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Li Z, Li Z, Ji Y, Wang C, Wang S, Shi Y, Le J, Zhang M. The heat shock factor 20-HSF4-cellulose synthase A2 module regulates heat stress tolerance in maize. THE PLANT CELL 2024; 36:2652-2667. [PMID: 38573521 PMCID: PMC11218781 DOI: 10.1093/plcell/koae106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 02/22/2024] [Accepted: 03/12/2024] [Indexed: 04/05/2024]
Abstract
Temperature shapes the geographical distribution and behavior of plants. Understanding the regulatory mechanisms underlying the plant heat stress response is important for developing climate-resilient crops, including maize (Zea mays). To identify transcription factors (TFs) that may contribute to the maize heat stress response, we generated a dataset of short- and long-term transcriptome changes following a heat treatment time course in the inbred line B73. Co-expression network analysis highlighted several TFs, including the class B2a heat shock factor (HSF) ZmHSF20. Zmhsf20 mutant seedlings exhibited enhanced tolerance to heat stress. Furthermore, DNA affinity purification sequencing and Cleavage Under Targets and Tagmentation assays demonstrated that ZmHSF20 binds to the promoters of Cellulose synthase A2 (ZmCesA2) and three class A Hsf genes, including ZmHsf4, repressing their transcription. We showed that ZmCesA2 and ZmHSF4 promote the heat stress response, with ZmHSF4 directly activating ZmCesA2 transcription. In agreement with the transcriptome analysis, ZmHSF20 inhibited cellulose accumulation and repressed the expression of cell wall-related genes. Importantly, the Zmhsf20 Zmhsf4 double mutant exhibited decreased thermotolerance, placing ZmHsf4 downstream of ZmHsf20. We proposed an expanded model of the heat stress response in maize, whereby ZmHSF20 lowers seedling heat tolerance by repressing ZmHsf4 and ZmCesA2, thus balancing seedling growth and defense.
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Affiliation(s)
- Ze Li
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zerui Li
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yulong Ji
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Chunyu Wang
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shufang Wang
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Yiting Shi
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, Center for Crop Functional Genomics and Molecular Breeding, China Agricultural University, Beijing 100193, China
| | - Jie Le
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Mei Zhang
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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2
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Kong X, Xiong Y, Song X, Wadey S, Yu S, Rao J, Lale A, Lombardi M, Fusi R, Bhosale R, Huang G. Ethylene regulates auxin-mediated root gravitropic machinery and controls root angle in cereal crops. PLANT PHYSIOLOGY 2024; 195:1969-1980. [PMID: 38446735 DOI: 10.1093/plphys/kiae134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Revised: 01/18/2024] [Accepted: 02/01/2024] [Indexed: 03/08/2024]
Abstract
Root angle is a critical factor in optimizing the acquisition of essential resources from different soil depths. The regulation of root angle relies on the auxin-mediated root gravitropism machinery. While the influence of ethylene on auxin levels is known, its specific role in governing root gravitropism and angle remains uncertain, particularly when Arabidopsis (Arabidopsis thaliana) core ethylene signaling mutants show no gravitropic defects. Our research, focusing on rice (Oryza sativa L.) and maize (Zea mays), clearly reveals the involvement of ethylene in root angle regulation in cereal crops through the modulation of auxin biosynthesis and the root gravitropism machinery. We elucidated the molecular components by which ethylene exerts its regulatory effect on auxin biosynthesis to control root gravitropism machinery. The ethylene-insensitive mutants ethylene insensitive2 (osein2) and ethylene insensitive like1 (oseil1), exhibited substantially shallower crown root angle compared to the wild type. Gravitropism assays revealed reduced root gravitropic response in these mutants. Hormone profiling analysis confirmed decreased auxin levels in the root tips of the osein2 mutant, and exogenous auxin (NAA) application rescued root gravitropism in both ethylene-insensitive mutants. Additionally, the auxin biosynthetic mutant mao hu zi10 (mhz10)/tryptophan aminotransferase2 (ostar2) showed impaired gravitropic response and shallow crown root angle phenotypes. Similarly, maize ethylene-insensitive mutants (zmein2) exhibited defective gravitropism and root angle phenotypes. In conclusion, our study highlights that ethylene controls the auxin-dependent root gravitropism machinery to regulate root angle in rice and maize, revealing a functional divergence in ethylene signaling between Arabidopsis and cereal crops. These findings contribute to a better understanding of root angle regulation and have implications for improving resource acquisition in agricultural systems.
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Affiliation(s)
- Xiuzhen Kong
- Joint International Research Laboratory of Metabolic and Developmental Sciences, State Key Laboratory of Hybrid Rice, SJTU-University of Adelaide Joint Centre for Agriculture and Health, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
- Shanghai Collaborative Innovation Center of Agri-Seeds/School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yali Xiong
- Joint International Research Laboratory of Metabolic and Developmental Sciences, State Key Laboratory of Hybrid Rice, SJTU-University of Adelaide Joint Centre for Agriculture and Health, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Xiaoyun Song
- Joint International Research Laboratory of Metabolic and Developmental Sciences, State Key Laboratory of Hybrid Rice, SJTU-University of Adelaide Joint Centre for Agriculture and Health, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Samuel Wadey
- Future Food Beacon and School of Biosciences, University of Nottingham, Nottingham LE12 5RD, UK
| | - Suhang Yu
- Joint International Research Laboratory of Metabolic and Developmental Sciences, State Key Laboratory of Hybrid Rice, SJTU-University of Adelaide Joint Centre for Agriculture and Health, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Jinliang Rao
- Joint International Research Laboratory of Metabolic and Developmental Sciences, State Key Laboratory of Hybrid Rice, SJTU-University of Adelaide Joint Centre for Agriculture and Health, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Aneesh Lale
- Future Food Beacon and School of Biosciences, University of Nottingham, Nottingham LE12 5RD, UK
| | - Marco Lombardi
- Future Food Beacon and School of Biosciences, University of Nottingham, Nottingham LE12 5RD, UK
| | - Riccardo Fusi
- Future Food Beacon and School of Biosciences, University of Nottingham, Nottingham LE12 5RD, UK
| | - Rahul Bhosale
- Future Food Beacon and School of Biosciences, University of Nottingham, Nottingham LE12 5RD, UK
- International Crops Research Institute for the Semi-Arid Tropics, Patancheru 502324, Hyderabad, India
| | - Guoqiang Huang
- Joint International Research Laboratory of Metabolic and Developmental Sciences, State Key Laboratory of Hybrid Rice, SJTU-University of Adelaide Joint Centre for Agriculture and Health, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
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3
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Zhao D, Chen S, Han Y, Liu G, Liu J, Yang Q, Zhang T, Shen J, Fan X, Zhang C, Zhang T, Li Q, Chen C, Liu Q. A CRISPR/Cas9-mediated mutant library of seed-preferred genes in rice. PLANT BIOTECHNOLOGY JOURNAL 2024. [PMID: 38925598 DOI: 10.1111/pbi.14422] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 05/27/2024] [Accepted: 06/11/2024] [Indexed: 06/28/2024]
Affiliation(s)
- Dongsheng Zhao
- Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, College of Agriculture, Yangzhou University, Yangzhou, China
- Zhongshan Biological Breeding Laboratory, Co-Innovation Centre for Modern Production Technology of Grain Crops of Jiangsu Province / Key Laboratory of Crop Genetics and Physiology of Jiangsu Province, Yangzhou University, Yangzhou, China
| | - Siyu Chen
- Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, College of Agriculture, Yangzhou University, Yangzhou, China
| | - Yangshuo Han
- Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, College of Agriculture, Yangzhou University, Yangzhou, China
| | - Guanqing Liu
- Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, College of Agriculture, Yangzhou University, Yangzhou, China
| | - Jinyu Liu
- Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, College of Agriculture, Yangzhou University, Yangzhou, China
| | - Qingqing Yang
- Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, College of Agriculture, Yangzhou University, Yangzhou, China
| | - Tao Zhang
- Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, College of Agriculture, Yangzhou University, Yangzhou, China
| | - Jilei Shen
- Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, College of Agriculture, Yangzhou University, Yangzhou, China
| | - Xiaolei Fan
- Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, College of Agriculture, Yangzhou University, Yangzhou, China
| | - Changquan Zhang
- Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, College of Agriculture, Yangzhou University, Yangzhou, China
- Zhongshan Biological Breeding Laboratory, Co-Innovation Centre for Modern Production Technology of Grain Crops of Jiangsu Province / Key Laboratory of Crop Genetics and Physiology of Jiangsu Province, Yangzhou University, Yangzhou, China
| | - Tao Zhang
- Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, College of Agriculture, Yangzhou University, Yangzhou, China
- Zhongshan Biological Breeding Laboratory, Co-Innovation Centre for Modern Production Technology of Grain Crops of Jiangsu Province / Key Laboratory of Crop Genetics and Physiology of Jiangsu Province, Yangzhou University, Yangzhou, China
| | - Qianfeng Li
- Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, College of Agriculture, Yangzhou University, Yangzhou, China
- Zhongshan Biological Breeding Laboratory, Co-Innovation Centre for Modern Production Technology of Grain Crops of Jiangsu Province / Key Laboratory of Crop Genetics and Physiology of Jiangsu Province, Yangzhou University, Yangzhou, China
| | - Chen Chen
- Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, College of Agriculture, Yangzhou University, Yangzhou, China
- Zhongshan Biological Breeding Laboratory, Co-Innovation Centre for Modern Production Technology of Grain Crops of Jiangsu Province / Key Laboratory of Crop Genetics and Physiology of Jiangsu Province, Yangzhou University, Yangzhou, China
| | - Qiaoquan Liu
- Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, College of Agriculture, Yangzhou University, Yangzhou, China
- Zhongshan Biological Breeding Laboratory, Co-Innovation Centre for Modern Production Technology of Grain Crops of Jiangsu Province / Key Laboratory of Crop Genetics and Physiology of Jiangsu Province, Yangzhou University, Yangzhou, China
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4
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Sun LQ, Bai Y, Wu J, Fan SJ, Chen SY, Zhang ZY, Xia JQ, Wang SM, Wang YP, Qin P, Li SG, Xu P, Zhao Z, Xiang CB, Zhang ZS. OsNLP3 enhances grain weight and reduces grain chalkiness in rice. PLANT COMMUNICATIONS 2024:100999. [PMID: 38853433 DOI: 10.1016/j.xplc.2024.100999] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Revised: 05/29/2024] [Accepted: 06/07/2024] [Indexed: 06/11/2024]
Abstract
Grain weight, a key determinant of yield in rice (Oryza sativa L.), is governed primarily by genetic factors, whereas grain chalkiness, a detriment to grain quality, is intertwined with environmental factors such as mineral nutrients. Nitrogen (N) is recognized for its effect on grain chalkiness, but the underlying molecular mechanisms remain to be clarified. This study revealed the pivotal role of rice NODULE INCEPTION-LIKE PROTEIN 3 (OsNLP3) in simultaneously regulating grain weight and grain chalkiness. Our investigation showed that loss of OsNLP3 leads to a reduction in both grain weight and dimension, in contrast to the enhancement observed with OsNLP3 overexpression. OsNLP3 directly suppresses the expression of OsCEP6.1 and OsNF-YA8, which were identified as negative regulators associated with grain weight. Consequently, two novel regulatory modules, OsNLP3-OsCEP6.1 and OsNLP3-OsNF-YA8, were identified as key players in grain weight regulation. Notably, the OsNLP3-OsNF-YA8 module not only increases grain weight but also mitigates grain chalkiness in response to N. This research clarifies the molecular mechanisms that orchestrate grain weight through the OsNLP3-OsCEP6.1 and OsNLP3-OsNF-YA8 modules, highlighting the pivotal role of the OsNLP3-OsNF-YA8 module in alleviating grain chalkiness. These findings reveal potential targets for simultaneous enhancement of rice yield and quality.
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Affiliation(s)
- Liang-Qi Sun
- Division of Life Sciences and Medicine, Division of Molecular & Cell Biophysics, Hefei National Science Center for Interdisciplinary Sciences at the Microscale, University of Science and Technology of China, The Innovation Academy of Seed Design, Chinese Academy of Sciences, Hefei, Anhui Province 230027, China
| | - Yu Bai
- Experimental Center of Engineering and Materials Science, University of Science and Technology of China, Hefei 230027, China
| | - Jie Wu
- Division of Life Sciences and Medicine, Division of Molecular & Cell Biophysics, Hefei National Science Center for Interdisciplinary Sciences at the Microscale, University of Science and Technology of China, The Innovation Academy of Seed Design, Chinese Academy of Sciences, Hefei, Anhui Province 230027, China
| | - Shi-Jun Fan
- Division of Life Sciences and Medicine, Division of Molecular & Cell Biophysics, Hefei National Science Center for Interdisciplinary Sciences at the Microscale, University of Science and Technology of China, The Innovation Academy of Seed Design, Chinese Academy of Sciences, Hefei, Anhui Province 230027, China
| | - Si-Yan Chen
- Division of Life Sciences and Medicine, Division of Molecular & Cell Biophysics, Hefei National Science Center for Interdisciplinary Sciences at the Microscale, University of Science and Technology of China, The Innovation Academy of Seed Design, Chinese Academy of Sciences, Hefei, Anhui Province 230027, China
| | - Zheng-Yi Zhang
- Division of Life Sciences and Medicine, Division of Molecular & Cell Biophysics, Hefei National Science Center for Interdisciplinary Sciences at the Microscale, University of Science and Technology of China, The Innovation Academy of Seed Design, Chinese Academy of Sciences, Hefei, Anhui Province 230027, China
| | - Jin-Qiu Xia
- Division of Life Sciences and Medicine, Division of Molecular & Cell Biophysics, Hefei National Science Center for Interdisciplinary Sciences at the Microscale, University of Science and Technology of China, The Innovation Academy of Seed Design, Chinese Academy of Sciences, Hefei, Anhui Province 230027, China
| | - Shi-Mei Wang
- Rice Research Institute, Anhui Academy of Agricultural Science, Hefei, China
| | - Yu-Ping Wang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Peng Qin
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Shi-Gui Li
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Ping Xu
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, Shanghai, China
| | - Zhong Zhao
- Division of Life Sciences and Medicine, Division of Molecular & Cell Biophysics, Hefei National Science Center for Interdisciplinary Sciences at the Microscale, University of Science and Technology of China, The Innovation Academy of Seed Design, Chinese Academy of Sciences, Hefei, Anhui Province 230027, China
| | - Cheng-Bin Xiang
- Division of Life Sciences and Medicine, Division of Molecular & Cell Biophysics, Hefei National Science Center for Interdisciplinary Sciences at the Microscale, University of Science and Technology of China, The Innovation Academy of Seed Design, Chinese Academy of Sciences, Hefei, Anhui Province 230027, China.
| | - Zi-Sheng Zhang
- Division of Life Sciences and Medicine, Division of Molecular & Cell Biophysics, Hefei National Science Center for Interdisciplinary Sciences at the Microscale, University of Science and Technology of China, The Innovation Academy of Seed Design, Chinese Academy of Sciences, Hefei, Anhui Province 230027, China.
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5
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Valentine M, Butruille D, Achard F, Beach S, Brower-Toland B, Cargill E, Hassebrock M, Rinehart J, Ream T, Chen Y. Simultaneous genetic transformation and genome editing of mixed lines in soybean ( Glycine max) and maize ( Zea mays). ABIOTECH 2024; 5:169-183. [PMID: 38974857 PMCID: PMC11224177 DOI: 10.1007/s42994-024-00173-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Accepted: 06/02/2024] [Indexed: 07/09/2024]
Abstract
Robust genome editing technologies are becoming part of the crop breeding toolbox. Currently, genome editing is usually conducted either at a single locus, or multiple loci, in a variety at one time. Massively parallel genomics platforms, multifaceted genome editing capabilities, and flexible transformation systems enable targeted variation at nearly any locus, across the spectrum of genotypes within a species. We demonstrate here the simultaneous transformation and editing of many genotypes, by targeting mixed seed embryo explants with genome editing machinery, followed by re-identification through genotyping after plant regeneration. Transformation and Editing of Mixed Lines (TREDMIL) produced transformed individuals representing 101 of 104 (97%) mixed elite genotypes in soybean; and 22 of 40 (55%) and 9 of 36 (25%) mixed maize female and male elite inbred genotypes, respectively. Characterization of edited genotypes for the regenerated individuals identified over 800 distinct edits at the Determinate1 (Dt1) locus in samples from 101 soybean genotypes and 95 distinct Brown midrib3 (Bm3) edits in samples from 17 maize genotypes. These results illustrate how TREDMIL can help accelerate the development and deployment of customized crop varieties for future precision breeding. Supplementary Information The online version contains supplementary material available at 10.1007/s42994-024-00173-5.
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Affiliation(s)
- Michelle Valentine
- Bayer Crop Science, 700 Chesterfield Parkway W, Chesterfield, MO 63017 USA
| | - David Butruille
- Bayer Crop Science, 700 Chesterfield Parkway W, Chesterfield, MO 63017 USA
| | - Frederic Achard
- Bayer Crop Science, 700 Chesterfield Parkway W, Chesterfield, MO 63017 USA
| | - Steven Beach
- Bayer Crop Science, 700 Chesterfield Parkway W, Chesterfield, MO 63017 USA
| | | | - Edward Cargill
- Bayer Crop Science, 700 Chesterfield Parkway W, Chesterfield, MO 63017 USA
| | - Megan Hassebrock
- Bayer Crop Science, 700 Chesterfield Parkway W, Chesterfield, MO 63017 USA
| | - Jennifer Rinehart
- Bayer Crop Science, 700 Chesterfield Parkway W, Chesterfield, MO 63017 USA
| | - Thomas Ream
- Bayer Crop Science, 700 Chesterfield Parkway W, Chesterfield, MO 63017 USA
| | - Yurong Chen
- Bayer Crop Science, 700 Chesterfield Parkway W, Chesterfield, MO 63017 USA
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6
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Liu Y, Li H, Liu J, Wang Y, Jiang C, Zhou Z, Zhuo L, Li W, Fernie AR, Jackson D, Yan J, Luo Y. The additive function of YIGE2 and YIGE1 in regulating maize ear length. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024. [PMID: 38804053 DOI: 10.1111/tpj.16851] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Revised: 05/06/2024] [Accepted: 05/10/2024] [Indexed: 05/29/2024]
Abstract
Ear length (EL) is a key trait that greatly contributes to yield in maize. Although dozens of EL quantitative trait loci have been mapped, very few causal genes have been cloned, and the molecular mechanisms remain largely unknown. Our previous study showed that YIGE1 is involved in sugar and auxin pathways to regulate ear inflorescence meristem (IM) development and thus affects EL in maize. Here, we reveal that YIGE2, the paralog of YIGE1, regulates maize ear development and EL through auxin pathway. Knockout of YIGE2 causes a significant decrease of auxin level, IM length, floret number, EL, and grain yield. yige1 yige2 double mutants had even shorter IM and ears implying that these two genes redundantly regulate IM development and EL. The genes controlling auxin levels are differential expressed in yige1 yige2 double mutants, leading to lower auxin level. These results elucidated the critical role of YIGE2 and the redundancy between YIGE2 and YIGE1 in maize ear development, providing a new genetic resource for maize yield improvement.
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Affiliation(s)
- Yu Liu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
- Hubei Hongshan Laboratory, Wuhan, 430070, China
| | - Huinan Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
- Hubei Hongshan Laboratory, Wuhan, 430070, China
| | - Jie Liu
- Yazhouwan National Laboratory, Sanya, 572024, China
| | - Yuebin Wang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
- Hubei Hongshan Laboratory, Wuhan, 430070, China
| | - Chenglin Jiang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
- Hubei Hongshan Laboratory, Wuhan, 430070, China
| | - Ziqi Zhou
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
- Hubei Hongshan Laboratory, Wuhan, 430070, China
| | - Lin Zhuo
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
- Hubei Hongshan Laboratory, Wuhan, 430070, China
| | - Wenqiang Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
- Hubei Hongshan Laboratory, Wuhan, 430070, China
| | - Alisdair R Fernie
- Department of Molecular Physiology, Max-Planck-Institute of Molecular Plant Physiology, Potsdam-Golm, 14476, Germany
| | - David Jackson
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, 11724, USA
| | - Jianbing Yan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
- Hubei Hongshan Laboratory, Wuhan, 430070, China
- Yazhouwan National Laboratory, Sanya, 572024, China
| | - Yun Luo
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
- Hubei Hongshan Laboratory, Wuhan, 430070, China
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7
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Zheng Z, Li W, Ding Y, Wu Y, Jiang Q, Wang Y. Integrative transcriptome analysis uncovers common components containing CPS2 regulated by maize lncRNA GARR2 in gibberellin response. PLANTA 2024; 259:146. [PMID: 38713242 DOI: 10.1007/s00425-024-04425-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Accepted: 04/26/2024] [Indexed: 05/08/2024]
Abstract
MAIN CONCLUSION The combined transcriptome outcome provides an important clue to the regulatory cascade centering on lncRNA GARR2 and CPS2 gene in GA response. Long non-coding RNAs (lncRNAs) serve as regulatory components in transcriptional hierarchy governing multiple aspects of biological processes. Dissecting regulatory mechanisms underpinning tetracyclic diterpenoid gibberellin (GA) cascade holds both theoretical and applied significance. However, roles of lncRNAs in transcriptional modulation of GA pathway remain largely elusive. Gypsy retrotransposon-derived GIBBERELLIN RESPONSIVE lncRNA2 (GARR2) has been reported as GA-responsive maize lncRNA. Here a novel GARR2-edited line garr2-1 was identified, characteristic of GA-induced phenotype of increased seedling height and elongated leaf sheath. Transcriptome analysis indicated that transcriptional abundance of five genes [ent-copalyl diphosphate synthase2 (CPS2), ent-kaurene synthase4 (KS4), ent-kaurene synthase6 (KS6), ent-kaurene oxidase2 (KO2), and ent-kaurenoic acid oxidase1/Dwarf3 (KAO1/D3)] was elevated in garr2-1 for early steps of GA biosynthesis. Five GA biosynthetic genes as hub regulators were interlaced to shape regulatory network of GA response. Different transcriptome resources were integrated to discover common differentially expressed genes (DEGs) in the independent GARR2-edited lines GARR2KO and garr2-1. A total of 320 common DEGs were retrieved. These common DEGs were enriched in diterpenoid biosynthetic pathway. Integrative transcriptome analysis revealed the common CPS2 encoding the CPS enzyme that catalyzes the conversion of the precursor trans-geranylgeranyl diphosphate to ent-copalyl diphosphate. The up-regulated CPS2 supported the GA-induced phenotype of slender seedlings observed in the independent GARR2-edited lines GARR2KO and garr2-1. Our integrative transcriptome analysis uncovers common components of the GA pathway regulated by lncRNA GARR2. These common components, especially for the GA biosynthetic gene CPS2, provide a valuable resource for further delineating the underlying mechanisms of lncRNA GARR2 in GA response.
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Affiliation(s)
- Zhongtian Zheng
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genetics and Physiology, Agricultural College of Yangzhou University, Yangzhou, 225009, China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, 225009, China
| | - Wei Li
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genetics and Physiology, Agricultural College of Yangzhou University, Yangzhou, 225009, China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, 225009, China
| | - Yuhang Ding
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genetics and Physiology, Agricultural College of Yangzhou University, Yangzhou, 225009, China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, 225009, China
| | - Yinting Wu
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genetics and Physiology, Agricultural College of Yangzhou University, Yangzhou, 225009, China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, 225009, China
| | - Qinyue Jiang
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genetics and Physiology, Agricultural College of Yangzhou University, Yangzhou, 225009, China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, 225009, China
| | - Yijun Wang
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genetics and Physiology, Agricultural College of Yangzhou University, Yangzhou, 225009, China.
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, 225009, China.
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8
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Yan Z, Zhang F, Mu C, Ma C, Yao G, Sun Y, Hou J, Leng B, Liu X. The ZmbHLH47-ZmSnRK2.9 Module Promotes Drought Tolerance in Maize. Int J Mol Sci 2024; 25:4957. [PMID: 38732175 PMCID: PMC11084430 DOI: 10.3390/ijms25094957] [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: 04/11/2024] [Revised: 04/29/2024] [Accepted: 04/30/2024] [Indexed: 05/13/2024] Open
Abstract
Drought stress globally poses a significant threat to maize (Zea mays L.) productivity and the underlying molecular mechanisms of drought tolerance remain elusive. In this study, we characterized ZmbHLH47, a basic helix-loop-helix (bHLH) transcription factor, as a positive regulator of drought tolerance in maize. ZmbHLH47 expression was notably induced by both drought stress and abscisic acid (ABA). Transgenic plants overexpressing ZmbHLH47 displayed elevated drought tolerance and ABA responsiveness, while the zmbhlh47 mutant exhibited increased drought sensitivity and reduced ABA sensitivity. Mechanistically, it was revealed that ZmbHLH47 could directly bind to the promoter of ZmSnRK2.9 gene, a member of the subgroup III SnRK2 kinases, activating its expression. Furthermore, ZmSnRK2.9-overexpressing plants exhibited enhanced ABA sensitivity and drought tolerance, whereas the zmsnrk2.9 mutant displayed a decreased sensitivity to both. Notably, overexpressing ZmbHLH47 in the zmsnrk2.9 mutant closely resembled the zmsnrk2.9 mutant, indicating the importance of the ZmbHLH47-ZmSnRK2.9 module in ABA response and drought tolerance. These findings provided valuable insights and a potential genetic resource for enhancing the environmental adaptability of maize.
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Affiliation(s)
- Zhenwei Yan
- Maize Research Institute, Shandong Academy of Agricultural Sciences, Jinan 250100, China; (Z.Y.); (F.Z.); (C.M.); (G.Y.)
| | - Fajun Zhang
- Maize Research Institute, Shandong Academy of Agricultural Sciences, Jinan 250100, China; (Z.Y.); (F.Z.); (C.M.); (G.Y.)
| | - Chunhua Mu
- Maize Research Institute, Shandong Academy of Agricultural Sciences, Jinan 250100, China; (Z.Y.); (F.Z.); (C.M.); (G.Y.)
| | - Changle Ma
- College of Life Sciences, Shandong Normal University, Jinan 250300, China;
| | - Guoqi Yao
- Maize Research Institute, Shandong Academy of Agricultural Sciences, Jinan 250100, China; (Z.Y.); (F.Z.); (C.M.); (G.Y.)
| | - Yue Sun
- College of Agronomy, Qingdao Agricultural University, Qingdao 266109, China;
| | - Jing Hou
- School of Agriculture, Ludong University, Yantai 264001, China;
| | - Bingying Leng
- Maize Research Institute, Shandong Academy of Agricultural Sciences, Jinan 250100, China; (Z.Y.); (F.Z.); (C.M.); (G.Y.)
| | - Xia Liu
- Maize Research Institute, Shandong Academy of Agricultural Sciences, Jinan 250100, China; (Z.Y.); (F.Z.); (C.M.); (G.Y.)
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9
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Bernal-Gallardo JJ, de Folter S. Plant genome information facilitates plant functional genomics. PLANTA 2024; 259:117. [PMID: 38592421 PMCID: PMC11004055 DOI: 10.1007/s00425-024-04397-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Accepted: 03/20/2024] [Indexed: 04/10/2024]
Abstract
MAIN CONCLUSION In this review, we give an overview of plant sequencing efforts and how this impacts plant functional genomics research. Plant genome sequence information greatly facilitates the studies of plant biology, functional genomics, evolution of genomes and genes, domestication processes, phylogenetic relationships, among many others. More than two decades of sequencing efforts have boosted the number of available sequenced plant genomes. The first plant genome, of Arabidopsis, was published in the year 2000 and currently, 4604 plant genomes from 1482 plant species have been published. Various large sequence initiatives are running, which are planning to produce tens of thousands of sequenced plant genomes in the near future. In this review, we give an overview on the status of sequenced plant genomes and on the use of genome information in different research areas.
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Affiliation(s)
- Judith Jazmin Bernal-Gallardo
- Unidad de Genómica Avanzada (UGA-Langebio), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (Cinvestav), Irapuato, Mexico
| | - Stefan de Folter
- Unidad de Genómica Avanzada (UGA-Langebio), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (Cinvestav), Irapuato, Mexico.
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10
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Cook GD, Stasulli NM. Employing synthetic biology to expand antibiotic discovery. SLAS Technol 2024; 29:100120. [PMID: 38340893 DOI: 10.1016/j.slast.2024.100120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Revised: 01/04/2024] [Accepted: 02/07/2024] [Indexed: 02/12/2024]
Abstract
Antimicrobial-resistant (AMR) bacterial pathogens are a continually growing threat as our methods for combating these infections continue to be overcome by the evolution of resistance mechanisms. Recent therapeutic methods have not staved off the concern of AMR infections, so continued research focuses on new ways of identifying small molecules to treat AMR pathogens. While chemical modification of existing antibiotics is possible, there has been rapid development of resistance by pathogens that were initially susceptible to these compounds. Synthetic biology is becoming a key strategy in trying to predict and induce novel, natural antibiotics. Advances in cloning and mutagenesis techniques applied through a synthetic biology lens can help characterize the native regulation of antibiotic biosynthetic gene clusters (BGCs) to identify potential modifications leading to more potent antibiotic activity. Additionally, many cryptic antibiotic BGCs are derived from non-ribosomal peptide synthase (NRPS) and polyketide synthase (PKS) biosynthetic pathways; complex, clustered genetic sequences that give rise to amino acid-derived natural products. Synthetic biology can be applied to modify and metabolically engineer these enzyme-based systems to promote rapid and sustainable production of natural products and their variants. This review will focus on recent advances related to synthetic biology as applied to genetic pathway characterization and identification of antibiotics from naturally occurring BGCs. Specifically, we will summarize recent efforts to characterize BGCs via general genomic mutagenesis, endogenous gene expression, and heterologous gene expression.
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Affiliation(s)
- Greta D Cook
- Department of Biology and Environmental Science, University of New Haven, 300 Boston Post Rd, Dodds Hall 316, West Haven 06516 USA
| | - Nikolas M Stasulli
- Department of Biology and Environmental Science, University of New Haven, 300 Boston Post Rd, Dodds Hall 316, West Haven 06516 USA.
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11
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Liu L, Zhan J, Yan J. Engineering the future cereal crops with big biological data: toward an intelligence-driven breeding by design. J Genet Genomics 2024:S1673-8527(24)00058-4. [PMID: 38531485 DOI: 10.1016/j.jgg.2024.03.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 03/17/2024] [Accepted: 03/17/2024] [Indexed: 03/28/2024]
Abstract
How to feed 10 billion human populations is one of the challenges that need to be addressed in the following decades, especially under an unpredicted climate change. Crop breeding, initiating from the phenotype-based selection by local farmers and developing into current biotechnology-based breeding, has played a critical role in securing the global food supply. However, regarding the changing environment and ever-increasing human population, can we breed outstanding crop varieties fast enough to achieve high productivity, good quality, and widespread adaptability? This review outlines the recent achievements in understanding cereal crop breeding, including the current knowledge about crop agronomic traits, newly developed techniques, crop big biological data research, and the possibility of integrating them for intelligence-driven breeding by design, which ushers in a new era of crop breeding practice and shapes the novel architecture of future crops. This review focuses on the major cereal crops, including rice, maize, and wheat, to explain how intelligence-driven breeding by design is becoming a reality.
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Affiliation(s)
- Lei Liu
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, Hubei 430070, China.
| | - Jimin Zhan
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Jianbing Yan
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, Hubei 430070, China
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12
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Xu X, Passalacqua M, Rice B, Demesa-Arevalo E, Kojima M, Takebayashi Y, Harris B, Sakakibara H, Gallavotti A, Gillis J, Jackson D. Large-scale single-cell profiling of stem cells uncovers redundant regulators of shoot development and yield trait variation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.04.583414. [PMID: 38496543 PMCID: PMC10942292 DOI: 10.1101/2024.03.04.583414] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
Stem cells in plant shoots are a rare population of cells that produce leaves, fruits and seeds, vital sources for food and bioethanol. Uncovering regulators expressed in these stem cells will inform crop engineering to boost productivity. Single-cell analysis is a powerful tool for identifying regulators expressed in specific groups of cells. However, accessing plant shoot stem cells is challenging. Recent single-cell analyses of plant shoots have not captured these cells, and failed to detect stem cell regulators like CLAVATA3 and WUSCHEL . In this study, we finely dissected stem cell-enriched shoot tissues from both maize and arabidopsis for single-cell RNA-seq profiling. We optimized protocols to efficiently recover thousands of CLAVATA3 and WUSCHEL expressed cells. A cross-species comparison identified conserved stem cell regulators between maize and arabidopsis. We also performed single-cell RNA-seq on maize stem cell overproliferation mutants to find additional candidate regulators. Expression of candidate stem cell genes was validated using spatial transcriptomics, and we functionally confirmed roles in shoot development. These candidates include a family of ribosome-associated RNA-binding proteins, and two families of sugar kinase genes related to hypoxia signaling and cytokinin hormone homeostasis. These large-scale single-cell profiling of stem cells provide a resource for mining stem cell regulators, which show significant association with yield traits. Overall, our discoveries advance the understanding of shoot development and open avenues for manipulating diverse crops to enhance food and energy security.
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13
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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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14
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Hao N, Yao H, Suzuki M, Li B, Wang C, Cao J, Fujiwara T, Wu T, Kamiya T. Novel lignin-based extracellular barrier in glandular trichome. NATURE PLANTS 2024; 10:381-389. [PMID: 38374437 DOI: 10.1038/s41477-024-01626-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Accepted: 01/16/2024] [Indexed: 02/21/2024]
Abstract
Successful biochemical reactions in organisms necessitate compartmentalization of the requisite components. Glandular trichomes (GTs) act as compartments for the synthesis and storage of specialized compounds. These compounds not only are crucial for the survival of plants under biotic and abiotic stresses but also have medical and commercial value for humans. However, the mechanisms underlying compartmentalization remain unclear. Here we identified a novel structure that is indispensable for the establishment of compartments in cucumber GTs. Silica, a specialized compound, is deposited on the GTs and is visible on the surface of the fruit as a white powder, known as bloom. This deposition provides resistance against pathogens and prevents water loss from the fruits1. Using the cucumber bloomless mutant2, we discovered that a lignin-based cell wall structure in GTs, named 'neck strip', achieves compartmentalization by acting as an extracellular barrier crucial for the silica polymerization. This structure is present in the GTs of diverse plant species. Our findings will enhance the understanding of the biosynthesis of unique compounds in trichomes and provide a basis for improving the production of compounds beneficial to humans.
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Affiliation(s)
- Ning Hao
- College of Horticulture/Yuelu Mountain Laboratory of Hunan Province, Hunan Agricultural University, Changsha, China
- Graduate School of Agricultural and Life Sciences, University of Tokyo, Tokyo, Japan
| | - Hongxin Yao
- College of Horticulture/Yuelu Mountain Laboratory of Hunan Province, Hunan Agricultural University, Changsha, China
| | - Michio Suzuki
- Graduate School of Agricultural and Life Sciences, University of Tokyo, Tokyo, Japan
| | - Baohai Li
- MOE Key Laboratory of Environment Remediation and Ecological Health, College of Environmental and Resource Science, Zhejiang University, Hangzhou, China
| | - Chunhua Wang
- College of Horticulture/Yuelu Mountain Laboratory of Hunan Province, Hunan Agricultural University, Changsha, China
| | - Jiajian Cao
- College of Horticulture/Yuelu Mountain Laboratory of Hunan Province, Hunan Agricultural University, Changsha, China
| | - Toru Fujiwara
- Graduate School of Agricultural and Life Sciences, University of Tokyo, Tokyo, Japan
| | - Tao Wu
- College of Horticulture/Yuelu Mountain Laboratory of Hunan Province, Hunan Agricultural University, Changsha, China.
| | - Takehiro Kamiya
- Graduate School of Agricultural and Life Sciences, University of Tokyo, Tokyo, Japan.
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15
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Liu N, Du Y, Yan S, Chen W, Deng M, Xu S, Wang H, Zhan W, Huang W, Yin Y, Yang X, Zhao Q, Fernie AR, Yan J. The light and hypoxia induced gene ZmPORB1 determines tocopherol content in the maize kernel. SCIENCE CHINA. LIFE SCIENCES 2024; 67:435-448. [PMID: 38289421 DOI: 10.1007/s11427-023-2489-2] [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: 08/10/2023] [Accepted: 11/11/2023] [Indexed: 03/05/2024]
Abstract
Tocopherol is an important lipid-soluble antioxidant beneficial for both human health and plant growth. Here, we fine mapped a major QTL-qVE1 affecting γ-tocopherol content in maize kernel, positionally cloned and confirmed the underlying gene ZmPORB1 (por1), as a protochlorophyllide oxidoreductase. A 13.7 kb insertion reduced the tocopherol and chlorophyll content, and the photosynthetic activity by repressing ZmPORB1 expression in embryos of NIL-K22, but did not affect the levels of the tocopherol precursors HGA (homogentisic acid) and PMP (phytyl monophosphate). Furthermore, ZmPORB1 is inducible by low oxygen and light, thereby involved in the hypoxia response in developing embryos. Concurrent with natural hypoxia in embryos, the redox state has been changed with NO increasing and H2O2 decreasing, which lowered γ-tocopherol content via scavenging reactive nitrogen species. In conclusion, we proposed that the lower light-harvesting chlorophyll content weakened embryo photosynthesis, leading to fewer oxygen supplies and consequently diverse hypoxic responses including an elevated γ-tocopherol consumption. Our findings shed light on the mechanism for fine-tuning endogenous oxygen concentration in the maize embryo through a novel feedback pathway involving the light and low oxygen regulation of ZmPORB1 expression and chlorophyll content.
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Affiliation(s)
- Nannan Liu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
- Hubei Hongshan Laboratory, Wuhan, 430070, China
| | - Yuanhao Du
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
- Hubei Hongshan Laboratory, Wuhan, 430070, China
| | - Shijuan Yan
- Agro-biological Gene Research Center, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
| | - Wei Chen
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
- Hubei Hongshan Laboratory, Wuhan, 430070, China
| | - Min Deng
- College of Agronomy, Hunan Agricultural University, Changsha, 410128, China
| | - Shutu Xu
- College of Agronomy, Northwest A&F University, Xi'an, 710000, China
| | - Hong Wang
- State Key Laboratory of North China Crop Improvement and Regulation, Hebei Sub-center of National Maize Improvement Center of China, College of Agronomy, Hebei Agricultural University, Baoding, 071001, China
| | - Wei Zhan
- College of Life Sciences, South-Central Minzu University, Wuhan, 430070, China
| | - Wenjie Huang
- Agro-biological Gene Research Center, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
| | - Yan Yin
- Plant Science Facility of the Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Xiaohong Yang
- National Maize Improvement Center of China, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Qiao Zhao
- Shenzhen Key Laboratory of Synthetic Genomics, Guangdong Provincial Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Alisdair R Fernie
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, 14476, Germany
| | - Jianbing Yan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China.
- Hubei Hongshan Laboratory, Wuhan, 430070, China.
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16
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Gupta P, Dholaniya PS, Princy K, Madhavan AS, Sreelakshmi Y, Sharma R. Augmenting tomato functional genomics with a genome-wide induced genetic variation resource. FRONTIERS IN PLANT SCIENCE 2024; 14:1290937. [PMID: 38328621 PMCID: PMC10848261 DOI: 10.3389/fpls.2023.1290937] [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: 09/08/2023] [Accepted: 12/22/2023] [Indexed: 02/09/2024]
Abstract
Induced mutations accelerate crop improvement by providing novel disease resistance and yield alleles. However, the alleles with no perceptible phenotype but have an altered function remain hidden in mutagenized plants. The whole-genome sequencing (WGS) of mutagenized individuals uncovers the complete spectrum of mutations in the genome. Genome-wide induced mutation resources can improve the targeted breeding of tomatoes and facilitate functional genomics. In this study, we sequenced 132 doubly ethyl methanesulfonate (EMS)-mutagenized lines of tomato and detected approximately 41 million novel mutations and 5.5 million short InDels not present in the parental cultivar. Approximately 97% of the genome had mutations, including the genes, promoters, UTRs, and introns. More than one-third of genes in the mutagenized population had one or more deleterious mutations predicted by Sorting Intolerant From Tolerant (SIFT). Nearly one-fourth of deleterious genes mapped on tomato metabolic pathways modulate multiple pathway steps. In addition to the reported GC>AT transition bias for EMS, our population also had a substantial number of AT>GC transitions. Comparing mutation frequency among synonymous codons revealed that the most preferred codon is the least mutagenic toward EMS. The validation of a potato leaf-like mutation, reduction in carotenoids in ζ-carotene isomerase mutant fruits, and chloroplast relocation loss in phototropin1 mutant validated the mutation discovery pipeline. Our database makes a large repertoire of mutations accessible to functional genomics studies and breeding of tomatoes.
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Affiliation(s)
- Prateek Gupta
- Repository of Tomato Genomics Resources, Department of Plant Sciences, University of Hyderabad, Hyderabad, India
- Department of Biological Sciences, SRM University-AP, Amaravati, Andhra Pradesh, India
| | - Pankaj Singh Dholaniya
- Department of Biotechnology and Bioinformatics, University of Hyderabad, Hyderabad, India
| | - Kunnappady Princy
- Repository of Tomato Genomics Resources, Department of Plant Sciences, University of Hyderabad, Hyderabad, India
| | - Athira Sethu Madhavan
- Repository of Tomato Genomics Resources, Department of Plant Sciences, University of Hyderabad, Hyderabad, India
| | - Yellamaraju Sreelakshmi
- Repository of Tomato Genomics Resources, Department of Plant Sciences, University of Hyderabad, Hyderabad, India
| | - Rameshwar Sharma
- Repository of Tomato Genomics Resources, Department of Plant Sciences, University of Hyderabad, Hyderabad, India
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Yan Z, Li K, Li Y, Wang W, Leng B, Yao G, Zhang F, Mu C, Liu X. The ZmbHLH32-ZmIAA9-ZmARF1 module regulates salt tolerance in maize. Int J Biol Macromol 2023; 253:126978. [PMID: 37741480 DOI: 10.1016/j.ijbiomac.2023.126978] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 09/02/2023] [Accepted: 09/16/2023] [Indexed: 09/25/2023]
Abstract
The growth and productivity of maize (Zea mays), along with other crop plants, can be significantly hindered by salt stress. Nevertheless, the precise molecular mechanism underlying salt tolerance in maize has yet to be fully elucidated. Hence, it was attempted to identify ZmIAA9, a member of the maize Aux/IAA gene family, as a positive regulator of salt tolerance in maize, which was accompanied by the increased ROS detoxification and elevated transcript abundances of ROS scavenging genes. Molecular and biochemical assays have provided compelling evidence that ZmbHLH32, a transcription factor belonging to the bHLH family, was capable of binding directly to the promoter region of ZmIAA9, thereby activating its expression. This interaction between ZmbHLH32 and ZmIAA9 could be critical for the regulation of salt tolerance in maize. As expected, overexpression of ZmbHLH32 led to the enhanced salt tolerance. In contrast, decreased salt tolerance was attained after application of knockout mutants of ZmbHLH32. Furthermore, ZmARF1, which could act as a downstream of ZmIAA9, was found to physically interact with ZmIAA9 and repress the expression levels of ROS scavenging genes. Thus, our work uncovers a novel mechanism of ZmbHLH32-ZmIAA9-ZmARF1 module-mediated salt tolerance in maize, which can be exploited for breeding salt-tolerant maize varieties.
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Affiliation(s)
- Zhenwei Yan
- Maize Research Institute, Shandong Academy of Agricultural Sciences, Jinan 250100, Shandong, China
| | - Ke Li
- Shandong Academy of Grape, Shandong Academy of Agricultural Sciences, Jinan 250100, Shandong, China
| | - Yanli Li
- Institute of Industrial Crops, Shandong Academy of Agricultural Sciences, Jinan 250100, Shandong, China
| | - Wenli Wang
- Maize Research Institute, Shandong Academy of Agricultural Sciences, Jinan 250100, Shandong, China
| | - Bingying Leng
- Maize Research Institute, Shandong Academy of Agricultural Sciences, Jinan 250100, Shandong, China
| | - Guoqi Yao
- Maize Research Institute, Shandong Academy of Agricultural Sciences, Jinan 250100, Shandong, China
| | - Fajun Zhang
- Maize Research Institute, Shandong Academy of Agricultural Sciences, Jinan 250100, Shandong, China.
| | - Chunhua Mu
- Maize Research Institute, Shandong Academy of Agricultural Sciences, Jinan 250100, Shandong, China.
| | - Xia Liu
- Maize Research Institute, Shandong Academy of Agricultural Sciences, Jinan 250100, Shandong, China.
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18
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Liu Y, Chen Z, Zhang C, Guo J, Liu Q, Yin Y, Hu Y, Xia H, Li B, Sun X, Li Y, Liu X. Gene editing of ZmGA20ox3 improves plant architecture and drought tolerance in maize. PLANT CELL REPORTS 2023; 43:18. [PMID: 38148416 DOI: 10.1007/s00299-023-03090-x] [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: 07/17/2023] [Accepted: 10/19/2023] [Indexed: 12/28/2023]
Abstract
KEY MESSAGE Editing ZmGA20ox3 can achieve the effect similar to applying Cycocel, which can reduce maize plant height and enhance stress resistance. Drought stress, a major plant abiotic stress, is capable of suppressing crop yield performance severely. However, the trade-off between crop drought tolerance and yield performance turns out to be significantly challenging in drought-resistant crop breeding. Several phytohormones [e.g., gibberellin (GA)] have been reported to play a certain role in plant drought response, which also take on critical significance in plant growth and development. In this study, the loss-of-function mutations of GA biosynthesis enzyme ZmGA20ox3 were produced using the CRISPR-Cas9 system in maize. As indicated by the result of 2-year field trials, the above-mentioned mutants displayed semi-dwarfing phenotype with the decrease of GA1, and almost no yield loss was generated compared with wild-type (WT) plants. Interestingly, as revealed by the transcriptome analysis, differential expressed genes (DEGs) were notably enriched in abiotic stress progresses, and biochemical tests indicated the significantly increased ABA, JA, and DIMBOA levels in mutants, suggesting that ZmGA20ox3 may take on vital significance in stress response in maize. The in-depth analysis suggested that the loss function of ZmGA20ox3 can enhance drought tolerance in maize seedling, reduce Anthesis-Silking Interval (ASI) delay while decreasing the yield loss significantly in the field under drought conditions. The results of this study supported that regulating ZmGA20ox3 can improve plant height while enhancing drought resistance in maize, thus serving as a novel method for drought-resistant genetic improvement in maize.
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Affiliation(s)
- Yang Liu
- Institute of Agricultural Biotechnology, Jilin Academy of Agricultural Sciences, Changchun, China
| | - Ziqi Chen
- Institute of Agricultural Biotechnology, Jilin Academy of Agricultural Sciences, Changchun, China
| | - Chuang Zhang
- Institute of Agricultural Biotechnology, Jilin Academy of Agricultural Sciences, Changchun, China
| | - Jia Guo
- Institute of Agricultural Biotechnology, Jilin Academy of Agricultural Sciences, Changchun, China
| | - Qing Liu
- Institute of Agricultural Biotechnology, Jilin Academy of Agricultural Sciences, Changchun, China
| | - Yuejia Yin
- Institute of Agricultural Biotechnology, Jilin Academy of Agricultural Sciences, Changchun, China
| | - Yang Hu
- Institute of Agricultural Biotechnology, Jilin Academy of Agricultural Sciences, Changchun, China
| | - Hanchao Xia
- Institute of Agricultural Biotechnology, Jilin Academy of Agricultural Sciences, Changchun, China
- Jilin Agricultural University, Changchun, China
| | - Bingyang Li
- Institute of Agricultural Biotechnology, Jilin Academy of Agricultural Sciences, Changchun, China
| | - Xiaopeng Sun
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China.
- Hubei Hongshan Laboratory, Wuhan, China.
| | - Yidan Li
- Institute of Agricultural Biotechnology, Jilin Academy of Agricultural Sciences, Changchun, China.
| | - Xiangguo Liu
- Institute of Agricultural Biotechnology, Jilin Academy of Agricultural Sciences, Changchun, China.
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19
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Wu J, Sun LQ, Song Y, Bai Y, Wan GY, Wang JX, Xia JQ, Zhang ZY, Zhang ZS, Zhao Z, Xiang CB. The OsNLP3/4-OsRFL module regulates nitrogen-promoted panicle architecture in rice. THE NEW PHYTOLOGIST 2023; 240:2404-2418. [PMID: 37845836 DOI: 10.1111/nph.19318] [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: 03/15/2023] [Accepted: 09/16/2023] [Indexed: 10/18/2023]
Abstract
Rice panicles, a major component of yield, are regulated by phytohormones and nutrients. How mineral nutrients promote panicle architecture remains largely unknown. Here, we report that NIN-LIKE PROTEIN3 and 4 (OsNLP3/4) are crucial positive regulators of rice panicle architecture in response to nitrogen (N). Loss-of-function mutants of either OsNLP3 or OsNLP4 produced smaller panicles with reduced primary and secondary branches and fewer grains than wild-type, whereas their overexpression plants showed the opposite phenotypes. The OsNLP3/4-regulated panicle architecture was positively correlated with N availability. OsNLP3/4 directly bind to the promoter of OsRFL and activate its expression to promote inflorescence meristem development. Furthermore, OsRFL activates OsMOC1 expression by binding to its promoter. Our findings reveal the novel N-responsive OsNLP3/4-OsRFL-OsMOC1 module that integrates N availability to regulate panicle architecture, shedding light on how N nutrient signals regulate panicle architecture and providing candidate targets for the improvement of crop yield.
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Affiliation(s)
- Jie Wu
- Division of Life Sciences and Medicine, Division of Molecular & Cell Biophysics, Hefei National Science Center for Interdisciplinary Sciences at the Microscale, MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, University of Science and Technology of China, The Innovation Academy of Seed Design, Chinese Academy of Sciences, Hefei, Anhui Province, 230027, China
| | - Liang-Qi Sun
- Division of Life Sciences and Medicine, Division of Molecular & Cell Biophysics, Hefei National Science Center for Interdisciplinary Sciences at the Microscale, MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, University of Science and Technology of China, The Innovation Academy of Seed Design, Chinese Academy of Sciences, Hefei, Anhui Province, 230027, China
| | - Ying Song
- Division of Life Sciences and Medicine, Division of Molecular & Cell Biophysics, Hefei National Science Center for Interdisciplinary Sciences at the Microscale, MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, University of Science and Technology of China, The Innovation Academy of Seed Design, Chinese Academy of Sciences, Hefei, Anhui Province, 230027, China
| | - Yu Bai
- Experimental Center of Engineering and Materials Science, University of Science and Technology of China, Hefei, 230027, China
| | - Guang-Yu Wan
- Division of Life Sciences and Medicine, Division of Molecular & Cell Biophysics, Hefei National Science Center for Interdisciplinary Sciences at the Microscale, MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, University of Science and Technology of China, The Innovation Academy of Seed Design, Chinese Academy of Sciences, Hefei, Anhui Province, 230027, China
| | - Jing-Xian Wang
- Division of Life Sciences and Medicine, Division of Molecular & Cell Biophysics, Hefei National Science Center for Interdisciplinary Sciences at the Microscale, MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, University of Science and Technology of China, The Innovation Academy of Seed Design, Chinese Academy of Sciences, Hefei, Anhui Province, 230027, China
| | - Jin-Qiu Xia
- Division of Life Sciences and Medicine, Division of Molecular & Cell Biophysics, Hefei National Science Center for Interdisciplinary Sciences at the Microscale, MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, University of Science and Technology of China, The Innovation Academy of Seed Design, Chinese Academy of Sciences, Hefei, Anhui Province, 230027, China
| | - Zheng-Yi Zhang
- Division of Life Sciences and Medicine, Division of Molecular & Cell Biophysics, Hefei National Science Center for Interdisciplinary Sciences at the Microscale, MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, University of Science and Technology of China, The Innovation Academy of Seed Design, Chinese Academy of Sciences, Hefei, Anhui Province, 230027, China
| | - Zi-Sheng Zhang
- Division of Life Sciences and Medicine, Division of Molecular & Cell Biophysics, Hefei National Science Center for Interdisciplinary Sciences at the Microscale, MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, University of Science and Technology of China, The Innovation Academy of Seed Design, Chinese Academy of Sciences, Hefei, Anhui Province, 230027, China
| | - Zhong Zhao
- Division of Life Sciences and Medicine, Division of Molecular & Cell Biophysics, Hefei National Science Center for Interdisciplinary Sciences at the Microscale, MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, University of Science and Technology of China, The Innovation Academy of Seed Design, Chinese Academy of Sciences, Hefei, Anhui Province, 230027, China
| | - Cheng-Bin Xiang
- Division of Life Sciences and Medicine, Division of Molecular & Cell Biophysics, Hefei National Science Center for Interdisciplinary Sciences at the Microscale, MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, University of Science and Technology of China, The Innovation Academy of Seed Design, Chinese Academy of Sciences, Hefei, Anhui Province, 230027, China
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20
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Bi M, Wang Z, Cheng K, Cui Y, He Y, Ma J, Qi M. Construction of transcription factor mutagenesis population in tomato using a pooled CRISPR/Cas9 plasmid library. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 205:108094. [PMID: 37995578 DOI: 10.1016/j.plaphy.2023.108094] [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: 05/18/2023] [Revised: 09/25/2023] [Accepted: 10/12/2023] [Indexed: 11/25/2023]
Abstract
Adequate mutant materials are the prerequisite for conducting gene function research or screening novel functional genes in plants. The strategy of constructing a large-scale mutant population using the pooled CRISPR/Cas9-sgRNA library has been implemented in several crops. However, the effective application of this CRISPR/Cas9 large-scale screening strategy to tomato remains to be attempted. Here, we identified 990 transcription factors in the tomato genome, designed and synthesized a CRISPR/Cas9 plasmid library containing 4379 sgRNAs. Using this pooled library, 487 T0 positive plants were obtained, among which 92 plants harbored a single sgRNA sequence, targeting 65 different transcription factors, with a mutation rate of 23%. In the T0 mutant population, the occurrence of homozygous and biallelic mutations was observed at higher frequencies. Additionally, the utilization of a small-scale CRISPR/Cas9 library targeting 30 transcription factors could enhance the efficacy of single sgRNA recognition in positive plants, increasing it from 19% to 42%. Phenotypic characterization of several mutants identified from the mutant population demonstrated the utility of our CRISPR/Cas9 mutant library. Taken together, our study offers insights into the implementation and optimization of CRISPR/Cas9-mediated large-scale knockout library in tomato.
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Affiliation(s)
- Mengxi Bi
- College of Horticulture, Shenyang Agricultural University, Shenyang, China; National & Local Joint Engineering Research Center of Northern Horticultural Facilities Design & Application Technology (Liaoning), Shenyang, China; Key Laboratory of Protected Horticulture (Shenyang Agricultural University), Ministry of Education, Shenyang, China; Key Laboratory of Horticultural Equipment, Ministry of Agriculture and Rural Affairs, Shenyang, China
| | - Zhijun Wang
- College of Horticulture, Shenyang Agricultural University, Shenyang, China; National & Local Joint Engineering Research Center of Northern Horticultural Facilities Design & Application Technology (Liaoning), Shenyang, China; Key Laboratory of Protected Horticulture (Shenyang Agricultural University), Ministry of Education, Shenyang, China; Key Laboratory of Horticultural Equipment, Ministry of Agriculture and Rural Affairs, Shenyang, China
| | - Keyan Cheng
- College of Horticulture, Shenyang Agricultural University, Shenyang, China; National & Local Joint Engineering Research Center of Northern Horticultural Facilities Design & Application Technology (Liaoning), Shenyang, China; Key Laboratory of Protected Horticulture (Shenyang Agricultural University), Ministry of Education, Shenyang, China; Key Laboratory of Horticultural Equipment, Ministry of Agriculture and Rural Affairs, Shenyang, China
| | - Yiqing Cui
- National & Local Joint Engineering Research Center of Northern Horticultural Facilities Design & Application Technology (Liaoning), Shenyang, China; Key Laboratory of Protected Horticulture (Shenyang Agricultural University), Ministry of Education, Shenyang, China
| | - Yi He
- National & Local Joint Engineering Research Center of Northern Horticultural Facilities Design & Application Technology (Liaoning), Shenyang, China; Key Laboratory of Protected Horticulture (Shenyang Agricultural University), Ministry of Education, Shenyang, China
| | - Jian Ma
- College of Horticulture, Shenyang Agricultural University, Shenyang, China; National & Local Joint Engineering Research Center of Northern Horticultural Facilities Design & Application Technology (Liaoning), Shenyang, China; Key Laboratory of Protected Horticulture (Shenyang Agricultural University), Ministry of Education, Shenyang, China; Key Laboratory of Horticultural Equipment, Ministry of Agriculture and Rural Affairs, Shenyang, China
| | - Mingfang Qi
- College of Horticulture, Shenyang Agricultural University, Shenyang, China; National & Local Joint Engineering Research Center of Northern Horticultural Facilities Design & Application Technology (Liaoning), Shenyang, China; Key Laboratory of Protected Horticulture (Shenyang Agricultural University), Ministry of Education, Shenyang, China; Key Laboratory of Horticultural Equipment, Ministry of Agriculture and Rural Affairs, Shenyang, China.
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21
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Yang N, Wang Y, Liu X, Jin M, Vallebueno-Estrada M, Calfee E, Chen L, Dilkes BP, Gui S, Fan X, Harper TK, Kennett DJ, Li W, Lu Y, Ding J, Chen Z, Luo J, Mambakkam S, Menon M, Snodgrass S, Veller C, Wu S, Wu S, Zhuo L, Xiao Y, Yang X, Stitzer MC, Runcie D, Yan J, Ross-Ibarra J. Two teosintes made modern maize. Science 2023; 382:eadg8940. [PMID: 38033071 DOI: 10.1126/science.adg8940] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Accepted: 10/02/2023] [Indexed: 12/02/2023]
Abstract
The origins of maize were the topic of vigorous debate for nearly a century, but neither the current genetic model nor earlier archaeological models account for the totality of available data, and recent work has highlighted the potential contribution of a wild relative, Zea mays ssp. mexicana. Our population genetic analysis reveals that the origin of modern maize can be traced to an admixture between ancient maize and Zea mays ssp. mexicana in the highlands of Mexico some 4000 years after domestication began. We show that variation in admixture is a key component of maize diversity, both at individual loci and for additive genetic variation underlying agronomic traits. Our results clarify the origin of modern maize and raise new questions about the anthropogenic mechanisms underlying dispersal throughout the Americas.
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Affiliation(s)
- Ning Yang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
- Hubei Hongshan Laboratory, Wuhan 430070, China
- Department of Evolution and Ecology, University of California, Davis, CA 95616, USA
| | - Yuebin Wang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Xiangguo Liu
- Institute of Agricultural Biotechnology, Jilin Academy of Agricultural Sciences, Changchun 130033, China
| | - Minliang Jin
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Miguel Vallebueno-Estrada
- Unidad de Genómica Avanzada, Laboratorio Nacional de Genómica para la Biodiversidad, CINVESTAV Irapuato, 36821 Guanajuato, México
| | - Erin Calfee
- Department of Evolution and Ecology, University of California, Davis, CA 95616, USA
- Center for Population Biology, University of California, Davis, CA 95616, USA
- Adaptive Biotechnologies, Seattle, WA 98109, USA
| | - Lu Chen
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Brian P Dilkes
- Department of Biochemistry, Purdue University, West Lafayette, IN 47907, USA
| | - Songtao Gui
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Xingming Fan
- Institute of Food Crops, Yunnan Academy of Agricultural Sciences, Kunming 650200, China
| | - Thomas K Harper
- Department of Anthropology, Pennsylvania State University, University Park, PA 16802, USA
| | - Douglas J Kennett
- Department of Anthropology, University of California, Santa Barbara, CA 93106, USA
| | - Wenqiang Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Yanli Lu
- Maize Research Institute, Sichuan Agricultural University, Wenjiang, Sichuan 611130, China
| | - Junqiang Ding
- College of Agronomy, Henan Agricultural University, Zhengzhou, Henan 450046, China
| | - Ziqi Chen
- Institute of Agricultural Biotechnology, Jilin Academy of Agricultural Sciences, Changchun 130033, China
| | - Jingyun Luo
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Sowmya Mambakkam
- Department of Evolution and Ecology, University of California, Davis, CA 95616, USA
| | - Mitra Menon
- Department of Evolution and Ecology, University of California, Davis, CA 95616, USA
- Center for Population Biology, University of California, Davis, CA 95616, USA
| | - Samantha Snodgrass
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA 50011, USA
| | - Carl Veller
- Department of Ecology and Evolution, University of Chicago, Chicago, IL 60637, USA
| | - Shenshen Wu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Siying Wu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Lin Zhuo
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Yingjie Xiao
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
- Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Xiaohong Yang
- National Maize Improvement Center of China, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Michelle C Stitzer
- Institute for Genomic Diversity and Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Daniel Runcie
- Department of Plant Sciences, University of California, Davis, CA 95616, USA
| | - Jianbing Yan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
- Hubei Hongshan Laboratory, Wuhan 430070, China
- Yazhouwan National Laboratory, Sanya 572024, China
| | - Jeffrey Ross-Ibarra
- Department of Evolution and Ecology, University of California, Davis, CA 95616, USA
- Center for Population Biology, University of California, Davis, CA 95616, USA
- Genome Center, University of California, Davis, CA 95616, USA
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22
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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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23
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Dinday S, Ghosh S. Recent advances in triterpenoid pathway elucidation and engineering. Biotechnol Adv 2023; 68:108214. [PMID: 37478981 DOI: 10.1016/j.biotechadv.2023.108214] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Revised: 07/10/2023] [Accepted: 07/11/2023] [Indexed: 07/23/2023]
Abstract
Triterpenoids are among the most assorted class of specialized metabolites found in all the taxa of living organisms. Triterpenoids are the leading active ingredients sourced from plant species and are utilized in pharmaceutical and cosmetic industries. The triterpenoid precursor 2,3-oxidosqualene, which is biosynthesized via the mevalonate (MVA) pathway is structurally diversified by the oxidosqualene cyclases (OSCs) and other scaffold-decorating enzymes such as cytochrome P450 monooxygenases (P450s), UDP-glycosyltransferases (UGTs) and acyltransferases (ATs). A majority of the bioactive triterpenoids are harvested from the native hosts using the traditional methods of extraction and occasionally semi-synthesized. These methods of supply are time-consuming and do not often align with sustainability goals. Recent advancements in metabolic engineering and synthetic biology have shown prospects for the green routes of triterpenoid pathway reconstruction in heterologous hosts such as Escherichia coli, Saccharomyces cerevisiae and Nicotiana benthamiana, which appear to be quite promising and might lead to the development of alternative source of triterpenoids. The present review describes the biotechnological strategies used to elucidate complex biosynthetic pathways and to understand their regulation and also discusses how the advances in triterpenoid pathway engineering might aid in the scale-up of triterpenoid production in engineered hosts.
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Affiliation(s)
- Sandeep Dinday
- CSIR-Central Institute of Medicinal and Aromatic Plants, Lucknow 226015, Uttar Pradesh, India; School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana 141004, Punjab, India
| | - Sumit Ghosh
- CSIR-Central Institute of Medicinal and Aromatic Plants, Lucknow 226015, Uttar Pradesh, India; Academy of Scientific and Innovative Research, Ghaziabad 201002, Uttar Pradesh, India.
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24
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Aguirre L, Hendelman A, Hutton SF, McCandlish DM, Lippman ZB. Idiosyncratic and dose-dependent epistasis drives variation in tomato fruit size. Science 2023; 382:315-320. [PMID: 37856609 PMCID: PMC10602613 DOI: 10.1126/science.adi5222] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Accepted: 09/06/2023] [Indexed: 10/21/2023]
Abstract
Epistasis between genes is traditionally studied with mutations that eliminate protein activity, but most natural genetic variation is in cis-regulatory DNA and influences gene expression and function quantitatively. In this study, we used natural and engineered cis-regulatory alleles in a plant stem-cell circuit to systematically evaluate epistatic relationships controlling tomato fruit size. Combining a promoter allelic series with two other loci, we collected over 30,000 phenotypic data points from 46 genotypes to quantify how allele strength transforms epistasis. We revealed a saturating dose-dependent relationship but also allele-specific idiosyncratic interactions, including between alleles driving a step change in fruit size during domestication. Our approach and findings expose an underexplored dimension of epistasis, in which cis-regulatory allelic diversity within gene regulatory networks elicits nonlinear, unpredictable interactions that shape phenotypes.
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Affiliation(s)
- Lyndsey Aguirre
- Cold Spring Harbor Laboratory, School of Biological Sciences, Cold Spring Harbor, NY, USA
| | - Anat Hendelman
- Cold Spring Harbor Laboratory; Cold Spring Harbor, NY, USA
| | - Samuel F. Hutton
- Gulf Coast Research and Education Center, University of Florida, Wimauma, FL, USA
| | | | - Zachary B. Lippman
- Cold Spring Harbor Laboratory, School of Biological Sciences, Cold Spring Harbor, NY, USA
- Cold Spring Harbor Laboratory; Cold Spring Harbor, NY, USA
- Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
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25
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Xu Z, Zhou Z, Cheng Z, Zhou Y, Wang F, Li M, Li G, Li W, Du Q, Wang K, Lu X, Tai Y, Chen R, Hao Z, Han J, Chen Y, Meng Q, Kong X, Tie S, Mu C, Song W, Wang Z, Yong H, Zhang D, Wang H, Weng J, Li X. A transcription factor ZmGLK36 confers broad resistance to maize rough dwarf disease in cereal crops. NATURE PLANTS 2023; 9:1720-1733. [PMID: 37709955 DOI: 10.1038/s41477-023-01514-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Accepted: 08/07/2023] [Indexed: 09/16/2023]
Abstract
Maize rough dwarf disease (MRDD), caused by maize rough dwarf virus (MRDV) or rice black-streaked dwarf virus (RBSDV), seriously threatens worldwide production of all major cereal crops, including maize, rice, wheat and barley. Here we report fine mapping and cloning of a previously reported major quantitative trait locus (QTL) (qMrdd2) for RBSDV resistance in maize. Subsequently, we show that qMrdd2 encodes a G2-like transcription factor named ZmGLK36 that promotes resistance to RBSDV by enhancing jasmonic acid (JA) biosynthesis and JA-mediated defence response. We identify a 26-bp indel located in the 5' UTR of ZmGLK36 that contributes to differential expression and resistance to RBSDV in maize inbred lines. Moreover, we show that ZmDBF2, an AP2/EREBP family transcription factor, directly binds to the 26-bp indel and represses ZmGLK36 expression. We further demonstrate that ZmGLK36 plays a conserved role in conferring resistance to RBSDV in rice and wheat using transgenic or marker-assisted breeding approaches. Our results provide insights into the molecular mechanisms of RBSDV resistance and effective strategies to breed RBSDV-resistant cereal crops.
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Affiliation(s)
- Zhennan Xu
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Zhiqiang Zhou
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Zixiang Cheng
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yu Zhou
- Northeast Agricultural University, Harbin, China
| | - Feifei Wang
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Mingshun Li
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Gongjian Li
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Wenxue Li
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Qingguo Du
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Ke Wang
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xin Lu
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yuxin Tai
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Runyi Chen
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Zhuanfang Hao
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jienan Han
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yanping Chen
- Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Qingchang Meng
- Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Xiaomin Kong
- Jining Academy of Agricultural Sciences, Jining, China
| | - Shuanggui Tie
- Henan Academy of Agricultural Sciences, Zhengzhou, China
| | - Chunhua Mu
- Shandong Academy of Agricultural Sciences, Jinan, China
| | - Weibin Song
- China Agricultural University, Beijing, China
| | - Zhenhua Wang
- Northeast Agricultural University, Harbin, China
| | - Hongjun Yong
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Degui Zhang
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Haiyang Wang
- Guangdong Laboratory for Lingnan Modern Agriculture, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China.
| | - Jianfeng Weng
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China.
| | - Xinhai Li
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China.
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26
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Yao L, Wang X, Ke R, Chen K, Xie K. FLASH Genome Editing Pipeline: An Efficient and High-Throughput Method to Construct Arrayed CRISPR Library for Plant Functional Genomics. Curr Protoc 2023; 3:e905. [PMID: 37755326 DOI: 10.1002/cpz1.905] [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] [Indexed: 09/28/2023]
Abstract
CRISPR/Cas9 genome editing is a revolutionary technology for plant functional genomics and crop breeding. In this system, the Cas9 nuclease is directed by a guide RNA (gRNA) to cut the DNA target and introduce mutation through error-prone DNA break repair. Owing to its simplicity, CRISPR/Cas9-mediated targeted gene knockout is widely used for high-throughput genetic screening in animal cell cultures and bacteria. However, high-throughput genetic screening using CRISPR/Cas9 is still challenging in plants. We recently established a new approach, named the FLASH genome editing pipeline, to construct an arrayed CRISPR library in plants. In this pipeline, a set of 12 PCR fragments with different lengths (referred to as FLASH tags) are used to index the Cas9/gRNA vectors. Subsequently, a mixture of 12 Agrobacterium strains, in which each strain contained a FLASH-tag indexed vector, was transformed into rice plants. As a result, a unique link between the target gene/gRNA and FLASH tag is generated, which allows reading gRNA information in bacterial strains and gene-edited plants using regular PCR and gel electrophoresis. This protocol includes step-by-step instructions for gRNA design, high throughput assembly of FLASH-tag indexed Cas9/gRNA plasmids, Agrobacterium-mediated transformation of 12 indexed plasmids, and fast assignment of target gene information in primary transformants. The arrayed CRISPR library described here is suitable for small- to large-scale genetic screening and allows fast and comprehensive gene function discovery in plants. © 2023 Wiley Periodicals LLC. Basic Protocol 1: Assembly of FLASH-tag-indexed Cas9/gRNA plasmids Basic Protocol 2: Preparation of the Cas9/gRNA plasmid library Basic Protocol 3: Library preparation of Agrobacterium strains and mixing FLASH-tag indexed strains Basic Protocol 4: Grouped transformation and assignments of gRNA information of gene-edited plants.
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Affiliation(s)
- Lu Yao
- National Key Laboratory of Crop Genetic Improvement and Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Xiaochun Wang
- National Key Laboratory of Crop Genetic Improvement and Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, People's Republic of China
- Current affiliation: Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, People's Republic of China
| | - Runnan Ke
- National Key Laboratory of Crop Genetic Improvement and Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Kaiyuan Chen
- National Key Laboratory of Crop Genetic Improvement and Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, People's Republic of China
- Current affiliation: Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, People's Republic of China
| | - Kabin Xie
- National Key Laboratory of Crop Genetic Improvement and Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, People's Republic of China
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Wang X, Li J, Han L, Liang C, Li J, Shang X, Miao X, Luo Z, Zhu W, Li Z, Li T, Qi Y, Li H, Lu X, Li L. QTG-Miner aids rapid dissection of the genetic base of tassel branch number in maize. Nat Commun 2023; 14:5232. [PMID: 37633966 PMCID: PMC10460418 DOI: 10.1038/s41467-023-41022-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 08/21/2023] [Indexed: 08/28/2023] Open
Abstract
Genetic dissection of agronomic traits is important for crop improvement and global food security. Phenotypic variation of tassel branch number (TBN), a major breeding target, is controlled by many quantitative trait loci (QTLs). The lack of large-scale QTL cloning methodology constrains the systematic dissection of TBN, which hinders modern maize breeding. Here, we devise QTG-Miner, a multi-omics data-based technique for large-scale and rapid cloning of quantitative trait genes (QTGs) in maize. Using QTG-Miner, we clone and verify seven genes underlying seven TBN QTLs. Compared to conventional methods, QTG-Miner performs well for both major- and minor-effect TBN QTLs. Selection analysis indicates that a substantial number of genes and network modules have been subjected to selection during maize improvement. Selection signatures are significantly enriched in multiple biological pathways between female heterotic groups and male heterotic groups. In summary, QTG-Miner provides a large-scale approach for rapid cloning of QTGs in crops and dissects the genetic base of TBN for further maize breeding.
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Affiliation(s)
- Xi Wang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
- Hubei Hongshan Laboratory, Wuhan, 430070, China
| | - Juan Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
- Hubei Hongshan Laboratory, Wuhan, 430070, China
| | - Linqian Han
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
- Hubei Hongshan Laboratory, Wuhan, 430070, China
| | - Chengyong Liang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
- Hubei Hongshan Laboratory, Wuhan, 430070, China
| | - Jiaxin Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
- Hubei Hongshan Laboratory, Wuhan, 430070, China
| | - Xiaoyang Shang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
- Hubei Hongshan Laboratory, Wuhan, 430070, China
| | - Xinxin Miao
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
- Hubei Hongshan Laboratory, Wuhan, 430070, China
| | - Zi Luo
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
- Hubei Hongshan Laboratory, Wuhan, 430070, China
| | - Wanchao Zhu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
- Hubei Hongshan Laboratory, Wuhan, 430070, China
| | - Zhao Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
- Hubei Hongshan Laboratory, Wuhan, 430070, China
| | - Tianhuan Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
- Hubei Hongshan Laboratory, Wuhan, 430070, China
| | - Yongwen Qi
- College of Agriculture and Biology, Zhongkai University of Agriculture and Engineering, Guangzhou, 510325, Guangdong, China
| | - Huihui Li
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, 100081, Beijing, China
| | - Xiaoduo Lu
- Institute of Molecular Breeding for Maize, Qilu Normal University, Jinan, 250200, China
| | - Lin Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China.
- Hubei Hongshan Laboratory, Wuhan, 430070, China.
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28
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Shi L, Su J, Cho MJ, Song H, Dong X, Liang Y, Zhang Z. Promoter editing for the genetic improvement of crops. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:4349-4366. [PMID: 37204916 DOI: 10.1093/jxb/erad175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Accepted: 05/06/2023] [Indexed: 05/21/2023]
Abstract
Gene expression plays a fundamental role in the regulation of agronomically important traits in crop plants. The genetic manipulation of plant promoters through genome editing has emerged as an effective strategy to create favorable traits in crops by altering the expression pattern of the pertinent genes. Promoter editing can be applied in a directed manner, where nucleotide sequences associated with favorable traits are precisely generated. Alternatively, promoter editing can also be exploited as a random mutagenic approach to generate novel genetic variations within a designated promoter, from which elite alleles are selected based on their phenotypic effects. Pioneering studies have demonstrated the potential of promoter editing in engineering agronomically important traits as well as in mining novel promoter alleles valuable for plant breeding. In this review, we provide an update on the application of promoter editing in crops for increased yield, enhanced tolerance to biotic and abiotic stresses, and improved quality. We also discuss several remaining technical bottlenecks and how this strategy may be better employed for the genetic improvement of crops in the future.
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Affiliation(s)
- Lu Shi
- Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base, Ministry of Science and Technology, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
| | - Jing Su
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Province and Ministry Co-sponsored Collaborative Innovation Center for Modern Crop Production, Jiangsu Engineering Research Center for Plant Genome Editing, Nanjing Agricultural University, Nanjing 210095, China
| | - Myeong-Je Cho
- Innovative Genomics Institute, University of California, Berkeley, CA 94704, USA
| | - Hao Song
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Province and Ministry Co-sponsored Collaborative Innovation Center for Modern Crop Production, Jiangsu Engineering Research Center for Plant Genome Editing, Nanjing Agricultural University, Nanjing 210095, China
| | - Xiaoou Dong
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Province and Ministry Co-sponsored Collaborative Innovation Center for Modern Crop Production, Jiangsu Engineering Research Center for Plant Genome Editing, Nanjing Agricultural University, Nanjing 210095, China
- Hainan Yazhou Bay Seed Laboratory, Sanya 572025, China
- Zhongshan Biological Breeding Laboratory, No. 50 Zhongling Street, Nanjing, Jiangsu 210014, China
| | - Ying Liang
- Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base, Ministry of Science and Technology, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
| | - Zhiyong Zhang
- Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base, Ministry of Science and Technology, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
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Impens L, Lorenzo CD, Vandeputte W, Wytynck P, Debray K, Haeghebaert J, Herwegh D, Jacobs TB, Ruttink T, Nelissen H, Inzé D, Pauwels L. Combining multiplex gene editing and doubled haploid technology in maize. THE NEW PHYTOLOGIST 2023; 239:1521-1532. [PMID: 37306056 PMCID: PMC7614789 DOI: 10.1111/nph.19021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 05/09/2023] [Indexed: 06/13/2023]
Abstract
A major advantage of using CRISPR/Cas9 for gene editing is multiplexing, that is, the simultaneous targeting of many genes. However, primary transformants typically contain hetero-allelic mutations or are genetic mosaic, while genetically stable lines that are homozygous are desired for functional analysis. Currently, a dedicated and labor-intensive effort is required to obtain such higher-order mutants through several generations of genetic crosses and genotyping. We describe the design and validation of a rapid and efficient strategy to produce lines of genetically identical plants carrying various combinations of homozygous edits, suitable for replicated analysis of phenotypical differences. This approach was achieved by combining highly multiplex gene editing in Zea mays (maize) with in vivo haploid induction and efficient in vitro generation of doubled haploid plants using embryo rescue doubling. By combining three CRISPR/Cas9 constructs that target in total 36 genes potentially involved in leaf growth, we generated an array of homozygous lines with various combinations of edits within three generations. Several genotypes show a reproducible 10% increase in leaf size, including a septuple mutant combination. We anticipate that our strategy will facilitate the study of gene families via multiplex CRISPR mutagenesis and the identification of allele combinations to improve quantitative crop traits.
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Affiliation(s)
- Lennert Impens
- department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium
- Center for Plant Systems Biology, VIB, B-9052 Ghent, Belgium
| | - Christian D. Lorenzo
- department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium
- Center for Plant Systems Biology, VIB, B-9052 Ghent, Belgium
| | - Wout Vandeputte
- department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium
- Center for Plant Systems Biology, VIB, B-9052 Ghent, Belgium
| | - Pieter Wytynck
- department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium
- Center for Plant Systems Biology, VIB, B-9052 Ghent, Belgium
| | - Kevin Debray
- department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium
- Center for Plant Systems Biology, VIB, B-9052 Ghent, Belgium
| | - Jari Haeghebaert
- department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium
- Center for Plant Systems Biology, VIB, B-9052 Ghent, Belgium
| | - Denia Herwegh
- department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium
- Center for Plant Systems Biology, VIB, B-9052 Ghent, Belgium
| | - Thomas B. Jacobs
- department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium
- Center for Plant Systems Biology, VIB, B-9052 Ghent, Belgium
| | - Tom Ruttink
- department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium
- Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), B-9820 Merelbeke, Belgium
| | - Hilde Nelissen
- department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium
- Center for Plant Systems Biology, VIB, B-9052 Ghent, Belgium
| | - Dirk Inzé
- department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium
- Center for Plant Systems Biology, VIB, B-9052 Ghent, Belgium
| | - Laurens Pauwels
- department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium
- Center for Plant Systems Biology, VIB, B-9052 Ghent, Belgium
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30
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Farinati S, Draga S, Betto A, Palumbo F, Vannozzi A, Lucchin M, Barcaccia G. Current insights and advances into plant male sterility: new precision breeding technology based on genome editing applications. FRONTIERS IN PLANT SCIENCE 2023; 14:1223861. [PMID: 37521915 PMCID: PMC10382145 DOI: 10.3389/fpls.2023.1223861] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 06/20/2023] [Indexed: 08/01/2023]
Abstract
Plant male sterility (MS) represents the inability of the plant to generate functional anthers, pollen, or male gametes. Developing MS lines represents one of the most important challenges in plant breeding programs, since the establishment of MS lines is a major goal in F1 hybrid production. For these reasons, MS lines have been developed in several species of economic interest, particularly in horticultural crops and ornamental plants. Over the years, MS has been accomplished through many different techniques ranging from approaches based on cross-mediated conventional breeding methods, to advanced devices based on knowledge of genetics and genomics to the most advanced molecular technologies based on genome editing (GE). GE methods, in particular gene knockout mediated by CRISPR/Cas-related tools, have resulted in flexible and successful strategic ideas used to alter the function of key genes, regulating numerous biological processes including MS. These precision breeding technologies are less time-consuming and can accelerate the creation of new genetic variability with the accumulation of favorable alleles, able to dramatically change the biological process and resulting in a potential efficiency of cultivar development bypassing sexual crosses. The main goal of this manuscript is to provide a general overview of insights and advances into plant male sterility, focusing the attention on the recent new breeding GE-based applications capable of inducing MS by targeting specific nuclear genic loci. A summary of the mechanisms underlying the recent CRISPR technology and relative success applications are described for the main crop and ornamental species. The future challenges and new potential applications of CRISPR/Cas systems in MS mutant production and other potential opportunities will be discussed, as generating CRISPR-edited DNA-free by transient transformation system and transgenerational gene editing for introducing desirable alleles and for precision breeding strategies.
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31
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Jin M, Liu H, Liu X, Guo T, Guo J, Yin Y, Ji Y, Li Z, Zhang J, Wang X, Qiao F, Xiao Y, Zan Y, Yan J. Complex genetic architecture underlying the plasticity of maize agronomic traits. PLANT COMMUNICATIONS 2023; 4:100473. [PMID: 36642074 DOI: 10.1016/j.xplc.2022.100473] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Revised: 08/21/2022] [Accepted: 11/07/2022] [Indexed: 05/11/2023]
Abstract
Phenotypic plasticity is the ability of a given genotype to produce multiple phenotypes in response to changing environmental conditions. Understanding the genetic basis of phenotypic plasticity and establishing a predictive model is highly relevant to future agriculture under a changing climate. Here we report findings on the genetic basis of phenotypic plasticity for 23 complex traits using a diverse maize population planted at five sites with distinct environmental conditions. We found that latitude-related environmental factors were the main drivers of across-site variation in flowering time traits but not in plant architecture or yield traits. For the 23 traits, we detected 109 quantitative trait loci (QTLs), 29 for mean values, 66 for plasticity, and 14 for both parameters, and 80% of the QTLs interacted with latitude. The effects of several QTLs changed in magnitude or sign, driving variation in phenotypic plasticity. We experimentally validated one plastic gene, ZmTPS14.1, whose effect was likely mediated by the compensation effect of ZmSPL6 from a downstream pathway. By integrating genetic diversity, environmental variation, and their interaction into a joint model, we could provide site-specific predictions with increased accuracy by as much as 9.9%, 2.2%, and 2.6% for days to tassel, plant height, and ear weight, respectively. This study revealed a complex genetic architecture involving multiple alleles, pleiotropy, and genotype-by-environment interaction that underlies variation in the mean and plasticity of maize complex traits. It provides novel insights into the dynamic genetic architecture of agronomic traits in response to changing environments, paving a practical way toward precision agriculture.
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Affiliation(s)
- Minliang Jin
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Haijun Liu
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna BioCenter, 1030 Vienna, Austria
| | - Xiangguo Liu
- Institute of Agricultural Biotechnology, Jilin Academy of Agricultural Sciences, Changchun 130033, China
| | - Tingting Guo
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China; Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Jia Guo
- Institute of Agricultural Biotechnology, Jilin Academy of Agricultural Sciences, Changchun 130033, China
| | - Yuejia Yin
- Institute of Agricultural Biotechnology, Jilin Academy of Agricultural Sciences, Changchun 130033, China
| | - Yan Ji
- Key Laboratory of Tobacco Improvement and Biotechnology, Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao 266000, China
| | - Zhenxian Li
- Institute of Agricultural Sciences of Xishuangbanna Prefecture of Yunnan Province, Jinghong 666100, China
| | - Jinhong Zhang
- Institute of Agricultural Sciences of Xishuangbanna Prefecture of Yunnan Province, Jinghong 666100, China
| | - Xiaqing Wang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Feng Qiao
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Yingjie Xiao
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China; Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Yanjun Zan
- Umeå Plant Science Center, Department of Forestry Genetics and Plant Physiology, Swedish University of Agricultural Sciences, 90736 Umeå, Sweden; Key Laboratory of Tobacco Improvement and Biotechnology, Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao 266000, China.
| | - Jianbing Yan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China; Hubei Hongshan Laboratory, Wuhan 430070, China.
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Gajardo HA, Gómez-Espinoza O, Boscariol Ferreira P, Carrer H, Bravo LA. The Potential of CRISPR/Cas Technology to Enhance Crop Performance on Adverse Soil Conditions. PLANTS (BASEL, SWITZERLAND) 2023; 12:plants12091892. [PMID: 37176948 PMCID: PMC10181257 DOI: 10.3390/plants12091892] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 04/22/2023] [Accepted: 04/24/2023] [Indexed: 05/15/2023]
Abstract
Worldwide food security is under threat in the actual scenery of global climate change because the major staple food crops are not adapted to hostile climatic and soil conditions. Significant efforts have been performed to maintain the actual yield of crops, using traditional breeding and innovative molecular techniques to assist them. However, additional strategies are necessary to achieve the future food demand. Clustered regularly interspaced short palindromic repeat/CRISPR-associated protein (CRISPR/Cas) technology, as well as its variants, have emerged as alternatives to transgenic plant breeding. This novelty has helped to accelerate the necessary modifications in major crops to confront the impact of abiotic stress on agriculture systems. This review summarizes the current advances in CRISPR/Cas applications in crops to deal with the main hostile soil conditions, such as drought, flooding and waterlogging, salinity, heavy metals, and nutrient deficiencies. In addition, the potential of extremophytes as a reservoir of new molecular mechanisms for abiotic stress tolerance, as well as their orthologue identification and edition in crops, is shown. Moreover, the future challenges and prospects related to CRISPR/Cas technology issues, legal regulations, and customer acceptance will be discussed.
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Affiliation(s)
- Humberto A Gajardo
- Laboratorio de Fisiología y Biología Molecular Vegetal, Instituto de Agroindustria, Departamento de Ciencias Agronómicas y Recursos Naturales, Facultad de Ciencias Agropecuarias y Medioambiente & Center of Plant, Soil Interaction and Natural Resources Biotechnology, Scientific and Technological Bioresource Nucleus, Universidad de La Frontera, Temuco 1145, Chile
| | - Olman Gómez-Espinoza
- Laboratorio de Fisiología y Biología Molecular Vegetal, Instituto de Agroindustria, Departamento de Ciencias Agronómicas y Recursos Naturales, Facultad de Ciencias Agropecuarias y Medioambiente & Center of Plant, Soil Interaction and Natural Resources Biotechnology, Scientific and Technological Bioresource Nucleus, Universidad de La Frontera, Temuco 1145, Chile
- Centro de Investigación en Biotecnología, Escuela de Biología, Instituto Tecnológico de Costa Rica, Cartago 30101, Costa Rica
| | - Pedro Boscariol Ferreira
- Department of Biological Sciences, Luiz de Queiroz College of Agriculture (ESALQ), University of São Paulo, Piracicaba 13418-900, Brazil
| | - Helaine Carrer
- Department of Biological Sciences, Luiz de Queiroz College of Agriculture (ESALQ), University of São Paulo, Piracicaba 13418-900, Brazil
| | - León A Bravo
- Laboratorio de Fisiología y Biología Molecular Vegetal, Instituto de Agroindustria, Departamento de Ciencias Agronómicas y Recursos Naturales, Facultad de Ciencias Agropecuarias y Medioambiente & Center of Plant, Soil Interaction and Natural Resources Biotechnology, Scientific and Technological Bioresource Nucleus, Universidad de La Frontera, Temuco 1145, Chile
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He J, Zhang K, Yan S, Tang M, Zhou W, Yin Y, Chen K, Zhang C, Li M. Genome-scale targeted mutagenesis in Brassica napus using a pooled CRISPR library. Genome Res 2023; 33:798-809. [PMID: 37290935 PMCID: PMC10317123 DOI: 10.1101/gr.277650.123] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Accepted: 04/19/2023] [Indexed: 06/10/2023]
Abstract
The recently constructed mutant libraries of diploid crops by the CRISPR-Cas9 system have provided abundant resources for functional genomics and crop breeding. However, because of the genome complexity, it is a big challenge to accomplish large-scale targeted mutagenesis in polyploid plants. Here, we demonstrate the feasibility of using a pooled CRISPR library to achieve genome-scale targeted editing in an allotetraploid crop of Brassica napus A total of 18,414 sgRNAs were designed to target 10,480 genes of interest, and afterward, 1104 regenerated transgenic plants harboring 1088 sgRNAs were obtained. Editing interrogation results revealed that 93 of the 178 genes were identified as mutated, thus representing an editing efficiency of 52.2%. Furthermore, we have discovered that Cas9-mediated DNA cleavages tend to occur at all the target sites guided by the same individual sgRNA, a novel finding in polyploid plants. Finally, we show the strong capability of reverse genetic screening for various traits with the postgenotyped plants. Several genes, which might dominate the fatty acid profile and seed oil content and have yet to be reported, were unveiled from the forward genetic studies. Our research provides valuable resources for functional genomics, elite crop breeding, and a good reference for high-throughput targeted mutagenesis in other polyploid plants.
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Affiliation(s)
- Jianjie He
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Wuhan 430074, China
| | - Kai Zhang
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Wuhan 430074, China
| | - Shuxiang Yan
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Wuhan 430074, China
| | - Mi Tang
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Wuhan 430074, China
| | - Weixian Zhou
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Wuhan 430074, China
| | - Yongtai Yin
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Wuhan 430074, China
| | - Kang Chen
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Wuhan 430074, China
| | - Chunyu Zhang
- National Key Laboratory of Crop Genetic Improvement and College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Maoteng Li
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China;
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Wuhan 430074, China
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Ma C, Li R, Sun Y, Zhang M, Li S, Xu Y, Song J, Li J, Qi J, Wang L, Wu J. ZmMYC2s play important roles in maize responses to simulated herbivory and jasmonate. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2023; 65:1041-1058. [PMID: 36349965 DOI: 10.1111/jipb.13404] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Accepted: 11/07/2022] [Indexed: 06/16/2023]
Abstract
Both herbivory and jasmonic acid (JA) activate the biosynthesis of defensive metabolites in maize, but the mechanism underlying this remains unclear. We generated maize mutants in which ZmMYC2a and ZmMYC2b, two transcription factor genes important in JA signaling, were individually or both knocked out. Genetic and biochemical analyses were used to elucidate the functions of ZmMYC2 proteins in the maize response to simulated herbivory and JA. Compared with the wild-type (WT) maize, the double mutant myc2ab was highly susceptible to insects, and the levels of benzoxazinoids and volatile terpenes, and the levels of their biosynthesis gene transcripts, were much lower in the mutants than in the WT maize after simulated insect feeding or JA treatment. Moreover, ZmMYC2a and ZmMYC2b played a redundant role in maize resistance to insects and JA signaling. Transcriptome and Cleavage Under Targets and Tagmentation-Sequencing (CUT&Tag-Seq) analysis indicated that ZmMYC2s physically targeted 60% of the JA-responsive genes, even though only 33% of these genes were transcriptionally ZmMYC2-dependent. Importantly, CUT&Tag-Seq and dual luciferase assays revealed that ZmMYC2s transactivate the benzoxazinoid and volatile terpene biosynthesis genes IGPS1/3, BX10/11/12/14, and TPS10/2/3/4/5/8 by directly binding to their promoters. Furthermore, several transcription factors physically targeted by ZmMYC2s were identified, and these are likely to function in the regulation of benzoxazinoid biosynthesis. This work reveals the transcriptional regulatory landscapes of both JA signaling and ZmMYC2s in maize and provides comprehensive mechanistic insight into how JA signaling modulates defenses in maize responses to herbivory through ZmMYC2s.
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Affiliation(s)
- Canrong Ma
- Department of Economic Plants and Biotechnology, Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, the Chinese Academy of Sciences, Kunming, 650201, China
- Chinese Academy of Science Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Ruoyue Li
- Department of Economic Plants and Biotechnology, Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, the Chinese Academy of Sciences, Kunming, 650201, China
| | - Yan Sun
- Department of Economic Plants and Biotechnology, Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, the Chinese Academy of Sciences, Kunming, 650201, China
| | - Mou Zhang
- Department of Economic Plants and Biotechnology, Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, the Chinese Academy of Sciences, Kunming, 650201, China
| | - Sen Li
- Department of Economic Plants and Biotechnology, Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, the Chinese Academy of Sciences, Kunming, 650201, China
| | - Yuxing Xu
- Department of Economic Plants and Biotechnology, Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, the Chinese Academy of Sciences, Kunming, 650201, China
- Chinese Academy of Science Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Juan Song
- Department of Economic Plants and Biotechnology, Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, the Chinese Academy of Sciences, Kunming, 650201, China
- Chinese Academy of Science Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jing Li
- Department of Economic Plants and Biotechnology, Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, the Chinese Academy of Sciences, Kunming, 650201, China
- Chinese Academy of Science Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jinfeng Qi
- Department of Economic Plants and Biotechnology, Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, the Chinese Academy of Sciences, Kunming, 650201, China
- Chinese Academy of Science Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Lei Wang
- Department of Economic Plants and Biotechnology, Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, the Chinese Academy of Sciences, Kunming, 650201, China
- Chinese Academy of Science Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jianqiang Wu
- Department of Economic Plants and Biotechnology, Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, the Chinese Academy of Sciences, Kunming, 650201, China
- Chinese Academy of Science Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, 100049, China
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35
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Hu Y, Patra P, Pisanty O, Shafir A, Belew ZM, Binenbaum J, Ben Yaakov S, Shi B, Charrier L, Hyams G, Zhang Y, Trabulsky M, Caldararu O, Weiss D, Crocoll C, Avni A, Vernoux T, Geisler M, Nour-Eldin HH, Mayrose I, Shani E. Multi-Knock-a multi-targeted genome-scale CRISPR toolbox to overcome functional redundancy in plants. NATURE PLANTS 2023; 9:572-587. [PMID: 36973414 PMCID: PMC7615256 DOI: 10.1038/s41477-023-01374-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Accepted: 02/15/2023] [Indexed: 06/18/2023]
Abstract
Plant genomes are characterized by large and complex gene families that often result in similar and partially overlapping functions. This genetic redundancy severely hampers current efforts to uncover novel phenotypes, delaying basic genetic research and breeding programmes. Here we describe the development and validation of Multi-Knock, a genome-scale clustered regularly interspaced short palindromic repeat toolbox that overcomes functional redundancy in Arabidopsis by simultaneously targeting multiple gene-family members, thus identifying genetically hidden components. We computationally designed 59,129 optimal single-guide RNAs that each target two to ten genes within a family at once. Furthermore, partitioning the library into ten sublibraries directed towards a different functional group allows flexible and targeted genetic screens. From the 5,635 single-guide RNAs targeting the plant transportome, we generated over 3,500 independent Arabidopsis lines that allowed us to identify and characterize the first known cytokinin tonoplast-localized transporters in plants. With the ability to overcome functional redundancy in plants at the genome-scale level, the developed strategy can be readily deployed by scientists and breeders for basic research and to expedite breeding efforts.
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Affiliation(s)
- Yangjie Hu
- School of Plant Sciences and Food Security, Tel Aviv University, Tel Aviv, Israel
| | - Priyanka Patra
- School of Plant Sciences and Food Security, Tel Aviv University, Tel Aviv, Israel
- Laboratoire Reproduction et Développement des Plantes, Université de Lyon, ENS de Lyon, CNRS, INRAE, Lyon, France
| | - Odelia Pisanty
- School of Plant Sciences and Food Security, Tel Aviv University, Tel Aviv, Israel
| | - Anat Shafir
- School of Plant Sciences and Food Security, Tel Aviv University, Tel Aviv, Israel
| | - Zeinu Mussa Belew
- DynaMo Center, Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Jenia Binenbaum
- School of Plant Sciences and Food Security, Tel Aviv University, Tel Aviv, Israel
| | - Shir Ben Yaakov
- School of Plant Sciences and Food Security, Tel Aviv University, Tel Aviv, Israel
| | - Bihai Shi
- Laboratoire Reproduction et Développement des Plantes, Université de Lyon, ENS de Lyon, CNRS, INRAE, Lyon, France
| | - Laurence Charrier
- Department of Biology, University of Fribourg, Fribourg, Switzerland
| | - Gal Hyams
- School of Plant Sciences and Food Security, Tel Aviv University, Tel Aviv, Israel
| | - Yuqin Zhang
- School of Plant Sciences and Food Security, Tel Aviv University, Tel Aviv, Israel
| | - Maor Trabulsky
- School of Plant Sciences and Food Security, Tel Aviv University, Tel Aviv, Israel
| | - Omer Caldararu
- School of Plant Sciences and Food Security, Tel Aviv University, Tel Aviv, Israel
| | - Daniela Weiss
- School of Plant Sciences and Food Security, Tel Aviv University, Tel Aviv, Israel
| | - Christoph Crocoll
- DynaMo Center, Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Adi Avni
- School of Plant Sciences and Food Security, Tel Aviv University, Tel Aviv, Israel
| | - Teva Vernoux
- Laboratoire Reproduction et Développement des Plantes, Université de Lyon, ENS de Lyon, CNRS, INRAE, Lyon, France
| | - Markus Geisler
- Department of Biology, University of Fribourg, Fribourg, Switzerland
| | - Hussam Hassan Nour-Eldin
- DynaMo Center, Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Itay Mayrose
- School of Plant Sciences and Food Security, Tel Aviv University, Tel Aviv, Israel.
| | - Eilon Shani
- School of Plant Sciences and Food Security, Tel Aviv University, Tel Aviv, Israel.
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36
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Zhang H, Yu F, Xie P, Sun S, Qiao X, Tang S, Chen C, Yang S, Mei C, Yang D, Wu Y, Xia R, Li X, Lu J, Liu Y, Xie X, Ma D, Xu X, Liang Z, Feng Z, Huang X, Yu H, Liu G, Wang Y, Li J, Zhang Q, Chen C, Ouyang Y, Xie Q. A Gγ protein regulates alkaline sensitivity in crops. Science 2023; 379:eade8416. [PMID: 36952416 DOI: 10.1126/science.ade8416] [Citation(s) in RCA: 60] [Impact Index Per Article: 60.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/25/2023]
Abstract
The use of alkaline salt lands for crop production is hindered by a scarcity of knowledge and breeding efforts for plant alkaline tolerance. Through genome association analysis of sorghum, a naturally high-alkaline-tolerant crop, we detected a major locus, Alkaline Tolerance 1 (AT1), specifically related to alkaline-salinity sensitivity. An at1 allele with a carboxyl-terminal truncation increased sensitivity, whereas knockout of AT1 increased tolerance to alkalinity in sorghum, millet, rice, and maize. AT1 encodes an atypical G protein γ subunit that affects the phosphorylation of aquaporins to modulate the distribution of hydrogen peroxide (H2O2). These processes appear to protect plants against oxidative stress by alkali. Designing knockouts of AT1 homologs or selecting its natural nonfunctional alleles could improve crop productivity in sodic lands.
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Affiliation(s)
- Huili Zhang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China
- Breeding Base of State Key Laboratory of Land Degradation and Ecological Restoration of North Western China, School of Agriculture, Ningxia University, Yinchuan 750021, China
| | - Feifei Yu
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China
- College of Grassland Science and Technology, China Agricultural University, Beijing 100083, China
| | - Peng Xie
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Shengyuan Sun
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
- Jiangsu Key Laboratory of Crop Genetics and Physiology and Co-Innovation Center for Modern Production Technology of Grain Crops, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou University, Yangzhou 225009, China
| | - Xinhua Qiao
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Sanyuan Tang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Chengxuan Chen
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Sen Yang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Cuo Mei
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Dekai Yang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yaorong Wu
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Ran Xia
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Xu Li
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Jun Lu
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Yuxi Liu
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Xiaowei Xie
- Breeding Base of State Key Laboratory of Land Degradation and Ecological Restoration of North Western China, School of Agriculture, Ningxia University, Yinchuan 750021, China
| | - Dongmei Ma
- Breeding Base of State Key Laboratory of Land Degradation and Ecological Restoration of North Western China, School of Agriculture, Ningxia University, Yinchuan 750021, China
| | - Xing Xu
- Breeding Base of State Key Laboratory of Land Degradation and Ecological Restoration of North Western China, School of Agriculture, Ningxia University, Yinchuan 750021, China
| | - Zhengwei Liang
- Northeast Institute of Geography and Agroecology, Daan National Station for Agro-ecosystem Observation and Research, Chinese Academy of Sciences, Changchun 130102, China
| | - Zhonghui Feng
- University of Chinese Academy of Sciences, Beijing 100049, China
- Northeast Institute of Geography and Agroecology, Daan National Station for Agro-ecosystem Observation and Research, Chinese Academy of Sciences, Changchun 130102, China
| | - Xiahe Huang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Hong Yu
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Guifu Liu
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Yingchun Wang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jiayang Li
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qifa Zhang
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Chang Chen
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yidan Ouyang
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Qi Xie
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- National Center of Technology Innovation for Maize, State Key Laboratory of Maize Germplasm Innovation and Molecular Breeding, Syngenta Group China, Beijing 102206, China
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37
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Tian Y, Zhong D, Li X, Shen R, Han H, Dai Y, Yao Q, Zhang X, Deng Q, Cao X, Zhu JK, Lu Y. High-throughput genome editing in rice with a virus-based surrogate system. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2023; 65:646-655. [PMID: 36218268 DOI: 10.1111/jipb.13381] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Accepted: 10/10/2022] [Indexed: 06/16/2023]
Abstract
With the widespread use of clustered regularly interspaced palindromic repeats (CRISPR)/CRISPR-associated nuclease (Cas) technologies in plants, large-scale genome editing is increasingly needed. Here, we developed a geminivirus-mediated surrogate system, called Wheat Dwarf Virus-Gate (WDV-surrogate), to facilitate high-throughput genome editing. WDV-Gate has two parts: one is the recipient callus from a transgenic rice line expressing Cas9 and a mutated hygromycin-resistant gene (HygM) for surrogate selection; the other is a WDV-based construct expressing two single guide RNAs (sgRNAs) targeting HygM and a gene of interest, respectively. We evaluated WDV-Gate on six rice loci by producing a total of 874 T0 plants. Compared with the conventional method, the WDV-Gate system, which was characterized by a transient and high level of sgRNA expression, significantly increased editing frequency (66.8% vs. 90.1%), plantlet regeneration efficiency (2.31-fold increase), and numbers of homozygous-edited plants (36.3% vs. 70.7%). Large-scale editing using pooled sgRNAs targeting the SLR1 gene resulted in a high editing frequency of 94.4%, further demonstrating its feasibility. We also tested WDV-Gate on sequence knock-in for protein tagging. By co-delivering a chemically modified donor DNA with the WDV-Gate plasmid, 3xFLAG peptides were successfully fused to three loci with an efficiency of up to 13%. Thus, by combining transiently expressed sgRNAs and a surrogate selection system, WDV-Gate could be useful for high-throughput gene knock-out and sequence knock-in.
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Affiliation(s)
- Yifu Tian
- Shanghai Center for Plant Stress Biology, Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 201602, China
- Center for Advanced Bioindustry Technologies, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- Hainan Yazhou Bay Seed Lab, Sanya, 572024, China
| | - Dating Zhong
- Shanghai Center for Plant Stress Biology, Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 201602, China
- 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
| | - Xinbo Li
- Shanghai Center for Plant Stress Biology, Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 201602, China
- Center for Advanced Bioindustry Technologies, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- Hainan Yazhou Bay Seed Lab, Sanya, 572024, China
| | - Rundong Shen
- Shanghai Center for Plant Stress Biology, Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 201602, China
- Center for Advanced Bioindustry Technologies, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- Hainan Yazhou Bay Seed Lab, Sanya, 572024, China
| | - Han Han
- 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
| | - Yuqin Dai
- Shanghai Center for Plant Stress Biology, Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 201602, China
| | - Qi Yao
- Shanghai Center for Plant Stress Biology, Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 201602, China
- 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 Center for Plant Stress Biology, Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 201602, China
- 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 Deng
- Center for Advanced Bioindustry Technologies, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Xuesong Cao
- Shanghai Center for Plant Stress Biology, Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 201602, China
| | - Jian-Kang Zhu
- Shanghai Center for Plant Stress Biology, Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 201602, China
- Center for Advanced Bioindustry Technologies, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- Hainan Yazhou Bay Seed Lab, Sanya, 572024, China
- Institute of Advanced Biotechnology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Yuming Lu
- Shanghai Center for Plant Stress Biology, Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 201602, China
- 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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38
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Chen G, Xiao Y, Dai S, Dai Z, Wang X, Li B, Jaqueth JS, Li W, Lai Z, Ding J, Yan J. Genetic basis of resistance to southern corn leaf blight in the maize multi-parent population and diversity panel. PLANT BIOTECHNOLOGY JOURNAL 2023; 21:506-520. [PMID: 36383026 PMCID: PMC9946143 DOI: 10.1111/pbi.13967] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Revised: 11/09/2022] [Accepted: 11/11/2022] [Indexed: 06/16/2023]
Abstract
Southern corn leaf blight (SLB), caused by the necrotrophic pathogen Cochliobolus heterostrophus, is one of the maize foliar diseases and poses a great threat to corn production around the world. Identification of genetic variations underlying resistance to SLB is of paramount importance to maize yield and quality. Here, we used a random-open-parent association mapping population containing eight recombinant inbred line populations and one association mapping panel consisting of 513 diversity maize inbred lines with high-density genetic markers to dissect the genetic basis of SLB resistance. Overall, 109 quantitative trait loci (QTLs) with predominantly small or moderate additive effects, and little epistatic effects were identified. We found 35 (32.1%) novel loci in comparison with the reported QTLs. We revealed that resistant alleles were significantly enriched in tropical accessions and the frequency of about half of resistant alleles decreased during the adaptation process owing to the selection of agronomic traits. A large number of annotated genes located in the SLB-resistant QTLs were shown to be involved in plant defence pathways. Integrating genome-wide association study, transcriptomic profiling, resequencing and gene editing, we identified ZmFUT1 and MYBR92 as the putative genes responsible for the major QTLs for resistance to C. heterostrophus. Our results present a comprehensive insight into the genetic basis of SLB resistance and provide resistant loci or genes as direct targets for crop genetic improvement.
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Affiliation(s)
- Gengshen Chen
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanChina
| | - Yingjie Xiao
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanChina
- Hubei Hongshan LaboratoryWuhanChina
| | - Sha Dai
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanChina
| | - Zhikang Dai
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanChina
| | - Xiaoming Wang
- Institute of Crop ScienceChinese Academy of Agricultural SciencesBeijingChina
| | | | | | - Wenqiang Li
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanChina
| | - Zhibing Lai
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanChina
| | - Junqiang Ding
- College of AgronomyHenan Agricultural UniversityZhengzhouChina
- The State Key Laboratory of Wheat and Maize Crop Science and Center for Crop Genome EngineeringHenan Agricultural UniversityZhengzhouChina
| | - Jianbing Yan
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanChina
- Hubei Hongshan LaboratoryWuhanChina
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39
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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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40
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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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41
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Ma Z, Ma L, Zhou J. Applications of CRISPR/Cas genome editing in economically important fruit crops: recent advances and future directions. MOLECULAR HORTICULTURE 2023; 3:1. [PMID: 37789479 PMCID: PMC10515014 DOI: 10.1186/s43897-023-00049-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Accepted: 01/10/2023] [Indexed: 10/05/2023]
Abstract
Fruit crops, consist of climacteric and non-climacteric fruits, are the major sources of nutrients and fiber for human diet. Since 2013, CRISPR/Cas (Clustered Regularly Interspersed Short Palindromic Repeats and CRISPR-Associated Protein) genome editing system has been widely employed in different plants, leading to unprecedented progress in the genetic improvement of many agronomically important fruit crops. Here, we summarize latest advancements in CRISPR/Cas genome editing of fruit crops, including efforts to decipher the mechanisms behind plant development and plant immunity, We also highlight the potential challenges and improvements in the application of genome editing tools to fruit crops, including optimizing the expression of CRISPR/Cas cassette, improving the delivery efficiency of CRISPR/Cas reagents, increasing the specificity of genome editing, and optimizing the transformation and regeneration system. In addition, we propose the perspectives on the application of genome editing in crop breeding especially in fruit crops and highlight the potential challenges. It is worth noting that efforts to manipulate fruit crops with genome editing systems are urgently needed for fruit crops breeding and demonstration.
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Affiliation(s)
- Zhimin Ma
- Peking University Institute of Advanced Agricultural Sciences, Weifang, 261000, Shandong, China
| | - Lijing Ma
- Peking University Institute of Advanced Agricultural Sciences, Weifang, 261000, Shandong, China
| | - Junhui Zhou
- Peking University Institute of Advanced Agricultural Sciences, Weifang, 261000, Shandong, China.
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42
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Chao Z, Chen Y, Ji C, Wang Y, Huang X, Zhang C, Yang J, Song T, Wu J, Guo L, Liu C, Han M, Wu Y, Yan J, Chao D. A genome-wide association study identifies a transporter for zinc uploading to maize kernels. EMBO Rep 2023; 24:e55542. [PMID: 36394374 PMCID: PMC9827554 DOI: 10.15252/embr.202255542] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Revised: 10/09/2022] [Accepted: 10/17/2022] [Indexed: 11/18/2022] Open
Abstract
The Zn content in cereal seeds is an important trait for crop production as well as for human health. However, little is known about how Zn is loaded to plant seeds. Here, through a genome-wide association study (GWAS), we identify the Zn-NA (nicotianamine) transporter gene ZmYSL2 that is responsible for loading Zn to maize kernels. High promoter sequence variation in ZmYSL2 most likely drives the natural variation in Zn concentrations in maize kernels. ZmYSL2 is specifically localized on the plasma membrane facing the maternal tissue of the basal endosperm transfer cell layer (BETL) and functions in loading Zn-NA into the BETL. Overexpression of ZmYSL2 increases the Zn concentration in the kernels by 31.6%, which achieves the goal of Zn biofortification of maize. These findings resolve the mystery underlying the loading of Zn into plant seeds, providing an efficient strategy for breeding or engineering maize varieties with enriched Zn nutrition.
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Affiliation(s)
- Zhen‐Fei Chao
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and EcologyChinese Academy of SciencesShanghaiChina
- University of Chinese Academy of SciencesBeijingChina
| | - Yuan‐Yuan Chen
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanChina
| | - Chen Ji
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and EcologyChinese Academy of SciencesShanghaiChina
- University of Chinese Academy of SciencesBeijingChina
| | - Ya‐Ling Wang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and EcologyChinese Academy of SciencesShanghaiChina
| | - Xing Huang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and EcologyChinese Academy of SciencesShanghaiChina
- University of Chinese Academy of SciencesBeijingChina
| | - Chu‐Ying Zhang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and EcologyChinese Academy of SciencesShanghaiChina
- School of Life Science, Henan UniversityKaifengChina
| | - Jun Yang
- National Engineering Laboratory of Crop Stress Resistance, School of Life ScienceAnhui Agricultural UniversityHefeiChina
| | - Tao Song
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and EcologyChinese Academy of SciencesShanghaiChina
- University of Chinese Academy of SciencesBeijingChina
| | - Jia‐Chen Wu
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and EcologyChinese Academy of SciencesShanghaiChina
- University of Chinese Academy of SciencesBeijingChina
| | - Liang‐Xing Guo
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and EcologyChinese Academy of SciencesShanghaiChina
- University of Chinese Academy of SciencesBeijingChina
| | - Chu‐Bin Liu
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and EcologyChinese Academy of SciencesShanghaiChina
- University of Chinese Academy of SciencesBeijingChina
| | - Mei‐Ling Han
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and EcologyChinese Academy of SciencesShanghaiChina
| | - Yong‐Rui Wu
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and EcologyChinese Academy of SciencesShanghaiChina
| | - Jianbing Yan
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanChina
| | - Dai‐Yin Chao
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and EcologyChinese Academy of SciencesShanghaiChina
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43
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High-Throughput Base Editing-Mediated Artificial Evolution Streamlines Trait Gene Identification in Rice. Methods Mol Biol 2023; 2606:191-202. [PMID: 36592317 DOI: 10.1007/978-1-0716-2879-9_15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Base Editing-Mediated Gene Evolution (BEMGE) method develops novel rice germplasms with mutations in any endogenous gene through employing both Cas9n-based cytosine and adenine base editors combined with an sgRNA library tiling the full-length coding region, for obtaining unknown functional SNPs. Here we describe the process of artificial evolution of OsALS1 in rice cells using BEMGE through Agrobacterium-mediated transformation. BEMGE method has the potential to generate numerous nucleotide changes to screen pivotal amino acids (AAs) and to accelerate crop improvement.
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44
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Lorenzo CD, Debray K, Herwegh D, Develtere W, Impens L, Schaumont D, Vandeputte W, Aesaert S, Coussens G, De Boe Y, Demuynck K, Van Hautegem T, Pauwels L, Jacobs TB, Ruttink T, Nelissen H, Inzé D. BREEDIT: a multiplex genome editing strategy to improve complex quantitative traits in maize. THE PLANT CELL 2023; 35:218-238. [PMID: 36066192 PMCID: PMC9806654 DOI: 10.1093/plcell/koac243] [Citation(s) in RCA: 22] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Accepted: 07/30/2022] [Indexed: 05/04/2023]
Abstract
Ensuring food security for an ever-growing global population while adapting to climate change is the main challenge for agriculture in the 21st century. Although new technologies are being applied to tackle this problem, we are approaching a plateau in crop improvement using conventional breeding. Recent advances in CRISPR/Cas9-mediated gene engineering have paved the way to accelerate plant breeding to meet this increasing demand. However, many traits are governed by multiple small-effect genes operating in complex interactive networks. Here, we present the gene discovery pipeline BREEDIT, which combines multiplex genome editing of whole gene families with crossing schemes to improve complex traits such as yield and drought tolerance. We induced gene knockouts in 48 growth-related genes into maize (Zea mays) using CRISPR/Cas9 and generated a collection of over 1,000 gene-edited plants. The edited populations displayed (on average) 5%-10% increases in leaf length and up to 20% increases in leaf width compared with the controls. For each gene family, edits in subsets of genes could be associated with enhanced traits, allowing us to reduce the gene space to be considered for trait improvement. BREEDIT could be rapidly applied to generate a diverse collection of mutants to identify promising gene modifications for later use in breeding programs.
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Affiliation(s)
| | | | - Denia Herwegh
- Center for Plant Systems Biology, VIB, B-9052 Gent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Gent, Belgium
| | - Ward Develtere
- Center for Plant Systems Biology, VIB, B-9052 Gent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Gent, Belgium
| | - Lennert Impens
- Center for Plant Systems Biology, VIB, B-9052 Gent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Gent, Belgium
| | - Dries Schaumont
- Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), B-9820 Merelbeke, Belgium
| | - Wout Vandeputte
- Center for Plant Systems Biology, VIB, B-9052 Gent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Gent, Belgium
| | - Stijn Aesaert
- Center for Plant Systems Biology, VIB, B-9052 Gent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Gent, Belgium
| | - Griet Coussens
- Center for Plant Systems Biology, VIB, B-9052 Gent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Gent, Belgium
| | - Yara De Boe
- Center for Plant Systems Biology, VIB, B-9052 Gent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Gent, Belgium
| | - Kirin Demuynck
- Center for Plant Systems Biology, VIB, B-9052 Gent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Gent, Belgium
| | - Tom Van Hautegem
- Center for Plant Systems Biology, VIB, B-9052 Gent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Gent, Belgium
| | - Laurens Pauwels
- Center for Plant Systems Biology, VIB, B-9052 Gent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Gent, Belgium
| | - Thomas B Jacobs
- Center for Plant Systems Biology, VIB, B-9052 Gent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Gent, Belgium
| | - Tom Ruttink
- Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), B-9820 Merelbeke, Belgium
| | - Hilde Nelissen
- Center for Plant Systems Biology, VIB, B-9052 Gent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Gent, Belgium
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45
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Han L, Zhong W, Qian J, Jin M, Tian P, Zhu W, Zhang H, Sun Y, Feng JW, Liu X, Chen G, Farid B, Li R, Xiong Z, Tian Z, Li J, Luo Z, Du D, Chen S, Jin Q, Li J, Li Z, Liang Y, Jin X, Peng Y, Zheng C, Ye X, Yin Y, Chen H, Li W, Chen LL, Li Q, Yan J, Yang F, Li L. A multi-omics integrative network map of maize. Nat Genet 2023; 55:144-153. [PMID: 36581701 DOI: 10.1038/s41588-022-01262-1] [Citation(s) in RCA: 22] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Accepted: 11/03/2022] [Indexed: 12/31/2022]
Abstract
Networks are powerful tools to uncover functional roles of genes in phenotypic variation at a system-wide scale. Here, we constructed a maize network map that contains the genomic, transcriptomic, translatomic and proteomic networks across maize development. This map comprises over 2.8 million edges in more than 1,400 functional subnetworks, demonstrating an extensive network divergence of duplicated genes. We applied this map to identify factors regulating flowering time and identified 2,651 genes enriched in eight subnetworks. We validated the functions of 20 genes, including 18 with previously unknown connections to flowering time in maize. Furthermore, we uncovered a flowering pathway involving histone modification. The multi-omics integrative network map illustrates the principles of how molecular networks connect different types of genes and potential pathways to map a genome-wide functional landscape in maize, which should be applicable in a wide range of species.
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Affiliation(s)
- Linqian Han
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China.,Hubei Hongshan Laboratory, Wuhan, China
| | - Wanshun Zhong
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China.,Hubei Hongshan Laboratory, Wuhan, China
| | - Jia Qian
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China.,Hubei Hongshan Laboratory, Wuhan, China
| | - Minliang Jin
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China.,Hubei Hongshan Laboratory, Wuhan, China
| | - Peng Tian
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China.,Hubei Hongshan Laboratory, Wuhan, China
| | - Wanchao Zhu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China.,Hubei Hongshan Laboratory, Wuhan, China
| | - Hongwei Zhang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yonghao Sun
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China.,Hubei Hongshan Laboratory, Wuhan, China
| | - Jia-Wu Feng
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Xiangguo Liu
- Institute of Agricultural Biotechnology, Jilin Academy of Agricultural Sciences, Changchun, China
| | - Guo Chen
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China.,Institute of Nuclear and Biological Technology, Xinjiang Academy of Agricultural Sciences, Urumqi, China
| | - Babar Farid
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China.,Institute of Plant Breeding and Biotechnology, Muhammad Nawaz Shareef University of Agriculture Multan, Multan, Pakistan
| | - Ruonan Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Zimo Xiong
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Zhihui Tian
- College of Science, Huazhong Agricultural University, Wuhan, China
| | - Juan Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China.,Hubei Hongshan Laboratory, Wuhan, China
| | - Zi Luo
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China.,Hubei Hongshan Laboratory, Wuhan, China
| | - Dengxiang Du
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Sijia Chen
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Qixiao Jin
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China.,Hubei Hongshan Laboratory, Wuhan, China
| | - Jiaxin Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Zhao Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China.,Hubei Hongshan Laboratory, Wuhan, China
| | - Yan Liang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Xiaomeng Jin
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Yong Peng
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Chang Zheng
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Xinnan Ye
- Institute of Agricultural Biotechnology, Jilin Academy of Agricultural Sciences, Changchun, China
| | - Yuejia Yin
- Institute of Agricultural Biotechnology, Jilin Academy of Agricultural Sciences, Changchun, China
| | - Hong Chen
- College of Science, Huazhong Agricultural University, Wuhan, China
| | - Weifu Li
- College of Science, Huazhong Agricultural University, Wuhan, China
| | - Ling-Ling Chen
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Qing Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China.,Hubei Hongshan Laboratory, Wuhan, China
| | - Jianbing Yan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China. .,Hubei Hongshan Laboratory, Wuhan, China.
| | - Fang Yang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China. .,Hubei Hongshan Laboratory, Wuhan, China.
| | - Lin Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China. .,Hubei Hongshan Laboratory, Wuhan, China.
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46
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Sun X, Xiang Y, Dou N, Zhang H, Pei S, Franco AV, Menon M, Monier B, Ferebee T, Liu T, Liu S, Gao Y, Wang J, Terzaghi W, Yan J, Hearne S, Li L, Li F, Dai M. The role of transposon inverted repeats in balancing drought tolerance and yield-related traits in maize. Nat Biotechnol 2023; 41:120-127. [PMID: 36229611 DOI: 10.1038/s41587-022-01470-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Accepted: 07/02/2022] [Indexed: 01/21/2023]
Abstract
The genomic basis underlying the selection for environmental adaptation and yield-related traits in maize remains poorly understood. Here we carried out genome-wide profiling of the small RNA (sRNA) transcriptome (sRNAome) and transcriptome landscapes of a global maize diversity panel under dry and wet conditions and uncover dozens of environment-specific regulatory hotspots. Transgenic and molecular studies of Drought-Related Environment-specific Super eQTL Hotspot on chromosome 8 (DRESH8) and ZmMYBR38, a target of DRESH8-derived small interfering RNAs, revealed a transposable element-mediated inverted repeats (TE-IR)-derived sRNA- and gene-regulatory network that balances plant drought tolerance with yield-related traits. A genome-wide scan revealed that TE-IRs associate with drought response and yield-related traits that were positively selected and expanded during maize domestication. These results indicate that TE-IR-mediated posttranscriptional regulation is a key molecular mechanism underlying the tradeoff between crop environmental adaptation and yield-related traits, providing potential genomic targets for the breeding of crops with greater stress tolerance but uncompromised yield.
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Affiliation(s)
- Xiaopeng Sun
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
| | - Yanli Xiang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Nannan Dou
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
| | - Hui Zhang
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan, China
| | - Surui Pei
- Annoroad Gene Tech (Beijing) Co., Ltd, Beijing, China
| | - Arcadio Valdes Franco
- School of Integrative Plant Sciences, Section of Plant Breeding and Genetics, Cornell University, Ithaca, NY, USA
| | - Mitra Menon
- Department of Evolution and Ecology, Center for Population Biology, and Genome Center, University of California, Davis, Davis, CA, USA
| | - Brandon Monier
- School of Integrative Plant Sciences, Section of Plant Breeding and Genetics, Cornell University, Ithaca, NY, USA
| | - Taylor Ferebee
- School of Integrative Plant Sciences, Section of Plant Breeding and Genetics, Cornell University, Ithaca, NY, USA
| | - Tao Liu
- Annoroad Gene Tech (Beijing) Co., Ltd, Beijing, China
| | - Sanyang Liu
- Annoroad Gene Tech (Beijing) Co., Ltd, Beijing, China
| | - Yuchi Gao
- Annoroad Gene Tech (Beijing) Co., Ltd, Beijing, China
| | - Jubin Wang
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan, China
| | | | - Jianbing Yan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
| | - Sarah Hearne
- CIMMYT, KM 45 Carretera Mexico-Veracruz, El Batan, Texcoco, Mexico
| | - Lin Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China.
- Hubei Hongshan Laboratory, Wuhan, China.
| | - Feng Li
- Hubei Hongshan Laboratory, Wuhan, China.
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan, China.
| | - Mingqiu Dai
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China.
- Hubei Hongshan Laboratory, Wuhan, China.
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47
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Wang Y, Tang Q, Pu L, Zhang H, Li X. CRISPR-Cas technology opens a new era for the creation of novel maize germplasms. FRONTIERS IN PLANT SCIENCE 2022; 13:1049803. [PMID: 36589095 PMCID: PMC9800880 DOI: 10.3389/fpls.2022.1049803] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Accepted: 11/25/2022] [Indexed: 06/17/2023]
Abstract
Maize (Zea mays) is one of the most important food crops in the world with the greatest global production, and contributes to satiating the demands for human food, animal feed, and biofuels. With population growth and deteriorating environment, efficient and innovative breeding strategies to develop maize varieties with high yield and stress resistance are urgently needed to augment global food security and sustainable agriculture. CRISPR-Cas-mediated genome-editing technology (clustered regularly interspaced short palindromic repeats (CRISPR)-Cas (CRISPR-associated)) has emerged as an effective and powerful tool for plant science and crop improvement, and is likely to accelerate crop breeding in ways dissimilar to crossbreeding and transgenic technologies. In this review, we summarize the current applications and prospects of CRISPR-Cas technology in maize gene-function studies and the generation of new germplasm for increased yield, specialty corns, plant architecture, stress response, haploid induction, and male sterility. Optimization of gene editing and genetic transformation systems for maize is also briefly reviewed. Lastly, the challenges and new opportunities that arise with the use of the CRISPR-Cas technology for maize genetic improvement are discussed.
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Affiliation(s)
- Youhua Wang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Qiaoling Tang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Li Pu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Haiwen Zhang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xinhai Li
- Institute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing, China
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48
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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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49
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Luo G, Najafi J, Correia PMP, Trinh MDL, Chapman EA, Østerberg JT, Thomsen HC, Pedas PR, Larson S, Gao C, Poland J, Knudsen S, DeHaan L, Palmgren M. Accelerated Domestication of New Crops: Yield is Key. PLANT & CELL PHYSIOLOGY 2022; 63:1624-1640. [PMID: 35583202 PMCID: PMC9680862 DOI: 10.1093/pcp/pcac065] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Revised: 04/17/2022] [Accepted: 05/17/2022] [Indexed: 05/05/2023]
Abstract
Sustainable agriculture in the future will depend on crops that are tolerant to biotic and abiotic stresses, require minimal input of water and nutrients and can be cultivated with a minimal carbon footprint. Wild plants that fulfill these requirements abound in nature but are typically low yielding. Thus, replacing current high-yielding crops with less productive but resilient species will require the intractable trade-off of increasing land area under cultivation to produce the same yield. Cultivating more land reduces natural resources, reduces biodiversity and increases our carbon footprint. Sustainable intensification can be achieved by increasing the yield of underutilized or wild plant species that are already resilient, but achieving this goal by conventional breeding programs may be a long-term prospect. De novo domestication of orphan or crop wild relatives using mutagenesis is an alternative and fast approach to achieve resilient crops with high yields. With new precise molecular techniques, it should be possible to reach economically sustainable yields in a much shorter period of time than ever before in the history of agriculture.
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Affiliation(s)
| | | | | | | | | | | | | | - Pai Rosager Pedas
- Carlsberg Research Laboratory, J.C. Jacobsens Gade 4, Copenhagen V DK-1799, Denmark
| | - Steve Larson
- US Department of Agriculture (USDA), USDA–ARS Forage & Range Research Lab, Utah State University Logan, Logan, UT 84322, USA
| | - Caixia Gao
- Center for Genome Editing, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Jesse Poland
- Center for Desert Agriculture, King Abdullah University of Science and Technology, Thuwal, Makkah 23955, Saudi Arabia
| | - Søren Knudsen
- Carlsberg Research Laboratory, J.C. Jacobsens Gade 4, Copenhagen V DK-1799, Denmark
| | - Lee DeHaan
- The Land Institute, Salina, KS 67401, USA
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50
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Jian L, Yan J, Liu J. De Novo Domestication in the Multi-Omics Era. PLANT & CELL PHYSIOLOGY 2022; 63:1592-1606. [PMID: 35762778 DOI: 10.1093/pcp/pcac077] [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: 01/14/2022] [Accepted: 06/27/2022] [Indexed: 06/15/2023]
Abstract
Most cereal crops were domesticated within the last 12,000 years and subsequently spread around the world. These crops have been nourishing the world by supplying a primary energy and nutrient source, thereby playing a critical role in determining the status of human health and sustaining the global population. Here, we review the major challenges of future agriculture and emphasize the utilization of wild germplasm. De novo domestication is one of the most straightforward strategies to manipulate domestication-related and/or other genes with known function, and thereby introduce desired traits into wild plants. We also summarize known causal variations and their corresponding pathways in order to better understand the genetic basis of crop evolution, and how this knowledge could facilitate de novo domestication. Indeed knowledge-driven de novo domestication has great potential for the development of new sustainable crops that have climate-resilient high yield with low resource input and meet individual nutrient needs. Finally, we discuss current opportunities for and barriers to knowledge-driven de novo domestication.
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Affiliation(s)
- Liumei Jian
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Jianbing Yan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
- Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Jie Liu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
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