10.3390/ijms23136963] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Revised: 06/16/2022] [Accepted: 06/20/2022] [Indexed: 02/04/2023] Open
Abstract
The CRISPR/Cas9 site-directed gene-editing system offers great advantages for identifying gene function and crop improvement. The circadian clock measures and conveys day length information to control rhythmic hypocotyl growth in photoperiodic conditions, to achieve optimal fitness, but operates through largely unknown mechanisms. Here, we generated core circadian clock evening components, Brassica rapa PSEUDO-RESPONSE REGULATOR (BrPRR) 1a, 1b, and 1ab (both 1a and 1b double knockout) mutants, using CRISPR/Cas9 genome editing in Chinese cabbage, where 9–16 genetic edited lines of each mutant were obtained. The targeted deep sequencing showed that each mutant had 2–4 different mutation types at the target sites in the BrPRR1a and BrPRR1b genes. To identify the functions of BrPRR1a and 1b genes, hypocotyl length, and mRNA and protein levels of core circadian clock morning components, BrCCA1 (CIRCADIAN CLOCK-ASSOCIATED 1) and BrLHY (LATE ELONGATED HYPOCOTYL) a and b were examined under light/dark cycles and continuous light conditions. The BrPRR1a and 1ab double mutants showed longer hypocotyls, lower core circadian clock morning component mRNA and protein levels, and a shorter circadian rhythm than wildtype (WT). On the other hand, the BrPRR1b mutant was not significantly different from WT. These results suggested that two paralogous genes may not be associated with the same regulatory function in Chinese cabbage. Taken together, our results demonstrated that CRISPR/Cas9 is an efficient tool for achieving targeted genome modifications and elucidating the biological functions of circadian clock genes in B. rapa, for both breeding and improvement.
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Affiliation(s)
- Nan-Sun Kim
- Department of Agricultural Biotechnology, National Institute of Agricultural Science, Rural Development Administration, Jeonju 54874, Korea; (N.-S.K.); (H.S.K.); (S.P.); (K.L.); (S.I.L.)
| | - Jihyeon Yu
- Division of Life Sciences, Korea Polar Research Institute, Incheon 21990, Korea;
| | - Sangsu Bae
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul 03080, Korea;
| | - Hyang Suk Kim
- Department of Agricultural Biotechnology, National Institute of Agricultural Science, Rural Development Administration, Jeonju 54874, Korea; (N.-S.K.); (H.S.K.); (S.P.); (K.L.); (S.I.L.)
| | - Soyoung Park
- Department of Agricultural Biotechnology, National Institute of Agricultural Science, Rural Development Administration, Jeonju 54874, Korea; (N.-S.K.); (H.S.K.); (S.P.); (K.L.); (S.I.L.)
| | - Kijong Lee
- Department of Agricultural Biotechnology, National Institute of Agricultural Science, Rural Development Administration, Jeonju 54874, Korea; (N.-S.K.); (H.S.K.); (S.P.); (K.L.); (S.I.L.)
| | - Soo In Lee
- Department of Agricultural Biotechnology, National Institute of Agricultural Science, Rural Development Administration, Jeonju 54874, Korea; (N.-S.K.); (H.S.K.); (S.P.); (K.L.); (S.I.L.)
| | - Jin A. Kim
- Department of Agricultural Biotechnology, National Institute of Agricultural Science, Rural Development Administration, Jeonju 54874, Korea; (N.-S.K.); (H.S.K.); (S.P.); (K.L.); (S.I.L.)
- Correspondence: ; Tel.: +82-63-238-4619
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18
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Li J, Yu X, Zhang C, Li N, Zhao J. The application of CRISPR/Cas technologies to Brassica crops: current progress and future perspectives. ABIOTECH 2022; 3:146-161. [PMID: 36304520 PMCID: PMC9590542 DOI: 10.1007/s42994-022-00076-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Accepted: 06/20/2022] [Indexed: 12/04/2022]
Abstract
Brassica species are a global source of nutrients and edible vegetable oil for humans. However, all commercially important Brassica crops underwent a whole-genome triplication event, hindering the development of functional genomics and breeding programs. Fortunately, clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated (Cas) technologies, by allowing multiplex and precise genome engineering, have become valuable genome-editing tools and opened up new avenues for biotechnology. Here, we review current progress in the use of CRISPR/Cas technologies with an emphasis on the latest breakthroughs in precise genome editing. We also summarize the application of CRISPR/Cas technologies to Brassica crops for trait improvements. Finally, we discuss the challenges and future directions of these technologies for comprehensive application in Brassica crops. Ongoing advancement in CRISPR/Cas technologies, in combination with other achievements, will play a significant role in the genetic improvement and molecular breeding of Brassica crops.
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Affiliation(s)
- Jun Li
- State Key Laboratory of North China Crop Improvement and Regulation, College of Life Sciences, Hebei Agricultural University, Baoding, 071001 China
| | - Xiaoxiao Yu
- State Key Laboratory of North China Crop Improvement and Regulation, College of Life Sciences, Hebei Agricultural University, Baoding, 071001 China
| | - Chao Zhang
- State Key Laboratory of North China Crop Improvement and Regulation, College of Life Sciences, Hebei Agricultural University, Baoding, 071001 China
| | - Na Li
- Key Laboratory of Vegetable Germplasm Innovation and Utilization of Hebei, Collaborative Innovation Center of Vegetable Industry in Hebei, College of Horticulture, Hebei Agricultural University, Baoding, 071001 China
| | - Jianjun Zhao
- State Key Laboratory of North China Crop Improvement and Regulation, College of Life Sciences, Hebei Agricultural University, Baoding, 071001 China
- Key Laboratory of Vegetable Germplasm Innovation and Utilization of Hebei, Collaborative Innovation Center of Vegetable Industry in Hebei, College of Horticulture, Hebei Agricultural University, Baoding, 071001 China
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19
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Das D, Singha DL, Paswan RR, Chowdhury N, Sharma M, Reddy PS, Chikkaputtaiah C. Recent advancements in CRISPR/Cas technology for accelerated crop improvement. PLANTA 2022; 255:109. [PMID: 35460444 DOI: 10.1007/s00425-022-03894-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 03/29/2022] [Indexed: 06/14/2023]
Abstract
Precise genome engineering approaches could be perceived as a second paradigm for targeted trait improvement in crop plants, with the potential to overcome the constraints imposed by conventional CRISPR/Cas technology. The likelihood of reduced agricultural production due to highly turbulent climatic conditions increases as the global population expands. The second paradigm of stress-resilient crops with enhanced tolerance and increased productivity against various stresses is paramount to support global production and consumption equilibrium. Although traditional breeding approaches have substantially increased crop production and yield, effective strategies are anticipated to restore crop productivity even further in meeting the world's increasing food demands. CRISPR/Cas, which originated in prokaryotes, has surfaced as a coveted genome editing tool in recent decades, reshaping plant molecular biology in unprecedented ways and paving the way for engineering stress-tolerant crops. CRISPR/Cas is distinguished by its efficiency, high target specificity, and modularity, enables precise genetic modification of crop plants, allowing for the creation of allelic variations in the germplasm and the development of novel and more productive agricultural practices. Additionally, a slew of advanced biotechnologies premised on the CRISPR/Cas methodologies have augmented fundamental research and plant synthetic biology toolkits. Here, we describe gene editing tools, including CRISPR/Cas and its imitative tools, such as base and prime editing, multiplex genome editing, chromosome engineering followed by their implications in crop genetic improvement. Further, we comprehensively discuss the latest developments of CRISPR/Cas technology including CRISPR-mediated gene drive, tissue-specific genome editing, dCas9 mediated epigenetic modification and programmed self-elimination of transgenes in plants. Finally, we highlight the applicability and scope of advanced CRISPR-based techniques in crop genetic improvement.
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Affiliation(s)
- Debajit Das
- Biological Sciences and Technology Division, CSIR-North East Institute of Science and Technology (CSIR-NEIST), Jorhat, Assam, 785006, India
| | - Dhanawantari L Singha
- Biological Sciences and Technology Division, CSIR-North East Institute of Science and Technology (CSIR-NEIST), Jorhat, Assam, 785006, India
| | - Ricky Raj Paswan
- Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat, Assam, 785013, India
| | - Naimisha Chowdhury
- Biological Sciences and Technology Division, CSIR-North East Institute of Science and Technology (CSIR-NEIST), Jorhat, Assam, 785006, India
| | - Monica Sharma
- Biological Sciences and Technology Division, CSIR-North East Institute of Science and Technology (CSIR-NEIST), Jorhat, Assam, 785006, India
| | - Palakolanu Sudhakar Reddy
- International Crop Research Institute for the Semi Arid Tropics (ICRISAT), Patancheru, Hyderabad, 502 324, India
| | - Channakeshavaiah Chikkaputtaiah
- Biological Sciences and Technology Division, CSIR-North East Institute of Science and Technology (CSIR-NEIST), Jorhat, Assam, 785006, India.
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201 002, India.
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20
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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: 3.5] [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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21
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Gupta P, Hirschberg J. The Genetic Components of a Natural Color Palette: A Comprehensive List of Carotenoid Pathway Mutations in Plants. FRONTIERS IN PLANT SCIENCE 2022; 12:806184. [PMID: 35069664 PMCID: PMC8770946 DOI: 10.3389/fpls.2021.806184] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Accepted: 12/08/2021] [Indexed: 05/16/2023]
Abstract
Carotenoids comprise the most widely distributed natural pigments. In plants, they play indispensable roles in photosynthesis, furnish colors to flowers and fruit and serve as precursor molecules for the synthesis of apocarotenoids, including aroma and scent, phytohormones and other signaling molecules. Dietary carotenoids are vital to human health as a source of provitamin A and antioxidants. Hence, the enormous interest in carotenoids of crop plants. Over the past three decades, the carotenoid biosynthesis pathway has been mainly deciphered due to the characterization of natural and induced mutations that impair this process. Over the year, numerous mutations have been studied in dozens of plant species. Their phenotypes have significantly expanded our understanding of the biochemical and molecular processes underlying carotenoid accumulation in crops. Several of them were employed in the breeding of crops with higher nutritional value. This compendium of all known random and targeted mutants available in the carotenoid metabolic pathway in plants provides a valuable resource for future research on carotenoid biosynthesis in plant species.
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Affiliation(s)
| | - Joseph Hirschberg
- Department of Genetics, Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
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22
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Zhang S, Wu S, Hu C, Yang Q, Dong T, Sheng O, Deng G, He W, Dou T, Li C, Sun C, Yi G, Bi F. Increased mutation efficiency of CRISPR/Cas9 genome editing in banana by optimized construct. PeerJ 2022; 10:e12664. [PMID: 35036088 PMCID: PMC8742547 DOI: 10.7717/peerj.12664] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 11/30/2021] [Indexed: 01/07/2023] Open
Abstract
The CRISPR/Cas9-mediated genome editing system has been used extensively to engineer targeted mutations in a wide variety of species. Its application in banana, however, has been hindered because of the species' triploid nature and low genome editing efficiency. This has delayed the development of a DNA-free genome editing approach. In this study, we reported that the endogenous U6 promoter and banana codon-optimized Cas9 apparently increased mutation frequency in banana, and we generated a method to validate the mutation efficiency of the CRISPR/Cas9-mediated genome editing system based on transient expression in protoplasts. The activity of the MaU6c promoter was approximately four times higher than that of the OsU6a promoter in banana protoplasts. The application of this promoter and banana codon-optimized Cas9 in CRISPR/Cas9 cassette resulted in a fourfold increase in mutation efficiency compared with the previous CRISPR/Cas9 cassette for banana. Our results indicated that the optimized CRISPR/Cas9 system was effective for mutating targeted genes in banana and thus will improve the applications for basic functional genomics. These findings are relevant to future germplasm improvement and provide a foundation for developing DNA-free genome editing technology in banana.
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Affiliation(s)
- Sen Zhang
- Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization (Ministry of Agriculture and Rural Affairs), Guangdong Key Laboratory of Tropical and Subtropical Fruit Tree Research, Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong, China,College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Shaoping Wu
- Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization (Ministry of Agriculture and Rural Affairs), Guangdong Key Laboratory of Tropical and Subtropical Fruit Tree Research, Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong, China,College of Life Sciences, Zhaoqing University, Zhaoqing, Guangdong, China
| | - Chunhua Hu
- Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization (Ministry of Agriculture and Rural Affairs), Guangdong Key Laboratory of Tropical and Subtropical Fruit Tree Research, Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong, China
| | - Qiaosong Yang
- Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization (Ministry of Agriculture and Rural Affairs), Guangdong Key Laboratory of Tropical and Subtropical Fruit Tree Research, Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong, China
| | - Tao Dong
- Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization (Ministry of Agriculture and Rural Affairs), Guangdong Key Laboratory of Tropical and Subtropical Fruit Tree Research, Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong, China
| | - Ou Sheng
- Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization (Ministry of Agriculture and Rural Affairs), Guangdong Key Laboratory of Tropical and Subtropical Fruit Tree Research, Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong, China
| | - Guiming Deng
- Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization (Ministry of Agriculture and Rural Affairs), Guangdong Key Laboratory of Tropical and Subtropical Fruit Tree Research, Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong, China
| | - Weidi He
- Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization (Ministry of Agriculture and Rural Affairs), Guangdong Key Laboratory of Tropical and Subtropical Fruit Tree Research, Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong, China
| | - Tongxin Dou
- Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization (Ministry of Agriculture and Rural Affairs), Guangdong Key Laboratory of Tropical and Subtropical Fruit Tree Research, Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong, China
| | - Chunyu Li
- Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization (Ministry of Agriculture and Rural Affairs), Guangdong Key Laboratory of Tropical and Subtropical Fruit Tree Research, Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong, China
| | - Chenkang Sun
- Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization (Ministry of Agriculture and Rural Affairs), Guangdong Key Laboratory of Tropical and Subtropical Fruit Tree Research, Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong, China,College of Life Sciences, South China Agricultural University, Guangzhou, Guangdong
| | - Ganjun Yi
- Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization (Ministry of Agriculture and Rural Affairs), Guangdong Key Laboratory of Tropical and Subtropical Fruit Tree Research, Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong, China
| | - Fangcheng Bi
- Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization (Ministry of Agriculture and Rural Affairs), Guangdong Key Laboratory of Tropical and Subtropical Fruit Tree Research, Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong, China
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23
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Wang T, Zhang C, Zhang H, Zhu H. CRISPR/Cas9-Mediated Gene Editing Revolutionizes the Improvement of Horticulture Food Crops. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:13260-13269. [PMID: 33734711 DOI: 10.1021/acs.jafc.1c00104] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Horticultural food crops are important sources of nutrients for humans. With the increase of the global population, enhanced horticulture food crop production has become a new challenge, and enriching their nutritional content has also been required. Gene editing systems, such as zinc finger nucleases, transcription activator-like effector nucleases, and clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated 9 (Cas9), have accelerated crop improvement through the modification of targeted genomes precisely. Here, we review the development of various gene editors and compare their advantages and shortcomings, especially the newly emerging CRISPR/Cas systems, such as base editing and prime editing. We also summarize their practical applications in crop trait improvement, including yield, nutritional quality, and other consumer traits.
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Affiliation(s)
- Tian Wang
- College of Life Science, Shandong Normal University, Jinan, Shandong 250014, People's Republic of China
| | - Chunjiao Zhang
- Supervision, Inspection & Testing Center of Agricultural Products Quality, Ministry of Agriculture and Rural Affairs, Beijing 100083, People's Republic of China
| | - Hongyan Zhang
- College of Life Science, Shandong Normal University, Jinan, Shandong 250014, People's Republic of China
| | - Hongliang Zhu
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, People's Republic of China
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24
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Kawall K. The Generic Risks and the Potential of SDN-1 Applications in Crop Plants. PLANTS (BASEL, SWITZERLAND) 2021; 10:2259. [PMID: 34834620 PMCID: PMC8622673 DOI: 10.3390/plants10112259] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Revised: 10/01/2021] [Accepted: 10/18/2021] [Indexed: 12/26/2022]
Abstract
The use of site-directed nucleases (SDNs) in crop plants to alter market-oriented traits is expanding rapidly. At the same time, there is an on-going debate around the safety and regulation of crops altered with the site-directed nuclease 1 (SDN-1) technology. SDN-1 applications can be used to induce a variety of genetic alterations ranging from fairly 'simple' genetic alterations to complex changes in plant genomes using, for example, multiplexing approaches. The resulting plants can contain modified alleles and associated traits, which are either known or unknown in conventionally bred plants. The European Commission recently published a study on new genomic techniques suggesting an adaption of the current GMO legislation by emphasizing that targeted mutagenesis techniques can produce genomic alterations that can also be obtained by natural mutations or conventional breeding techniques. This review highlights the need for a case-specific risk assessment of crop plants derived from SDN-1 applications considering both the characteristics of the product and the process to ensure a high level of protection of human and animal health and the environment. The published literature on so-called market-oriented traits in crop plants altered with SDN-1 applications is analyzed here to determine the types of SDN-1 application in plants, and to reflect upon the complexity and the naturalness of such products. Furthermore, it demonstrates the potential of SDN-1 applications to induce complex alterations in plant genomes that are relevant to generic SDN-associated risks. In summary, it was found that nearly half of plants with so-called market-oriented traits contain complex genomic alterations induced by SDN-1 applications, which may also pose new types of risks. It further underscores the need for data on both the process and the end-product for a case-by-case risk assessment of plants derived from SDN-1 applications.
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Affiliation(s)
- Katharina Kawall
- Fachstelle Gentechnik und Umwelt, Frohschammerstr. 14, 80807 Munich, Germany
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Abstract
Broccoli (Brassica oleracea L. var. italica) is one of the most important vegetable crops cultivated worldwide. The market demand for broccoli is still increasing due to its richness in vitamins, anthocyanins, mineral substances, fiber, secondary metabolites and other nutrients. The famous secondary metabolites, glucosinolates, sulforaphane and selenium have protective effects against cancer. Significant progress has been made in fine-mapping and cloning genes that are responsible for important traits; this progress provides a foundation for marker-assisted selection (MAS) in broccoli breeding. Genetic engineering by the well-developed Agrobacterium tumefaciens-mediated transformation in broccoli has contributed to the improvement of quality; postharvest life; glucosinolate and sulforaphane content; and resistance to insects, pathogens and abiotic stresses. Here, we review recent progress in the genetics and molecular breeding of broccoli. Future perspectives for improving broccoli are also briefly discussed.
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Peng H, Zheng Y, Zhao Z, Li J. Multigene editing: current approaches and beyond. Brief Bioinform 2021; 22:bbaa396. [PMID: 33428725 DOI: 10.1093/bib/bbaa396] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Revised: 11/15/2020] [Accepted: 12/03/2020] [Indexed: 11/14/2022] Open
Abstract
CRISPR/Cas9 multigene editing is an active and widely studied topic in the fields of biomedicine and biology. It involves a simultaneous participation of multiple single-guide RNAs (sgRNAs) to edit multiple target genes in a way that each gene is edited by one of these sgRNAs. There are possibly numerous sgRNA candidates capable of on-target editing on each of these genes with various efficiencies. Meanwhile, each of these sgRNA candidates may cause unwanted off-target editing at many other genes. Therefore, selection optimization of these multiple sgRNAs is demanded so as to minimize the number of sgRNAs and thus reduce the collective negative effects caused by the off-target editing. This survey reviews wet-laboratory approaches to the implementation of multigene editing and their needs of computational tools for better design. We found that though off-target editing is unavoidable during the gene editing, those disfavored cuttings by some target genes' sgRNAs can potentially become on-target editing sites for some other genes of interests. This off-to-on role conversion is beneficial to optimize the sgRNA selection in multigene editing. We present a preference cutting score to assess those beneficial off-target cutting sites, which have a few mismatches with their host genes' on-target editing sites. These potential sgRNAs can be prioritized for recommendation via ranking their on-target average cutting efficiency, the total off-target site number and their average preference cutting score. We also present case studies on cancer-associated genes to demonstrate tremendous usefulness of the new method.
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Affiliation(s)
- Hui Peng
- Data Science Institute, University of Technology Sydney, PO Box 123, Ultimo, NSW 2007, Australia
- School of Computing, National University of Singapore, 13 Computing Drive, 117417, Singapore
| | - Yi Zheng
- Data Science Institute, University of Technology Sydney, PO Box 123, Ultimo, NSW 2007, Australia
| | - Zhixun Zhao
- Data Science Institute, University of Technology Sydney, PO Box 123, Ultimo, NSW 2007, Australia
| | - Jinyan Li
- Data Science Institute, University of Technology Sydney, PO Box 123, Ultimo, NSW 2007, Australia
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Improvement of glucosinolates by metabolic engineering in Brassica crops. ABIOTECH 2021; 2:314-329. [PMID: 36303883 PMCID: PMC9590530 DOI: 10.1007/s42994-021-00057-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2021] [Accepted: 07/07/2021] [Indexed: 02/08/2023]
Abstract
Glucosinolates (GSLs) are a class of sulfur- and nitrogen-containing, and amino acid-derived important secondary metabolites, which mainly present in plants of Brassicaceae family, including Brassica crops, such as broccoli, cabbage, and oilseed rape. The bioactive GSL metabolites confer benefits to plant defense, human health, and the unique flavor of some Brassica crops. However, certain GSL profiles have adverse effects and are known as anti-nutritional factors. This has attracted mounting attempts to increase beneficial GSLs and reduce detrimental ones in the most commonly consumed Brassica crops. We provide a comprehensive overview of metabolic engineering applied in Brassica crops to achieve this purpose, including modulation of GSL biosynthesis, ablation of GSL hydrolysis, inhibition of GSL transport processes, and redirection of metabolic flux to GSL. Moreover, advances in omics approaches, i.e., genomics, transcriptome, and metabolome, applied in the elucidation of GSL metabolism in Brassica crops, as well as promising and potential genome-editing technologies are also discussed.
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Pavese V, Moglia A, Corredoira E, Martínez MT, Torello Marinoni D, Botta R. First Report of CRISPR/Cas9 Gene Editing in Castanea sativa Mill. FRONTIERS IN PLANT SCIENCE 2021; 12:728516. [PMID: 34512704 PMCID: PMC8424114 DOI: 10.3389/fpls.2021.728516] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Accepted: 07/26/2021] [Indexed: 06/13/2023]
Abstract
CRISPR/Cas9 has emerged as the most important tool for genome engineering due to its simplicity, design flexibility, and high efficiency. This technology makes it possible to induce point mutations in one or some target sequences simultaneously, as well as to introduce new genetic variants by homology-directed recombination. However, this approach remains largely unexplored in forest species. In this study, we reported the first example of CRISPR/Cas9-mediated gene editing in Castanea genus. As a proof of concept, we targeted the gene encoding phytoene desaturase (pds), whose mutation disrupts chlorophyll biosynthesis allowing for the visual assessment of knockout efficiency. Globular and early torpedo-stage somatic embryos of Castanea sativa (European chestnut) were cocultured for 5 days with a CRISPR/Cas9 construct targeting two conserved gene regions of pds and subsequently cultured on a selection medium with kanamycin. After 8 weeks of subculture on selection medium, four kanamycin-resistant embryogenetic lines were isolated. Genotyping of these lines through target Sanger sequencing of amplicons revealed successful gene editing. Cotyledonary somatic embryos were maturated on maltose 3% and cold-stored at 4°C for 2 months. Subsequently, embryos were subjected to the germination process to produce albino plants. This study opens the way to the use of the CRISPR/Cas9 system in European chestnut for biotechnological applications.
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Affiliation(s)
- Vera Pavese
- Dipartimento di Scienze Agrarie, Forestali e Alimentari (DISAFA), Università degli Studi di Torino, Grugliasco, Italy
| | - Andrea Moglia
- Dipartimento di Scienze Agrarie, Forestali e Alimentari (DISAFA), Università degli Studi di Torino, Grugliasco, Italy
| | - Elena Corredoira
- Instituto de Investigaciones Agrobiológicas de Galicia (IIAG)-Consejo Superior de Investigaciones Científicas, Santiago de Compostela, Spain
| | - Mª Teresa Martínez
- Instituto de Investigaciones Agrobiológicas de Galicia (IIAG)-Consejo Superior de Investigaciones Científicas, Santiago de Compostela, Spain
| | - Daniela Torello Marinoni
- Dipartimento di Scienze Agrarie, Forestali e Alimentari (DISAFA), Università degli Studi di Torino, Grugliasco, Italy
| | - Roberto Botta
- Dipartimento di Scienze Agrarie, Forestali e Alimentari (DISAFA), Università degli Studi di Torino, Grugliasco, Italy
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Kim YC, Kang Y, Yang EY, Cho MC, Schafleitner R, Lee JH, Jang S. Applications and Major Achievements of Genome Editing in Vegetable Crops: A Review. FRONTIERS IN PLANT SCIENCE 2021; 12:688980. [PMID: 34178006 PMCID: PMC8231707 DOI: 10.3389/fpls.2021.688980] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 05/18/2021] [Indexed: 05/04/2023]
Abstract
The emergence of genome-editing technology has allowed manipulation of DNA sequences in genomes to precisely remove or replace specific sequences in organisms resulting in targeted mutations. In plants, genome editing is an attractive method to alter gene functions to generate improved crop varieties. Genome editing is thought to be simple to use and has a lower risk of off-target effects compared to classical mutation breeding. Furthermore, genome-editing technology tools can also be applied directly to crops that contain complex genomes and/or are not easily bred using traditional methods. Currently, highly versatile genome-editing tools for precise and predictable editing of almost any locus in the plant genome make it possible to extend the range of application, including functional genomics research and molecular crop breeding. Vegetables are essential nutrient sources for humans and provide vitamins, minerals, and fiber to diets, thereby contributing to human health. In this review, we provide an overview of the brief history of genome-editing technologies and the components of genome-editing tool boxes, and illustrate basic modes of operation in representative systems. We describe the current and potential practical application of genome editing for the development of improved nutritious vegetables and present several case studies demonstrating the potential of the technology. Finally, we highlight future directions and challenges in applying genome-editing systems to vegetable crops for research and product development.
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Affiliation(s)
- Young-Cheon Kim
- Division of Life Sciences, Jeonbuk National University, Jeonju, South Korea
| | - Yeeun Kang
- World Vegetable Center Korea Office, Wanju-gun, South Korea
| | - Eun-Young Yang
- National Institute of Horticultural and Herbal Science (NIHHS), Rural Development Administration (RDA), Wanju-gun, South Korea
| | - Myeong-Cheoul Cho
- National Institute of Horticultural and Herbal Science (NIHHS), Rural Development Administration (RDA), Wanju-gun, South Korea
| | | | - Jeong Hwan Lee
- Division of Life Sciences, Jeonbuk National University, Jeonju, South Korea
| | - Seonghoe Jang
- World Vegetable Center Korea Office, Wanju-gun, South Korea
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Mohd Saad NS, Severn-Ellis AA, Pradhan A, Edwards D, Batley J. Genomics Armed With Diversity Leads the Way in Brassica Improvement in a Changing Global Environment. Front Genet 2021; 12:600789. [PMID: 33679880 PMCID: PMC7930750 DOI: 10.3389/fgene.2021.600789] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Accepted: 01/15/2021] [Indexed: 12/14/2022] Open
Abstract
Meeting the needs of a growing world population in the face of imminent climate change is a challenge; breeding of vegetable and oilseed Brassica crops is part of the race in meeting these demands. Available genetic diversity constituting the foundation of breeding is essential in plant improvement. Elite varieties, land races, and crop wild species are important resources of useful variation and are available from existing genepools or genebanks. Conservation of diversity in genepools, genebanks, and even the wild is crucial in preventing the loss of variation for future breeding efforts. In addition, the identification of suitable parental lines and alleles is critical in ensuring the development of resilient Brassica crops. During the past two decades, an increasing number of high-quality nuclear and organellar Brassica genomes have been assembled. Whole-genome re-sequencing and the development of pan-genomes are overcoming the limitations of the single reference genome and provide the basis for further exploration. Genomic and complementary omic tools such as microarrays, transcriptomics, epigenetics, and reverse genetics facilitate the study of crop evolution, breeding histories, and the discovery of loci associated with highly sought-after agronomic traits. Furthermore, in genomic selection, predicted breeding values based on phenotype and genome-wide marker scores allow the preselection of promising genotypes, enhancing genetic gains and substantially quickening the breeding cycle. It is clear that genomics, armed with diversity, is set to lead the way in Brassica improvement; however, a multidisciplinary plant breeding approach that includes phenotype = genotype × environment × management interaction will ultimately ensure the selection of resilient Brassica varieties ready for climate change.
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Affiliation(s)
| | | | | | | | - Jacqueline Batley
- School of Biological Sciences Western Australia and UWA Institute of Agriculture, University of Western Australia, Perth, WA, Australia
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Anupriya C, Shradha N, Prasun B, Abha A, Pankaj S, Abdin MZ, Neeraj S. Genomic and Molecular Perspectives of Host-pathogen Interaction and Resistance Strategies against White Rust in Oilseed Mustard. Curr Genomics 2020; 21:179-193. [PMID: 33071612 PMCID: PMC7521032 DOI: 10.2174/1389202921999200508075410] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Revised: 02/25/2020] [Accepted: 03/14/2020] [Indexed: 11/29/2022] Open
Abstract
Oilseed brassicas stand as the second most valuable source of vegetable oil and the third most traded one across the globe. However, the yield can be severely affected by infections caused by phytopathogens. White rust is a major oomycete disease of oilseed brassicas resulting in up to 60% yield loss globally. So far, success in the development of oomycete resistant Brassicas through conventional breeding has been limited. Hence, there is an imperative need to blend conventional and frontier biotechnological means to breed for improved crop protection and yield. This review provides a deep insight into the white rust disease and explains the oomycete-plant molecular events with special reference to Albugo candida describing the role of effector molecules, A. candida secretome, and disease response mechanism along with nucleotide-binding leucine-rich repeat receptor (NLR) signaling. Based on these facts, we further discussed the recent progress and future scopes of genomic approaches to transfer white rust resistance in the susceptible varieties of oilseed brassicas, while elucidating the role of resistance and susceptibility genes. Novel genomic technologies have been widely used in crop sustainability by deploying resistance in the host. Enrichment of NLR repertoire, over-expression of R genes, silencing of avirulent and disease susceptibility genes through RNA interference and CRSPR-Cas are technologies which have been successfully applied against pathogen-resistance mechanism. The article provides new insight into Albugo and Brassica genomics which could be useful for producing high yielding and WR resistant oilseed cultivars across the globe.
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Affiliation(s)
- Chatterjee Anupriya
- 1Amity Institute of Microbial Technology, Amity University, Uttar Pradesh, Noida-201313, India; 2International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi-110067, India; 3Centre for Agricultural Biotechnology, Amity Institute of Microbial Technology, Amity University Uttar Pradesh, Noida-201313, India; 4Amity Institute of Biotechnology, Amity University Uttar Pradesh, Noida-201313, India; 5Department of Biotechnology, Jamia Hamdard University, New Delhi-110062, India
| | - Nirwan Shradha
- 1Amity Institute of Microbial Technology, Amity University, Uttar Pradesh, Noida-201313, India; 2International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi-110067, India; 3Centre for Agricultural Biotechnology, Amity Institute of Microbial Technology, Amity University Uttar Pradesh, Noida-201313, India; 4Amity Institute of Biotechnology, Amity University Uttar Pradesh, Noida-201313, India; 5Department of Biotechnology, Jamia Hamdard University, New Delhi-110062, India
| | - Bandyopadhyay Prasun
- 1Amity Institute of Microbial Technology, Amity University, Uttar Pradesh, Noida-201313, India; 2International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi-110067, India; 3Centre for Agricultural Biotechnology, Amity Institute of Microbial Technology, Amity University Uttar Pradesh, Noida-201313, India; 4Amity Institute of Biotechnology, Amity University Uttar Pradesh, Noida-201313, India; 5Department of Biotechnology, Jamia Hamdard University, New Delhi-110062, India
| | - Agnihotri Abha
- 1Amity Institute of Microbial Technology, Amity University, Uttar Pradesh, Noida-201313, India; 2International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi-110067, India; 3Centre for Agricultural Biotechnology, Amity Institute of Microbial Technology, Amity University Uttar Pradesh, Noida-201313, India; 4Amity Institute of Biotechnology, Amity University Uttar Pradesh, Noida-201313, India; 5Department of Biotechnology, Jamia Hamdard University, New Delhi-110062, India
| | - Sharma Pankaj
- 1Amity Institute of Microbial Technology, Amity University, Uttar Pradesh, Noida-201313, India; 2International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi-110067, India; 3Centre for Agricultural Biotechnology, Amity Institute of Microbial Technology, Amity University Uttar Pradesh, Noida-201313, India; 4Amity Institute of Biotechnology, Amity University Uttar Pradesh, Noida-201313, India; 5Department of Biotechnology, Jamia Hamdard University, New Delhi-110062, India
| | - Malik Zainul Abdin
- 1Amity Institute of Microbial Technology, Amity University, Uttar Pradesh, Noida-201313, India; 2International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi-110067, India; 3Centre for Agricultural Biotechnology, Amity Institute of Microbial Technology, Amity University Uttar Pradesh, Noida-201313, India; 4Amity Institute of Biotechnology, Amity University Uttar Pradesh, Noida-201313, India; 5Department of Biotechnology, Jamia Hamdard University, New Delhi-110062, India
| | - Shrivastava Neeraj
- 1Amity Institute of Microbial Technology, Amity University, Uttar Pradesh, Noida-201313, India; 2International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi-110067, India; 3Centre for Agricultural Biotechnology, Amity Institute of Microbial Technology, Amity University Uttar Pradesh, Noida-201313, India; 4Amity Institute of Biotechnology, Amity University Uttar Pradesh, Noida-201313, India; 5Department of Biotechnology, Jamia Hamdard University, New Delhi-110062, India
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Bhatta BP, Malla S. Improving Horticultural Crops via CRISPR/Cas9: Current Successes and Prospects. PLANTS (BASEL, SWITZERLAND) 2020; 9:E1360. [PMID: 33066510 PMCID: PMC7602190 DOI: 10.3390/plants9101360] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Revised: 10/03/2020] [Accepted: 10/12/2020] [Indexed: 12/23/2022]
Abstract
Horticultural crops include a diverse array of crops comprising fruits, vegetables, nuts, flowers, aromatic and medicinal plants. They provide nutritional, medicinal, and aesthetic benefits to mankind. However, these crops undergo many biotic (e.g., diseases, pests) and abiotic stresses (e.g., drought, salinity). Conventional breeding strategies to improve traits in crops involve the use of a series of backcrossing and selection for introgression of a beneficial trait into elite germplasm, which is time and resource consuming. Recent new plant breeding tools such as clustered regularly interspaced short palindromic repeats (CRISPR) /CRISPR-associated protein-9 (Cas9) technique have the potential to be rapid, cost-effective, and precise tools for crop improvement. In this review article, we explore the CRISPR/Cas9 technology, its history, classification, general applications, specific uses in horticultural crops, challenges, existing resources, associated regulatory aspects, and the way forward.
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Affiliation(s)
- Bed Prakash Bhatta
- Department of Horticultural Sciences, Texas A&M University, College Station, TX 77843, USA;
- Texas A&M AgriLife Research and Extension Center, Uvalde, TX 78801, USA
| | - Subas Malla
- Texas A&M AgriLife Research and Extension Center, Uvalde, TX 78801, USA
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33
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Applications of CRISPR-Cas in agriculture and plant biotechnology. Nat Rev Mol Cell Biol 2020; 21:661-677. [PMID: 32973356 DOI: 10.1038/s41580-020-00288-9] [Citation(s) in RCA: 306] [Impact Index Per Article: 76.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/11/2020] [Indexed: 12/26/2022]
Abstract
The prokaryote-derived CRISPR-Cas genome editing technology has altered plant molecular biology beyond all expectations. Characterized by robustness and high target specificity and programmability, CRISPR-Cas allows precise genetic manipulation of crop species, which provides the opportunity to create germplasms with beneficial traits and to develop novel, more sustainable agricultural systems. Furthermore, the numerous emerging biotechnologies based on CRISPR-Cas platforms have expanded the toolbox of fundamental research and plant synthetic biology. In this Review, we first briefly describe gene editing by CRISPR-Cas, focusing on the newest, precise gene editing technologies such as base editing and prime editing. We then discuss the most important applications of CRISPR-Cas in increasing plant yield, quality, disease resistance and herbicide resistance, breeding and accelerated domestication. We also highlight the most recent breakthroughs in CRISPR-Cas-related plant biotechnologies, including CRISPR-Cas reagent delivery, gene regulation, multiplexed gene editing and mutagenesis and directed evolution technologies. Finally, we discuss prospective applications of this game-changing technology.
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Zhang Y, Held MA, Showalter AM. Elucidating the roles of three β-glucuronosyltransferases (GLCATs) acting on arabinogalactan-proteins using a CRISPR-Cas9 multiplexing approach in Arabidopsis. BMC PLANT BIOLOGY 2020; 20:221. [PMID: 32423474 PMCID: PMC7236193 DOI: 10.1186/s12870-020-02420-5] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Accepted: 04/29/2020] [Indexed: 05/20/2023]
Abstract
BACKGROUND Arabinogalactan-proteins (AGPs) are one of the most complex protein families in the plant kingdom and are present in the cell walls of all land plants. AGPs are implicated in diverse biological processes such as plant growth, development, reproduction, and stress responses. AGPs are extensively glycosylated by the addition of type II arabinogalactan (AG) polysaccharides to hydroxyproline residues in their protein cores. Glucuronic acid (GlcA) is the only negatively charged sugar added to AGPs and the functions of GlcA residues on AGPs remain to be elucidated. RESULTS Three members of the CAZy GT14 family (GLCAT14A-At5g39990, GLCAT14B-At5g15050, and GLCAT14C-At2g37585), which are responsible for transferring glucuronic acid (GlcA) to AGPs, were functionally characterized using a CRISPR/Cas9 gene editing approach in Arabidopsis. RNA seq and qRT-PCR data showed all three GLCAT genes were broadly expressed in different plant tissues, with GLCAT14A and GLCAT14B showing particularly high expression in the micropylar endosperm. Biochemical analysis of the AGPs from knock-out mutants of various glcat single, double, and triple mutants revealed that double and triple mutants generally had small increases of Ara and Gal and concomitant reductions of GlcA, particularly in the glcat14a glcat14b and glcat14a glcat14b glcat14c mutants. Moreover, AGPs isolated from all the glcat mutants displayed significant reductions in calcium binding compared to WT. Further phenotypic analyses found that the glcat14a glcat14b and glcat14a glcat14b glcat14c mutants exhibited significant delays in seed germination, reductions in root hair length, reductions in trichome branching, and accumulation of defective pollen grains. Additionally, both glcat14b glcat14c and glcat14a glcat14b glcat14c displayed significantly shorter siliques and reduced seed set. Finally, all higher-order mutants exhibited significant reductions in adherent seed coat mucilage. CONCLUSIONS This research provides genetic evidence that GLCAT14A-C function in the transfer of GlcA to AGPs, which in turn play a role in a variety of biochemical and physiological phenotypes including calcium binding by AGPs, seed germination, root hair growth, trichome branching, pollen development, silique development, seed set, and adherent seed coat mucilage accumulation.
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Affiliation(s)
- Yuan Zhang
- Molecular and Cellular Biology Program, Ohio University, Athens, OH 45701–2979 USA
- Department of Environmental & Plant Biology, Ohio University, Athens, OH 45701–2979 USA
| | - Michael A. Held
- Molecular and Cellular Biology Program, Ohio University, Athens, OH 45701–2979 USA
- Department of Chemistry & Biochemistry, Ohio University, Athens, OH 45701–2979 USA
| | - Allan M. Showalter
- Molecular and Cellular Biology Program, Ohio University, Athens, OH 45701–2979 USA
- Department of Environmental & Plant Biology, Ohio University, Athens, OH 45701–2979 USA
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Lv H, Fang Z, Yang L, Zhang Y, Wang Y. An update on the arsenal: mining resistance genes for disease management of Brassica crops in the genomic era. HORTICULTURE RESEARCH 2020; 7:34. [PMID: 32194970 PMCID: PMC7072071 DOI: 10.1038/s41438-020-0257-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Revised: 01/12/2020] [Accepted: 01/15/2020] [Indexed: 05/18/2023]
Abstract
Brassica species include many economically important crops that provide nutrition and health-promoting substances to humans worldwide. However, as with all crops, their production is constantly threatened by emerging viral, bacterial, and fungal diseases, whose incidence has increased in recent years. Traditional methods of control are often costly, present limited effectiveness, and cause environmental damage; instead, the ideal approach is to mine and utilize the resistance genes of the Brassica crop hosts themselves. Fortunately, the development of genomics, molecular genetics, and biological techniques enables us to rapidly discover and apply resistance (R) genes. Herein, the R genes identified in Brassica crops are summarized, including their mapping and cloning, possible molecular mechanisms, and application in resistance breeding. Future perspectives concerning how to accurately discover additional R gene resources and efficiently utilize these genes in the genomic era are also discussed.
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Affiliation(s)
- Honghao Lv
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, 12# Zhongguancun South Street, Beijing, 100081 China
| | - Zhiyuan Fang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, 12# Zhongguancun South Street, Beijing, 100081 China
| | - Limei Yang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, 12# Zhongguancun South Street, Beijing, 100081 China
| | - Yangyong Zhang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, 12# Zhongguancun South Street, Beijing, 100081 China
| | - Yong Wang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, 12# Zhongguancun South Street, Beijing, 100081 China
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Cheng Q, Li T, Ai Y, Lu Q, Wang Y, Wu L, Liu J, Sun L, Shen H. Phenotypic, genetic, and molecular function of msc-2, a genic male sterile mutant in pepper (Capsicum annuum L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2020; 133:843-855. [PMID: 31863155 DOI: 10.1007/s00122-019-03510-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Accepted: 12/11/2019] [Indexed: 06/10/2023]
Abstract
Bulked segregant analysis and fine mapping delimited the pepper genic male sterile (msc-2) locus into a 336 kb region on chromosome 5. A strong candidate gene, Capana05g000766, a homolog of AtMS1, was indentified in this region. Genic male sterility (msc-2) is used to produce hybrid seeds in Northern China. However, no co-segregated markers have been reported or candidate genes controlling this trait have been cloned. Here, bulked segregant analysis and genotyping of an F2 population and a 18Q5431AB line were employed to fine map msc-2, which was delimited to a 336 kb region. In this region, Capana05g000766 was a homolog of AtMS1, which encodes a plant homeodomain finger involved in tapetum development. A "T" deletion in the Capana05g000766 locus leads to a premature stop codon, which may cause a loss-of-function mutation. Real-time PCR analysis revealed that Capana05g000766 was an anther-specific gene and down-regulation of the gene resulted in male sterility. Therefore, Capana05g000766 was identified as the strongest candidate gene for the msc-2 locus. Allelism tests showed that msc-1 and msc-2 were nonallelic, and bimolecular fluorescence complementation analysis indicated that the two genes did not interact directly with each other at the protein level. As msc-1 and msc-2 are homologs of AtDYT1 and AtMS1 in Arabidopsis, they may play similar roles in tapetum development in genic male sterile peppers, and Msc-1 might be up stream of Msc-2 in the regulation of other genes involved in tapetum development.
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Affiliation(s)
- Qing Cheng
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, Department of Vegetable Science, College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Ting Li
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, Department of Vegetable Science, College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Yixin Ai
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, Department of Vegetable Science, College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Qiaohua Lu
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, Department of Vegetable Science, College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Yihao Wang
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, Department of Vegetable Science, College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Lang Wu
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, Department of Vegetable Science, College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Jinqiu Liu
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, Department of Vegetable Science, College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Liang Sun
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, Department of Vegetable Science, College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Huolin Shen
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, Department of Vegetable Science, College of Horticulture, China Agricultural University, Beijing, 100193, China.
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Erpen-Dalla Corte L, M. Mahmoud L, S. Moraes T, Mou Z, W. Grosser J, Dutt M. Development of Improved Fruit, Vegetable, and Ornamental Crops Using the CRISPR/Cas9 Genome Editing Technique. PLANTS (BASEL, SWITZERLAND) 2019; 8:E601. [PMID: 31847196 PMCID: PMC6963220 DOI: 10.3390/plants8120601] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/17/2019] [Revised: 12/06/2019] [Accepted: 12/11/2019] [Indexed: 02/06/2023]
Abstract
Horticultural crops, including fruit, vegetable, and ornamental plants are an important component of the agriculture production systems and play an important role in sustaining human life. With a steady growth in the world's population and the consequent need for more food, sustainable and increased fruit and vegetable crop production is a major challenge to guarantee future food security. Although conventional breeding techniques have significantly contributed to the development of important varieties, new approaches are required to further improve horticultural crop production. Clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9) has emerged as a valuable genome-editing tool able to change DNA sequences at precisely chosen loci. The CRISPR/Cas9 system was developed based on the bacterial adaptive immune system and comprises of an endonuclease guided by one or more single-guide RNAs to generate double-strand breaks. These breaks can then be repaired by the natural cellular repair mechanisms, during which genetic mutations are introduced. In a short time, the CRISPR/Cas9 system has become a popular genome-editing technique, with numerous examples of gene mutation and transcriptional regulation control in both model and crop plants. In this review, various aspects of the CRISPR/Cas9 system are explored, including a general presentation of the function of the CRISPR/Cas9 system in bacteria and its practical application as a biotechnological tool for editing plant genomes, particularly in horticultural crops.
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Affiliation(s)
| | - Lamiaa M. Mahmoud
- Pomology Department, Faculty of Agriculture, Mansoura University, 35516 Mansoura, Egypt;
- Citrus Research and Education Center, University of Florida, Lake Alfred, FL 33850, USA;
| | - Tatiana S. Moraes
- Centro de Energia Nuclear na Agricultura, Universidade de São Paulo, Piracicaba 13416-000, SP, Brazil;
| | - Zhonglin Mou
- Department of Microbiology and Cell Sciences, University of Florida, Gainesville, FL 32603, USA;
| | - Jude W. Grosser
- Citrus Research and Education Center, University of Florida, Lake Alfred, FL 33850, USA;
| | - Manjul Dutt
- Citrus Research and Education Center, University of Florida, Lake Alfred, FL 33850, USA;
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Fan Y, Wang Q, Dong Z, Yin Y, Teixeira da Silva JA, Yu X. Advances in molecular biology of Paeonia L. PLANTA 2019; 251:23. [PMID: 31784828 DOI: 10.1007/s00425-019-03299-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Accepted: 10/11/2019] [Indexed: 06/10/2023]
Abstract
Molecular biology can serve as a tool to solve the limitations of traditional breeding and cultivation techniques related to flower patterns, the improvement of flower color, and the regulation of flowering and stress resistance. These characteristics of molecular biology ensured its significant role in improving the efficiency of breeding and germplasm amelioration of Paeonia. This review describes the advances in molecular biology of Paeonia, including: (1) the application of molecular markers; (2) genomics, transcriptomics, proteomics, metabolomics, and microRNA studies; (3) studies of functional genes; and (4) molecular biology techniques. This review also points out select limitations in current molecular biology, analyzes the direction of Paeonia molecular biology research, and provides advice for future research objectives.
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Affiliation(s)
- Yongming Fan
- College of Landscape Architecture, Beijing Forestry University, Beijing, 100083, People's Republic of China
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Beijing, 100083, People's Republic of China
| | - Qi Wang
- College of Landscape Architecture, Beijing Forestry University, Beijing, 100083, People's Republic of China
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Beijing, 100083, People's Republic of China
| | - Zhijun Dong
- College of Landscape Architecture, Beijing Forestry University, Beijing, 100083, People's Republic of China
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Beijing, 100083, People's Republic of China
| | - Yijia Yin
- College of Landscape Architecture, Beijing Forestry University, Beijing, 100083, People's Republic of China
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Beijing, 100083, People's Republic of China
| | | | - Xiaonan Yu
- College of Landscape Architecture, Beijing Forestry University, Beijing, 100083, People's Republic of China.
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Beijing, 100083, People's Republic of China.
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Walawage SL, Zaini PA, Mubarik MS, Martinelli F, Balan B, Caruso T, Leslie CA, Dandekar AM. Deploying Genome Editing Tools for Dissecting the Biology of Nut Trees. FRONTIERS IN SUSTAINABLE FOOD SYSTEMS 2019. [DOI: 10.3389/fsufs.2019.00100] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
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Ghogare R, Williamson-Benavides B, Ramírez-Torres F, Dhingra A. CRISPR-associated nucleases: the Dawn of a new age of efficient crop improvement. Transgenic Res 2019; 29:1-35. [PMID: 31677059 DOI: 10.1007/s11248-019-00181-y] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Accepted: 10/23/2019] [Indexed: 12/26/2022]
Abstract
The world stands at a new threshold today. As a planet, we face various challenges, and the key one is how to continue to produce enough food, feed, fiber, and fuel to support the burgeoning population. In the past, plant breeding and the ability to genetically engineer crops contributed to increasing food production. However, both approaches rely on random mixing or integration of genes, and the process can be unpredictable and time-consuming. Given the challenge of limited availability of natural resources and changing environmental conditions, the need to rapidly and precisely improve crops has become urgent. The discovery of CRISPR-associated endonucleases offers a precise yet versatile platform for rapid crop improvement. This review summarizes a brief history of the discovery of CRISPR-associated nucleases and their application in genome editing of various plant species. Also provided is an overview of several new endonucleases reported recently, which can be utilized for editing of specific genes in plants through various forms of DNA sequence alteration. Genome editing, with its ever-expanding toolset, increased efficiency, and its potential integration with the emerging synthetic biology approaches hold promise for efficient crop improvement to meet the challenge of supporting the needs of future generations.
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Xu J, Hua K, Lang Z. Genome editing for horticultural crop improvement. HORTICULTURE RESEARCH 2019; 6:113. [PMID: 31645967 PMCID: PMC6804600 DOI: 10.1038/s41438-019-0196-5] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Revised: 07/18/2019] [Accepted: 08/13/2019] [Indexed: 05/06/2023]
Abstract
Horticultural crops provide humans with many valuable products. The improvement of the yield and quality of horticultural crops has been receiving increasing research attention. Given the development and advantages of genome-editing technologies, research that uses genome editing to improve horticultural crops has substantially increased in recent years. Here, we briefly review the different genome-editing systems used in horticultural research with a focus on clustered regularly interspaced palindromic repeats (CRISPR)/CRISPR-associated 9 (Cas9)-mediated genome editing. We also summarize recent progress in the application of genome editing for horticultural crop improvement. The combination of rapidly advancing genome-editing technology with breeding will greatly increase horticultural crop production and quality.
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Affiliation(s)
- Jiemeng Xu
- Shanghai Center for Plant Stress Biology, National Key Laboratory of Plant Molecular Genetics, Center of Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032 China
| | - Kai Hua
- Shanghai Center for Plant Stress Biology, National Key Laboratory of Plant Molecular Genetics, Center of Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032 China
| | - Zhaobo Lang
- Shanghai Center for Plant Stress Biology, National Key Laboratory of Plant Molecular Genetics, Center of Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032 China
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