1
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Sun Y, Hu J, Hu Z, Zhou H, Gao Y, Liu Y, Ji Y, Xu G, Guo Y, Zhang Y, Tian Y, Liu X, Zhou S, Liu Y, Li T, Li C, Wan J. Engineer and split an efficient hypercompact CRISPR-CasΦ genome editor in plants. PLANT COMMUNICATIONS 2024; 5:100881. [PMID: 38486456 PMCID: PMC11287130 DOI: 10.1016/j.xplc.2024.100881] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Revised: 03/04/2024] [Accepted: 03/12/2024] [Indexed: 04/07/2024]
Affiliation(s)
- Yan Sun
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Jiangsu Engineering Research Center for Plant Genome Editing, National Observation and Research Station of Rice Germplasm Resources, Nanjing Agricultural University, Nanjing 210095, China
| | - Jianjian Hu
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Jiangsu Engineering Research Center for Plant Genome Editing, National Observation and Research Station of Rice Germplasm Resources, Nanjing Agricultural University, Nanjing 210095, China
| | - Zhichao Hu
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Jiangsu Engineering Research Center for Plant Genome Editing, National Observation and Research Station of Rice Germplasm Resources, Nanjing Agricultural University, Nanjing 210095, China
| | - Hejie Zhou
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Jiangsu Engineering Research Center for Plant Genome Editing, National Observation and Research Station of Rice Germplasm Resources, Nanjing Agricultural University, Nanjing 210095, China
| | - Yuhong Gao
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Jiangsu Engineering Research Center for Plant Genome Editing, National Observation and Research Station of Rice Germplasm Resources, Nanjing Agricultural University, Nanjing 210095, China
| | - Yini Liu
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Jiangsu Engineering Research Center for Plant Genome Editing, National Observation and Research Station of Rice Germplasm Resources, Nanjing Agricultural University, Nanjing 210095, China
| | - Yuan Ji
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Jiangsu Engineering Research Center for Plant Genome Editing, National Observation and Research Station of Rice Germplasm Resources, Nanjing Agricultural University, Nanjing 210095, China
| | - Gencheng Xu
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Jiangsu Engineering Research Center for Plant Genome Editing, National Observation and Research Station of Rice Germplasm Resources, Nanjing Agricultural University, Nanjing 210095, China
| | - Yifan Guo
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Jiangsu Engineering Research Center for Plant Genome Editing, National Observation and Research Station of Rice Germplasm Resources, Nanjing Agricultural University, Nanjing 210095, China
| | - Yuanyan Zhang
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Jiangsu Engineering Research Center for Plant Genome Editing, National Observation and Research Station of Rice Germplasm Resources, Nanjing Agricultural University, Nanjing 210095, China
| | - Yunlu Tian
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Jiangsu Engineering Research Center for Plant Genome Editing, National Observation and Research Station of Rice Germplasm Resources, Nanjing Agricultural University, Nanjing 210095, China; Zhongshan Biological Breeding Laboratory, Nanjing 210095, China
| | - Xi Liu
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Jiangsu Engineering Research Center for Plant Genome Editing, National Observation and Research Station of Rice Germplasm Resources, Nanjing Agricultural University, Nanjing 210095, China; Zhongshan Biological Breeding Laboratory, Nanjing 210095, China
| | - Shirong Zhou
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Jiangsu Engineering Research Center for Plant Genome Editing, National Observation and Research Station of Rice Germplasm Resources, Nanjing Agricultural University, Nanjing 210095, China; Zhongshan Biological Breeding Laboratory, Nanjing 210095, China
| | - Yuqiang Liu
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Jiangsu Engineering Research Center for Plant Genome Editing, National Observation and Research Station of Rice Germplasm Resources, Nanjing Agricultural University, Nanjing 210095, China; Zhongshan Biological Breeding Laboratory, Nanjing 210095, China; Sanya Institute of Nanjing Agricultural University, Hainan Seed Industry Laboratory, Sanya 572025, China
| | - Tingdong Li
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling 712100, China
| | - Chao Li
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Jiangsu Engineering Research Center for Plant Genome Editing, National Observation and Research Station of Rice Germplasm Resources, Nanjing Agricultural University, Nanjing 210095, China; Zhongshan Biological Breeding Laboratory, Nanjing 210095, China; Sanya Institute of Nanjing Agricultural University, Hainan Seed Industry Laboratory, Sanya 572025, China.
| | - Jianmin Wan
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Jiangsu Engineering Research Center for Plant Genome Editing, National Observation and Research Station of Rice Germplasm Resources, Nanjing Agricultural University, Nanjing 210095, China; Zhongshan Biological Breeding Laboratory, Nanjing 210095, China; State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
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2
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Chen C, Hu Y, Ikeuchi M, Jiao Y, Prasad K, Su YH, Xiao J, Xu L, Yang W, Zhao Z, Zhou W, Zhou Y, Gao J, Wang JW. Plant regeneration in the new era: from molecular mechanisms to biotechnology applications. SCIENCE CHINA. LIFE SCIENCES 2024; 67:1338-1367. [PMID: 38833085 DOI: 10.1007/s11427-024-2581-2] [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: 01/31/2024] [Accepted: 03/26/2024] [Indexed: 06/06/2024]
Abstract
Plants or tissues can be regenerated through various pathways. Like animal regeneration, cell totipotency and pluripotency are the molecular basis of plant regeneration. Detailed systematic studies on Arabidopsis thaliana gradually unravel the fundamental mechanisms and principles underlying plant regeneration. Specifically, plant hormones, cell division, epigenetic remodeling, and transcription factors play crucial roles in reprogramming somatic cells and reestablishing meristematic cells. Recent research on basal non-vascular plants and monocot crops has revealed that plant regeneration differs among species, with various plant species using distinct mechanisms and displaying significant differences in regenerative capacity. Conducting multi-omics studies at the single-cell level, tracking plant regeneration processes in real-time, and deciphering the natural variation in regenerative capacity will ultimately help understand the essence of plant regeneration, improve crop regeneration efficiency, and contribute to future crop design.
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Affiliation(s)
- Chunli Chen
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China.
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China.
| | - Yuxin Hu
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences (CAS), China National Botanical Garden, Beijing, 100093, China.
| | - Momoko Ikeuchi
- Division of Biological Sciences, Graduate School of Science and Technology, Nara Institute of Science and Technology, Nara, 630-0192, Japan.
| | - Yuling Jiao
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, 100871, China.
- Peking-Tsinghua Center for Life Sciences, Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, 100871, China.
| | - Kalika Prasad
- Indian Institute of Science Education and Research, Pune, 411008, India.
- , Thiruvananthapuram, 695551, India.
| | - Ying Hua Su
- State Key Laboratory of Wheat Improvement, College of Life Sciences, Shandong Agricultural University, Tai'an, 271018, China.
- Sino-German Joint Research Center on Agricultural Biology, Shandong Agricultural University, Tai'an, 271018, China.
| | - Jun Xiao
- Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology (IGDB), CAS, Beijing, 100101, China.
- CAS-JIC Centre of Excellence for Plant and Microbial Science (CEPAMS), IGDB, CAS, Beijing, 100101, China.
| | - Lin Xu
- National Key Laboratory of Plant Molecular Genetics, CEMPS, Institute of Plant Physiology and Ecology (SIPPE), CAS, Shanghai, 200032, China.
| | - Weibing Yang
- National Key Laboratory of Plant Molecular Genetics, CEMPS, Institute of Plant Physiology and Ecology (SIPPE), CAS, Shanghai, 200032, China.
- CEPAMS, SIPPE, CAS, Shanghai, 200032, China.
| | - Zhong Zhao
- Hefei National Laboratory for Physical Sciences at the Microscale, CEMPS, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230027, China.
| | - Wenkun Zhou
- State Key Laboratory of Plant Environmental Resilience, College of Biological Sciences, China Agricultural University, Beijing, 100193, China.
| | - Yun Zhou
- Department of Botany and Plant Pathology and Center for Plant Biology, Purdue University, West Lafayette, 47907, USA.
| | - Jian Gao
- National Key Laboratory of Plant Molecular Genetics, CEMPS, Institute of Plant Physiology and Ecology (SIPPE), CAS, Shanghai, 200032, China
| | - Jia-Wei Wang
- National Key Laboratory of Plant Molecular Genetics, CEMPS, Institute of Plant Physiology and Ecology (SIPPE), CAS, Shanghai, 200032, China.
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China.
- Key Laboratory of Plant Carbon Capture, CAS, Shanghai, 200032, China.
- New Cornerstone Science Laboratory, Shanghai, 200032, China.
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3
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Shen Y, Ye T, Li Z, Kimutai TH, Song H, Dong X, Wan J. Exploiting viral vectors to deliver genome editing reagents in plants. ABIOTECH 2024; 5:247-261. [PMID: 38974861 PMCID: PMC11224180 DOI: 10.1007/s42994-024-00147-7] [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: 11/30/2023] [Accepted: 03/02/2024] [Indexed: 07/09/2024]
Abstract
Genome editing holds great promise for the molecular breeding of plants, yet its application is hindered by the shortage of simple and effective means of delivering genome editing reagents into plants. Conventional plant transformation-based methods for delivery of genome editing reagents into plants often involve prolonged tissue culture, a labor-intensive and technically challenging process for many elite crop cultivars. In this review, we describe various virus-based methods that have been employed to deliver genome editing reagents, including components of the CRISPR/Cas machinery and donor DNA for precision editing in plants. We update the progress in these methods with recent successful examples of genome editing achieved through virus-based delivery in different plant species, highlight the advantages and limitations of these delivery approaches, and discuss the remaining challenges.
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Affiliation(s)
- Yilin Shen
- State Key Laboratory of Crop Genetics and Germplasm Enhancement and Utilization, Jiangsu Collaborative Innovation Centre for Modern Crop Production, Jiangsu Engineering Research Center for Plant Genome Editing, Nanjing Agricultural University, Nanjing, 210095 China
- Zhongshan Biological Breeding Laboratory, Nanjing, 210014 China
| | - Tao Ye
- State Key Laboratory of Crop Genetics and Germplasm Enhancement and Utilization, Jiangsu Collaborative Innovation Centre for Modern Crop Production, Jiangsu Engineering Research Center for Plant Genome Editing, Nanjing Agricultural University, Nanjing, 210095 China
- Zhongshan Biological Breeding Laboratory, Nanjing, 210014 China
| | - Zihan Li
- State Key Laboratory of Crop Genetics and Germplasm Enhancement and Utilization, Jiangsu Collaborative Innovation Centre for Modern Crop Production, Jiangsu Engineering Research Center for Plant Genome Editing, Nanjing Agricultural University, Nanjing, 210095 China
- Zhongshan Biological Breeding Laboratory, Nanjing, 210014 China
| | - Torotwa Herman Kimutai
- State Key Laboratory of Crop Genetics and Germplasm Enhancement and Utilization, Jiangsu Collaborative Innovation Centre for Modern Crop Production, Jiangsu Engineering Research Center for Plant Genome Editing, Nanjing Agricultural University, Nanjing, 210095 China
- Zhongshan Biological Breeding Laboratory, Nanjing, 210014 China
| | - Hao Song
- State Key Laboratory of Crop Genetics and Germplasm Enhancement and Utilization, Jiangsu Collaborative Innovation Centre for Modern Crop Production, Jiangsu Engineering Research Center for Plant Genome Editing, Nanjing Agricultural University, Nanjing, 210095 China
- Zhongshan Biological Breeding Laboratory, Nanjing, 210014 China
| | - Xiaoou Dong
- State Key Laboratory of Crop Genetics and Germplasm Enhancement and Utilization, Jiangsu Collaborative Innovation Centre for Modern Crop Production, Jiangsu Engineering Research Center for Plant Genome Editing, Nanjing Agricultural University, Nanjing, 210095 China
- Zhongshan Biological Breeding Laboratory, Nanjing, 210014 China
- Hainan Seed Industry Laboratory, Sanya, 572025 China
| | - Jianmin Wan
- State Key Laboratory of Crop Genetics and Germplasm Enhancement and Utilization, Jiangsu Collaborative Innovation Centre for Modern Crop Production, Jiangsu Engineering Research Center for Plant Genome Editing, Nanjing Agricultural University, Nanjing, 210095 China
- Zhongshan Biological Breeding Laboratory, Nanjing, 210014 China
- Hainan Seed Industry Laboratory, Sanya, 572025 China
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
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4
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Yue N, Jiang Z, Pi Q, Yang M, Gao Z, Wang X, Zhang H, Wu F, Jin X, Li M, Wang Y, Zhang Y, Li D. Zn2+-dependent association of cysteine-rich protein with virion orchestrates morphogenesis of rod-shaped viruses. PLoS Pathog 2024; 20:e1012311. [PMID: 38885273 PMCID: PMC11213338 DOI: 10.1371/journal.ppat.1012311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2023] [Revised: 06/28/2024] [Accepted: 05/31/2024] [Indexed: 06/20/2024] Open
Abstract
The majority of rod-shaped and some filamentous plant viruses encode a cysteine-rich protein (CRP) that functions in viral virulence; however, the roles of these CRPs in viral infection remain largely unknown. Here, we used barley stripe mosaic virus (BSMV) as a model to investigate the essential role of its CRP in virus morphogenesis. The CRP protein γb directly interacts with BSMV coat protein (CP), the mutations either on the His-85 site in γb predicted to generate a potential CCCH motif or on the His-13 site in CP exposed to the surface of the virions abolish the zinc-binding activity and their interaction. Immunogold-labeling assays show that γb binds to the surface of rod-shaped BSMV virions in a Zn2+-dependent manner, which enhances the RNA binding activity of CP and facilitates virion assembly and stability, suggesting that the Zn2+-dependent physical association of γb with the virion is crucial for BSMV morphogenesis. Intriguingly, the tightly binding of diverse CRPs to their rod-shaped virions is a general feature employed by the members in the families Virgaviridae (excluding the genus Tobamovirus) and Benyviridae. Together, these results reveal a hitherto unknown role of CRPs in the assembly and stability of virus particles, and expand our understanding of the molecular mechanism underlying virus morphogenesis.
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Affiliation(s)
- Ning Yue
- State Key Laboratory of Plant Environmental Resilience, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Zhihao Jiang
- State Key Laboratory of Plant Environmental Resilience, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Qinglin Pi
- State Key Laboratory of Plant Environmental Resilience, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Meng Yang
- State Key Laboratory of Plant Environmental Resilience, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Zongyu Gao
- State Key Laboratory of Plant Environmental Resilience, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Xueting Wang
- State Key Laboratory of Plant Environmental Resilience, College of Biological Sciences, China Agricultural University, Beijing, China
| | - He Zhang
- State Key Laboratory of Plant Environmental Resilience, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Fengtong Wu
- State Key Laboratory of Plant Environmental Resilience, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Xuejiao Jin
- State Key Laboratory of Plant Environmental Resilience, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Menglin Li
- College of Plant Protection, China Agricultural University, Beijing, China
| | - Ying Wang
- College of Plant Protection, China Agricultural University, Beijing, China
| | - Yongliang Zhang
- State Key Laboratory of Plant Environmental Resilience, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Dawei Li
- State Key Laboratory of Plant Environmental Resilience, College of Biological Sciences, China Agricultural University, Beijing, China
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5
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Wang Q, Zhang D, Dai YR, Liu CC. Efficient tobacco rattle virus-induced gene editing in tomato mediated by the CRISPR/Cas9 system. Biotechnol J 2024; 19:e2400204. [PMID: 38797722 DOI: 10.1002/biot.202400204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2024] [Revised: 05/04/2024] [Accepted: 05/07/2024] [Indexed: 05/29/2024]
Abstract
Plant virus-based sgRNA delivery strategy has been widely applied for efficient genome editing across various plant species, leveraging its significant advantages in the rapid expression and expansion of sgRNA through virus replication and movement. However, the efficacy of the virus-induced gene editing (VIGE) tool in tomato has yet to be explored. In this paper, we established a TRV-mediated CRISPR/Cas9 genome editing system in the somatic cells of tomato, reporting the validation of VIGE and evaluating the mutagenesis efficiency in both tomato leaves and fruits using high-throughput sequencing. The results demonstrated an approximate 65% efficiency of VIGE in tomato leaves for the selected target genes, with VIGE efficiency reaching up to 50% in tomato fruits. This research not only introduces an efficient tool for reverse genetics but also reveals substantial potential of VIGE in surpassing traditional tissue culture techniques for creating heritable mutations in tomato.
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Affiliation(s)
- Qiong Wang
- College of Plant Protection, Yangzhou University, Yangzhou, China
| | - Dan Zhang
- College of Plant Protection, Yangzhou University, Yangzhou, China
| | - Yu-Ru Dai
- College of Plant Protection, Yangzhou University, Yangzhou, China
| | - Chao-Chao Liu
- College of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, China
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6
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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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7
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Liu D, Myers EA, Xuan S, Prichard LE, Donahue LI, Ellison EE, Starker CG, Voytas DF. Heritable, multinucleotide deletions in plants using viral delivery of a repair exonuclease and guide RNAs. PLANT PHYSIOLOGY 2024; 194:2229-2239. [PMID: 38243587 DOI: 10.1093/plphys/kiae015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 12/08/2023] [Accepted: 12/12/2023] [Indexed: 01/21/2024]
Abstract
CRISPR/Cas9-mediated mutagenesis typically results in short insertion/deletion mutations, which are often too small to disrupt the function of cis-acting regulatory elements. Here, we describe a highly efficient in planta gene editing approach called VirTREX2-HLDel that achieves heritable multinucleotide deletions in both protein-coding genes and noncoding DNA regulatory elements. VirTREX2-HLDel uses RNA viruses to deliver both the 3 prime repair exonuclease 2 (TREX2) and single-guide RNAs. Our method enables recovery of multiplexed heritable deletions and increases the heritable gene editing frequency at poorly edited sites. We identified functional conservation and divergence of MICRORNA164 (miR164) in Nicotiana benthamiana and tomato (Solanum lycopersicum) using VirTREX2-HLDel and observed previously uncharacterized phenotypes in plants with large deletions at this locus. Our viral delivery method reduces the need for tissue culture and will accelerate the understanding of protein-coding and regulatory regions in plants.
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Affiliation(s)
- Degao Liu
- Department of Genetics, Cell Biology and Development, University of Minnesota, St. Paul, MN 55108, USA
- Center for Precision Plant Genomics, University of Minnesota, St. Paul, MN 55108, USA
| | - Erik A Myers
- Department of Genetics, Cell Biology and Development, University of Minnesota, St. Paul, MN 55108, USA
- Center for Precision Plant Genomics, University of Minnesota, St. Paul, MN 55108, USA
| | - Shuya Xuan
- Department of Genetics, Cell Biology and Development, University of Minnesota, St. Paul, MN 55108, USA
- Center for Precision Plant Genomics, University of Minnesota, St. Paul, MN 55108, USA
| | - Lynn E Prichard
- Department of Genetics, Cell Biology and Development, University of Minnesota, St. Paul, MN 55108, USA
- Center for Precision Plant Genomics, University of Minnesota, St. Paul, MN 55108, USA
| | - Lilee I Donahue
- Department of Genetics, Cell Biology and Development, University of Minnesota, St. Paul, MN 55108, USA
- Center for Precision Plant Genomics, University of Minnesota, St. Paul, MN 55108, USA
| | - Evan E Ellison
- Department of Genetics, Cell Biology and Development, University of Minnesota, St. Paul, MN 55108, USA
- Center for Precision Plant Genomics, University of Minnesota, St. Paul, MN 55108, USA
| | - Colby G Starker
- Department of Genetics, Cell Biology and Development, University of Minnesota, St. Paul, MN 55108, USA
- Center for Precision Plant Genomics, University of Minnesota, St. Paul, MN 55108, USA
| | - Daniel F Voytas
- Department of Genetics, Cell Biology and Development, University of Minnesota, St. Paul, MN 55108, USA
- Center for Precision Plant Genomics, University of Minnesota, St. Paul, MN 55108, USA
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8
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Wu J, Zhang Y, Li F, Zhang X, Ye J, Wei T, Li Z, Tao X, Cui F, Wang X, Zhang L, Yan F, Li S, Liu Y, Li D, Zhou X, Li Y. Plant virology in the 21st century in China: Recent advances and future directions. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2024; 66:579-622. [PMID: 37924266 DOI: 10.1111/jipb.13580] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Accepted: 11/02/2023] [Indexed: 11/06/2023]
Abstract
Plant viruses are a group of intracellular pathogens that persistently threaten global food security. Significant advances in plant virology have been achieved by Chinese scientists over the last 20 years, including basic research and technologies for preventing and controlling plant viral diseases. Here, we review these milestones and advances, including the identification of new crop-infecting viruses, dissection of pathogenic mechanisms of multiple viruses, examination of multilayered interactions among viruses, their host plants, and virus-transmitting arthropod vectors, and in-depth interrogation of plant-encoded resistance and susceptibility determinants. Notably, various plant virus-based vectors have also been successfully developed for gene function studies and target gene expression in plants. We also recommend future plant virology studies in China.
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Affiliation(s)
- Jianguo Wu
- State Key Laboratory for Ecological Pest Control of Fujian and Taiwan Crops, Vector-borne Virus Research Center, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Yongliang Zhang
- State Key Laboratory of Plant Environmental Resilience and Ministry of Agriculture Key Laboratory of Soil Microbiology, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Fangfang Li
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Xiaoming Zhang
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
- CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jian Ye
- CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, 100049, China
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Taiyun Wei
- State Key Laboratory for Ecological Pest Control of Fujian and Taiwan Crops, Vector-borne Virus Research Center, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Zhenghe Li
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Xiaorong Tao
- Department of Plant Pathology, The Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing, 210095, China
| | - Feng Cui
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
- CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xianbing Wang
- State Key Laboratory of Plant Environmental Resilience and Ministry of Agriculture Key Laboratory of Soil Microbiology, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Lili Zhang
- CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, 100049, China
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Fei Yan
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Plant Virology, Ningbo University, Ningbo, 315211, China
| | - Shifang Li
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Yule Liu
- MOE Key Laboratory of Bioinformatics, Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Dawei Li
- State Key Laboratory of Plant Environmental Resilience and Ministry of Agriculture Key Laboratory of Soil Microbiology, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Xueping Zhou
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Yi Li
- State Key Laboratory for Ecological Pest Control of Fujian and Taiwan Crops, Vector-borne Virus Research Center, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, 100871, China
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9
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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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10
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Ahmar S, Usman B, Hensel G, Jung KH, Gruszka D. CRISPR enables sustainable cereal production for a greener future. TRENDS IN PLANT SCIENCE 2024; 29:179-195. [PMID: 37981496 DOI: 10.1016/j.tplants.2023.10.016] [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: 07/04/2023] [Revised: 10/16/2023] [Accepted: 10/26/2023] [Indexed: 11/21/2023]
Abstract
The clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9) system has become the most important tool for targeted genome editing in many plant and animal species over the past decade. The CRISPR/Cas9 technology has also sparked a flood of applications and technical advancements in genome editing in the key cereal crops, including rice, wheat, maize, and barley. Here, we review advanced uses of CRISPR/Cas9 and derived systems in genome editing of cereal crops to enhance a variety of agronomically important features. We also highlight new technological advances for delivering preassembled Cas9-gRNA ribonucleoprotein (RNP)-editing systems, multiplex editing, gain-of-function strategies, the use of artificial intelligence (AI)-based tools, and combining CRISPR with novel speed breeding (SB) and vernalization strategies.
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Affiliation(s)
- Sunny Ahmar
- Institute of Biology, Biotechnology, and Environmental Protection, Faculty of Natural Sciences, University of Silesia, Jagiellonska 28, 40-032 Katowice, Poland
| | - Babar Usman
- Graduate School of Green-Bio Science & Crop Biotech Institute, Kyung Hee University, 1732 Deogyeong-daero, Giheung-gu, Yongin-si, Gyeonggi-do 17104, Republic of Korea
| | - Goetz Hensel
- Centre for Plant Genome Engineering, Institute of Plant Biochemistry, Heinrich-Heine-University, D-40225 Duesseldorf, Germany; Centre of Region Haná for Biotechnological and Agricultural Research, Czech Advanced Technology and Research Institute, Palacký University Olomouc, 783 71 Olomouc, Czech Republic
| | - Ki-Hong Jung
- Graduate School of Green-Bio Science & Crop Biotech Institute, Kyung Hee University, 1732 Deogyeong-daero, Giheung-gu, Yongin-si, Gyeonggi-do 17104, Republic of Korea; Research Center for Plant Plasticity, Seoul National University, Seoul 08826, Republic of Korea.
| | - Damian Gruszka
- Institute of Biology, Biotechnology, and Environmental Protection, Faculty of Natural Sciences, University of Silesia, Jagiellonska 28, 40-032 Katowice, Poland.
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11
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Chicowski AS, Bredow M, Utiyama AS, Marcelino‐Guimarães FC, Whitham SA. Soybean-Phakopsora pachyrhizi interactions: towards the development of next-generation disease-resistant plants. PLANT BIOTECHNOLOGY JOURNAL 2024; 22:296-315. [PMID: 37883664 PMCID: PMC10826999 DOI: 10.1111/pbi.14206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Revised: 09/19/2023] [Accepted: 10/08/2023] [Indexed: 10/28/2023]
Abstract
Soybean rust (SBR), caused by the obligate biotrophic fungus Phakopsora pachyrhizi, is a devastating foliar disease threatening soybean production. To date, no commercial cultivars conferring durable resistance to SBR are available. The development of long-lasting SBR resistance has been hindered by the lack of understanding of this complex pathosystem, encompassing challenges posed by intricate genetic structures in both the host and pathogen, leading to a gap in the knowledge of gene-for-gene interactions between soybean and P. pachyrhizi. In this review, we focus on recent advancements and emerging technologies that can be used to improve our understanding of the P. pachyrhizi-soybean molecular interactions. We further explore approaches used to combat SBR, including conventional breeding, transgenic approaches and RNA interference, and how advances in our understanding of plant immune networks, the availability of new molecular tools, and the recent sequencing of the P. pachyrhizi genome could be used to aid in the development of better genetic resistance against SBR. Lastly, we discuss the research gaps of this pathosystem and how new technologies can be used to shed light on these questions and to develop durable next-generation SBR-resistant soybean plants.
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Affiliation(s)
- Aline Sartor Chicowski
- Department of Plant Pathology, Entomology and MicrobiologyIowa State UniversityAmesIowaUSA
| | - Melissa Bredow
- Department of Plant Pathology, Entomology and MicrobiologyIowa State UniversityAmesIowaUSA
| | - Alice Satiko Utiyama
- Brazilian Agricultural Research Corporation – National Soybean Research Center (Embrapa Soja)LondrinaParanáBrazil
- Department of AgronomyFederal University of ViçosaViçosaMinas GeraisBrazil
| | | | - Steven A. Whitham
- Department of Plant Pathology, Entomology and MicrobiologyIowa State UniversityAmesIowaUSA
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12
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Nagalakshmi U, Meier N, Dinesh-Kumar SP. Virus-Induced Heritable Gene Editing in Plants. Methods Mol Biol 2024; 2724:273-288. [PMID: 37987913 DOI: 10.1007/978-1-0716-3485-1_20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2023]
Abstract
Gene editing using clustered, regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated (Cas) nuclease is an excellent tool for assessing gene function in plants. However, delivery of CRISPR/Cas-editing components into plant cells is still a major bottleneck and requires tissue culture-based approaches and regeneration of plants. To overcome this limitation, several plant viral vectors have recently been engineered to deliver single-guide RNA (sgRNA) targets into SpCas9-expressing plants. Here, we describe an optimized, step-by-step protocol based on the tobacco rattle virus (TRV)-based vector system to deliver sgRNAs fused to mobile tRNA sequences for efficient heritable editing in Nicotiana benthamiana and Arabidopsis thaliana model systems. The protocol described here could be adopted to study the function of any gene of interest.
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Affiliation(s)
- Ugrappa Nagalakshmi
- Department of Plant Biology and The Genome Center, College of Biological Sciences, University of California, Davis, Davis, CA, USA.
| | - Nathan Meier
- Department of Plant Biology and The Genome Center, College of Biological Sciences, University of California, Davis, Davis, CA, USA
| | - Savithramma P Dinesh-Kumar
- Department of Plant Biology and The Genome Center, College of Biological Sciences, University of California, Davis, Davis, CA, USA.
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13
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Wu X, Zhang Y, Jiang X, Ma T, Guo Y, Wu X, Guo Y, Cheng X. Considerations in engineering viral vectors for genome editing in plants. Virology 2024; 589:109922. [PMID: 37924727 DOI: 10.1016/j.virol.2023.109922] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Revised: 10/24/2023] [Accepted: 10/27/2023] [Indexed: 11/06/2023]
Abstract
Plant viruses have been engineered to express proteins and induce gene silencing for decades. Recently, plant viruses have also been used to deliver components into plant cells for genome editing, a technique called virus-induced genome editing (VIGE). Although more than a dozen plant viruses have been engineered into VIGE vectors and VIGE has been successfully accomplished in some plant species, application of VIGE to crops that are difficult to tissue culture and/or have low regeneration efficiency is still tough. This paper discusses factors to consider for an ideal VIGE vector, including insertion capacity for foreign DNA, vertical transmission ability, expression level of the target gene, stability of foreign DNA insertion, and biosafety. We also proposed a step-by-step schedule for excavating the suitable viral vector for VIGE.
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Affiliation(s)
- Xiaoyun Wu
- College of Plant Protection, Northeast Agricultural University, Harbin, 150030, Heilongjiang, PR China; Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region of Chinese Education Ministry, Northeast Agricultural University, Harbin, 150030, PR China
| | - Ying Zhang
- College of Plant Protection, Northeast Agricultural University, Harbin, 150030, Heilongjiang, PR China
| | - Xue Jiang
- College of Plant Protection, Northeast Agricultural University, Harbin, 150030, Heilongjiang, PR China
| | - Tingshuai Ma
- College of Plant Protection, Northeast Agricultural University, Harbin, 150030, Heilongjiang, PR China
| | - Yating Guo
- College of Plant Protection, Northeast Agricultural University, Harbin, 150030, Heilongjiang, PR China
| | - Xiaoxia Wu
- College of Agriculture, Northeast Agricultural University, Harbin, 150030, PR China
| | - Yushuang Guo
- Key Laboratory of Molecular Genetics, Guizhou Academy of Tobacco Science, Guiyang, 550081, Guizhou, PR China.
| | - Xiaofei Cheng
- College of Plant Protection, Northeast Agricultural University, Harbin, 150030, Heilongjiang, PR China; Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region of Chinese Education Ministry, Northeast Agricultural University, Harbin, 150030, PR China.
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14
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Yao L, Wu X, Jiang X, Shan M, Zhang Z, Li Y, Yang A, Li Y, Yang C. Subcellular compartmentalization in the biosynthesis and engineering of plant natural products. Biotechnol Adv 2023; 69:108258. [PMID: 37722606 DOI: 10.1016/j.biotechadv.2023.108258] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Revised: 09/07/2023] [Accepted: 09/11/2023] [Indexed: 09/20/2023]
Abstract
Plant natural products (PNPs) are specialized metabolites with diverse bioactivities. They are extensively used in the pharmaceutical, cosmeceutical and food industries. PNPs are synthesized in plant cells by enzymes that are distributed in different subcellular compartments with unique microenvironments, such as ions, co-factors and substrates. Plant metabolic engineering is an emerging and promising approach for the sustainable production of PNPs, for which the knowledge of the subcellular compartmentalization of their biosynthesis is instrumental. In this review we describe the state of the art on the role of subcellular compartments in the biosynthesis of major types of PNPs, including terpenoids, phenylpropanoids, alkaloids and glucosinolates, and highlight the efforts to target biosynthetic pathways to subcellular compartments in plants. In addition, we will discuss the challenges and strategies in the field of plant synthetic biology and subcellular engineering. We expect that newly developed methods and tools, together with the knowledge gained from the microbial chassis, will greatly advance plant metabolic engineering.
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Affiliation(s)
- Lu Yao
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, Shandong 266100, China
| | - Xiuming Wu
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, Shandong 266100, China
| | - Xun Jiang
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, Shandong 266100, China
| | - Muhammad Shan
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, Shandong 266100, China
| | - Zhuoxiang Zhang
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, Shandong 266100, China
| | - Yiting Li
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, Shandong 266100, China
| | - Aiguo Yang
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, Shandong 266100, China
| | - Yu Li
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
| | - Changqing Yang
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, Shandong 266100, China.
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15
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Zhou X, Zhao Y, Ni P, Ni Z, Sun Q, Zong Y. CRISPR-mediated acceleration of wheat improvement: advances and perspectives. J Genet Genomics 2023; 50:815-834. [PMID: 37741566 DOI: 10.1016/j.jgg.2023.09.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Revised: 09/13/2023] [Accepted: 09/14/2023] [Indexed: 09/25/2023]
Abstract
Common wheat (Triticum aestivum) is one of the most widely cultivated and consumed crops globally. In the face of limited arable land and climate changes, it is a great challenge to maintain current and increase future wheat production. Enhancing agronomic traits in wheat by introducing mutations across all three homoeologous copies of each gene has proven to be a difficult task due to its large genome with high repetition. However, clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated nuclease (Cas) genome editing technologies offer a powerful means of precisely manipulating the genomes of crop species, thereby opening up new possibilities for biotechnology and breeding. In this review, we first focus on the development and optimization of the current CRISPR-based genome editing tools in wheat, emphasizing recent breakthroughs in precise and multiplex genome editing. We then describe the general procedure of wheat genome editing and highlight different methods to deliver the genome editing reagents into wheat cells. Furthermore, we summarize the recent applications and advancements of CRISPR/Cas technologies for wheat improvement. Lastly, we discuss the remaining challenges specific to wheat genome editing and its future prospects.
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Affiliation(s)
- Ximeng Zhou
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Yidi Zhao
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Pei Ni
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Zhongfu Ni
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Qixin Sun
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Yuan Zong
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China.
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16
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He YH, Chen SY, Chen XY, Xu YP, Liang Y, Cai XZ. RALF22 promotes plant immunity and amplifies the Pep3 immune signal. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2023; 65:2519-2534. [PMID: 37698076 DOI: 10.1111/jipb.13566] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Accepted: 09/04/2023] [Indexed: 09/13/2023]
Abstract
Rapid alkalinization factors (RALFs) in plants have been reported to dampen pathogen-associated molecular pattern (PAMP)-triggered immunity via suppressing PAMP-induced complex formation between the pattern recognition receptor (PRR) and its co-receptor BAK1. However, the direct and positive role of RALFs in plant immunity remains largely unknown. Herein, we report the direct and positive roles of a typical RALF, RALF22, in plant immunity. RALF22 alone directly elicited a variety of typical immune responses and triggered resistance against the devastating necrotrophic fungal pathogen Sclerotinia sclerotiorum in a FERONIA (FER)-dependent manner. LORELEI (LRE)-like glycosylphosphatidylinositol (GPI)-anchored protein 1 (LLG1) and NADPH oxidase RBOHD were required for RALF22-elicited reactive oxygen species (ROS) generation. The mutation of cysteines conserved in the C terminus of RALFs abolished, while the constitutive formation of two disulfide bridges between these cysteines promoted the RALF22-elicited ROS production and resistance against S. sclerotiorum, demonstrating the requirement of these cysteines in the functions of RALF22 in plant immunity. Furthermore, RALF22 amplified the Pep3-induced immune signal by dramatically increasing the abundance of PROPEP3 transcript and protein. Supply with RALF22 induced resistance against S. sclerotiorum in Brassica crop plants. Collectively, our results reveal that RALF22 triggers immune responses and augments the Pep3-induced immune signal in a FER-dependent manner, and exhibits the potential to be exploited as an immune elicitor in crop protection.
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Affiliation(s)
- Yu-Han He
- Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Biotechnology, College of Agriculture and Biotechnology, Zhejiang University, 866 Yu Hang Tang Road, Hangzhou, 310058, China
| | - Song-Yu Chen
- Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Biotechnology, College of Agriculture and Biotechnology, Zhejiang University, 866 Yu Hang Tang Road, Hangzhou, 310058, China
| | - Xing-Yan Chen
- Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Biotechnology, College of Agriculture and Biotechnology, Zhejiang University, 866 Yu Hang Tang Road, Hangzhou, 310058, China
| | - You-Ping Xu
- Centre of Analysis and Measurement, Zhejiang University, 866 Yu Hang Tang Road, Hangzhou, 310058, China
| | - Yan Liang
- Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Biotechnology, College of Agriculture and Biotechnology, Zhejiang University, 866 Yu Hang Tang Road, Hangzhou, 310058, China
| | - Xin-Zhong Cai
- Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Biotechnology, College of Agriculture and Biotechnology, Zhejiang University, 866 Yu Hang Tang Road, Hangzhou, 310058, China
- Hainan Institute, Zhejiang University, Sanya, 572025, China
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17
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Shahriari Z, Su X, Zheng K, Zhang Z. Advances and Prospects of Virus-Resistant Breeding in Tomatoes. Int J Mol Sci 2023; 24:15448. [PMID: 37895127 PMCID: PMC10607384 DOI: 10.3390/ijms242015448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Revised: 10/15/2023] [Accepted: 10/16/2023] [Indexed: 10/29/2023] Open
Abstract
Plant viruses are the main pathogens which cause significant quality and yield losses in tomato crops. The important viruses that infect tomatoes worldwide belong to five genera: Begomovirus, Orthotospovirus, Tobamovirus, Potyvirus, and Crinivirus. Tomato resistance genes against viruses, including Ty gene resistance against begomoviruses, Sw gene resistance against orthotospoviruses, Tm gene resistance against tobamoviruses, and Pot 1 gene resistance against potyviruses, have been identified from wild germplasm and introduced into cultivated cultivars via hybrid breeding. However, these resistance genes mainly exhibit qualitative resistance mediated by single genes, which cannot protect against virus mutations, recombination, mixed-infection, or emerging viruses, thus posing a great challenge to tomato antiviral breeding. Based on the epidemic characteristics of tomato viruses, we propose that future studies on tomato virus resistance breeding should focus on rapidly, safely, and efficiently creating broad-spectrum germplasm materials resistant to multiple viruses. Accordingly, we summarized and analyzed the advantages and characteristics of the three tomato antiviral breeding strategies, including marker-assisted selection (MAS)-based hybrid breeding, RNA interference (RNAi)-based transgenic breeding, and CRISPR/Cas-based gene editing. Finally, we highlighted the challenges and provided suggestions for improving tomato antiviral breeding in the future using the three breeding strategies.
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Affiliation(s)
- Zolfaghar Shahriari
- Biotechnology and Germplasm Resources Research Institute, Yunnan Academy of Agricultural Sciences, Yunnan Seed Laboratory, 2238# Beijing Rd, Panlong District, Kunming 650205, China; (Z.S.); (X.S.)
- Crop and Horticultural Science Research Department, Fars Agricultural and Natural Resources Research and Education Center, Agricultural Research, Education and Extension Organization (AREEO), Shiraz 617-71555, Iran
| | - Xiaoxia Su
- Biotechnology and Germplasm Resources Research Institute, Yunnan Academy of Agricultural Sciences, Yunnan Seed Laboratory, 2238# Beijing Rd, Panlong District, Kunming 650205, China; (Z.S.); (X.S.)
| | - Kuanyu Zheng
- Biotechnology and Germplasm Resources Research Institute, Yunnan Academy of Agricultural Sciences, Yunnan Seed Laboratory, 2238# Beijing Rd, Panlong District, Kunming 650205, China; (Z.S.); (X.S.)
| | - Zhongkai Zhang
- Biotechnology and Germplasm Resources Research Institute, Yunnan Academy of Agricultural Sciences, Yunnan Seed Laboratory, 2238# Beijing Rd, Panlong District, Kunming 650205, China; (Z.S.); (X.S.)
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18
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Tsakirpaloglou N, Septiningsih EM, Thomson MJ. Guidelines for Performing CRISPR/Cas9 Genome Editing for Gene Validation and Trait Improvement in Crops. PLANTS (BASEL, SWITZERLAND) 2023; 12:3564. [PMID: 37896028 PMCID: PMC10610170 DOI: 10.3390/plants12203564] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Revised: 10/10/2023] [Accepted: 10/11/2023] [Indexed: 10/29/2023]
Abstract
With the rapid advances in plant genome editing techniques over the past 10 years, more efficient and powerful crop genome editing applications are now possible. Candidate genes for key traits can be validated using CRISPR/Cas9-based knockouts and through the up- and down-regulation of gene expression. Likewise, new trait improvement approaches can take advantage of targeted editing to improve stress tolerance, disease resistance, and nutritional traits. However, several key steps in the process can prove tricky for researchers who might be new to plant genome editing. Here, we present step-by-step guidelines and best practices for a crop genome editing pipeline that should help to improve the rate of success. Important factors in the process include proper target sequence analysis and single guide RNA (sgRNA) design, sequencing of the target site in the genotypes of interest, performing an in vitro CRISPR/Cas9 ribonucleoprotein (RNP) assay to validate the designed sgRNAs, preparing the transformation constructs, considering a protoplast editing step as further validation, and, finally, stable plant transformation and mutation detection by Sanger and/or next-generation sequencing. With these detailed guidelines, a new user should be able to quickly set up a genome editing pipeline in their crop of interest and start making progress with the different CRISPR/Cas-based editing variants for gene validation and trait improvement purposes.
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Affiliation(s)
| | | | - Michael J. Thomson
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX 77843, USA; (N.T.); (E.M.S.)
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19
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Baghini SS, Razeghian E, Malayer SK, Pecho RDC, Obaid M, Awfi ZS, Zainab HA, Shamsara M. Recent advances in the application of genetic and epigenetic modalities in the improvement of antibody-producing cell lines. Int Immunopharmacol 2023; 123:110724. [PMID: 37582312 DOI: 10.1016/j.intimp.2023.110724] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 07/25/2023] [Accepted: 07/26/2023] [Indexed: 08/17/2023]
Abstract
There are numerous applications for recombinant antibodies (rAbs) in biological and toxicological research. Monoclonal antibodies are synthesized using genetic engineering and other related processes involved in the generation of rAbs. Because they can identify specific antigenic sites on practically any molecule, including medicines, hormones, microbial antigens, and cell receptors, rAbs are particularly useful in scientific research. The key benefits of rAbs are improved repeatability, control, and consistency, shorter manufacturing times than with hybridoma technology, an easier transition from one format of antibody to another, and an animal-free process. The engineering of the host cell has recently been developed method for enhancing the production efficiency and improving the quality of antibodies from mammalian cell lines. In this light, genetic engineering is mostly utilized to manage cellular chaperones, decrease cell death, increase cell viability, change the microRNAs (miRNAs) pattern in mammalian cells, and glycoengineered cell lines. Here, we shed light on how genetic engineering can be used therapeutically to produce antibodies at higher levels with greater potency and effectiveness.
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Affiliation(s)
- Sadegh Shojaei Baghini
- Plant Biotechnology Department, National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran, Iran.
| | - Ehsan Razeghian
- Human Genetics Division, Medical Biotechnology Department, National Institute of Genetics Engineering and Biotechnology (NIGEB), Tehran, Iran
| | - Setare Kakavand Malayer
- Department of Biology, Faculty of Biological Science, Tehran North Branch, Islamic Azad University, Tehran, Iran
| | | | | | - Zinah Salem Awfi
- Department of Dental Industry Techniques, Al-Noor University College, Nineveh, Iraq.
| | - H A Zainab
- Department of Pharmacy, Al-Zahrawi University College, Karbala, Iraq.
| | - Mehdi Shamsara
- Department of Animal Biotechnology, National Institute of Genetic Engineering and Biotechnology, Tehran, Iran.
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20
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Cardi T, Murovec J, Bakhsh A, Boniecka J, Bruegmann T, Bull SE, Eeckhaut T, Fladung M, Galovic V, Linkiewicz A, Lukan T, Mafra I, Michalski K, Kavas M, Nicolia A, Nowakowska J, Sági L, Sarmiento C, Yıldırım K, Zlatković M, Hensel G, Van Laere K. CRISPR/Cas-mediated plant genome editing: outstanding challenges a decade after implementation. TRENDS IN PLANT SCIENCE 2023; 28:1144-1165. [PMID: 37331842 DOI: 10.1016/j.tplants.2023.05.012] [Citation(s) in RCA: 24] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 05/09/2023] [Accepted: 05/15/2023] [Indexed: 06/20/2023]
Abstract
The discovery of the CRISPR/Cas genome-editing system has revolutionized our understanding of the plant genome. CRISPR/Cas has been used for over a decade to modify plant genomes for the study of specific genes and biosynthetic pathways as well as to speed up breeding in many plant species, including both model and non-model crops. Although the CRISPR/Cas system is very efficient for genome editing, many bottlenecks and challenges slow down further improvement and applications. In this review we discuss the challenges that can occur during tissue culture, transformation, regeneration, and mutant detection. We also review the opportunities provided by new CRISPR platforms and specific applications related to gene regulation, abiotic and biotic stress response improvement, and de novo domestication of plants.
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Affiliation(s)
- Teodoro Cardi
- Consiglio Nazionale delle Ricerche (CNR), Institute of Biosciences and Bioresources (IBBR), Portici, Italy; CREA Research Centre for Vegetable and Ornamental Crops, Pontecagnano, Italy
| | - Jana Murovec
- University of Ljubljana, Biotechnical Faculty, Ljubljana, Slovenia
| | - Allah Bakhsh
- Department of Agricultural Genetic Engineering, Faculty of Agricultural Sciences and Technologies, Nigde Omer Halisdemir University, Nigde, Turkey; Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Justyna Boniecka
- Department of Genetics, Faculty of Biological and Veterinary Sciences, Nicolaus Copernicus University, Toruń, Poland; Centre for Modern Interdisciplinary Technologies, Nicolaus Copernicus University, Toruń, Poland
| | | | - Simon E Bull
- Molecular Plant Breeding, Institute of Agricultural Sciences, Eidgenössische Technische Hochschule (ETH) Zurich, Switzerland; Plant Biochemistry, Institute of Molecular Plant Biology, ETH, Zurich, Switzerland
| | - Tom Eeckhaut
- Flanders Research Institute for Agricultural, Fisheries and Food, Melle, Belgium
| | | | - Vladislava Galovic
- University of Novi Sad, Institute of Lowland Forestry and Environment (ILFE), Novi Sad, Serbia
| | - Anna Linkiewicz
- Molecular Biology and Genetics Department, Institute of Biological Sciences, Faculty of Biology and Environmental Sciences, Cardinal Stefan Wyszyński University, Warsaw, Poland
| | - Tjaša Lukan
- National Institute of Biology, Department of Biotechnology and Systems Biology, Ljubljana, Slovenia
| | - Isabel Mafra
- Rede de Química e Tecnologia (REQUIMTE) Laboratório Associado para a Química Verde (LAQV), Faculdade de Farmácia, Universidade do Porto, Porto, Portugal
| | - Krzysztof Michalski
- Plant Breeding and Acclimatization Institute, National Research Institute, Błonie, Poland
| | - Musa Kavas
- Department of Molecular Biology and Genetics, Faculty of Science, Ondokuz Mayis University, Samsun, Turkey
| | - Alessandro Nicolia
- CREA Research Centre for Vegetable and Ornamental Crops, Pontecagnano, Italy
| | - Justyna Nowakowska
- Molecular Biology and Genetics Department, Institute of Biological Sciences, Faculty of Biology and Environmental Sciences, Cardinal Stefan Wyszyński University, Warsaw, Poland
| | - Laszlo Sági
- Centre for Agricultural Research, Loránd Eötvös Research Network, Martonvásár, Hungary
| | - Cecilia Sarmiento
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Tallinn, Estonia
| | - Kubilay Yıldırım
- Department of Molecular Biology and Genetics, Faculty of Science, Ondokuz Mayis University, Samsun, Turkey
| | - Milica Zlatković
- University of Novi Sad, Institute of Lowland Forestry and Environment (ILFE), Novi Sad, Serbia
| | - Goetz Hensel
- Heinrich-Heine-University, Institute of Plant Biochemistry, Centre for Plant Genome Engineering, Düsseldorf, Germany; Division of Molecular Biology, Centre of the Region Hana for Biotechnological and Agriculture Research, Faculty of Science, Palacký University, Olomouc, Czech Republic
| | - Katrijn Van Laere
- Flanders Research Institute for Agricultural, Fisheries and Food, Melle, Belgium.
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21
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Cui Y, Cao Q, Li Y, He M, Liu X. Advances in cis-element- and natural variation-mediated transcriptional regulation and applications in gene editing of major crops. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:5441-5457. [PMID: 37402253 DOI: 10.1093/jxb/erad248] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Accepted: 06/28/2023] [Indexed: 07/06/2023]
Abstract
Transcriptional regulation is crucial to control of gene expression. Both spatio-temporal expression patterns and expression levels of genes are determined by the interaction between cis-acting elements and trans-acting factors. Numerous studies have focused on the trans-acting factors that mediate transcriptional regulatory networks. However, cis-acting elements, such as enhancers, silencers, transposons, and natural variations in the genome, are also vital for gene expression regulation and could be utilized by clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9)-mediated gene editing to improve crop quality and yield. In this review, we discuss current understanding of cis-element-mediated transcriptional regulation in major crops, including rice (Oryza sativa), wheat (Triticum aestivum), and maize (Zea mays), as well as the latest advancements in gene editing techniques and their applications in crops to highlight prospective strategies for crop breeding.
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Affiliation(s)
- Yue Cui
- College of Teacher Education, Molecular and Cellular Postdoctoral Research Station, Hebei Normal University, Shijiazhuang 050024, China
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Hebei Collaboration Innovation Center for Cell Signaling, Hebei Research Center of the Basic Discipline Cell Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang 050024, China
| | - Qiao Cao
- Shijiazhuang Academy of Agricultural and Forestry Sciences, Shijiazhuang, Hebei Province 050041, China
| | - Yongpeng Li
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Hebei Collaboration Innovation Center for Cell Signaling, Hebei Research Center of the Basic Discipline Cell Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang 050024, China
| | - Mingqi He
- Shijiazhuang Academy of Agricultural and Forestry Sciences, Shijiazhuang, Hebei Province 050041, China
| | - Xigang Liu
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Hebei Collaboration Innovation Center for Cell Signaling, Hebei Research Center of the Basic Discipline Cell Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang 050024, China
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22
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Li H, Hua L, Zhao S, Hao M, Song R, Pang S, Liu Y, Chen H, Zhang W, Shen T, Gou JY, Mao H, Wang G, Hao X, Li J, Song B, Lan C, Li Z, Deng XW, Dubcovsky J, Wang X, Chen S. Cloning of the wheat leaf rust resistance gene Lr47 introgressed from Aegilops speltoides. Nat Commun 2023; 14:6072. [PMID: 37770474 PMCID: PMC10539295 DOI: 10.1038/s41467-023-41833-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 09/20/2023] [Indexed: 09/30/2023] Open
Abstract
Leaf rust, caused by Puccinia triticina Eriksson (Pt), is one of the most severe foliar diseases of wheat. Breeding for leaf rust resistance is a practical and sustainable method to control this devastating disease. Here, we report the identification of Lr47, a broadly effective leaf rust resistance gene introgressed into wheat from Aegilops speltoides. Lr47 encodes a coiled-coil nucleotide-binding leucine-rich repeat protein that is both necessary and sufficient to confer Pt resistance, as demonstrated by loss-of-function mutations and transgenic complementation. Lr47 introgression lines with no or reduced linkage drag are generated using the Pairing homoeologous1 mutation, and a diagnostic molecular marker for Lr47 is developed. The coiled-coil domain of the Lr47 protein is unable to induce cell death, nor does it have self-protein interaction. The cloning of Lr47 expands the number of leaf rust resistance genes that can be incorporated into multigene transgenic cassettes to control this devastating disease.
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Affiliation(s)
- Hongna Li
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences in Weifang, 261325, Shandong, China
| | - Lei Hua
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences in Weifang, 261325, Shandong, China
| | - Shuqing Zhao
- State Key Laboratory of North China Crop Improvement and Regulation, College of Plant Protection, Hebei Agricultural University, 071000, Baoding, Hebei, China
| | - Ming Hao
- Triticeae Research Institute, Sichuan Agricultural University, 611130, Chengdu, China
| | - Rui Song
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences in Weifang, 261325, Shandong, China
| | - Shuyong Pang
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences in Weifang, 261325, Shandong, China
- State Key Laboratory of North China Crop Improvement and Regulation, College of Plant Protection, Hebei Agricultural University, 071000, Baoding, Hebei, China
| | - Yanna Liu
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences in Weifang, 261325, Shandong, China
| | - Hong Chen
- Triticeae Research Institute, Sichuan Agricultural University, 611130, Chengdu, China
| | - Wenjun Zhang
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA
| | - Tao Shen
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences in Weifang, 261325, Shandong, China
| | - Jin-Ying Gou
- Key Laboratory of Crop Heterosis and Utilization (MOE) and Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, 100193, Beijing, China
| | - Hailiang Mao
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, 430070, Wuhan, China
| | - Guiping Wang
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences in Weifang, 261325, Shandong, China
| | - Xiaohua Hao
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences in Weifang, 261325, Shandong, China
| | - Jian Li
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences in Weifang, 261325, Shandong, China
| | - Baoxing Song
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences in Weifang, 261325, Shandong, China
| | - Caixia Lan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, 430070, Wuhan, China
| | - Zaifeng Li
- State Key Laboratory of North China Crop Improvement and Regulation, College of Plant Protection, Hebei Agricultural University, 071000, Baoding, Hebei, China
| | - Xing Wang Deng
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences in Weifang, 261325, Shandong, China
| | - Jorge Dubcovsky
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, 20815, USA
| | - Xiaodong Wang
- State Key Laboratory of North China Crop Improvement and Regulation, College of Plant Protection, Hebei Agricultural University, 071000, Baoding, Hebei, China.
| | - Shisheng Chen
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences in Weifang, 261325, Shandong, China.
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23
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Islam T, Kasfy SH. CRISPR enables heritable genome editing in planta. Trends Genet 2023; 39:646-648. [PMID: 37429772 DOI: 10.1016/j.tig.2023.06.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2023] [Revised: 06/24/2023] [Accepted: 06/26/2023] [Indexed: 07/12/2023]
Abstract
Recent exciting developments in clustered regularly interspaced short palindromic repeats (CRISPR)-based genome editing showcase its potential to rapidly and efficiently edit genomes in planta, eliminating long processes of tissue culture and extensive breeding for crop improvement. These new methods offer heritable transgene-free edits in one generation, making them an attractive option for improving commercially important crops.
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Affiliation(s)
- Tofazzal Islam
- Institute of Biotechnology and Genetic Engineering (IBGE), Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur 1706, Bangladesh.
| | - Shamfin Hossain Kasfy
- Institute of Biotechnology and Genetic Engineering (IBGE), Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur 1706, Bangladesh
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24
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Awan MJA, Akram A, Amin I, Mansoor S. Viral vectors as carriers of genome-editing reagents. TRENDS IN PLANT SCIENCE 2023; 28:981-983. [PMID: 37236860 DOI: 10.1016/j.tplants.2023.05.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 05/14/2023] [Accepted: 05/15/2023] [Indexed: 05/28/2023]
Abstract
The presence of a transgene in the genome of plants is a regulatory challenge. Recently, Liu et al. reported an engineered tomato spotted wilt virus (TSWV) that can carry large clustered regularly interspaced palindromic repeats (CRISPR)/Cas reagents for targeted genome editing in various crops without the integration of the transgene into the genome.
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Affiliation(s)
- Muhammad Jawad Akbar Awan
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Constituent College of Pakistan Institute of Engineering and Applied Sciences, Jhang Road, Faisalabad, Pakistan
| | - Afzal Akram
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Constituent College of Pakistan Institute of Engineering and Applied Sciences, Jhang Road, Faisalabad, Pakistan
| | - Imran Amin
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Constituent College of Pakistan Institute of Engineering and Applied Sciences, Jhang Road, Faisalabad, Pakistan
| | - Shahid Mansoor
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Constituent College of Pakistan Institute of Engineering and Applied Sciences, Jhang Road, Faisalabad, Pakistan; International Center for Chemical and Biological Sciences, University of Karachi, Karachi, Pakistan.
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25
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Wang B, Meng T, Xiao B, Yu T, Yue T, Jin Y, Ma P. Fighting wheat powdery mildew: from genes to fields. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:196. [PMID: 37606731 DOI: 10.1007/s00122-023-04445-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 08/07/2023] [Indexed: 08/23/2023]
Abstract
KEY MESSAGE Host resistance conferred by Pm genes provides an effective strategy to control powdery mildew. The study of Pm genes helps modern breeding develop toward more intelligent and customized. Powdery mildew of wheat is one of the most destructive diseases seriously threatening the crop yield and quality worldwide. The genetic research on powdery mildew (Pm) resistance has entered a new era. Many Pm genes from wheat and its wild and domesticated relatives have been mined and cloned. Meanwhile, modern breeding strategies based on high-throughput sequencing and genome editing are emerging and developing toward more intelligent and customized. This review highlights mining and cloning of Pm genes, molecular mechanism studies on the resistance and avirulence genes, and prospects for genomic-assisted breeding for powdery mildew resistance in wheat.
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Affiliation(s)
- Bo Wang
- Yantai Key Laboratory of Characteristic Agricultural Biological Resource Conservation and Germplasm Innovative Utilization, College of Life Sciences, Yantai University, Yantai, 264005, China
| | - Ting Meng
- Yantai Key Laboratory of Characteristic Agricultural Biological Resource Conservation and Germplasm Innovative Utilization, College of Life Sciences, Yantai University, Yantai, 264005, China
| | - Bei Xiao
- Yantai Key Laboratory of Characteristic Agricultural Biological Resource Conservation and Germplasm Innovative Utilization, College of Life Sciences, Yantai University, Yantai, 264005, China
| | - Tianying Yu
- Yantai Key Laboratory of Characteristic Agricultural Biological Resource Conservation and Germplasm Innovative Utilization, College of Life Sciences, Yantai University, Yantai, 264005, China
| | - Tingyan Yue
- Yantai Key Laboratory of Characteristic Agricultural Biological Resource Conservation and Germplasm Innovative Utilization, College of Life Sciences, Yantai University, Yantai, 264005, China
| | - Yuli Jin
- Yantai Key Laboratory of Characteristic Agricultural Biological Resource Conservation and Germplasm Innovative Utilization, College of Life Sciences, Yantai University, Yantai, 264005, China
| | - Pengtao Ma
- Yantai Key Laboratory of Characteristic Agricultural Biological Resource Conservation and Germplasm Innovative Utilization, College of Life Sciences, Yantai University, Yantai, 264005, China.
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26
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Bekalu ZE, Panting M, Bæksted Holme I, Brinch-Pedersen H. Opportunities and Challenges of In Vitro Tissue Culture Systems in the Era of Crop Genome Editing. Int J Mol Sci 2023; 24:11920. [PMID: 37569295 PMCID: PMC10419073 DOI: 10.3390/ijms241511920] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 07/17/2023] [Accepted: 07/21/2023] [Indexed: 08/13/2023] Open
Abstract
Currently, the development of genome editing (GE) tools has provided a wide platform for targeted modification of plant genomes. However, the lack of versatile DNA delivery systems for a large variety of crop species has been the main bottleneck for improving crops with beneficial traits. Currently, the generation of plants with heritable mutations induced by GE tools mostly goes through tissue culture. Unfortunately, current tissue culture systems restrict successful results to only a limited number of plant species and genotypes. In order to release the full potential of the GE tools, procedures need to be species and genotype independent. This review provides an in-depth summary and insights into the various in vitro tissue culture systems used for GE in the economically important crops barley, wheat, rice, sorghum, soybean, maize, potatoes, cassava, and millet and uncovers new opportunities and challenges of already-established tissue culture platforms for GE in the crops.
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27
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Kocsisova Z, Coneva V. Strategies for delivery of CRISPR/Cas-mediated genome editing to obtain edited plants directly without transgene integration. Front Genome Ed 2023; 5:1209586. [PMID: 37545761 PMCID: PMC10398581 DOI: 10.3389/fgeed.2023.1209586] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Accepted: 06/28/2023] [Indexed: 08/08/2023] Open
Abstract
Increased understanding of plant genetics and the development of powerful and easier-to-use gene editing tools over the past century have revolutionized humankind's ability to deliver precise genotypes in crops. Plant transformation techniques are well developed for making transgenic varieties in certain crops and model organisms, yet reagent delivery and plant regeneration remain key bottlenecks to applying the technology of gene editing to most crops. Typical plant transformation protocols to produce transgenic, genetically modified (GM) varieties rely on transgenes, chemical selection, and tissue culture. Typical protocols to make gene edited (GE) varieties also use transgenes, even though these may be undesirable in the final crop product. In some crops, the transgenes are routinely segregated away during meiosis by performing crosses, and thus only a minor concern. In other crops, particularly those propagated vegetatively, complex hybrids, or crops with long generation times, such crosses are impractical or impossible. This review highlights diverse strategies to deliver CRISPR/Cas gene editing reagents to regenerable plant cells and to recover edited plants without unwanted integration of transgenes. Some examples include delivering DNA-free gene editing reagents such as ribonucleoproteins or mRNA, relying on reagent expression from non-integrated DNA, using novel delivery mechanisms such as viruses or nanoparticles, using unconventional selection methods to avoid integration of transgenes, and/or avoiding tissue culture altogether. These methods are advancing rapidly and already enabling crop scientists to make use of the precision of CRISPR gene editing tools.
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28
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Beernink BM, Whitham SA. Foxtail mosaic virus: A tool for gene function analysis in maize and other monocots. MOLECULAR PLANT PATHOLOGY 2023; 24:811-822. [PMID: 37036421 PMCID: PMC10257046 DOI: 10.1111/mpp.13330] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 02/20/2023] [Accepted: 03/08/2023] [Indexed: 06/11/2023]
Abstract
Many plant viruses have been engineered into vectors for use in functional genomics studies, expression of heterologous proteins, and, most recently, gene editing applications. The use of viral vectors overcomes bottlenecks associated with mutagenesis and transgenesis approaches often implemented for analysis of gene function. There are several engineered viruses that are demonstrated or suggested to be useful in maize through proof-of-concept studies. However, foxtail mosaic virus (FoMV), which has a relatively broad host range, is emerging as a particularly useful virus for gene function studies in maize and other monocot crop or weed species. A few clones of FoMV have been independently engineered, and they have different features and capabilities for virus-induced gene silencing (VIGS) and virus-mediated overexpression (VOX) of proteins. In addition, FoMV can be used to deliver functional guide RNAs in maize and other plants expressing the Cas9 protein, demonstrating its potential utility in virus-induced gene editing applications. There is a growing number of studies in which FoMV vectors are being applied for VIGS or VOX in maize and the vast majority of these are related to maize-microbe interactions. In this review, we highlight the biology and engineering of FoMV as well as its applications in maize-microbe interactions and more broadly in the context of the monocot functional genomics toolbox.
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Affiliation(s)
- Bliss M. Beernink
- Department of Plant Pathology, Entomology, and MicrobiologyIowa State UniversityAmesIowaUSA
- Department of BiologyUniversity of ManitobaWinnipegManitobaCanada
| | - Steven A. Whitham
- Department of Plant Pathology, Entomology, and MicrobiologyIowa State UniversityAmesIowaUSA
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29
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Tamilselvan-Nattar-Amutha S, Hiekel S, Hartmann F, Lorenz J, Dabhi RV, Dreissig S, Hensel G, Kumlehn J, Heckmann S. Barley stripe mosaic virus-mediated somatic and heritable gene editing in barley ( Hordeum vulgare L.). FRONTIERS IN PLANT SCIENCE 2023; 14:1201446. [PMID: 37404527 PMCID: PMC10315673 DOI: 10.3389/fpls.2023.1201446] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Accepted: 06/02/2023] [Indexed: 07/06/2023]
Abstract
Genome editing strategies in barley (Hordeum vulgare L.) typically rely on Agrobacterium-mediated genetic transformation for the delivery of required genetic reagents involving tissue culture techniques. These approaches are genotype-dependent, time-consuming, and labor-intensive, which hampers rapid genome editing in barley. More recently, plant RNA viruses have been engineered to transiently express short guide RNAs facilitating CRISPR/Cas9-based targeted genome editing in plants that constitutively express Cas9. Here, we explored virus-induced genome editing (VIGE) based on barley stripe mosaic virus (BSMV) in Cas9-transgenic barley. Somatic and heritable editing in the ALBOSTRIANS gene (CMF7) resulting in albino/variegated chloroplast-defective barley mutants is shown. In addition, somatic editing in meiosis-related candidate genes in barley encoding ASY1 (an axis-localized HORMA domain protein), MUS81 (a DNA structure-selective endonuclease), and ZYP1 (a transverse filament protein of the synaptonemal complex) was achieved. Hence, the presented VIGE approach using BSMV enables rapid somatic and also heritable targeted gene editing in barley.
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30
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Awan MJA, Aslam MQ, Naqvi RZ, Amin I, Mansoor S. A graft that crafts nontransgenic and genome-edited plants. TRENDS IN PLANT SCIENCE 2023; 28:614-616. [PMID: 36997438 DOI: 10.1016/j.tplants.2023.03.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 03/20/2023] [Accepted: 03/20/2023] [Indexed: 05/13/2023]
Abstract
Grafting in plants facilitates the transmission of biomolecules across the union formation. Recently, Yang et al. demonstrated that inter- and intraspecific grafting in plants can be exploited for trafficking tRNA-tagged mobile reagents of the clustered regularly interspaced short palindromic repeats (CRISPR)/Cas system from the transgenic rootstock to wild-type scion for genetic improvement in plants through targeted mutagenesis.
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Affiliation(s)
- Muhammad Jawad Akbar Awan
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Constituent College of Pakistan Institute of Engineering and Applied Sciences, Jhang Road, Faisalabad, Pakistan
| | - Muhammad Qasim Aslam
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Constituent College of Pakistan Institute of Engineering and Applied Sciences, Jhang Road, Faisalabad, Pakistan
| | - Rubab Zahra Naqvi
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Constituent College of Pakistan Institute of Engineering and Applied Sciences, Jhang Road, Faisalabad, Pakistan
| | - Imran Amin
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Constituent College of Pakistan Institute of Engineering and Applied Sciences, Jhang Road, Faisalabad, Pakistan
| | - Shahid Mansoor
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Constituent College of Pakistan Institute of Engineering and Applied Sciences, Jhang Road, Faisalabad, Pakistan; International Center for Chemical and Biological Sciences, University of Karachi, Karachi, Pakistan.
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31
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Daròs JA, Pasin F, Merwaiss F. CRISPR-Cas-based plant genome engineering goes viral. MOLECULAR PLANT 2023; 16:660-661. [PMID: 36950734 DOI: 10.1016/j.molp.2023.03.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Revised: 03/19/2023] [Accepted: 03/19/2023] [Indexed: 06/18/2023]
Affiliation(s)
- José-Antonio Daròs
- Instituto de Biología Molecular y Celular de Plantas (CSIC-Universitat Politècnica de València), 46022 Valencia, Spain.
| | - Fabio Pasin
- Instituto de Biología Molecular y Celular de Plantas (CSIC-Universitat Politècnica de València), 46022 Valencia, Spain
| | - Fernando Merwaiss
- Instituto de Biología Molecular y Celular de Plantas (CSIC-Universitat Politècnica de València), 46022 Valencia, Spain
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32
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Uranga M, Aragonés V, Daròs JA, Pasin F. Heritable CRISPR-Cas9 editing of plant genomes using RNA virus vectors. STAR Protoc 2023; 4:102091. [PMID: 36853698 PMCID: PMC9943877 DOI: 10.1016/j.xpro.2023.102091] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 12/05/2022] [Accepted: 01/17/2023] [Indexed: 02/11/2023] Open
Abstract
Viral vectors hold enormous potential for genome editing in plants as transient delivery vehicles of CRISPR-Cas components. Here, we describe a protocol to assemble plant viral vectors for single-guide RNA (sgRNA) delivery. The obtained viral constructs are based on compact T-DNA binary vectors of the pLX series and are delivered into Cas9-expressing plants through agroinoculation. This approach allows rapidly assessing sgRNA design for plant genome targeting, as well as the recovery of progeny with heritable mutations at targeted loci. For complete details on the use and execution of this protocol, please refer to Uranga et al. (2021)1 and Aragonés et al. (2022).2.
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Affiliation(s)
- Mireia Uranga
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas - Universitat Politècnica de València, Avenida de los Naranjos s/n, 46022 Valencia, Spain.
| | - Verónica Aragonés
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas - Universitat Politècnica de València, Avenida de los Naranjos s/n, 46022 Valencia, Spain.
| | - José-Antonio Daròs
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas - Universitat Politècnica de València, Avenida de los Naranjos s/n, 46022 Valencia, Spain.
| | - Fabio Pasin
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas - Universitat Politècnica de València, Avenida de los Naranjos s/n, 46022 Valencia, Spain.
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Virus-Induced Gene Silencing (VIGS): A Powerful Tool for Crop Improvement and Its Advancement towards Epigenetics. Int J Mol Sci 2023; 24:ijms24065608. [PMID: 36982682 PMCID: PMC10057534 DOI: 10.3390/ijms24065608] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Revised: 01/26/2023] [Accepted: 02/02/2023] [Indexed: 03/17/2023] Open
Abstract
Virus-induced gene silencing (VIGS) is an RNA-mediated reverse genetics technology that has evolved into an indispensable approach for analyzing the function of genes. It downregulates endogenous genes by utilizing the posttranscriptional gene silencing (PTGS) machinery of plants to prevent systemic viral infections. Based on recent advances, VIGS can now be used as a high-throughput tool that induces heritable epigenetic modifications in plants through the viral genome by transiently knocking down targeted gene expression. As a result of the progression of DNA methylation induced by VIGS, new stable genotypes with desired traits are being developed in plants. In plants, RNA-directed DNA methylation (RdDM) is a mechanism where epigenetic modifiers are guided to target loci by small RNAs, which play a major role in the silencing of the target gene. In this review, we described the molecular mechanisms of DNA and RNA-based viral vectors and the knowledge obtained through altering the genes in the studied plants that are not usually accessible to transgenic techniques. We showed how VIGS-induced gene silencing can be used to characterize transgenerational gene function(s) and altered epigenetic marks, which can improve future plant breeding programs.
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Liu Q, Zhao C, Sun K, Deng Y, Li Z. Engineered biocontainable RNA virus vectors for non-transgenic genome editing across crop species and genotypes. MOLECULAR PLANT 2023; 16:616-631. [PMID: 36751129 DOI: 10.1016/j.molp.2023.02.003] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2022] [Revised: 01/13/2023] [Accepted: 02/01/2023] [Indexed: 06/18/2023]
Abstract
CRISPR/Cas genome-editing tools provide unprecedented opportunities for basic plant biology research and crop breeding. However, the lack of robust delivery methods has limited the widespread adoption of these revolutionary technologies in plant science. Here, we report an efficient, non-transgenic CRISPR/Cas delivery platform based on the engineered tomato spotted wilt virus (TSWV), an RNA virus with a host range of over 1000 plant species. We eliminated viral elements essential for insect transmission to liberate genome space for accommodating large genetic cargoes without sacrificing the ability to infect plant hosts. The resulting non-insect-transmissible viral vectors enabled effective and stable in planta delivery of Cas12a and Cas9 nucleases as well as adenine and cytosine base editors. In systemically infected plant tissues, the deconstructed TSWV-derived vectors induced efficient somatic gene mutations and base conversions in multiple crop species with little genotype dependency. Plants with heritable, bi-allelic mutations could be readily regenerated by culturing the virus-infected tissues in vitro without antibiotic selection. Moreover, we showed that antiviral treatment with ribavirin during tissue culture cleared the viral vectors in 100% of regenerated plants and further augmented the recovery of heritable mutations. Because many plants are recalcitrant to stable transformation, the viral delivery system developed in this work provides a promising tool to overcome gene delivery bottlenecks for genome editing in various crop species and elite varieties.
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Affiliation(s)
- Qian Liu
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, China
| | - Chenglu Zhao
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, China
| | - Kai Sun
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, China
| | - Yinlu Deng
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, China
| | - Zhenghe Li
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, China; Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insect Pests, Zhejiang University, Hangzhou, China; Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Zhejiang University, Hangzhou, China.
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Mahmood MA, Naqvi RZ, Rahman SU, Amin I, Mansoor S. Plant Virus-Derived Vectors for Plant Genome Engineering. Viruses 2023; 15:v15020531. [PMID: 36851743 PMCID: PMC9958682 DOI: 10.3390/v15020531] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 01/25/2023] [Accepted: 02/10/2023] [Indexed: 02/17/2023] Open
Abstract
Advances in genome engineering (GE) tools based on sequence-specific programmable nucleases have revolutionized precise genome editing in plants. However, only the traditional approaches are used to deliver these GE reagents, which mostly rely on Agrobacterium-mediated transformation or particle bombardment. These techniques have been successfully used for the past decades for the genetic engineering of plants with some limitations relating to lengthy time-taking protocols and transgenes integration-related regulatory concerns. Nevertheless, in the era of climate change, we require certain faster protocols for developing climate-smart resilient crops through GE to deal with global food security. Therefore, some alternative approaches are needed to robustly deliver the GE reagents. In this case, the plant viral vectors could be an excellent option for the delivery of GE reagents because they are efficient, effective, and precise. Additionally, these are autonomously replicating and considered as natural specialists for transient delivery. In the present review, we have discussed the potential use of these plant viral vectors for the efficient delivery of GE reagents. We have further described the different plant viral vectors, such as DNA and RNA viruses, which have been used as efficient gene targeting systems in model plants, and in other important crops including potato, tomato, wheat, and rice. The achievements gained so far in the use of viral vectors as a carrier for GE reagent delivery are depicted along with the benefits and limitations of each viral vector. Moreover, recent advances have been explored in employing viral vectors for GE and adapting this technology for future research.
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Affiliation(s)
- Muhammad Arslan Mahmood
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), College of Pakistan Institute of Engineering and Applied Sciences (PIEAS), Jhang Road, Faisalabad 38000, Pakistan
- Department of Biological Sciences, University of Sialkot, Sialkot 51310, Pakistan
| | - Rubab Zahra Naqvi
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), College of Pakistan Institute of Engineering and Applied Sciences (PIEAS), Jhang Road, Faisalabad 38000, Pakistan
| | - Saleem Ur Rahman
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), College of Pakistan Institute of Engineering and Applied Sciences (PIEAS), Jhang Road, Faisalabad 38000, Pakistan
| | - Imran Amin
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), College of Pakistan Institute of Engineering and Applied Sciences (PIEAS), Jhang Road, Faisalabad 38000, Pakistan
| | - Shahid Mansoor
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), College of Pakistan Institute of Engineering and Applied Sciences (PIEAS), Jhang Road, Faisalabad 38000, Pakistan
- International Center for Chemical and Biological Sciences, University of Karachi, Karachi 74000, Pakistan
- Correspondence:
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36
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Pan C, Li G, Bandyopadhyay A, Qi Y. Guide RNA library-based CRISPR screens in plants: opportunities and challenges. Curr Opin Biotechnol 2023; 79:102883. [PMID: 36603502 DOI: 10.1016/j.copbio.2022.102883] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 11/21/2022] [Accepted: 12/08/2022] [Indexed: 01/04/2023]
Abstract
Next-generation sequencing technologies have revolutionized our ability to read sequence information at the genome and transcriptome levels in a high-throughput manner. However, genetic screening at a large or genomic scale remains challenging in plants. Recently, the RNA-guided CRISPR-Cas nucleases have been optimized for high-throughput functional genomic screens combined with guide RNA (gRNA) libraries in plants. This approach has shown great promise in facilitating genetic screening, directed evolution, and quantitative trait engineering. However, this technology is still in its infancy. In this short review, we describe the recent progress in gRNA library-based CRISPR screens in plants. We provide a critical assessment of the current approaches and emerging delivery methods for CRISPR screens. We also highlight the challenges and present future perspectives on CRISPR screens in plants.
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Affiliation(s)
- Changtian Pan
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD 20742, USA
| | - Gen Li
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD 20742, USA
| | | | - Yiping Qi
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD 20742, USA; Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, MD 20850, USA.
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37
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Liu T, Zhang X, Li K, Yao Q, Zhong D, Deng Q, Lu Y. Large-scale genome editing in plants: approaches, applications, and future perspectives. Curr Opin Biotechnol 2023; 79:102875. [PMID: 36610369 DOI: 10.1016/j.copbio.2022.102875] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 11/22/2022] [Accepted: 12/05/2022] [Indexed: 01/07/2023]
Abstract
As a powerful genome editing technology, CRISPR/Cas is revolutionizing both fundamental research and crop breeding, and has now evolved into large-scale editing tools that are efficient, simple, and programmable. With such CRISPR screening technologies, the numbers of genome-edited crops are rapidly increasing. Here, we describe the general workflow of a CRISPR screen in plants, including the selection of appropriate editors, genome-wide guide RNA design, pooled library construction, massive transformation, and high-throughput genotyping. We also discuss applications for the screening of candidate genes, the optimization of spatiotemporal expression, the evolution of protein activities, and the establishment of genome-wide libraries of knockout mutant. After considering the current challenges and limitations, we finally envision a virus-mediated strategy to improve CRISPR screens.
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Affiliation(s)
- Tianzhen Liu
- Shanghai Collaborative Innovation Center of Agri-Seeds, Joint Center for Single Cell Biology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Xuening Zhang
- Shanghai Collaborative Innovation Center of Agri-Seeds, Joint Center for Single Cell Biology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China; Shanghai Center for Plant Stress Biology, Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 201602, China
| | - Kai Li
- Shanghai Collaborative Innovation Center of Agri-Seeds, Joint Center for Single Cell Biology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Qi Yao
- Shanghai Collaborative Innovation Center of Agri-Seeds, Joint Center for Single Cell Biology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China; Shanghai Center for Plant Stress Biology, Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 201602, China
| | - Dating Zhong
- Shanghai Collaborative Innovation Center of Agri-Seeds, Joint Center for Single Cell Biology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China; Shanghai Center for Plant Stress Biology, Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 201602, China
| | - Qi Deng
- Shanghai Collaborative Innovation Center of Agri-Seeds, Joint Center for Single Cell Biology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yuming Lu
- Shanghai Collaborative Innovation Center of Agri-Seeds, Joint Center for Single Cell Biology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China.
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May D, Paldi K, Altpeter F. Targeted mutagenesis with sequence-specific nucleases for accelerated improvement of polyploid crops: Progress, challenges, and prospects. THE PLANT GENOME 2023:e20298. [PMID: 36692095 DOI: 10.1002/tpg2.20298] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Accepted: 11/20/2022] [Indexed: 06/17/2023]
Abstract
Many of the world's most important crops are polyploid. The presence of more than two sets of chromosomes within their nuclei and frequently aberrant reproductive biology in polyploids present obstacles to conventional breeding. The presence of a larger number of homoeologous copies of each gene makes random mutation breeding a daunting task for polyploids. Genome editing has revolutionized improvement of polyploid crops as multiple gene copies and/or alleles can be edited simultaneously while preserving the key attributes of elite cultivars. Most genome-editing platforms employ sequence-specific nucleases (SSNs) to generate DNA double-stranded breaks at their target gene. Such DNA breaks are typically repaired via the error-prone nonhomologous end-joining process, which often leads to frame shift mutations, causing loss of gene function. Genome editing has enhanced the disease resistance, yield components, and end-use quality of polyploid crops. However, identification of candidate targets, genotyping, and requirement of high mutagenesis efficiency remain bottlenecks for targeted mutagenesis in polyploids. In this review, we will survey the tremendous progress of SSN-mediated targeted mutagenesis in polyploid crop improvement, discuss its challenges, and identify optimizations needed to sustain further progress.
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Affiliation(s)
- David May
- Agronomy Department, University of Florida Institute of Food and Agricultural Sciences, Gainesville, FL, USA
- DOE Center for Advanced Bioenergy and Bioproducts Innovation, Gainesville, FL, USA
| | - Katalin Paldi
- Agronomy Department, University of Florida Institute of Food and Agricultural Sciences, Gainesville, FL, USA
- DOE Center for Advanced Bioenergy and Bioproducts Innovation, Gainesville, FL, USA
| | - Fredy Altpeter
- Agronomy Department, University of Florida Institute of Food and Agricultural Sciences, Gainesville, FL, USA
- DOE Center for Advanced Bioenergy and Bioproducts Innovation, Gainesville, FL, USA
- Plant Cellular and Molecular Biology Program, Genetics Institute, University of Florida Institute of Food and Agricultural Sciences, Gainesville, FL, USA
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39
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Yang L, Machin F, Wang S, Saplaoura E, Kragler F. Heritable transgene-free genome editing in plants by grafting of wild-type shoots to transgenic donor rootstocks. Nat Biotechnol 2023:10.1038/s41587-022-01585-8. [PMID: 36593415 DOI: 10.1038/s41587-022-01585-8] [Citation(s) in RCA: 51] [Impact Index Per Article: 51.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Accepted: 10/20/2022] [Indexed: 01/03/2023]
Abstract
Generation of stable gene-edited plant lines using clustered regularly interspaced short palindromic repeats (CRISPR)-CRISPR-associated protein 9 (Cas9) requires a lengthy process of outcrossing to eliminate CRISPR-Cas9-associated sequences and produce transgene-free lines. We have addressed this issue by designing fusions of Cas9 and guide RNA transcripts to tRNA-like sequence motifs that move RNAs from transgenic rootstocks to grafted wild-type shoots (scions) and achieve heritable gene editing, as demonstrated in wild-type Arabidopsis thaliana and Brassica rapa. The graft-mobile gene editing system enables the production of transgene-free offspring in one generation without the need for transgene elimination, culture recovery and selection, or use of viral editing vectors. We anticipate that using graft-mobile editing systems for transgene-free plant production may be applied to a wide range of breeding programs and crop plants.
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Affiliation(s)
- Lei Yang
- Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany
| | - Frank Machin
- Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany
| | - Shuangfeng Wang
- Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany
| | | | - Friedrich Kragler
- Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany.
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40
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Affiliation(s)
- Jiacheng Hu
- State Key Laboratory of Plant Cell and Chromosome Engineering, 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
| | - Caixia Gao
- State Key Laboratory of Plant Cell and Chromosome Engineering, 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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41
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Li Z, Zhong F, Guo J, Chen Z, Song J, Zhang Y. Improving Wheat Salt Tolerance for Saline Agriculture. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:14989-15006. [PMID: 36442507 DOI: 10.1021/acs.jafc.2c06381] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Salinity is a major abiotic stress that threatens crop yield and food supply in saline soil areas. Crops have evolved various strategies to facilitate survival and production of harvestable yield under salinity stress. Wheat (Triticum aestivum L.) is the main crop in arid and semiarid land areas, which are often affected by soil salinity. In this review, we summarize the conventional approaches to enhance wheat salt tolerance, including cross-breeding, exogenous application of chemical compounds, beneficial soil microorganisms, and transgenic engineering. We also propose several new breeding techniques for increasing salt tolerance in wheat, such as identifying new quantitative trait loci or genes related to salt tolerance, gene stacking and multiple genome editing, and wheat wild relatives and orphan crops domestication. The challenges and possible countermeasures in enhancing wheat salinity tolerance are also discussed.
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Affiliation(s)
- Zihan Li
- Shandong Provincial Key Laboratory of Plant Stress, College of Life Sciences, Shandong Normal University, Jinan 250014, China
| | - Fan Zhong
- Shandong Provincial Key Laboratory of Plant Stress, College of Life Sciences, Shandong Normal University, Jinan 250014, China
| | - Jianrong Guo
- Shandong Provincial Key Laboratory of Plant Stress, College of Life Sciences, Shandong Normal University, Jinan 250014, China
| | - Zhuo Chen
- Shandong Provincial Key Laboratory of Plant Stress, College of Life Sciences, Shandong Normal University, Jinan 250014, China
| | - Jie Song
- Shandong Provincial Key Laboratory of Plant Stress, College of Life Sciences, Shandong Normal University, Jinan 250014, China
| | - Yi Zhang
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an 271018, China
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42
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Wang W, Yu Z, He F, Bai G, Trick HN, Akhunova A, Akhunov E. Multiplexed promoter and gene editing in wheat using a virus-based guide RNA delivery system. PLANT BIOTECHNOLOGY JOURNAL 2022; 20:2332-2341. [PMID: 36070109 PMCID: PMC9674318 DOI: 10.1111/pbi.13910] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 07/20/2022] [Accepted: 08/07/2022] [Indexed: 06/15/2023]
Abstract
The low efficiency of genetic transformation and gene editing across diverse cultivars hinder the broad application of CRISPR technology for crop improvement. The development of virus-based methods of CRISPR-Cas system delivery into the plant cells holds great promise to overcome these limitations. Here, we perform direct inoculation of wheat leaves with the barley stripe mosaic virus (BSMV) transcripts to deliver guide RNAs (sgRNA) into the Cas9-expressing wheat. We demonstrate that wheat inoculation with the pool of BSMV-sgRNAs could be used to generate heritable precise deletions in the promoter region of a transcription factor and to perform multiplexed editing of agronomic genes. We transfer the high-expressing locus of Cas9 into adapted spring and winter cultivars by marker-assisted introgression and use of the BSMV-sgRNAs to edit two agronomic genes. A strategy presented in our study could be applied to any adapted cultivar for creating new cis-regulatory diversity or large-scale editing of multiple genes in biological pathways or QTL regions, opening possibilities for the effective engineering of crop genomes, and accelerating gene discovery and trait improvement efforts.
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Affiliation(s)
- Wei Wang
- Department of Plant PathologyKansas State UniversityManhattanKSUSA
- Wheat Genetic Resources CenterKansas State UniversityManhattanKSUSA
| | - Zitong Yu
- Department of Plant PathologyKansas State UniversityManhattanKSUSA
- Wheat Genetic Resources CenterKansas State UniversityManhattanKSUSA
| | - Fei He
- Department of Plant PathologyKansas State UniversityManhattanKSUSA
- Present address:
State Key Laboratory of Plant Cell and Chromosome EngineeringInstitute of Genetics and Developmental Biology, Chinese Academy of SciencesBeijingChina
| | - Guihua Bai
- Hard Winter Wheat Genetics Research UnitUSDA‐ARSManhattanKSUSA
| | - Harold N. Trick
- Department of Plant PathologyKansas State UniversityManhattanKSUSA
| | - Alina Akhunova
- Department of Plant PathologyKansas State UniversityManhattanKSUSA
- Integrated Genomic FacilityKansas State UniversityManhattanKSUSA
| | - Eduard Akhunov
- Department of Plant PathologyKansas State UniversityManhattanKSUSA
- Wheat Genetic Resources CenterKansas State UniversityManhattanKSUSA
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43
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Chen Z, Debernardi JM, Dubcovsky J, Gallavotti A. Recent advances in crop transformation technologies. NATURE PLANTS 2022; 8:1343-1351. [PMID: 36522447 DOI: 10.1038/s41477-022-01295-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 10/30/2022] [Indexed: 05/12/2023]
Abstract
Agriculture is experiencing a technological inflection point in its history, while also facing unprecedented challenges posed by human population growth and global climate changes. Key advancements in precise genome editing and new methods for rapid generation of bioengineered crops promise to both revolutionize the speed and breadth of breeding programmes and increase our ability to feed and sustain human population growth. Although genome editing enables targeted and specific modifications of DNA sequences, several existing barriers prevent the widespread adoption of editing technologies for basic and applied research in established and emerging crop species. Inefficient methods for the transformation and regeneration of recalcitrant species and the genotype dependency of the transformation process remain major hurdles. These limitations are frequent in monocotyledonous crops, which alone provide most of the calories consumed by human populations. Somatic embryogenesis and de novo induction of meristems - pluripotent groups of stem cells responsible for plant developmental plasticity - are essential strategies to quickly generate transformed plants. Here we review recent discoveries that are rapidly advancing nuclear transformation technologies and promise to overcome the obstacles that have so far impeded the widespread adoption of genome editing in crop species.
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Affiliation(s)
- Zongliang Chen
- Waksman Institute of Microbiology, Rutgers University, Piscataway, NJ, USA
| | - Juan M Debernardi
- Department of Plant Sciences, University of California Davis, Davis, CA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Jorge Dubcovsky
- Department of Plant Sciences, University of California Davis, Davis, CA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Andrea Gallavotti
- Waksman Institute of Microbiology, Rutgers University, Piscataway, NJ, USA.
- Department of Plant Biology, Rutgers University, New Brunswick, NJ, USA.
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44
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Lei J, Li Y, Dai P, Liu C, Zhao Y, You Y, Qu Y, Chen Q, Liu X. Efficient virus-mediated genome editing in cotton using the CRISPR/Cas9 system. FRONTIERS IN PLANT SCIENCE 2022; 13:1032799. [PMID: 36466231 PMCID: PMC9709312 DOI: 10.3389/fpls.2022.1032799] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 10/19/2022] [Indexed: 06/17/2023]
Abstract
Plant virus-mediated sgRNA delivery and expression have great advantages; sgRNA expression can rapidly expand and accumulate along with virus replication and movement, resulting in efficient gene editing efficiency. In this study, a VIGE system based on cotton leaf crumple virus (CLCrV) was established using cotton overexpressing Cas9 (Cas9-OE) as the VIGE receptor. CLCrV-mediated VIGE could not only target and knock out the GhMAPKKK2, GhCLA1 and GhPDS genes subgroup A and D genome sequences but also achieve double mutation of GhCLA1 and GhPDS genes at the same time. These results verified the effectiveness and efficiency of this system. In addition, the off-target effect assay demonstrated that the CLCrV-mediated VIGE system not only has high gene editing efficiency but also high gene editing specificity in cotton. We further explored whether the FT-sgRNA strategy could transport sgRNA to cotton apical meristem (SAM) over long distances to avoid using tissue culture to obtain stable genetic mutants. The results showed that the sgRNA fused with FT mRNA at the 5' end could also efficiently achieve targeted editing of endogenous genes in cotton, but it was difficult to detect heritable mutant progeny. The above results showed that the CLCrV-mediated VIGE system provided an accurate and rapid validation tool for screening effective sgRNAs in cotton.
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Affiliation(s)
- Jianfeng Lei
- College of Agriculture, Xinjiang Agricultural University, Engineering Research Centre of Cotton, Ministry of Education, Urumqi, China
| | - Yue Li
- College of Life Sciences, Xinjiang Agricultural University, Urumqi, China
| | - Peihong Dai
- College of Life Sciences, Xinjiang Agricultural University, Urumqi, China
| | - Chao Liu
- College of Life Sciences, Xinjiang Agricultural University, Urumqi, China
| | - Yi Zhao
- College of Life Sciences, Xinjiang Agricultural University, Urumqi, China
| | - Yangzi You
- College of Life Sciences, Xinjiang Agricultural University, Urumqi, China
| | - Yanying Qu
- College of Agriculture, Xinjiang Agricultural University, Engineering Research Centre of Cotton, Ministry of Education, Urumqi, China
| | - Quanjia Chen
- College of Agriculture, Xinjiang Agricultural University, Engineering Research Centre of Cotton, Ministry of Education, Urumqi, China
| | - Xiaodong Liu
- College of Life Sciences, Xinjiang Agricultural University, Urumqi, China
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45
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Wang X, Chang C. Exploring and exploiting cuticle biosynthesis for abiotic and biotic stress tolerance in wheat and barley. FRONTIERS IN PLANT SCIENCE 2022; 13:1064390. [PMID: 36438119 PMCID: PMC9685406 DOI: 10.3389/fpls.2022.1064390] [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: 10/08/2022] [Accepted: 10/24/2022] [Indexed: 06/16/2023]
Abstract
Wheat and barley are widely distributed cereal crops whose yields are adversely affected by environmental stresses such as drought, salinity, extreme temperatures, and attacks of pathogens and pests. As the interphase between aerial plant organs and their environments, hydrophobic cuticle largely consists of a cutin matrix impregnated and sealed with cuticular waxes. Increasing evidence supports that the cuticle plays a key role in plant adaptation to abiotic and biotic stresses, which could be harnessed for wheat and barley improvement. In this review, we highlighted recent advances in cuticle biosynthesis and its multifaceted roles in abiotic and biotic stress tolerance of wheat and barley. Current strategies, challenges, and future perspectives on manipulating cuticle biosynthesis for abiotic and biotic stress tolerance in wheat and barley are discussed.
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46
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Lu K, Chen X, Yao X, An Y, Wang X, Qin L, Li X, Wang Z, Liu S, Sun Z, Zhang L, Chen L, Li B, Liu B, Wang W, Ding X, Yang Y, Zhang M, Zou S, Dong H. Phosphorylation of a wheat aquaporin at two sites enhances both plant growth and defense. MOLECULAR PLANT 2022; 15:1772-1789. [PMID: 36207815 DOI: 10.1016/j.molp.2022.10.003] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 08/30/2022] [Accepted: 10/05/2022] [Indexed: 06/16/2023]
Abstract
Eukaryotic aquaporins share the characteristic of functional multiplicity in transporting distinct substrates and regulating various processes, but the underlying molecular basis for this is largely unknown. Here, we report that the wheat (Triticum aestivum) aquaporin TaPIP2;10 undergoes phosphorylation to promote photosynthesis and productivity and to confer innate immunity against pathogens and a generalist aphid pest. In response to elevated atmospheric CO2 concentrations, TaPIP2;10 is phosphorylated at the serine residue S280 and thereafter transports CO2 into wheat cells, resulting in enhanced photosynthesis and increased grain yield. In response to apoplastic H2O2 induced by pathogen or insect attacks, TaPIP2;10 is phosphorylated at S121 and this phosphorylated form transports H2O2 into the cytoplasm, where H2O2 intensifies host defenses, restricting further attacks. Wheat resistance and grain yield could be simultaneously increased by TaPIP2;10 overexpression or by expressing a TaPIP2;10 phosphomimic with aspartic acid substitutions at S121 and S280, thereby improving both crop productivity and immunity.
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Affiliation(s)
- Kai Lu
- College of Plant Protection, State Key Laboratory of Crop Biology, Qilu College, Shandong Agricultural University, Taian 271018, China
| | - Xiaochen Chen
- College of Plant Protection, State Key Laboratory of Crop Biology, Qilu College, Shandong Agricultural University, Taian 271018, China
| | - Xiaohui Yao
- College of Plant Protection, State Key Laboratory of Crop Biology, Qilu College, Shandong Agricultural University, Taian 271018, China
| | - Yuyan An
- College of Life Sciences, Shaanxi Normal University, Xi'an 710019, China
| | - Xuan Wang
- Institute of Plant Molecular Biology, State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Lina Qin
- College of Plant Protection, State Key Laboratory of Crop Biology, Qilu College, Shandong Agricultural University, Taian 271018, China
| | - Xiaoxu Li
- College of Plant Protection, State Key Laboratory of Crop Biology, Qilu College, Shandong Agricultural University, Taian 271018, China
| | - Zuodong Wang
- College of Plant Protection, State Key Laboratory of Crop Biology, Qilu College, Shandong Agricultural University, Taian 271018, China
| | - Shuo Liu
- College of Plant Protection, State Key Laboratory of Crop Biology, Qilu College, Shandong Agricultural University, Taian 271018, China
| | - Zhimao Sun
- College of Life Sciences, Shaanxi Normal University, Xi'an 710019, China
| | - Liyuan Zhang
- College of Plant Protection, State Key Laboratory of Crop Biology, Qilu College, Shandong Agricultural University, Taian 271018, China
| | - Lei Chen
- College of Plant Protection, State Key Laboratory of Crop Biology, Qilu College, Shandong Agricultural University, Taian 271018, China
| | - Baoyan Li
- Institute of Plant Protection & Resource and Environment, Yantai Academy of Agricultural Sciences, Yantai 265599, China
| | - Baoyou Liu
- Institute of Plant Protection & Resource and Environment, Yantai Academy of Agricultural Sciences, Yantai 265599, China
| | - Weiyang Wang
- College of Plant Protection, State Key Laboratory of Crop Biology, Qilu College, Shandong Agricultural University, Taian 271018, China
| | - Xinhua Ding
- College of Plant Protection, State Key Laboratory of Crop Biology, Qilu College, Shandong Agricultural University, Taian 271018, China
| | - Yonghua Yang
- Institute of Plant Molecular Biology, State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Meixiang Zhang
- College of Life Sciences, Shaanxi Normal University, Xi'an 710019, China.
| | - Shenshen Zou
- College of Plant Protection, State Key Laboratory of Crop Biology, Qilu College, Shandong Agricultural University, Taian 271018, China.
| | - Hansong Dong
- College of Plant Protection, State Key Laboratory of Crop Biology, Qilu College, Shandong Agricultural University, Taian 271018, China.
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Cao X, Xie H, Song M, Lu J, Ma P, Huang B, Wang M, Tian Y, Chen F, Peng J, Lang Z, Li G, Zhu JK. Cut-dip-budding delivery system enables genetic modifications in plants without tissue culture. Innovation (N Y) 2022; 4:100345. [PMID: 36387605 PMCID: PMC9661722 DOI: 10.1016/j.xinn.2022.100345] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Accepted: 10/24/2022] [Indexed: 11/07/2022] Open
Abstract
Of the more than 370 000 species of higher plants in nature, fewer than 0.1% can be genetically modified due to limitations of the current gene delivery systems. Even for those that can be genetically modified, the modification involves a tedious and costly tissue culture process. Here, we describe an extremely simple cut-dip-budding (CDB) delivery system, which uses Agrobacterium rhizogene to inoculate explants, generating transformed roots that produce transformed buds due to root suckering. We have successfully used CDB to achieve the heritable transformation of plant species in multiple plant families, including two herbaceous plants (Taraxacum kok-saghyz and Coronilla varia), a tuberous root plant (sweet potato), and three woody plant species (Ailanthus altissima, Aralia elata, and Clerodendrum chinense). These plants have previously been difficult or impossible to transform, but the CDB method enabled efficient transformation or gene editing in them using a very simple explant dipping protocol, under non-sterile conditions and without the need for tissue culture. Our work suggests that large numbers of plants could be amenable to genetic modifications using the CDB method.
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Affiliation(s)
- Xuesong Cao
- Shanghai Center for Plant Stress Biology, Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 201602, China
- University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Hongtao Xie
- Shandong Shunfeng Biotechnology Co., Ltd., Jinan 250000, China
| | - Minglei Song
- Shanghai Center for Plant Stress Biology, Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 201602, China
- University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Jinghua Lu
- Hainan Yazhou Bay Seed Laboratory, Sanya 572025, China
| | - Ping Ma
- Shandong Shunfeng Biotechnology Co., Ltd., Jinan 250000, China
| | - Boyu Huang
- Shanghai Center for Plant Stress Biology, Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 201602, China
- University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Mugui Wang
- Shanghai Center for Plant Stress Biology, Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 201602, China
| | - Yifu Tian
- Center for Advanced Bioindustry Technologies, Chinese Academy of Agricultural Sciences, Beijing 100081, China
- Hainan Yazhou Bay Seed Laboratory, Sanya 572025, China
| | - Fan Chen
- Hainan Yazhou Bay Seed Laboratory, Sanya 572025, China
| | - Jun Peng
- Center for Advanced Bioindustry Technologies, Chinese Academy of Agricultural Sciences, Beijing 100081, China
- Hainan Yazhou Bay Seed Laboratory, Sanya 572025, China
| | - Zhaobo Lang
- Institute of Advanced Biotechnology and School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China
| | - Guofu Li
- Shandong Shunfeng Biotechnology Co., Ltd., Jinan 250000, China
- Corresponding author
| | - Jian-Kang Zhu
- Institute of Advanced Biotechnology and School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China
- Center for Advanced Bioindustry Technologies, Chinese Academy of Agricultural Sciences, Beijing 100081, China
- Hainan Yazhou Bay Seed Laboratory, Sanya 572025, China
- Corresponding author
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Rustgi S, Naveed S, Windham J, Zhang H, Demirer GS. Plant biomacromolecule delivery methods in the 21st century. Front Genome Ed 2022; 4:1011934. [PMID: 36311974 PMCID: PMC9614364 DOI: 10.3389/fgeed.2022.1011934] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Accepted: 10/03/2022] [Indexed: 11/06/2022] Open
Abstract
The 21st century witnessed a boom in plant genomics and gene characterization studies through RNA interference and site-directed mutagenesis. Specifically, the last 15 years marked a rapid increase in discovering and implementing different genome editing techniques. Methods to deliver gene editing reagents have also attempted to keep pace with the discovery and implementation of gene editing tools in plants. As a result, various transient/stable, quick/lengthy, expensive (requiring specialized equipment)/inexpensive, and versatile/specific (species, developmental stage, or tissue) methods were developed. A brief account of these methods with emphasis on recent developments is provided in this review article. Additionally, the strengths and limitations of each method are listed to allow the reader to select the most appropriate method for their specific studies. Finally, a perspective for future developments and needs in this research area is presented.
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Affiliation(s)
- Sachin Rustgi
- Department of Plant and Environmental Sciences, School of Health Research, Clemson University Pee Dee Research and Education Center, Florence, SC, United States,*Correspondence: Sachin Rustgi, ; Gözde S. Demirer,
| | - Salman Naveed
- Department of Plant and Environmental Sciences, School of Health Research, Clemson University Pee Dee Research and Education Center, Florence, SC, United States
| | - Jonathan Windham
- Department of Plant and Environmental Sciences, School of Health Research, Clemson University Pee Dee Research and Education Center, Florence, SC, United States
| | - Huan Zhang
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Gözde S. Demirer
- Department of Chemical Engineering, California Institute of Technology, Pasadena, CA, United States,*Correspondence: Sachin Rustgi, ; Gözde S. Demirer,
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49
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Sharma KK, Palakolanu SR, Bhattacharya J, Shankhapal AR, Bhatnagar-Mathur P. CRISPR for accelerating genetic gains in under-utilized crops of the drylands: Progress and prospects. Front Genet 2022; 13:999207. [PMID: 36276961 PMCID: PMC9582247 DOI: 10.3389/fgene.2022.999207] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Accepted: 09/09/2022] [Indexed: 12/12/2022] Open
Abstract
Technologies and innovations are critical for addressing the future food system needs where genetic resources are an essential component of the change process. Advanced breeding tools like "genome editing" are vital for modernizing crop breeding to provide game-changing solutions to some of the "must needed" traits in agriculture. CRISPR/Cas-based tools have been rapidly repurposed for editing applications based on their improved efficiency, specificity and reduced off-target effects. Additionally, precise gene-editing tools such as base editing, prime editing, and multiplexing provide precision in stacking of multiple traits in an elite variety, and facilitating specific and targeted crop improvement. This has helped in advancing research and delivery of products in a short time span, thereby enhancing the rate of genetic gains. A special focus has been on food security in the drylands through crops including millets, teff, fonio, quinoa, Bambara groundnut, pigeonpea and cassava. While these crops contribute significantly to the agricultural economy and resilience of the dryland, improvement of several traits including increased stress tolerance, nutritional value, and yields are urgently required. Although CRISPR has potential to deliver disruptive innovations, prioritization of traits should consider breeding product profiles and market segments for designing and accelerating delivery of locally adapted and preferred crop varieties for the drylands. In this context, the scope of regulatory environment has been stated, implying the dire impacts of unreasonable scrutiny of genome-edited plants on the evolution and progress of much-needed technological advances.
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Affiliation(s)
- Kiran K. Sharma
- Sustainable Agriculture Programme, The Energy and Resources Institute (TERI), India Habitat Center, New Delhi, India
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Hyderabad, India
| | - Sudhakar Reddy Palakolanu
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Hyderabad, India
| | - Joorie Bhattacharya
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Hyderabad, India
- Department of Genetics, Osmania University, Hyderabad, Telangana, India
| | - Aishwarya R. Shankhapal
- Division of Plant and Crop Sciences, School of Biosciences, University of Nottingham, Nottingham, United Kingdom
- Plant Sciences and the Bioeconomy, Rothamsted Research, Harpenden, Hertfordshire, United Kingdom
| | - Pooja Bhatnagar-Mathur
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Hyderabad, India
- International Maize and Wheat Improvement Center (CIMMYT), México, United Kingdom
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50
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Mahmood MA, Naqvi RZ, Mansoor S. Engineering crop resistance by manipulating disease susceptibility genes. MOLECULAR PLANT 2022; 15:1511-1513. [PMID: 36127871 DOI: 10.1016/j.molp.2022.09.010] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2022] [Revised: 09/18/2022] [Accepted: 09/18/2022] [Indexed: 06/15/2023]
Affiliation(s)
- Muhammad Arslan Mahmood
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), College of Pakistan Institute of Engineering and Applied Sciences (PIEAS), Jhang Road, Faisalabad, Pakistan; Department of Biological Sciences, University of Sialkot, Sialkot, Pakistan
| | - Rubab Zahra Naqvi
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), College of Pakistan Institute of Engineering and Applied Sciences (PIEAS), Jhang Road, Faisalabad, Pakistan
| | - Shahid Mansoor
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), College of Pakistan Institute of Engineering and Applied Sciences (PIEAS), Jhang Road, Faisalabad, Pakistan.
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