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Kim JS, Chae S, Jo JE, Kim KD, Song SI, Park SH, Choi SB, Jun KM, Shim SH, Jeon JS, Lee GS, Kim YK. OsMYB14, an R2R3-MYB transcription factor, regulates plant height through the control of hormone metabolism in rice. Mol Cells 2024; 47:100093. [PMID: 39004308 PMCID: PMC11342784 DOI: 10.1016/j.mocell.2024.100093] [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: 05/20/2024] [Revised: 06/26/2024] [Accepted: 07/09/2024] [Indexed: 07/16/2024] Open
Abstract
Plant growth must be regulated throughout the plant life cycle. The myeloblastosis (MYB) transcription factor (TF) family is one of the largest TF families and is involved in metabolism, lignin biosynthesis, and developmental processes. Here, we showed that OsMYB14, a rice R2R3-MYB TF, was expressed in leaves and roots, especially in rice culm and panicles, and that it localized to the nucleus. Overexpression of OsMYB14 (OsMYB14-ox) in rice resulted in a 30% reduction in plant height compared to that of the wild type (WT), while the height of the osmyb14-knockout (osmyb14-ko) mutant generated using the CRISPR/Cas9 system was not significantly different. Microscopic observations of the first internode revealed that the cell size did not differ significantly among the lines. RNA sequencing analysis revealed that genes associated with plant development, regulation, lipid metabolism, carbohydrate metabolism, and gibberellin (GA) and auxin metabolic processes were downregulated in the OsMYB14-ox line. Hormone quantitation revealed that inactive GA19 accumulated in OsMYB14-ox but not in the WT or knockout plants, suggesting that GA20 generation was repressed. Indole-3-acetic acid (IAA) and IAA-aspartate accumulated in OsMYB14-ox and osmyb14-ko, respectively. Indeed, real-time PCR analysis revealed that the expression of OsGA20ox1, encoding GA20 oxidase 1, and OsGH3-2, encoding IAA-amido synthetase, was downregulated in OsMYB14-ox and upregulated in osmyb14-ko. A protein-binding microarray revealed the presence of a consensus DNA-binding sequence, the ACCTACC-like motif, in the promoters of the OsGA20ox1 and GA20ox2 genes. These results suggest that OsMYB14 may act as a negative regulator of biological processes affecting plant height in rice by regulating GA biosynthesis and auxin metabolism.
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Affiliation(s)
- Joung Sug Kim
- Department of Biosciences and Bioinformatics, Myongji University, Yongin, Gyeonggi-do 17058, Republic of Korea
| | - Songhwa Chae
- Department of Biosciences and Bioinformatics, Myongji University, Yongin, Gyeonggi-do 17058, Republic of Korea
| | - Jae Eun Jo
- Department of Biosciences and Bioinformatics, Myongji University, Yongin, Gyeonggi-do 17058, Republic of Korea
| | - Kyung Do Kim
- Department of Biosciences and Bioinformatics, Myongji University, Yongin, Gyeonggi-do 17058, Republic of Korea
| | - Sang-Ik Song
- Department of Biosciences and Bioinformatics, Myongji University, Yongin, Gyeonggi-do 17058, Republic of Korea
| | - Su Hyun Park
- Department of Biosciences and Bioinformatics, Myongji University, Yongin, Gyeonggi-do 17058, Republic of Korea
| | - Sang-Bong Choi
- Department of Biosciences and Bioinformatics, Myongji University, Yongin, Gyeonggi-do 17058, Republic of Korea
| | - Kyong Mi Jun
- Genomics Genetics Institute, GreenGene Biotech Inc, Yongin, Gyeonggi-do 17058, Republic of Korea
| | - Su-Hyeon Shim
- Graduate School of Green-Bio Science and Crop Biotech Institute, Kyung Hee University, Yongin, Gyeonggi-do 17104, Republic of Korea
| | - Jong-Seong Jeon
- Graduate School of Green-Bio Science and Crop Biotech Institute, Kyung Hee University, Yongin, Gyeonggi-do 17104, Republic of Korea
| | - Gang-Seob Lee
- Department of Agricultural Biotechnology, National Institute of Agricultural Sciences, Jeonju, Jeollabuk-do 54875, Republic of Korea
| | - Yeon-Ki Kim
- Department of Biosciences and Bioinformatics, Myongji University, Yongin, Gyeonggi-do 17058, Republic of Korea.
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Hu Z, Huang X, Xia H, Zhang Z, Lu H, Wang X, Sun Y, Cui M, Yang S, Kant S, Xu G, Sun S. Transcription factor OsSHR2 regulates rice architecture and yield per plant in response to nitrogen. PLANTA 2024; 259:148. [PMID: 38717679 DOI: 10.1007/s00425-024-04400-7] [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: 12/27/2023] [Accepted: 03/28/2024] [Indexed: 05/23/2024]
Abstract
MAIN CONCLUSION Mutation of OsSHR2 adversely impacted root and shoot growth and impaired plant response to N conditions, further reducing the yield per plant. Nitrogen (N) is a crucial factor that regulates the plant architecture. There is still a lack of research on it. In our study, it was observed that the knockout of the SHORTROOT 2 (OsSHR2) which was induced by N deficiency, can significantly affect the regulation of plant architecture response to N in rice. Under N deficiency, the mutation of OsSHR2 significantly reduced root growth, and impaired the sensitivity of the root meristem length to N deficiency. The mutants were found to have approximately a 15% reduction in plant height compared to wild type. But mutants showed a significant increase in tillering at post-heading stage, approximately 26% more than the wild type, particularly in high N conditions. In addition, due to reduced seed setting rate and 1000-grain weight, mutant yield was significantly decreased by approximately 33% under low N fertilizer supply. The mutation also changed the distribution of N between the vegetative and reproductive organs. Our findings suggest that the transcription factor OsSHR2 plays a regulatory role in the response of plant architecture and yield per plant to N in rice.
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Affiliation(s)
- Zhi Hu
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xu Huang
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Huihuang Xia
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Zhantian Zhang
- Yantai Academy of Agricultural Sciences, Yantai, 265500, China
| | - Huixin Lu
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xiaowen Wang
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yafei Sun
- Institute of Eco-Environment and Plant Protection, Shanghai Academy of Agriculture Science, Shanghai, 201403, China
| | - Mengyuan Cui
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Shanshan Yang
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Surya Kant
- Agriculture Victoria, Grains Innovation Park, Horsham, VIC, 3400, Australia
| | - Guohua Xu
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Shubin Sun
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China.
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Hong J, Su S, Wang L, Bai S, Xu J, Li Z, Betts N, Liang W, Wang W, Shi J, Zhang D. Combined genome-wide association study and epistasis analysis reveal multifaceted genetic architectures of plant height in Asian cultivated rice. PLANT, CELL & ENVIRONMENT 2023; 46:1295-1311. [PMID: 36734269 DOI: 10.1111/pce.14557] [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: 10/25/2022] [Revised: 01/08/2023] [Accepted: 02/01/2023] [Indexed: 06/18/2023]
Abstract
Plant height (PH) in rice (Oryza sativa) is an important trait for its adaptation and agricultural performance. Discovery of the semi-dwarf1 (SD1) mutation initiated the Green Revolution, boosting rice yield and fitness, but the underlying genetic regulation of PH in rice remains largely unknown. Here, we performed genome-wide association study (GWAS) and identified 12 non-repetitive QTL/genes regulating PH variation in 619 Asian cultivated rice accessions. One of these was an SD1 structural variant, not normally detected in standard GWAS analyses. Given the strong effect of SD1 on PH, we also divided 619 accessions into subgroups harbouring distinct SD1 haplotypes, and found a further 85 QTL/genes for PH, revealing genetic heterogeneity that may be missed by analysing a broad, diverse population. Moreover, we uncovered two epistatic interaction networks of PH-associated QTL/genes in the japonica (Geng)-dominant SD1NIP subgroup. In one of them, the hub QTL/gene qphSN1.4/GAMYB interacted with qphSN3.1/OsINO80, qphSN3.4/HD16/EL1, qphSN6.2/LOC_Os06g11130, and qphSN10.2/MADS56. Sequence variations in GAMYB and MADS56 were associated with their expression levels and PH variations, and MADS56 was shown to physically interact with MADS57 to coregulate expression of gibberellin (GA) metabolic genes OsGA2ox3 and Elongated Uppermost Internode1 (EUI1). Our study uncovered the multifaceted genetic architectures of rice PH, and provided novel and abundant genetic resources for breeding semi-dwarf rice and new candidates for further mechanistic studies on regulation of PH in rice.
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Affiliation(s)
- Jun Hong
- Joint International Research Laboratory of Metabolic and Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Yazhou Bay Institute of Deepsea Sci-Tech, Shanghai Jiao Tong University, Shanghai, China
| | - Su Su
- Joint International Research Laboratory of Metabolic and Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Yazhou Bay Institute of Deepsea Sci-Tech, Shanghai Jiao Tong University, Shanghai, China
| | - Li Wang
- Joint International Research Laboratory of Metabolic and Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Yazhou Bay Institute of Deepsea Sci-Tech, Shanghai Jiao Tong University, Shanghai, China
| | - Shaoxing Bai
- Joint International Research Laboratory of Metabolic and Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Yazhou Bay Institute of Deepsea Sci-Tech, Shanghai Jiao Tong University, Shanghai, China
| | - Jianlong Xu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Zhikang Li
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Natalie Betts
- School of Agriculture, Food and Wine, University of Adelaide, Urrbrae, South Australia, Australia
| | - Wanqi Liang
- Joint International Research Laboratory of Metabolic and Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Yazhou Bay Institute of Deepsea Sci-Tech, Shanghai Jiao Tong University, Shanghai, China
| | - Wensheng Wang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jianxin Shi
- Joint International Research Laboratory of Metabolic and Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Yazhou Bay Institute of Deepsea Sci-Tech, Shanghai Jiao Tong University, Shanghai, China
| | - Dabing Zhang
- Joint International Research Laboratory of Metabolic and Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Yazhou Bay Institute of Deepsea Sci-Tech, Shanghai Jiao Tong University, Shanghai, China
- School of Agriculture, Food and Wine, University of Adelaide, Urrbrae, South Australia, Australia
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Applications and Prospects of CRISPR/Cas9-Mediated Base Editing in Plant Breeding. Curr Issues Mol Biol 2023; 45:918-935. [PMID: 36826004 PMCID: PMC9955079 DOI: 10.3390/cimb45020059] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2022] [Revised: 01/10/2023] [Accepted: 01/17/2023] [Indexed: 01/20/2023] Open
Abstract
The clustered regularly interspaced short palindromic repeats (CRISPR)/associated protein 9 system (Cas9) has been used at length to optimize multiple aspects of germplasm resources. However, large-scale genomic research has indicated that novel variations in crop plants are attributed to single-nucleotide polymorphisms (SNPs). Therefore, substituting single bases into a plant genome may produce desirable traits. Gene editing by CRISPR/Cas9 techniques frequently results in insertions-deletions (indels). Base editing allows precise single-nucleotide changes in the genome in the absence of double-strand breaks (DSBs) and donor repair templates (DRTs). Therefore, BEs have provided a new way of thinking about genome editing, and base editing techniques are currently being utilized to edit the genomes of many different organisms. As traditional breeding techniques and modern molecular breeding technologies complement each other, various genome editing technologies have emerged. How to realize the greater potential of BE applications is the question we need to consider. Here, we explain various base editings such as CBEs, ABEs, and CGBEs. In addition, the latest applications of base editing technologies in agriculture are summarized, including crop yield, quality, disease, and herbicide resistance. Finally, the challenges and future prospects of base editing technologies are presented. The aim is to provide a comprehensive overview of the application of BE in crop breeding to further improve BE and make the most of its value.
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Cheng X, Huang Y, Tan Y, Tan L, Yin J, Zou G. Potentially Useful Dwarfing or Semi-dwarfing Genes in Rice Breeding in Addition to the sd1 Gene. RICE (NEW YORK, N.Y.) 2022; 15:66. [PMID: 36542176 PMCID: PMC9772376 DOI: 10.1186/s12284-022-00615-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Accepted: 12/13/2022] [Indexed: 06/17/2023]
Abstract
The "Green revolution" gene sd1 has been used widely in the breeding of modern rice varieties for over half a century. The application of this gene has increased rice yields and thereby supported a significant proportion of the global population. The use of a single gene, however, has raised concerns in the scientific community regarding its durability, especially given the bottleneck in genetic background and the need for large input of fertilizer. New dwarfing or semi-dwarfing genes are needed to alleviate our dependence on the sole "Green revolution" gene. In the past few years, several new dwarfing and semi-dwarfing genes as well as their mutants have been reported. Here, we provide an extensive review of the recent discoveries concerning newly identified genes that are potentially useful in rice breeding, including methods employed to create and effectively screen new rice mutants, the phenotypic characteristics of the new dwarfing and semi-dwarfing mutants, potential values of the new dwarfing and semi-dwarfing genes in rice breeding, and potential molecular mechanisms associated with the newly identified genes.
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Affiliation(s)
- Xiaoyan Cheng
- National Engineering Research Center of Rice (Nanchang), Rice Research Institute, Jiangxi Academy of Agricultural Sciences, Nanchang, 330200, Jiangxi, People's Republic of China
- Jiangxi Tiandao Liangan Seed Industry Co., Ltd., 568 South Huancheng Rd., Yuanzhou Dist., Yi Chun, 336000, Jiangxi, People's Republic of China
| | - Yongping Huang
- National Engineering Research Center of Rice (Nanchang), Rice Research Institute, Jiangxi Academy of Agricultural Sciences, Nanchang, 330200, Jiangxi, People's Republic of China
| | - Yong Tan
- Jiangxi Tiandao Liangan Seed Industry Co., Ltd., 568 South Huancheng Rd., Yuanzhou Dist., Yi Chun, 336000, Jiangxi, People's Republic of China
| | - Lin Tan
- Jiangxi Tiandao Liangan Seed Industry Co., Ltd., 568 South Huancheng Rd., Yuanzhou Dist., Yi Chun, 336000, Jiangxi, People's Republic of China
| | - Jianhua Yin
- National Engineering Research Center of Rice (Nanchang), Rice Research Institute, Jiangxi Academy of Agricultural Sciences, Nanchang, 330200, Jiangxi, People's Republic of China
| | - Guoxing Zou
- National Engineering Research Center of Rice (Nanchang), Rice Research Institute, Jiangxi Academy of Agricultural Sciences, Nanchang, 330200, Jiangxi, People's Republic of China.
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6
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Zhang X, Wang Y, Wang X, Zhu Z, Zhang X, Jia L, Li Y, Tian W, Chen H, Zhu X, He G, Sang X. A very-long-chain fatty acid synthesis gene, SD38, influences plant height by activating ethylene biosynthesis in rice. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 112:1084-1097. [PMID: 36196616 DOI: 10.1111/tpj.15998] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 09/18/2022] [Accepted: 10/02/2022] [Indexed: 06/16/2023]
Abstract
As an important trait in crop breeding, plant height is associated with lodging resistance and yield. With the identification and cloning of several semi-dwarfing genes, increasing numbers of semi-dwarf cultivars have emerged, which has led to a 'green revolution' in rice (Oryza sativa) production. In this study, we identified a rice semi-dwarf mutant, semi-dwarf 38 (sd38), which showed significantly reduced cell length. SD38 encodes a fatty acid elongase, β-ketoacyl-CoA synthase, which is involved in the synthesis of very-long-chain fatty acids (VLCFAs). Expression analysis showed that SD38 was localized on the membrane of the endoplasmic reticulum, and was expressed in all analyzed tissues with differential abundance. The mutation of SD38 affected lipid metabolism in the sd38 mutant. A functional complementarity test in Saccharomyces cerevisiae indicated that SD38 was capable of complementing the deficiency of ELO3p activity in BY4741-elo3 knockout yeast cells by participating in the synthesis of C24:0 VLCFA. Significant changes were observed in the expression of genes involved in ethylene synthesis, which resulted in reduced content of the ethylene precursor 1-aminocyclopropane-1-carboxylic acid (ACC) in the sd38 mutant. Exogenously supplied VLCFA (C24:0) increased the expression levels of OsACS3, OsACS4, and OsACO7 and the plant height of sd38 mutant seedlings, similar to the effect of exogenous application of ACC and ethephon. These results reveal a relationship among VLCFAs, ethylene biosynthesis, and plant height and improve our understanding of plant height development in crops.
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Affiliation(s)
- Xiaobo Zhang
- Rice Research Institute, Key Laboratory of Application and Safety Control of Genetically Modified Crops, Academy of Agricultural Sciences, Southwest University, Chongqing, 400715, People's Republic of China
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing, 400715, People's Republic of China
| | - Ying Wang
- Rice Research Institute, Key Laboratory of Application and Safety Control of Genetically Modified Crops, Academy of Agricultural Sciences, Southwest University, Chongqing, 400715, People's Republic of China
| | - Xiaowen Wang
- Rice Research Institute, Key Laboratory of Application and Safety Control of Genetically Modified Crops, Academy of Agricultural Sciences, Southwest University, Chongqing, 400715, People's Republic of China
| | - Zhu Zhu
- Rice Research Institute, Key Laboratory of Application and Safety Control of Genetically Modified Crops, Academy of Agricultural Sciences, Southwest University, Chongqing, 400715, People's Republic of China
| | - Xuefei Zhang
- Rice Research Institute, Key Laboratory of Application and Safety Control of Genetically Modified Crops, Academy of Agricultural Sciences, Southwest University, Chongqing, 400715, People's Republic of China
| | - Luqi Jia
- Rice Research Institute, Key Laboratory of Application and Safety Control of Genetically Modified Crops, Academy of Agricultural Sciences, Southwest University, Chongqing, 400715, People's Republic of China
| | - Yangyang Li
- Rice Research Institute, Key Laboratory of Application and Safety Control of Genetically Modified Crops, Academy of Agricultural Sciences, Southwest University, Chongqing, 400715, People's Republic of China
| | - Weijiang Tian
- Rice Research Institute, Key Laboratory of Application and Safety Control of Genetically Modified Crops, Academy of Agricultural Sciences, Southwest University, Chongqing, 400715, People's Republic of China
| | - Hongyan Chen
- Rice Research Institute, Key Laboratory of Application and Safety Control of Genetically Modified Crops, Academy of Agricultural Sciences, Southwest University, Chongqing, 400715, People's Republic of China
| | - Xiaoyan Zhu
- Rice Research Institute, Key Laboratory of Application and Safety Control of Genetically Modified Crops, Academy of Agricultural Sciences, Southwest University, Chongqing, 400715, People's Republic of China
| | - Guanghua He
- Rice Research Institute, Key Laboratory of Application and Safety Control of Genetically Modified Crops, Academy of Agricultural Sciences, Southwest University, Chongqing, 400715, People's Republic of China
| | - Xianchun Sang
- Rice Research Institute, Key Laboratory of Application and Safety Control of Genetically Modified Crops, Academy of Agricultural Sciences, Southwest University, Chongqing, 400715, People's Republic of China
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Liu X, Jiang H, Yang J, Han J, Jin M, Zhang H, Chen L, Chen S, Teng S. Comprehensive QTL analyses of nitrogen use efficiency in indica rice. FRONTIERS IN PLANT SCIENCE 2022; 13:992225. [PMID: 36212385 PMCID: PMC9539535 DOI: 10.3389/fpls.2022.992225] [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: 07/12/2022] [Accepted: 08/29/2022] [Indexed: 06/16/2023]
Abstract
Nitrogen-use efficiency (NUE) in rice is a complex quantitative trait involved in multiple biological processes and agronomic traits; however, the genetic basis and regulatory network of NUE remain largely unknown. We constructed a high-resolution microarray-based genetic map for 261 recombinant inbred lines derived from two indica parents. Using 2,345 bin markers, comprehensive analyses of quantitative trait loci (QTLs) of seven key agronomic traits under two different N levels were performed. A total of 11 non-redundant QTLs for effective panicle number (EPN), 7 for grain number per panicle, 13 for thousand-grain weight, 2 for seed-setting percentage, 15 for plant height, 12 for panicle length, and 6 for grain yield per plant were identified. The QTL regions were as small as 512 kb on average, and more than half spanned an interval smaller than 100 kb. Using this advantage, we identified possible candidate genes of two major EPN-related QTLs. One QTL detected under both N levels possibly encodes a DELLA protein SLR1, which is known to regulate NUE, although the natural variations of this protein have not been reported. The other QTL detected only under a high N level could encode the transcription factor OsbZIP59. We also predicted the possible candidate genes for another three of the NUE-related QTLs. Our results provide a reference for improving NUE-related QTL cloning and promote our understanding of NUE regulation in indica rice.
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Affiliation(s)
- Xiuyan Liu
- College of Material and Environmental Engineering, Hangzhou Dianzi University, Hangzhou, China
- Laboratory of Photosynthesis and Environmental Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Hong Jiang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Jiangsu Province Engineering Research Center of Seed Industry Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Jing Yang
- Laboratory of Photosynthesis and Environmental Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Jiajia Han
- Laboratory of Photosynthesis and Environmental Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Mengxian Jin
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Jiangsu Province Engineering Research Center of Seed Industry Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Hongsheng Zhang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Jiangsu Province Engineering Research Center of Seed Industry Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Liang Chen
- Shanghai Agrobiological Gene Center, Shanghai, China
| | - Sunlu Chen
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Jiangsu Province Engineering Research Center of Seed Industry Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Sheng Teng
- Laboratory of Photosynthesis and Environmental Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
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8
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Liu Q, Wu K, Song W, Zhong N, Wu Y, Fu X. Improving Crop Nitrogen Use Efficiency Toward Sustainable Green Revolution. ANNUAL REVIEW OF PLANT BIOLOGY 2022; 73:523-551. [PMID: 35595292 DOI: 10.1146/annurev-arplant-070121-015752] [Citation(s) in RCA: 58] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
The Green Revolution of the 1960s improved crop yields in part through the widespread cultivation of semidwarf plant varieties, which resist lodging but require a high-nitrogen (N) fertilizer input. Because environmentally degrading synthetic fertilizer use underlies current worldwide cereal yields, future agricultural sustainability demands enhanced N use efficiency (NUE). Here, we summarize the current understanding of how plants sense, uptake, and respond to N availability in the model plants that can be used to improve sustainable productivity in agriculture. Recent progress in unlocking the genetic basis of NUE within the broader context of plant systems biology has provided insights into the coordination of plant growth and nutrient assimilation and inspired the implementation of a new breeding strategy to cut fertilizer use in high-yield cereal crops. We conclude that identifying fresh targets for N sensing and response in crops would simultaneously enable improved grain productivity and NUE to launch a new Green Revolution and promote future food security.
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Affiliation(s)
- Qian Liu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, China;
| | - Kun Wu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, China;
| | - Wenzhen Song
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, China;
| | - Nan Zhong
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, China;
| | - Yunzhe Wu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, China;
| | - Xiangdong Fu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, China;
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
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9
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Das D, Singha DL, Paswan RR, Chowdhury N, Sharma M, Reddy PS, Chikkaputtaiah C. Recent advancements in CRISPR/Cas technology for accelerated crop improvement. PLANTA 2022; 255:109. [PMID: 35460444 DOI: 10.1007/s00425-022-03894-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 03/29/2022] [Indexed: 06/14/2023]
Abstract
Precise genome engineering approaches could be perceived as a second paradigm for targeted trait improvement in crop plants, with the potential to overcome the constraints imposed by conventional CRISPR/Cas technology. The likelihood of reduced agricultural production due to highly turbulent climatic conditions increases as the global population expands. The second paradigm of stress-resilient crops with enhanced tolerance and increased productivity against various stresses is paramount to support global production and consumption equilibrium. Although traditional breeding approaches have substantially increased crop production and yield, effective strategies are anticipated to restore crop productivity even further in meeting the world's increasing food demands. CRISPR/Cas, which originated in prokaryotes, has surfaced as a coveted genome editing tool in recent decades, reshaping plant molecular biology in unprecedented ways and paving the way for engineering stress-tolerant crops. CRISPR/Cas is distinguished by its efficiency, high target specificity, and modularity, enables precise genetic modification of crop plants, allowing for the creation of allelic variations in the germplasm and the development of novel and more productive agricultural practices. Additionally, a slew of advanced biotechnologies premised on the CRISPR/Cas methodologies have augmented fundamental research and plant synthetic biology toolkits. Here, we describe gene editing tools, including CRISPR/Cas and its imitative tools, such as base and prime editing, multiplex genome editing, chromosome engineering followed by their implications in crop genetic improvement. Further, we comprehensively discuss the latest developments of CRISPR/Cas technology including CRISPR-mediated gene drive, tissue-specific genome editing, dCas9 mediated epigenetic modification and programmed self-elimination of transgenes in plants. Finally, we highlight the applicability and scope of advanced CRISPR-based techniques in crop genetic improvement.
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Affiliation(s)
- Debajit Das
- Biological Sciences and Technology Division, CSIR-North East Institute of Science and Technology (CSIR-NEIST), Jorhat, Assam, 785006, India
| | - Dhanawantari L Singha
- Biological Sciences and Technology Division, CSIR-North East Institute of Science and Technology (CSIR-NEIST), Jorhat, Assam, 785006, India
| | - Ricky Raj Paswan
- Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat, Assam, 785013, India
| | - Naimisha Chowdhury
- Biological Sciences and Technology Division, CSIR-North East Institute of Science and Technology (CSIR-NEIST), Jorhat, Assam, 785006, India
| | - Monica Sharma
- Biological Sciences and Technology Division, CSIR-North East Institute of Science and Technology (CSIR-NEIST), Jorhat, Assam, 785006, India
| | - Palakolanu Sudhakar Reddy
- International Crop Research Institute for the Semi Arid Tropics (ICRISAT), Patancheru, Hyderabad, 502 324, India
| | - Channakeshavaiah Chikkaputtaiah
- Biological Sciences and Technology Division, CSIR-North East Institute of Science and Technology (CSIR-NEIST), Jorhat, Assam, 785006, India.
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201 002, India.
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10
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Fang X, Bo C, Wang M, Yuan H, Li W, Chen H, Ma Q, Cai R. Overexpression of the maize WRKY114 gene in transgenic rice reduce plant height by regulating the biosynthesis of GA. PLANT SIGNALING & BEHAVIOR 2021; 16:1967635. [PMID: 34498544 PMCID: PMC8525977 DOI: 10.1080/15592324.2021.1967635] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 08/09/2021] [Accepted: 08/10/2021] [Indexed: 05/30/2023]
Abstract
WRKYs represent an important family of transcription factors that are widely involved in plant development, defense regulation and stress response. Transgenic rice that constitutively expressed ZmWRKY114 had shorter plant height and showed less sensitivity to gibberellic acid (GA3). Further investigation proved that transgenic rice accumulated lower levels of bioactive GAs than that in wild-type plants. Application of exogenous GA3 fully rescued the semi-dwarf phenotype of ZmWRKY114 transgenic plants. Transcriptome and qRT-PCR analyses indicated that the expression of OsGA2ox4, encoding the repressor of GA biosynthesis, was markedly increased. Electrophoretic mobility shift assay and dual-luciferase reporter assay indicated that ZmWRKY114 directly binds to a W-box motif in the OsGA2ox4 promoter. Taken together, these results confirm that ZmWRKY114 is a GA-responsive gene and is participated in the regulation of plant height in rice.
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Affiliation(s)
- Xiu Fang
- National Engineering Laboratory of Crop Stress Resistance Breeding, School of Life Sciences, Anhui Agricultural University, Hefei, China
| | - Chen Bo
- National Engineering Laboratory of Crop Stress Resistance Breeding, School of Life Sciences, Anhui Agricultural University, Hefei, China
| | - Mengjie Wang
- School of Life Sciences, Anhui Agricultural University, Hefei, China
| | - Haotian Yuan
- National Engineering Laboratory of Crop Stress Resistance Breeding, School of Life Sciences, Anhui Agricultural University, Hefei, China
| | - Wei Li
- National Engineering Laboratory of Crop Stress Resistance Breeding, School of Life Sciences, Anhui Agricultural University, Hefei, China
| | - Haowei Chen
- National Engineering Laboratory of Crop Stress Resistance Breeding, School of Life Sciences, Anhui Agricultural University, Hefei, China
| | - Qing Ma
- National Engineering Laboratory of Crop Stress Resistance Breeding, School of Life Sciences, Anhui Agricultural University, Hefei, China
- Engineering Research Center for Maize of Anhui Province, School of Life Sciences, Anhui Agricultural University, Hefei, China
| | - Ronghao Cai
- National Engineering Laboratory of Crop Stress Resistance Breeding, School of Life Sciences, Anhui Agricultural University, Hefei, China
- Engineering Research Center for Maize of Anhui Province, School of Life Sciences, Anhui Agricultural University, Hefei, China
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11
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Wei X, Zhou H, Xie D, Li J, Yang M, Chang T, Wang D, Hu L, Xie G, Wang J, Wang L. Genome-Wide Association Study in Rice Revealed a Novel Gene in Determining Plant Height and Stem Development, by Encoding a WRKY Transcription Factor. Int J Mol Sci 2021; 22:ijms22158192. [PMID: 34360958 PMCID: PMC8347446 DOI: 10.3390/ijms22158192] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 07/17/2021] [Indexed: 11/27/2022] Open
Abstract
Semi-dwarfism is a main agronomic trait in crop breeding. In this study, we performed genome-wide association study (GWAS) and identified a new quantitative trait nucleotide (QTN) for rice shoot length. The peak QTN (C/T) was located in the first coding region of a group III WRKY transcription factor OsWRKY21 (LOC_Os01g60640). Interestingly, further haplotype analysis showed that C/T difference only existed in the indica group but not in the japonica group, resulting in significant differences in plant height among the different indica rice varieties. OsWRKY21 was expressed in embryo, radicle, shoots, leaves, and stems. Most notably, overexpressing OsWRKY21 resulted in the semi-dwarf phenotype, early heading date and short internodes compared to the wild type, while the knockout mutant plants by CRISPR/Cas9 technology yielded the opposite. The overexpressing lines exhibited the decreased length of the cells near sclerenchyma epidermis, accompanied with the lower levels of indole-3-acetic acid (IAA) and gibberellin 3 (GA3), but increased levels of the abscisic acid (ABA) and salicylic acid (SA) in the internodes at heading stage. Moreover, the semi-dwarf phenotype could be fully rescued by exogenous GA3 application at seedling stage. The RNA-seq and qRT-PCR analysis confirmed the differential expression levels of genes in development and the stress responses in rice, including GA metabolism (GA20ox2, GA2ox6, and YABY1) and cell wall biosynthesis (CesA4, 7, and 9) and regulation (MYB103L). These data suggest the essential role of OsWRKY21 in regulation of internode elongation and plant height in rice.
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Affiliation(s)
- Xiaoshuang Wei
- State Key Laboratory for Conservation & Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning 530004, China; (X.W.); (H.Z.); (J.L.); (M.Y.); (T.C.)
| | - Hailian Zhou
- State Key Laboratory for Conservation & Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning 530004, China; (X.W.); (H.Z.); (J.L.); (M.Y.); (T.C.)
| | - Deying Xie
- College of Plant Science & Technology, Huazhong Agricultural University, Wuhan 430070, China; (D.X.); (G.X.)
| | - Jianguo Li
- State Key Laboratory for Conservation & Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning 530004, China; (X.W.); (H.Z.); (J.L.); (M.Y.); (T.C.)
- College of Plant Science & Technology, Huazhong Agricultural University, Wuhan 430070, China; (D.X.); (G.X.)
| | - Mingchong Yang
- State Key Laboratory for Conservation & Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning 530004, China; (X.W.); (H.Z.); (J.L.); (M.Y.); (T.C.)
| | - Tianli Chang
- State Key Laboratory for Conservation & Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning 530004, China; (X.W.); (H.Z.); (J.L.); (M.Y.); (T.C.)
| | - Dongxin Wang
- College of Life Science & Technology, Guangxi University, Nanning 530004, China; (D.W.); (L.H.)
| | - Lihua Hu
- College of Life Science & Technology, Guangxi University, Nanning 530004, China; (D.W.); (L.H.)
| | - Guosheng Xie
- College of Plant Science & Technology, Huazhong Agricultural University, Wuhan 430070, China; (D.X.); (G.X.)
| | - Jihong Wang
- Department of Life Science, Tangshan Normal University, Tangshan 063000, China;
| | - Lingqiang Wang
- State Key Laboratory for Conservation & Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning 530004, China; (X.W.); (H.Z.); (J.L.); (M.Y.); (T.C.)
- College of Plant Science & Technology, Huazhong Agricultural University, Wuhan 430070, China; (D.X.); (G.X.)
- Correspondence:
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12
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Sarwar R, Jiang T, Ding P, Gao Y, Tan X, Zhu K. Genome-wide analysis and functional characterization of the DELLA gene family associated with stress tolerance in B. napus. BMC PLANT BIOLOGY 2021; 21:286. [PMID: 34157966 PMCID: PMC8220683 DOI: 10.1186/s12870-021-03054-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Accepted: 05/13/2021] [Indexed: 05/07/2023]
Abstract
BACKGROUND Brassica napus is an essential crop for oil and livestock feed. Eventually, this crop's economic interest is at the most risk due to anthropogenic climate change. DELLA proteins constitute a significant repressor of plant growth to facilitate survival under constant stress conditions. DELLA proteins lack DNA binding domain but can interact with various transcription factors or transcription regulators of different hormonal families. Significant progress has been made on Arabidopsis and cereal plants. However, no comprehensive study regarding DELLA proteins has been delineated in rapeseed. RESULTS In our study, we have identified 10 BnaDELLA genes. All of the BnaDELLA genes are closely related to five AtDELLA genes, suggesting a relative function and structure. Gene duplication and synteny relationship among Brassica. napus, Arabidopsis. thaliana, Brassica rapa, Brassica oleracea, and Brassica nigra genomes were also predicted to provide valuable insights into the BnaDELLA gene family evolutionary characteristics. Chromosomal mapping revealed the uneven distribution of BnaDELLA genes on eight chromosomes, and site-specific selection assessment proposes BnaDELLA genes purifying selection. The motifs composition in all BnaDELLA genes is inconsistent; however, every BnaDELLA gene contains 12 highly conserved motifs, encoding DELLA and GRAS domains. The two known miRNAs (bna-miR6029 and bna-miR603) targets BnaC07RGA and BnaA09GAI, were also predicted. Furthermore, quantitative real-time PCR (qRT-PCR) analysis has exhibited the BnaDELLA genes diverse expression patterns in the root, mature-silique, leaf, flower, flower-bud, stem, shoot-apex, and seed. Additionally, cis-acting element prediction shows that all BnaDELLA genes contain light, stress, and hormone-responsive elements on their promoters. The gene ontology (GO) enrichment report indicated that the BnaDELLA gene family might regulate stress responses. Combine with transcriptomic data used in this study, we detected the distinct expression patterns of BnaDELLA genes under biotic and abiotic stresses. CONCLUSION In this study, we investigate evolution feature, genomic structure, miRNAs targets, and expression pattern of the BnaDELLA gene family in B. napus, which enrich our understanding of BnaDELLA genes in B. napus and suggests modulating individual BnaDELLA expression is a promising way to intensify rapeseed stress tolerance and harvest index.
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Affiliation(s)
- Rehman Sarwar
- Institute of Life Sciences, Jiangsu University, Zhenjiang, China
| | - Ting Jiang
- Institute of Life Sciences, Jiangsu University, Zhenjiang, China
| | - Peng Ding
- Institute of Life Sciences, Jiangsu University, Zhenjiang, China
| | - Yue Gao
- Institute of Life Sciences, Jiangsu University, Zhenjiang, China
| | - Xiaoli Tan
- Institute of Life Sciences, Jiangsu University, Zhenjiang, China
| | - Keming Zhu
- Institute of Life Sciences, Jiangsu University, Zhenjiang, China.
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13
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Numan M, Khan AL, Asaf S, Salehin M, Beyene G, Tadele Z, Ligaba-Osena A. From Traditional Breeding to Genome Editing for Boosting Productivity of the Ancient Grain Tef [ Eragrostis tef (Zucc.) Trotter]. PLANTS (BASEL, SWITZERLAND) 2021; 10:628. [PMID: 33806233 PMCID: PMC8066236 DOI: 10.3390/plants10040628] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 03/19/2021] [Accepted: 03/22/2021] [Indexed: 02/07/2023]
Abstract
Tef (Eragrostis tef (Zucc.) Trotter) is a staple food crop for 70% of the Ethiopian population and is currently cultivated in several countries for grain and forage production. It is one of the most nutritious grains, and is also more resilient to marginal soil and climate conditions than major cereals such as maize, wheat and rice. However, tef is an extremely low-yielding crop, mainly due to lodging, which is when stalks fall on the ground irreversibly, and prolonged drought during the growing season. Climate change is triggering several biotic and abiotic stresses which are expected to cause severe food shortages in the foreseeable future. This has necessitated an alternative and robust approach in order to improve resilience to diverse types of stresses and increase crop yields. Traditional breeding has been extensively implemented to develop crop varieties with traits of interest, although the technique has several limitations. Currently, genome editing technologies are receiving increased interest among plant biologists as a means of improving key agronomic traits. In this review, the potential application of clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated proteins (CRISPR-Cas) technology in improving stress resilience in tef is discussed. Several putative abiotic stress-resilient genes of the related monocot plant species have been discussed and proposed as target genes for editing in tef through the CRISPR-Cas system. This is expected to improve stress resilience and boost productivity, thereby ensuring food and nutrition security in the region where it is needed the most.
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Affiliation(s)
- Muhammad Numan
- Laboratory of Molecular Biology and Biotechnology, Department of Biology, University of North Carolina at Greensboro, Greensboro, NC 27412, USA; (M.N.); (M.S.)
| | - Abdul Latif Khan
- Natural and Medical Sciences Research Center, Biotechnology and OMICs Laboratory, University of Nizwa, Nizwa 616, Oman; (A.L.K.); (S.A.)
| | - Sajjad Asaf
- Natural and Medical Sciences Research Center, Biotechnology and OMICs Laboratory, University of Nizwa, Nizwa 616, Oman; (A.L.K.); (S.A.)
| | - Mohammad Salehin
- Laboratory of Molecular Biology and Biotechnology, Department of Biology, University of North Carolina at Greensboro, Greensboro, NC 27412, USA; (M.N.); (M.S.)
| | - Getu Beyene
- Donald Danforth Plant Science Center, St. Louis, MO 63132, USA;
| | - Zerihun Tadele
- Institute of Plant Sciences, University of Bern, Altenbergrain 21, CH-3013 Bern, Switzerland;
| | - Ayalew Ligaba-Osena
- Laboratory of Molecular Biology and Biotechnology, Department of Biology, University of North Carolina at Greensboro, Greensboro, NC 27412, USA; (M.N.); (M.S.)
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14
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Liu Y, Wang W. Characterization of the GRAS gene family reveals their contribution to the high adaptability of wheat. PeerJ 2021; 9:e10811. [PMID: 33665016 PMCID: PMC7908883 DOI: 10.7717/peerj.10811] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Accepted: 12/30/2020] [Indexed: 01/18/2023] Open
Abstract
GRAS transcription factors play important roles in many processes of plant development as well as abiotic and biotic stress responses. However, little is known about this gene family in bread wheat (Triticum aestivum), one of the most important crops worldwide. The completion of a quality draft genome allows genome-wide detection and evolutionary analysis of the GRAS gene family in wheat. In this study, 188 TaGRAS genes were detected and divided into 12 subfamilies based on phylogenetic analyses: DELLA, DLT, HAM, LISCL, SCL3, SCL4/7, SCR, SHR, PAT1, Os19, Os4 and LAS. Tandem and segmental duplications are the main contributors to the expansion of TaGRAS, which may contribute to the adaptation of wheat to various environmental conditions. A high rate of homoeolog retention during hexaploidization was detected, suggesting the nonredundancy and biological importance of TaGRAS homoeologs. Systematic analyses of TaGRAS indicated the conserved expression pattern and function of the same subfamily during evolution. In addition, we detected five genes belonging to the LISCL subfamily induced by both biotic and abiotic stresses and they may be potential targets for further research through gene editing. Using degradome and ChIP-seq data, we identified the targets of miR171 and histone modifications and further analyzed the contribution of epigenetic modification to the subfunctionalization of TaGRAS. This study laid a foundation for further functional elucidation of TaGRAS genes.
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Affiliation(s)
- Yanfeng Liu
- School of Resources and Environmental Engineering, Ludong University, Yantai, Shandong, China
| | - Wei Wang
- School of Resources and Environmental Engineering, Ludong University, Yantai, Shandong, China
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15
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Zhan X, Lu Y, Zhu JK, Botella JR. Genome editing for plant research and crop improvement. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2021; 63:3-33. [PMID: 33369120 DOI: 10.1111/jipb.13063] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2020] [Accepted: 12/22/2020] [Indexed: 05/27/2023]
Abstract
The advent of clustered regularly interspaced short palindromic repeat (CRISPR) has had a profound impact on plant biology, and crop improvement. In this review, we summarize the state-of-the-art development of CRISPR technologies and their applications in plants, from the initial introduction of random small indel (insertion or deletion) mutations at target genomic loci to precision editing such as base editing, prime editing and gene targeting. We describe advances in the use of class 2, types II, V, and VI systems for gene disruption as well as for precise sequence alterations, gene transcription, and epigenome control.
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Affiliation(s)
- Xiangqiang Zhan
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Horticulture, Northwest A&F University, Xianyang, 712100, China
| | - Yuming Lu
- Shanghai Center for Plant Stress Biology, CAS Center of Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Jian-Kang Zhu
- Shanghai Center for Plant Stress Biology, CAS Center of Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, Indiana, 47907, USA
| | - Jose Ramon Botella
- School of Agriculture and Food Sciences, University of Queensland, Brisbane, Queensland, 4072, Australia
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16
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Systematic Analysis of Gibberellin Pathway Components in Medicago truncatula Reveals the Potential Application of Gibberellin in Biomass Improvement. Int J Mol Sci 2020; 21:ijms21197180. [PMID: 33003317 PMCID: PMC7582545 DOI: 10.3390/ijms21197180] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Revised: 09/26/2020] [Accepted: 09/27/2020] [Indexed: 12/02/2022] Open
Abstract
Gibberellins (GAs), a class of phytohormones, act as an essential natural regulator of plant growth and development. Many studies have shown that GA is related to rhizobial infection and nodule organogenesis in legume species. However, thus far, GA metabolism and signaling components are largely unknown in the model legume Medicago truncatula. In this study, a genome-wide analysis of GA metabolism and signaling genes was carried out. In total 29 components, including 8 MtGA20ox genes, 2 MtGA3ox genes, 13 MtGA2ox genes, 3 MtGID1 genes, and 3 MtDELLA genes were identified in M. truncatula genome. Expression profiles revealed that most members of MtGAox, MtGID1, and MtDELLA showed tissue-specific expression patterns. In addition, the GA biosynthesis and deactivation genes displayed a feedback regulation on GA treatment, respectively. Yeast two-hybrid assays showed that all the three MtGID1s interacted with MtDELLA1 and MtDELLA2, suggesting that the MtGID1s are functional GA receptors. More importantly, M. truncatula exhibited increased plant height and biomass by ectopic expression of the MtGA20ox1, suggesting that enhanced GA response has the potential for forage improvement.
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17
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Bhuvaneswari S, Gopala Krishnan S, Ellur RK, Vinod KK, Bollinedi H, Bhowmick PK, Bansal VP, Nagarajan M, Singh AK. Discovery of a Novel Induced Polymorphism in SD1 Gene Governing Semi-Dwarfism in Rice and Development of a Functional Marker for Marker-Assisted Selection. PLANTS 2020; 9:plants9091198. [PMID: 32937792 PMCID: PMC7570060 DOI: 10.3390/plants9091198] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 08/31/2020] [Accepted: 09/07/2020] [Indexed: 11/16/2022]
Abstract
The semi-dwarfing allele, sd1-d, has been widely utilized in developing high-yielding rice cultivars across the world. Originally identified from the rice cultivar Dee-Geo-Woo-Gen (DGWG), sd1-d, derived from a spontaneous mutation, has a 383-bp deletion in the SD1 gene. To date, as many as seven alleles of the SD1 gene have been identified and used in rice improvement, either with a functional single-nucleotide polymorphism (SNP), with insertion–deletions (InDels), or both. Here, we report discovery of a novel SNP in the SD1 gene from the rice genotype, Pusa 1652. Genetic analysis revealed that the inheritance of the semi-dwarfism in Pusa 1652 is monogenic and recessive, but it did not carry the sd1-d allele. However, response to exogenous gibberellic acid (GA3) application and the subsequent bulked segregant and linkage analyses confirmed that the SD1 gene is involved in the plant height reduction in Pusa 1652. Sequencing of the SD1 gene from Pusa 1652 revealed a novel transition in exon 3 (T/A) causing a nonsense mutation at the 300th codon. The stop codon leads to premature termination, resulting in a truncated protein of OsGA20ox2 obstructing the GA3 biosynthesis pathway. This novel recessive allele, named sd1-bm, is derived from Bindli Mutant 34 (BM34), a γ-ray induced mutant of a short-grain aromatic landrace, Bindli. BM34 is the parent of an aromatic semi-dwarf cultivar, Pusa 1176, from which Pusa 1652 is derived. The semi-dwarfing allele, sd1-bm, was further validated by developing a derived cleaved amplified polymorphic sequence (dCAPS) marker, AKS-sd1. This allele provides an alternative to the most widely used sd1-d in rice improvement programs and the functional dCAPS marker will facilitate marker-assisted introgression of the semi-dwarf trait into tall genotypes.
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Affiliation(s)
- Shivashankar Bhuvaneswari
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi 110012, Delhi, India; (S.B.); (S.G.K.); (R.K.E.); (K.K.V.); (H.B.); (P.K.B.); (V.P.B.)
- Division of Plant Breeding, ICAR RC NEH Region, Manipur Centre, Imphal 795004, Manipur, India
| | - Subbaiyan Gopala Krishnan
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi 110012, Delhi, India; (S.B.); (S.G.K.); (R.K.E.); (K.K.V.); (H.B.); (P.K.B.); (V.P.B.)
| | - Ranjith Kumar Ellur
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi 110012, Delhi, India; (S.B.); (S.G.K.); (R.K.E.); (K.K.V.); (H.B.); (P.K.B.); (V.P.B.)
| | - Kunnummal Kurungara Vinod
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi 110012, Delhi, India; (S.B.); (S.G.K.); (R.K.E.); (K.K.V.); (H.B.); (P.K.B.); (V.P.B.)
| | - Haritha Bollinedi
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi 110012, Delhi, India; (S.B.); (S.G.K.); (R.K.E.); (K.K.V.); (H.B.); (P.K.B.); (V.P.B.)
| | - Prolay Kumar Bhowmick
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi 110012, Delhi, India; (S.B.); (S.G.K.); (R.K.E.); (K.K.V.); (H.B.); (P.K.B.); (V.P.B.)
| | - Vijay Prakash Bansal
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi 110012, Delhi, India; (S.B.); (S.G.K.); (R.K.E.); (K.K.V.); (H.B.); (P.K.B.); (V.P.B.)
| | - Mariappan Nagarajan
- Rice Breeding and Genetics Research Centre, ICAR- Indian Agricultural Research Institute, Aduthurai 612101, Tamil Nadu, India;
| | - Ashok Kumar Singh
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi 110012, Delhi, India; (S.B.); (S.G.K.); (R.K.E.); (K.K.V.); (H.B.); (P.K.B.); (V.P.B.)
- Correspondence: ; Tel.: +91-11-2584-3375
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18
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Jung YJ, Kim JH, Lee HJ, Kim DH, Yu J, Bae S, Cho YG, Kang KK. Generation and Transcriptome Profiling of Slr1-d7 and Slr1-d8 Mutant Lines with a New Semi-Dominant Dwarf Allele of SLR1 Using the CRISPR/Cas9 System in Rice. Int J Mol Sci 2020; 21:ijms21155492. [PMID: 32752068 PMCID: PMC7432230 DOI: 10.3390/ijms21155492] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 07/29/2020] [Accepted: 07/29/2020] [Indexed: 01/18/2023] Open
Abstract
The rice SLR1 gene encodes the DELLA protein (protein with DELLA amino acid motif), and a loss-of-function mutation is dwarfed by inhibiting plant growth. We generate slr1-d mutants with a semi-dominant dwarf phenotype to target mutations of the DELLA/TVHYNP domain using CRISPR/Cas9 genome editing in rice. Sixteen genetic edited lines out of 31 transgenic plants were generated. Deep sequencing results showed that the mutants had six different mutation types at the target site of the TVHYNP domain of the SLR1 gene. The homo-edited plants selected individuals without DNA (T-DNA) transcribed by segregation in the T1 generation. The slr1-d7 and slr1-d8 plants caused a gibberellin (GA)-insensitive dwarf phenotype with shrunken leaves and shortened internodes. A genome-wide gene expression analysis by RNA-seq indicated that the expression levels of two GA-related genes, GA20OX2 (Gibberellin oxidase) and GA3OX2, were increased in the edited mutant plants, suggesting that GA20OX2 acts as a convert of GA12 signaling. These mutant plants are required by altering GA responses, at least partially by a defect in the phytohormone signaling system process and prevented cell elongation. The new mutants, namely, the slr1-d7 and slr1-d8 lines, are valuable semi-dominant dwarf alleles with potential application value for molecule breeding using the CRISPR/Cas9 system in rice.
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Affiliation(s)
- Yu Jin Jung
- Division of Horticultural Biotechnology, Hankyong National University, Anseong 17579, Korea; (Y.J.J.); (J.H.K.); (H.J.L.); (D.H.K.)
- Institute of Genetic Engineering, Hankyong National University, Anseong 17579, Korea
| | - Jong Hee Kim
- Division of Horticultural Biotechnology, Hankyong National University, Anseong 17579, Korea; (Y.J.J.); (J.H.K.); (H.J.L.); (D.H.K.)
| | - Hyo Ju Lee
- Division of Horticultural Biotechnology, Hankyong National University, Anseong 17579, Korea; (Y.J.J.); (J.H.K.); (H.J.L.); (D.H.K.)
| | - Dong Hyun Kim
- Division of Horticultural Biotechnology, Hankyong National University, Anseong 17579, Korea; (Y.J.J.); (J.H.K.); (H.J.L.); (D.H.K.)
| | - Jihyeon Yu
- Department of Chemistry, Hanyang University, Seoul 04763, Korea; (J.Y.); (S.B.)
| | - Sangsu Bae
- Department of Chemistry, Hanyang University, Seoul 04763, Korea; (J.Y.); (S.B.)
| | - Yong-Gu Cho
- Department of Crop Science, Chungbuk National University, Cheongju 28644, Korea;
| | - Kwon Kyoo Kang
- Division of Horticultural Biotechnology, Hankyong National University, Anseong 17579, Korea; (Y.J.J.); (J.H.K.); (H.J.L.); (D.H.K.)
- Institute of Genetic Engineering, Hankyong National University, Anseong 17579, Korea
- Correspondence: ; Tel.: +82-31-670-5104
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Systems Metabolic Alteration in a Semi-Dwarf Rice Mutant Induced by OsCYP96B4 Gene Mutation. Int J Mol Sci 2020; 21:ijms21061924. [PMID: 32168953 PMCID: PMC7139402 DOI: 10.3390/ijms21061924] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Revised: 03/07/2020] [Accepted: 03/08/2020] [Indexed: 02/06/2023] Open
Abstract
Dwarfism and semi-dwarfism are among the most valuable agronomic traits in crop breeding, which were adopted by the “Green Revolution”. Previously, we reported a novel semi-dwarf rice mutant (oscyp96b4) derived from the insertion of a single copy of Dissociator (Ds) transposon into the gene OsCYP96B4. However, the systems metabolic effect of the mutation is not well understood, which is important for understanding the gene function and developing new semi-dwarf mutants. Here, the metabolic phenotypes in the semi-dwarf mutant (M) and ectopic expression (ECE) rice line were compared to the wild-type (WT) rice, by using nuclear magnetic resonance (NMR) metabolomics and quantitative real-time polymerase chain reaction (qRT-PCR). Compared with WT, ECE of the OsCYP96B4 gene resulted in significant increase of γ-aminobutyrate (GABA), glutamine, and alanine, but significant decrease of glutamate, aromatic and branched-chain amino acids, and some other amino acids. The ECE caused significant increase of monosaccharides (glucose, fructose), but significant decrease of disaccharide (sucrose); induced significant changes of metabolites involved in choline metabolism (phosphocholine, ethanolamine) and nucleotide metabolism (adenosine, adenosine monophosphate, uridine). These metabolic profile alterations were accompanied with changes in the gene expression levels of some related enzymes, involved in GABA shunt, glutamate and glutamine metabolism, choline metabolism, sucrose metabolism, glycolysis/gluconeogenesis pathway, tricarboxylic acid (TCA) cycle, nucleotide metabolism, and shikimate-mediated secondary metabolism. The semi-dwarf mutant showed corresponding but less pronounced changes, especially in the gene expression levels. It indicates that OsCYP96B4 gene mutation in rice causes significant alteration in amino acid metabolism, carbohydrate metabolism, nucleotide metabolism, and shikimate-mediated secondary metabolism. The present study will provide essential information for the OsCYP96B4 gene function analysis and may serve as valuable reference data for the development of new semi-dwarf mutants.
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Mishra R, Joshi RK, Zhao K. Base editing in crops: current advances, limitations and future implications. PLANT BIOTECHNOLOGY JOURNAL 2020; 18:20-31. [PMID: 31365173 PMCID: PMC6920333 DOI: 10.1111/pbi.13225] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Revised: 07/23/2019] [Accepted: 07/29/2019] [Indexed: 05/19/2023]
Abstract
Targeted mutagenesis via genome-editing technologies holds great promise in developing improved crop varieties to meet future demands. Point mutations or single nucleotide polymorphisms often determine important agronomic traits of crops. Genome-editing-based single-base changes could generate elite trait variants in crop plants which help in accelerating crop improvement. Among the genome-editing technologies, base editing has emerged as a novel and efficient genome-editing approach which enables direct and irreversible conversion of one target base into another in a programmable manner. A base editor is a fusion of catalytically inactive CRISPR-Cas9 domain (Cas9 variants) and cytosine or adenosine deaminase domain that introduces desired point mutations in the target region enabling precise editing of genomes. In the present review, we have summarized the development of different base-editing platforms. Then, we have focussed on the current advances and the potential applications of this precise technology in crop improvement. The review also sheds light on the limitations associated with this technology. Finally, the future perspectives of this emerging technology towards crop improvement have been highlighted.
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Affiliation(s)
- Rukmini Mishra
- National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Institute of Crop ScienceChinese Academy of Agriculture Sciences (CAAS)BeijingChina
| | - Raj Kumar Joshi
- Department of BiotechnologyRama Devi Women's UniversityBhubaneswarOdishaIndia
| | - Kaijun Zhao
- National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Institute of Crop ScienceChinese Academy of Agriculture Sciences (CAAS)BeijingChina
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21
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Ferrero-Serrano Á, Cantos C, Assmann SM. The Role of Dwarfing Traits in Historical and Modern Agriculture with a Focus on Rice. Cold Spring Harb Perspect Biol 2019; 11:a034645. [PMID: 31358515 PMCID: PMC6824242 DOI: 10.1101/cshperspect.a034645] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Semidwarf stature is a valuable agronomic trait in grain crops that reduces lodging and increases harvest index. A fundamental advance during the 1960s Green Revolution was the introduction of semidwarf cultivars of rice and wheat. Essentially, all semidwarf varieties of rice under cultivation today owe their diminished stature to a specific null mutation in the gibberellic acid (GA) biosynthesis gene, SD1 However, it is now well-established that, in addition to GAs, brassinosteroids and strigolactones also control plant height. In this review, we describe the synthesis and signaling pathways of these three hormones as understood in rice and discuss the mutants and transgenics in these pathways that confer semidwarfism and other valuable architectural traits. We propose that such genes offer underexploited opportunities for broadening the genetic basis and germplasm in semidwarf rice breeding.
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Affiliation(s)
| | - Christian Cantos
- Biology Department, Penn State University, University Park, Pennsylvania 16802, USA
| | - Sarah M Assmann
- Biology Department, Penn State University, University Park, Pennsylvania 16802, USA
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22
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Zou X, Wang Q, Chen P, Yin C, Lin Y. Strigolactones regulate shoot elongation by mediating gibberellin metabolism and signaling in rice (Oryza sativa L.). JOURNAL OF PLANT PHYSIOLOGY 2019; 237:72-79. [PMID: 31026778 DOI: 10.1016/j.jplph.2019.04.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Revised: 04/04/2019] [Accepted: 04/05/2019] [Indexed: 05/18/2023]
Abstract
Strigolactones (SLs) are plant hormones that regulate diverse physiological processes including shoot elongation. However, little is known about the regulatory mechanism of SLs in rice shoot elongation. Our results demonstrate that defects in SL biosynthesis or signaling led to dwarfism, and the dwarf statures of SL-deficient mutant (d17) and SL-insensitive mutant (d14) were restored to wild-type (WT) by gibberellin (GA) treatment, indicating that their dwarfism was associated with decreased GA content or weakened GA sensitivity. Our results indicate that the bioactive GA1 contents in d17 and d14 were lower than those in WT, due to the downregulated transcription of GA biosynthesis genes and upregulated transcription of GA inactivation genes. Moreover, d17 and d14 exhibited weakened GA-responsive sensitivity compared with WT. Although the transcription levels of cell division- and cell elongation-related genes were upregulated by GA3 treatment, the increase in transcription of d17 and d14 was lower than that in WT. These results suggest that SL is required for rice shoot elongation by mediating GA metabolism and signaling. Therefore, a deficiency in SL biosynthesis or signaling leads to decreased GA content and weakened GA response, which in turn reduces shoot length by downregulating transcription levels of cell division- and cell elongation-related genes.
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Affiliation(s)
- Xiao Zou
- MOA Key Laboratory of Crop Ecophysiology and Farming System in the Middle Reaches of the Yangtze River, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China.
| | - Qi Wang
- MOA Key Laboratory of Crop Ecophysiology and Farming System in the Middle Reaches of the Yangtze River, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China.
| | - Peisai Chen
- MOA Key Laboratory of Crop Ecophysiology and Farming System in the Middle Reaches of the Yangtze River, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China.
| | - Changxi Yin
- MOA Key Laboratory of Crop Ecophysiology and Farming System in the Middle Reaches of the Yangtze River, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Huazhong Agricultural University, Wuhan 430070, China.
| | - Yongjun Lin
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Huazhong Agricultural University, Wuhan 430070, China.
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23
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Tomlinson L, Yang Y, Emenecker R, Smoker M, Taylor J, Perkins S, Smith J, MacLean D, Olszewski NE, Jones JDG. Using CRISPR/Cas9 genome editing in tomato to create a gibberellin-responsive dominant dwarf DELLA allele. PLANT BIOTECHNOLOGY JOURNAL 2019; 17:132-140. [PMID: 29797460 PMCID: PMC6330640 DOI: 10.1111/pbi.12952] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Revised: 05/01/2018] [Accepted: 05/16/2018] [Indexed: 05/05/2023]
Abstract
The tomato PROCERA gene encodes a DELLA protein, and loss-of-function mutations derepress growth. We used CRISPR/Cas9 and a single guide RNAs (sgRNA) to target mutations to the PROCERA DELLA domain, and recovered several loss-of-function mutations and a dominant dwarf mutation that carries a deletion of one amino acid in the DELLA domain. This is the first report of a dominant dwarf PROCERA allele. This allele retains partial responsiveness to exogenously applied gibberellin. Heterozygotes show an intermediate phenotype at the seedling stage, but adult heterozygotes are as dwarfed as homozygotes.
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Affiliation(s)
| | - Ying Yang
- The Sainsbury LaboratoryNorwich Research ParkNorwichUK
| | - Ryan Emenecker
- Department of Plant and Microbial BiologyUniversity of MinnesotaSt. PaulMNUSA
| | | | - Jodie Taylor
- The Sainsbury LaboratoryNorwich Research ParkNorwichUK
| | - Sara Perkins
- The Sainsbury LaboratoryNorwich Research ParkNorwichUK
| | - Justine Smith
- The Sainsbury LaboratoryNorwich Research ParkNorwichUK
| | - Dan MacLean
- The Sainsbury LaboratoryNorwich Research ParkNorwichUK
| | - Neil E. Olszewski
- Department of Plant and Microbial BiologyUniversity of MinnesotaSt. PaulMNUSA
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Alamin M, Zeng DD, Sultana MH, Qin R, Jin XL, Shi CH. Rice SDSFL1 plays a critical role in the regulation of plant structure through the control of different phytohormones and altered cell structure. JOURNAL OF PLANT PHYSIOLOGY 2018; 231:110-123. [PMID: 30253267 DOI: 10.1016/j.jplph.2018.09.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Revised: 09/09/2018] [Accepted: 09/09/2018] [Indexed: 06/08/2023]
Abstract
Semi-dwarfism is one of the most important agronomic traits for many cereal crops. In the present study, a mutant with semi-dwarf and short flag leaf 1, sdsfl1, was identified and characterized. The sdsfl1 mutant demonstrated some distinguished structural alterations, including shorter plant height and flag leaf length, increased tiller numbers and flag leaf width, and decreased panicle length compared with those of wild type (WT). Genetic analysis suggested that the mutant traits were completely controlled by a single recessive gene. The SDSFL1 gene was mapped to the long arm of chromosome 3 within a region of 44.6 kb between InDel markers A3P8.3 and A3P8.4. The DNA sequence analysis revealed that there was only a T to C substitution in the coding region of LOC_Os03g63970, resulting in the substitution of Tryptophan (Try) to Arginine (Arg) and encoding a GA 20 oxidase 1 protein of 372 amino acid residues. Photosynthesis analysis showed that the photosynthetic rate (Pn), stomatal conductance (Gs), and intercellular CO2 concentration (Ci) were significantly increased in sdsfl1. Chlorophyll a (Chl a), total Chl, and carotenoid contents were significantly increased in sdsfl1 compared with those in WT. sdsfl1 carried a reduced level of GA3 but reacted to exogenously applied gibberellins (GA). Moreover, the levels of abscisic acid (ABA), indole 3-acetic acid (IAA), and salicylic acid (SA) were notably improved in sdsfl1, whereas there was no noteworthy change in jasmonic acid (JA). The results thus offer a visible foundation for the molecular and physiological analysis of the SDSFL1 gene, which might participate in various functional pathways for controlling plant height and leaf length in rice breeding.
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Affiliation(s)
- Md Alamin
- Department of Agronomy, Zhejiang University, Hangzhou 310058, China
| | - Dong-Dong Zeng
- Department of Agronomy, Zhejiang University, Hangzhou 310058, China
| | | | - Ran Qin
- Department of Agronomy, Zhejiang University, Hangzhou 310058, China
| | - Xiao-Li Jin
- Department of Agronomy, Zhejiang University, Hangzhou 310058, China
| | - Chun-Hai Shi
- Department of Agronomy, Zhejiang University, Hangzhou 310058, China.
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Chen X, Xu P, Zhou J, Tao D, Yu D. Mapping and breeding value evaluation of a semi-dominant semi-dwarf gene in upland rice. PLANT DIVERSITY 2018; 40:238-244. [PMID: 30740570 PMCID: PMC6224660 DOI: 10.1016/j.pld.2018.09.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Revised: 08/29/2018] [Accepted: 09/03/2018] [Indexed: 06/01/2023]
Abstract
Plant height is an important trait related to yield potential and plant architecture. A suitable plant height plays a crucial role in improvement of rice yield and lodging resistance. In this study, we found that the traditional upland landrace 'Kaowenghan' (KWH) showed a special semi-dwarf phenotype. To identify the semi-dwarf gene from KWH, we raised BC2F4 semi-dwarf introgression lines (IL) by hybridization of the japonica rice cultivar 'Dianjingyou1' (DJY1) and KWH in a DJY1 background. The plant height of the homozygous semi-dwarf IL (IL-87) was significantly reduced compared with that of DJY1. The phenotype of the F1 progeny of the semi-dwarf IL-87 and DJY1 showed that the semi-dwarf phenotype was semi-dominant. QTL mapping indicated that the semi-dwarf phenotype was controlled by a major QTL qDH1 and was localized between the markers RM6696 and RM12047 on chromosome 1. We also developed near-isogenic lines (NIL) from the BC3F3 population, and found that the yield of homozygous NIL (NIL-2) was not significantly different compared to DJY1. Breeding value evaluation through investigation of the plant height of the progeny of NIL (NIL-2) and cultivars from different genetic background indicate that the novel semi-dwarf gene shows potential as a genetic resource for rice breeding.
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Affiliation(s)
- Xiaoqian Chen
- Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Peng Xu
- Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China
| | - Jiawu Zhou
- Food Crops Research Institute, Yunnan Academy of Agricultural Sciences (YAAS), Kunming, 650200, China
| | - Dayun Tao
- Food Crops Research Institute, Yunnan Academy of Agricultural Sciences (YAAS), Kunming, 650200, China
| | - Diqiu Yu
- Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China
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26
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Wu Z, Tang D, Liu K, Miao C, Zhuo X, Li Y, Tan X, Sun M, Luo Q, Cheng Z. Characterization of a new semi-dominant dwarf allele of SLR1 and its potential application in hybrid rice breeding. JOURNAL OF EXPERIMENTAL BOTANY 2018; 69:4703-4713. [PMID: 29955878 PMCID: PMC6137977 DOI: 10.1093/jxb/ery243] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Accepted: 06/26/2018] [Indexed: 05/04/2023]
Affiliation(s)
- Zhigang Wu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, China
- Institute of Rice Research, Agriculture College, Yunnan Agricultural University, Kunming, China
| | - Ding Tang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Kai Liu
- Institute of Agricultural Science in Jiangsu Coastal Areas, Yancheng, China
| | - Chunbo Miao
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Xiaoxuan Zhuo
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, China
| | - Yafei Li
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Xuelin Tan
- Institute of Rice Research, Agriculture College, Yunnan Agricultural University, Kunming, China
| | - Mingfa Sun
- Institute of Agricultural Science in Jiangsu Coastal Areas, Yancheng, China
| | - Qiong Luo
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, China
| | - Zhukuan Cheng
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
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27
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Li ZF, Guo Y, Ou L, Hong H, Wang J, Liu ZX, Guo B, Zhang L, Qiu L. Identification of the dwarf gene GmDW1 in soybean (Glycine max L.) by combining mapping-by-sequencing and linkage analysis. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2018; 131:1001-1016. [PMID: 29550969 PMCID: PMC5895683 DOI: 10.1007/s00122-017-3044-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Accepted: 12/17/2017] [Indexed: 05/10/2023]
Abstract
KEY MESSAGE GmDW1 encodes an ent-kaurene synthase (KS) acting at the early step of the biosynthesis pathway for gibberellins (GAs) and regulates the development of plant height in soybean. Plant height is an important component of plant architecture, and significantly affects crop breeding practices and yield. Here, we report the characterization of an EMS-induced dwarf mutant (dw) of the soybean cultivar Zhongpin 661 (ZDD23893). The dw mutant displayed reduced plant height and shortened internodes, both of which were mainly attributed to the longitudinally decreased cell length. The bioactive GA1 (gibberellin A1) and GA4 (gibberellin A4) were not detectable in the stem of dw, and the dwarf phenotype could be rescued by treatment with exogenous GA3. Genetic analysis showed that the dwarf trait of dw was controlled by a recessive nuclear gene. By combining linkage analysis and mapping-by-sequencing, we mapped the GmDW1 gene to an approximately 460-kb region on chromosome (Chr.) 8, containing 36 annotated genes in the reference Willliams 82 genome. Of these genes, we identified two nonsynonymous single nucleotide polymorphisms (SNPs) that are present in the encoding regions of Gmdw1 and Glyma.08G165100 in dw, respectively. However, only the SNP mutation (T>A) at nucleotide 1224 in Gmdw1 cosegregated with the dwarf phenotype. GmDW1 encodes an ent-kaurene synthase, and was expressed in various tissues including root, stem, and leaf. Further phenotypic analysis of the allelic variations in soybean accessions strongly indicated that GmDW1 is responsible for the dwarf phenotype in dw. Our results provide important information for improving our understanding of the genetics of soybean plant height and crop breeding.
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Affiliation(s)
- Zhong-Feng Li
- National Key Facility for Gene Resources and Genetic Improvement/Key Laboratory of Crop Germplasm Utilization, Ministry of Agriculture, Institute of Crop Sciences, Chinese Academy of Agricultural Science, No. 12 Zhongguancun South Street, Haidian District, Beijing, 100081, People's Republic of China
| | - Yong Guo
- National Key Facility for Gene Resources and Genetic Improvement/Key Laboratory of Crop Germplasm Utilization, Ministry of Agriculture, Institute of Crop Sciences, Chinese Academy of Agricultural Science, No. 12 Zhongguancun South Street, Haidian District, Beijing, 100081, People's Republic of China
| | - Lin Ou
- College of Agriculture, Yangzi University, Jingzhou, 434025, People's Republic of China
| | - Huilong Hong
- National Key Facility for Gene Resources and Genetic Improvement/Key Laboratory of Crop Germplasm Utilization, Ministry of Agriculture, Institute of Crop Sciences, Chinese Academy of Agricultural Science, No. 12 Zhongguancun South Street, Haidian District, Beijing, 100081, People's Republic of China
| | - Jun Wang
- College of Agriculture, Yangzi University, Jingzhou, 434025, People's Republic of China
| | - Zhang-Xiong Liu
- National Key Facility for Gene Resources and Genetic Improvement/Key Laboratory of Crop Germplasm Utilization, Ministry of Agriculture, Institute of Crop Sciences, Chinese Academy of Agricultural Science, No. 12 Zhongguancun South Street, Haidian District, Beijing, 100081, People's Republic of China
| | - Bingfu Guo
- National Key Facility for Gene Resources and Genetic Improvement/Key Laboratory of Crop Germplasm Utilization, Ministry of Agriculture, Institute of Crop Sciences, Chinese Academy of Agricultural Science, No. 12 Zhongguancun South Street, Haidian District, Beijing, 100081, People's Republic of China
| | - Lijuan Zhang
- National Key Facility for Gene Resources and Genetic Improvement/Key Laboratory of Crop Germplasm Utilization, Ministry of Agriculture, Institute of Crop Sciences, Chinese Academy of Agricultural Science, No. 12 Zhongguancun South Street, Haidian District, Beijing, 100081, People's Republic of China
| | - Lijuan Qiu
- National Key Facility for Gene Resources and Genetic Improvement/Key Laboratory of Crop Germplasm Utilization, Ministry of Agriculture, Institute of Crop Sciences, Chinese Academy of Agricultural Science, No. 12 Zhongguancun South Street, Haidian District, Beijing, 100081, People's Republic of China.
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28
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Hua K, Tao X, Yuan F, Wang D, Zhu JK. Precise A·T to G·C Base Editing in the Rice Genome. MOLECULAR PLANT 2018; 11:627-630. [PMID: 29476916 DOI: 10.1016/j.molp.2018.02.007] [Citation(s) in RCA: 136] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Revised: 01/23/2018] [Accepted: 02/11/2018] [Indexed: 05/19/2023]
Affiliation(s)
- Kai Hua
- Shanghai Center for Plant Stress Biology, CAS Center of Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaoping Tao
- Shanghai Center for Plant Stress Biology, CAS Center of Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Fengtong Yuan
- Shanghai Center for Plant Stress Biology, CAS Center of Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Dong Wang
- Laboratory of Molecular Biology and Gene Engineering in Jiangxi Province, College of Life Science, Nanchang University, Jiangxi 330031, China
| | - Jian-Kang Zhu
- Shanghai Center for Plant Stress Biology, CAS Center of Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China; Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN 47907, USA.
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29
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Yimer HZ, Nahar K, Kyndt T, Haeck A, Van Meulebroek L, Vanhaecke L, Demeestere K, Höfte M, Gheysen G. Gibberellin antagonizes jasmonate-induced defense against Meloidogyne graminicola in rice. THE NEW PHYTOLOGIST 2018; 218:646-660. [PMID: 29464725 DOI: 10.1111/nph.15046] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Accepted: 01/10/2018] [Indexed: 05/23/2023]
Abstract
Gibberellin (GA) regulates various plant growth and developmental processes, but its role in pathogen attack, and especially nematode-plant interactions, still remains to be elucidated. An in-depth characterization of the role of GA in nematode infection was conducted using mutant lines of rice, chemical inhibitors, and phytohormone measurements. Our results showed that GA influences rice-Meloidogyne graminicola interactions in a concentration-dependent manner. Foliar spray of plants with a low concentration of gibberellic acid enhanced nematode infection. Biosynthetic and signaling mutants confirmed the importance of gibberellin for rice susceptibility to M. graminicola infection. Our study also demonstrates that GA signaling suppresses jasmonate (JA)-mediated defense against M. graminicola, and likewise the JA-induced defense against M. graminicola requires SLENDER RICE1 (SLR1)-mediated repression of the GA pathway. In contrast to observations from other plant-pathogen interactions, GA plays a dominant role over JA in determining susceptibility to M. graminicola in rice. This GA-induced nematode susceptibility was largely independent of auxin biosynthesis, but relied on auxin transport. In conclusion, we showed that GA-JA antagonistic crosstalk is at the forefront of the interaction between rice and M. graminicola, and SLR1 plays a central role in the JA-mediated defense response in rice against this nematode.
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Affiliation(s)
- Henok Zemene Yimer
- Department of Molecular Biotechnology, Ghent University, 9000, Ghent, Belgium
- Department of Crop protection, Ghent University, Ghent, Belgium
| | - Kamrun Nahar
- Department of Molecular Biotechnology, Ghent University, 9000, Ghent, Belgium
| | - Tina Kyndt
- Department of Molecular Biotechnology, Ghent University, 9000, Ghent, Belgium
| | - Ashley Haeck
- Research Group EnVOC, Department of Sustainable Organic Chemistry and Technology, Ghent University, Ghent, Belgium
| | - Lieven Van Meulebroek
- Department of Veterinary Public Health and Food Safety, Laboratory of Chemical Analysis, Ghent University, Merelbeke, Belgium
| | - Lynn Vanhaecke
- Department of Veterinary Public Health and Food Safety, Laboratory of Chemical Analysis, Ghent University, Merelbeke, Belgium
| | - Kristof Demeestere
- Research Group EnVOC, Department of Sustainable Organic Chemistry and Technology, Ghent University, Ghent, Belgium
| | - Monica Höfte
- Department of Crop protection, Ghent University, Ghent, Belgium
| | - Godelieve Gheysen
- Department of Molecular Biotechnology, Ghent University, 9000, Ghent, Belgium
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30
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Liu C, Zheng S, Gui J, Fu C, Yu H, Song D, Shen J, Qin P, Liu X, Han B, Yang Y, Li L. Shortened Basal Internodes Encodes a Gibberellin 2-Oxidase and Contributes to Lodging Resistance in Rice. MOLECULAR PLANT 2018; 11:288-299. [PMID: 29253619 DOI: 10.1016/j.molp.2017.12.004] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2017] [Revised: 12/08/2017] [Accepted: 12/08/2017] [Indexed: 05/05/2023]
Abstract
Breeding semi-dwarf varieties to improve lodging resistance has been proven to be enormously successful in increasing grain yield since the advent of the "green revolution." However, the breeding of the majority of semi-dwarf rice varieties in Asia has been dependent mainly on genetic introduction of the mutant alleles of SD1, which encodes a gibberellin (GA) 20-oxidase, OsGA20ox2, for catalyzing GA biosynthesis. Here, we report a new rice lodging-resistance gene, Shortened Basal Internodes (SBI), which encodes a gibberellin 2-oxidase and specifically controls the elongation of culm basal internodes through deactivating GA activity. SBI is predominantly expressed in culm basal internodes. Genetic analyses indicate that SBI is a semi-dominant gene affecting rice height and lodging resistance. SBI allelic variants display different activities and are associated with the height of rice varieties. Breeding with higher activity of the SBI allele generates new rice varieties with improved lodging resistance and increased yield. The discovery of the SBI provides a desirable gene resource for producing semi-dwarf rice phenotypes and offers an effective strategy for breeding rice varieties with enhanced lodging resistance and high yield.
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Affiliation(s)
- Chang Liu
- National Key Laboratory of Plant Molecular Genetics and CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China; University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Shuai Zheng
- National Key Laboratory of Plant Molecular Genetics and CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China; University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Jinshan Gui
- National Key Laboratory of Plant Molecular Genetics and CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Chenjian Fu
- Yuan Longping Agriculture High-Tech Co., Ltd., Hunan 410001, China
| | - Hasi Yu
- National Key Laboratory of Plant Molecular Genetics and CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China; University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Dongliang Song
- National Key Laboratory of Plant Molecular Genetics and CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Junhui Shen
- National Key Laboratory of Plant Molecular Genetics and CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Peng Qin
- Yuan Longping Agriculture High-Tech Co., Ltd., Hunan 410001, China
| | | | - Bin Han
- National Center of Plant Gene Research and CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200233, China
| | - Yuanzhu Yang
- Yuan Longping Agriculture High-Tech Co., Ltd., Hunan 410001, China; Hunan Ava Seed Research Institute, Hunan 410119, China; Hunan Engineering Laboratory for Disease and Insect-Resistant Rice Breeding, Hunan 410119, China.
| | - Laigeng Li
- National Key Laboratory of Plant Molecular Genetics and CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China.
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Liu F, Wang P, Zhang X, Li X, Yan X, Fu D, Wu G. The genetic and molecular basis of crop height based on a rice model. PLANTA 2018; 247:1-26. [PMID: 29110072 DOI: 10.1007/s00425-017-2798-1] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Accepted: 10/15/2017] [Indexed: 05/04/2023]
Abstract
This review presents genetic and molecular basis of crop height using a rice crop model. Height is controlled by multiple genes with potential to be manipulated through breeding strategies to improve productivity. Height is an important factor affecting crop architecture, apical dominance, biomass, resistance to lodging, tolerance to crowding and mechanical harvesting. The impressive increase in wheat and rice yield during the 'green revolution' benefited from a combination of breeding for high-yielding dwarf varieties together with advances in agricultural mechanization, irrigation and agrochemical/fertilizer use. To maximize yield under irrigation and high fertilizer use, semi-dwarfing is optimal, whereas extreme dwarfing leads to decreased yield. Rice plant height is controlled by genes that lie in a complex regulatory network, mainly involved in the biosynthesis or signal transduction of phytohormones such as gibberellins, brassinosteroids and strigolactones. Additional dwarfing genes have been discovered that are involved in other pathways, some of which are uncharacterized. This review discusses our current understanding of the regulation of plant height using rice as a well-characterized model and highlights some of the most promising research that could lead to the development of new, high-yielding varieties. This knowledge underpins future work towards the genetic improvement of plant height in rice and other crops.
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Affiliation(s)
- Fang Liu
- Key Laboratory of Oil Crop Biology of the Ministry of Agriculture, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Pandi Wang
- Key Laboratory of Oil Crop Biology of the Ministry of Agriculture, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Xiaobo Zhang
- State Key Laboratory of Crop Breeding Technology Innovation and Integration, China National Seed Group Co., Ltd., Wuhan, 430206, China
| | - Xiaofei Li
- Key Laboratory of Oil Crop Biology of the Ministry of Agriculture, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Xiaohong Yan
- Key Laboratory of Oil Crop Biology of the Ministry of Agriculture, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Donghui Fu
- The Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Agronomy College, Jiangxi Agricultural University, Nanchang, China.
| | - Gang Wu
- Key Laboratory of Oil Crop Biology of the Ministry of Agriculture, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, China.
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Mishra R, Joshi RK, Zhao K. Genome Editing in Rice: Recent Advances, Challenges, and Future Implications. FRONTIERS IN PLANT SCIENCE 2018; 9:1361. [PMID: 30283477 PMCID: PMC6156261 DOI: 10.3389/fpls.2018.01361] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Accepted: 08/28/2018] [Indexed: 05/03/2023]
Abstract
Rice (Oryza sativa L.) is the major food source for more than three billion people of the world. In the last few decades, the classical, mutational, and molecular breeding approaches have brought about tremendous increase in rice productivity with the development of novel rice varieties. However, stagnation in rice yield has been reported in recent decade owing to several factors including the emergence of pests and phyto pathogens, climate change, and other environmental issues posing great threat to global food security. There is an urgent need to produce more rice and associated cereals to satisfy the mammoth task of feeding a still growing population expected to reach 9.7 billion by 2050. Advances in genomics and emergence of multiple genome-editing technologies through use of engineered site-specific nucleases (SSNs) have revolutionized the field of plant science and agriculture. Among them, the CRISPR/Cas9 system is the most advanced and widely accepted because of its simplicity, robustness, and high efficiency. The availability of huge genomic resources together with a small genome size makes rice more suitable and feasible for genetic manipulation. As such, rice has been increasingly used to test the efficiency of different types of genome editing technologies to study the functions of various genes and demonstrate their potential in genetic improvement. Recently developed approaches including CRISPR/Cpf1 system and base editors have evolved as more efficient and accurate genome editing tools which might accelerate the pace of crop improvement. In the present review, we focus on the genome editing strategies for rice improvement, thereby highlighting the applications and advancements of CRISPR/Cas9 system. This review also sheds light on the role of CRISPR/Cpf1 and base editors in the field of genome editing highlighting major challenges and future implications of these tools in rice improvement.
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Affiliation(s)
- Rukmini Mishra
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Raj Kumar Joshi
- Department of Biotechnology, Rama Devi Women’s University, Bhubaneswar, India
| | - Kaijun Zhao
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
- *Correspondence: Kaijun Zhao,
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Mishra R, Joshi RK, Zhao K. Genome Editing in Rice: Recent Advances, Challenges, and Future Implications. FRONTIERS IN PLANT SCIENCE 2018; 9:1361. [PMID: 30283477 DOI: 10.33389/fpls.2018.01361] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Accepted: 08/28/2018] [Indexed: 05/18/2023]
Abstract
Rice (Oryza sativa L.) is the major food source for more than three billion people of the world. In the last few decades, the classical, mutational, and molecular breeding approaches have brought about tremendous increase in rice productivity with the development of novel rice varieties. However, stagnation in rice yield has been reported in recent decade owing to several factors including the emergence of pests and phyto pathogens, climate change, and other environmental issues posing great threat to global food security. There is an urgent need to produce more rice and associated cereals to satisfy the mammoth task of feeding a still growing population expected to reach 9.7 billion by 2050. Advances in genomics and emergence of multiple genome-editing technologies through use of engineered site-specific nucleases (SSNs) have revolutionized the field of plant science and agriculture. Among them, the CRISPR/Cas9 system is the most advanced and widely accepted because of its simplicity, robustness, and high efficiency. The availability of huge genomic resources together with a small genome size makes rice more suitable and feasible for genetic manipulation. As such, rice has been increasingly used to test the efficiency of different types of genome editing technologies to study the functions of various genes and demonstrate their potential in genetic improvement. Recently developed approaches including CRISPR/Cpf1 system and base editors have evolved as more efficient and accurate genome editing tools which might accelerate the pace of crop improvement. In the present review, we focus on the genome editing strategies for rice improvement, thereby highlighting the applications and advancements of CRISPR/Cas9 system. This review also sheds light on the role of CRISPR/Cpf1 and base editors in the field of genome editing highlighting major challenges and future implications of these tools in rice improvement.
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Affiliation(s)
- Rukmini Mishra
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Raj Kumar Joshi
- Department of Biotechnology, Rama Devi Women's University, Bhubaneswar, India
| | - Kaijun Zhao
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
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Hirano K, Masuda R, Takase W, Morinaka Y, Kawamura M, Takeuchi Y, Takagi H, Yaegashi H, Natsume S, Terauchi R, Kotake T, Matsushita Y, Sazuka T. Screening of rice mutants with improved saccharification efficiency results in the identification of CONSTITUTIVE PHOTOMORPHOGENIC 1 and GOLD HULL AND INTERNODE 1. PLANTA 2017; 246:61-74. [PMID: 28357539 DOI: 10.1007/s00425-017-2685-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Accepted: 03/27/2017] [Indexed: 05/28/2023]
Abstract
The screening of rice mutants with improved cellulose to glucose saccharification efficiency (SE) identifies reduced xylan and/or ferulic acid, and a qualitative change of lignin to impact SE. To ensure the availability of sustainable energy, considerable effort is underway to utilize lignocellulosic plant biomass as feedstock for the production of biofuels. However, the high cost of degrading plant cell wall components to fermentable sugars (saccharification) has been problematic. One way to overcome this barrier is to develop plants possessing cell walls that are amenable to saccharification. In this study, we aimed to identify new molecular factors that influence saccharification efficiency (SE) in rice. By screening 22 rice mutants, we identified two lines, 122 and 108, with improved SE. Reduced xylan and ferulic acid within the cell wall of line 122 were probable reasons of improved SE. Line 108 showed reduced levels of thioglycolic-released lignin; however, the amount of Klason lignin was comparable to the wild-type, indicating that structural changes had occurred in the 108 lignin polymer which resulted in improved SE. Positional cloning revealed that the genes responsible for improved SE in 122 and 108 were rice CONSTITUTIVE PHOTOMORPHOGENIC 1 (OsCOP1) and GOLD HULL AND INTERNODE 1 (GH1), respectively, which have not been previously reported to influence SE. The screening of mutants for improved SE is an efficient approach to identify novel genes that affect SE, which is relevant in the development of crops as biofuel sources.
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Affiliation(s)
- Ko Hirano
- Bioscience and Biotechnology Center, Nagoya University, Nagoya, Aichi, 464-8601, Japan.
| | - Reiko Masuda
- Bioscience and Biotechnology Center, Nagoya University, Nagoya, Aichi, 464-8601, Japan
| | - Wakana Takase
- Bioscience and Biotechnology Center, Nagoya University, Nagoya, Aichi, 464-8601, Japan
| | - Yoichi Morinaka
- Bioscience and Biotechnology Center, Nagoya University, Nagoya, Aichi, 464-8601, Japan
- Zensho Holdings Co., Ltd., Tokyo, Japan
| | - Mayuko Kawamura
- Bioscience and Biotechnology Center, Nagoya University, Nagoya, Aichi, 464-8601, Japan
| | - Yoshinobu Takeuchi
- Rice Breeding Research Team, NARO Institute of Crop Science, Tsukuba, Ibaraki, Japan
| | - Hiroki Takagi
- Iwate Biotechnology Research Center, Kitakami, Iwate, Japan
| | | | | | | | - Toshihisa Kotake
- Graduate School of Science and Engineering, Saitama University, Saitama, Japan
- Institute for Environmental Science and Technology, Saitama University, Saitama, Japan
| | - Yasuyuki Matsushita
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Aichi, Japan
| | - Takashi Sazuka
- Bioscience and Biotechnology Center, Nagoya University, Nagoya, Aichi, 464-8601, Japan
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Zhao B, Li H, Li J, Wang B, Dai C, Wang J, Liu K. Brassica napus DS-3, encoding a DELLA protein, negatively regulates stem elongation through gibberellin signaling pathway. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2017; 130:727-741. [PMID: 28093630 DOI: 10.1007/s00122-016-2846-4] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2016] [Accepted: 12/22/2016] [Indexed: 05/20/2023]
Abstract
Identification and characterization of a semi-dwarfing gene ds-3 encoding a mutant DELLA protein regulating plant height through gibberellin signaling pathway. Lodging is one of the most important factors causing severe yield loss in oilseed rape. Utilization of semi-dwarf varieties has been proved the most effective way to increase lodging resistance and yield in many crops. To develop semi-dwarf germplasm in oilseed rape, we identified a semi-dwarf mutant ds-3 which showed a reduced response to phytohormones gibberellins (GAs). Genetic analysis indicated the dwarfism was controlled by a single semi-dominant gene, ds-3. The DS-3 gene was mapped to a genomic region on chromosome C07, which is syntenic to the region of a previously identified semi-dwarf gene ds-1 (BnaA06.RGA). In this region, DS-3 (BnaC07.RGA) gene was identified to encode a DELLA protein that functions as a repressor in GA signaling pathway. A substitution of proline to leucine was identified in ds-3 in the conserved VHYNP motif, which is essential for GA-dependent interaction between gibberellin receptor GID1 and DELLA proteins. Segregation analysis in the F2 population derived from the cross between ds-1 and ds-3 demonstrated that BnaA06.RGA displayed a stronger effect on plant height than BnaC07.RGA, indicating that different RGA genes may play different roles in stem elongation. In addition to BnaA06.RGA and BnaC07.RGA, two more RGA genes (BnaA09.RGA and BnaC09.RGA) were identified in the Brassica napus (B. napus) genome. Reverse-transcription polymerase chain reaction (RT-PCR) and yeast two-hybrid (Y2H) assays suggest that both BnaA09.RGA and BnaC09.RGA are transcribed in leaves and stems and can mediate GA signaling in vivo. These genes represent potential targets for screening ideal semi-dwarfing alleles for oilseed rape breeding.
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Affiliation(s)
- Bo Zhao
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Haitao Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Juanjuan Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Bo Wang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Cheng Dai
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Jing Wang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Kede Liu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China.
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Lu Y, Zhu JK. Precise Editing of a Target Base in the Rice Genome Using a Modified CRISPR/Cas9 System. MOLECULAR PLANT 2017; 10:523-525. [PMID: 27932049 DOI: 10.1016/j.molp.2016.11.013] [Citation(s) in RCA: 238] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2016] [Revised: 11/27/2016] [Accepted: 11/29/2016] [Indexed: 05/20/2023]
Affiliation(s)
- Yuming Lu
- 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; Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN 47907, USA.
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37
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Plum Fruit Development Occurs via Gibberellin-Sensitive and -Insensitive DELLA Repressors. PLoS One 2017; 12:e0169440. [PMID: 28076366 PMCID: PMC5226729 DOI: 10.1371/journal.pone.0169440] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2016] [Accepted: 12/17/2016] [Indexed: 01/16/2023] Open
Abstract
Fruit growth depends on highly coordinated hormonal activities. The phytohormone gibberellin (GA) promotes growth by triggering degradation of the growth-repressing DELLA proteins; however, the extent to which such proteins contribute to GA-mediated fruit development remains to be clarified. Three new plum genes encoding DELLA proteins, PslGAI, PslRGL and PslRGA were isolated and functionally characterized. Analysis of expression profile during fruit development suggested that PslDELLA are transcriptionally regulated during flower and fruit ontogeny with potential positive regulation by GA and ethylene, depending on organ and developmental stage. PslGAI and PslRGL deduced proteins contain all domains present in typical DELLA proteins. However, PslRGA exhibited a degenerated DELLA domain and subsequently lacks in GID1–DELLA interaction property. PslDELLA–overexpression in WT Arabidopsis caused dramatic disruption in overall growth including root length, stem elongation, plant architecture, flower structure, fertility, and considerable retardation in development due to dramatic distortion in GA-metabolic pathway. GA treatment enhanced PslGAI/PslRGL interaction with PslGID1 receptors, causing protein destabilization and relief of growth-restraining effect. By contrast, PslRGA protein was not degraded by GA due to its inability to interact with PslGID1. Relative to other PslDELLA–mutants, PslRGA–plants displayed stronger constitutive repressive growth that was irreversible by GA application. The present results describe additional complexities in GA-signalling during plum fruit development, which may be particularly important to optimize successful reproductive growth.
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38
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Fan S, Yao X, Liu J, Dong X, Mao T, Wang J. Characterization and fine mapping of osh15(t), a novel dwarf mutant gene in rice (Oryza sativa L.). Genes Genomics 2016. [DOI: 10.1007/s13258-016-0430-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Cho SH, Kang K, Lee SH, Lee IJ, Paek NC. OsWOX3A is involved in negative feedback regulation of the gibberellic acid biosynthetic pathway in rice (Oryza sativa). JOURNAL OF EXPERIMENTAL BOTANY 2016; 67:1677-87. [PMID: 26767749 PMCID: PMC4783357 DOI: 10.1093/jxb/erv559] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
The plant-specific WUSCHEL-related homeobox (WOX) nuclear proteins have important roles in the transcriptional regulation of many developmental processes. Among the rice (Oryza sativa) WOX proteins, a loss of OsWOX3A function in narrow leaf2 (nal2) nal3 double mutants (termed nal2/3) causes pleiotropic effects, such as narrow and curly leaves, opened spikelets, narrow grains, more tillers, and fewer lateral roots, but almost normal plant height. To examine OsWOX3A function in more detail, transgenic rice overexpressing OsWOX3A (OsWOX3A-OX) were generated; unexpectedly, all of them consistently exhibited severe dwarfism with very short and wide leaves, a phenotype that resembles that of gibberellic acid (GA)-deficient or GA-insensitive mutants. Exogenous GA3 treatment fully rescued the developmental defects of OsWOX3A-OX plants, suggesting that constitutive overexpression of OsWOX3A downregulates GA biosynthesis. Quantitative analysis of GA intermediates revealed significantly reduced levels of GA20 and bioactive GA1 in OsWOX3A-OX, possibly due to downregulation of the expression of KAO, which encodes ent-kaurenoic acid oxidase, a GA biosynthetic enzyme. Yeast one-hybrid and electrophoretic mobility shift assays revealed that OsWOX3A directly interacts with the KAO promoter. OsWOX3A expression is drastically and temporarily upregulated by GA3 and downregulated by paclobutrazol, a blocker of GA biosynthesis. These data indicate that OsWOX3A is a GA-responsive gene and functions in the negative feedback regulation of the GA biosynthetic pathway for GA homeostasis to maintain the threshold levels of endogenous GA intermediates throughout development.
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Affiliation(s)
- Sung-Hwan Cho
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Republic of Korea Present address: Division of Plant Science and Biochemistry, University of Missouri, Columbia, MO 65211, USA
| | - Kiyoon Kang
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Republic of Korea
| | - Sang-Hwa Lee
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Republic of Korea
| | - In-Jung Lee
- Division of Plant Biosciences, Kyungpook National University, Daegu, 702-701, Republic of Korea
| | - Nam-Chon Paek
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Republic of Korea
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Tamiru M, Undan JR, Takagi H, Abe A, Yoshida K, Undan JQ, Natsume S, Uemura A, Saitoh H, Matsumura H, Urasaki N, Yokota T, Terauchi R. A cytochrome P450, OsDSS1, is involved in growth and drought stress responses in rice (Oryza sativa L.). PLANT MOLECULAR BIOLOGY 2015; 88:85-99. [PMID: 25800365 DOI: 10.1007/s11103-015-0310-5] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2014] [Accepted: 03/16/2015] [Indexed: 05/05/2023]
Abstract
Cytochrome P450s are among the largest protein coding gene families in plant genomes. However, majority of the genes remain uncharacterized. Here, we report the characterization of dss1, a rice mutant showing dwarfism and reduced grain size. The dss1 phenotype is caused by a non-synonymous point mutation we identified in DSS1, which is member of a P450 gene cluster located on rice chromosome 3 and corresponds to the previously reported CYP96B4/SD37 gene. Phenotypes of several dwarf mutants characterized in rice are associated with defects in the biosynthesis or perception of the phytohormones gibberellins (GAs) and brassinosteroids (BRs). However, both GA and BR failed to rescue the dss1 phenotype. Hormone profiling revealed the accumulation of abscisic acid (ABA) and ABA metabolites, as well as significant reductions in GA19 and GA53 levels, precursors of the bioactive GA1, in the mutant. The dss1 contents of cytokinin and auxins were not significantly different from wild-type plants. Consistent with the accumulation of ABA and metabolites, germination and early growth was delayed in dss1, which also exhibited an enhanced tolerance to drought. Additionally, expressions of members of the DSS1/CYP96B gene cluster were regulated by drought stress and exogenous ABA. RNA-seq-based transcriptome profiling revealed, among others, that cell wall-related genes and genes involved in lipid metabolism were up- and down-regulated in dss1, respectively. Taken together, these findings suggest that DSS1 mediates growth and stress responses in rice by fine-tuning GA-to-ABA balance, and might as well play a role in lipid metabolism.
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Affiliation(s)
- Muluneh Tamiru
- Iwate Biotechnology Research Center, 22-174-4 Narita, Kitakami, Iwate, 024-0003, Japan,
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42
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A substitution mutation in OsCCD7 cosegregates with dwarf and increased tillering phenotype in rice. J Genet 2015; 93:389-401. [PMID: 25189234 DOI: 10.1007/s12041-014-0389-5] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
Dwarf plant height and tillering ability are two of the most important agronomic traits that determine the plant architecture, and have profound influence on grain yield in rice. To understand the molecular mechanism controlling these two traits, an EMS-induced recessive dwarf and increased tillering1 (dit1) mutant was characterized. The mutant showed proportionate reduction in each internode as compared to wild type revealing that it belonged to the category of dn-type of dwarf mutants. Besides, exogenous application of GA3 and 24-epibrassinolide, did not have any effect on the phenotype of the mutant. The gene was mapped on the long arm of chromosome 4, identified through positional candidate approach and verified by cosegregation analysis. It was found to encode carotenoid cleavage dioxygenase7 (CCD7) and identified as an allele of htd1. The mutant carried substitution of two nucleotides CC to AA in the sixth exon of the gene that resulted in substitution of serine by a stop codon in the mutant, and thus formation of a truncated protein, unlike amino acid substitution event in htd1. The new allele will facilitate further functional characterization of this gene, which may lead to unfolding of newer signalling pathways involving plant development and architecture.
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43
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Ayano M, Kani T, Kojima M, Sakakibara H, Kitaoka T, Kuroha T, Angeles-Shim RB, Kitano H, Nagai K, Ashikari M. Gibberellin biosynthesis and signal transduction is essential for internode elongation in deepwater rice. PLANT, CELL & ENVIRONMENT 2014; 37:2313-24. [PMID: 24891164 PMCID: PMC4282320 DOI: 10.1111/pce.12377] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2013] [Revised: 05/15/2014] [Accepted: 05/21/2014] [Indexed: 05/17/2023]
Abstract
Under flooded conditions, the leaves and internodes of deepwater rice can elongate above the water surface to capture oxygen and prevent drowning. Our previous studies showed that three major quantitative trait loci (QTL) regulate deepwater-dependent internode elongation in deepwater rice. In this study, we investigated the age-dependent internode elongation in deepwater rice. We also investigated the relationship between deepwater-dependent internode elongation and the phytohormone gibberellin (GA) by physiological and genetic approach using a QTL pyramiding line (NIL-1 + 3 + 12). Deepwater rice did not show internode elongation before the sixth leaf stage under deepwater condition. Additionally, deepwater-dependent internode elongation occurred on the sixth and seventh internodes during the sixth leaf stage. These results indicate that deepwater rice could not start internode elongation until the sixth leaf stage. Ultra-performance liquid chromatography tandem mass-spectrometry (UPLC-MS/MS) method for the phytohormone contents showed a deepwater-dependent GA1 and GA4 accumulation in deepwater rice. Additionally, a GA inhibitor abolished deepwater-dependent internode elongation in deepwater rice. On the contrary, GA feeding mimicked internode elongation under ordinary growth conditions. However, mutations in GA biosynthesis and signal transduction genes blocked deepwater-dependent internode elongation. These data suggested that GA biosynthesis and signal transduction are essential for deepwater-dependent internode elongation in deepwater rice.
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Affiliation(s)
- Madoka Ayano
- Bioscience and Biotechnology Center, Nagoya University, Nagoya, Aichi, 464-8601
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44
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Sakata T, Oda S, Tsunaga Y, Shomura H, Kawagishi-Kobayashi M, Aya K, Saeki K, Endo T, Nagano K, Kojima M, Sakakibara H, Watanabe M, Matsuoka M, Higashitani A. Reduction of gibberellin by low temperature disrupts pollen development in rice. PLANT PHYSIOLOGY 2014; 164:2011-9. [PMID: 24569847 PMCID: PMC3982758 DOI: 10.1104/pp.113.234401] [Citation(s) in RCA: 73] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2013] [Accepted: 02/24/2014] [Indexed: 05/18/2023]
Abstract
Microsporogenesis in rice (Oryza sativa) plants is susceptible to moderate low temperature (LT; approximately 19°C) that disrupts pollen development and causes severe reductions in grain yields. Although considerable research has been invested in the study of cool-temperature injury, a full understanding of the molecular mechanism has not been achieved. Here, we show that endogenous levels of the bioactive gibberellins (GAs) GA4 and GA7, and expression levels of the GA biosynthesis genes GA20ox3 and GA3ox1, decrease in the developing anthers by exposure to LT. By contrast, the levels of precursor GA12 were higher in response to LT. In addition, the expression of the dehydration-responsive element-binding protein DREB2B and SLENDER RICE1 (SLR1)/DELLA was up-regulated in response to LT. Mutants involved in GA biosynthetic and response pathways were hypersensitive to LT stress, including the semidwarf mutants sd1 and d35, the gain-of-function mutant slr1-d, and gibberellin insensitive dwarf1. The reduction in the number of sporogenous cells and the abnormal enlargement of tapetal cells occurred most severely in the GA-insensitive mutant. Application of exogenous GA significantly reversed the male sterility caused by LT, and simultaneous application of exogenous GA with sucrose substantially improved the extent of normal pollen development. Modern rice varieties carrying the sd1 mutation are widely cultivated, and the sd1 mutation is considered one of the greatest achievements of the Green Revolution. The protective strategy achieved by our work may help sustain steady yields of rice under global climate change.
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New approach to increasing rice lodging resistance and biomass yield through the use of high gibberellin producing varieties. PLoS One 2014; 9:e86870. [PMID: 24586255 PMCID: PMC3929325 DOI: 10.1371/journal.pone.0086870] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2013] [Accepted: 12/17/2013] [Indexed: 11/19/2022] Open
Abstract
Traditional breeding for high-yielding rice has been dependent on the widespread use of fertilizers and the cultivation of gibberellin (GA)-deficient semi-dwarf varieties. The use of semi-dwarf plants facilitates high grain yield since these varieties possess high levels of lodging resistance, and thus could support the high grain weight. Although this approach has been successful in increasing grain yield, it is desirable to further improve grain production and also to breed for high biomass. In this study, we re-examined the effect of GA on rice lodging resistance and biomass yield using several GA-deficient mutants (e.g. having defects in the biosynthesis or perception of GA), and high-GA producing line or mutant. GA-deficient mutants displayed improved bending-type lodging resistance due to their short stature; however they showed reduced breaking-type lodging resistance and reduced total biomass. In plants producing high amounts of GA, the bending-type lodging resistance was inferior to the original cultivars. The breaking-type lodging resistance was improved due to increased lignin accumulation and/or larger culm diameters. Further, these lines had an increase in total biomass weight. These results show that the use of rice cultivars producing high levels of GA would be a novel approach to create higher lodging resistance and biomass.
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Isolation and characterization of a dominant dwarf gene, d-h, in rice. PLoS One 2014; 9:e86210. [PMID: 24498271 PMCID: PMC3911911 DOI: 10.1371/journal.pone.0086210] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2013] [Accepted: 12/08/2013] [Indexed: 11/19/2022] Open
Abstract
Plant height is an important agronomic trait that affects grain yield. Previously, we reported a novel semi-dominant dwarfmutant, HD1, derived from chemical mutagenesis using N-methyl-N-nitrosourea (MNU) on a japonica rice cultivar, Hwacheong. In this study, we cloned the gene responsible for the dwarf mutant using a map-based approach. Fine mapping revealed that the mutant gene was located on the short arm of chromosome 1 in a 48 kb region. Sequencing of the candidate genes and rapid amplification of cDNA ends-polymerase chain reaction (RACE-PCR) analysis identified the gene, d-h, which encodes a protein of unknown function but whose sequence is conserved in other cereal crops. Real-time (RT)-PCR analysis and promoter activity assays showed that the d-h gene was primarily expressed in the nodes and the panicle. In the HD1 plant, the d-h gene was found to carry a 63-bp deletion in the ORF region that was subsequently confirmed by transgenic experiments to be directly responsible for the gain-of-function phenotype observed in the mutant. Since the mutant plants exhibit a defect in GA response, but not in the GA synthetic pathway, it appears that the d-h gene may be involved in a GA signaling pathway.
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Zhang J, Liu X, Li S, Cheng Z, Li C. The rice semi-dwarf mutant sd37, caused by a mutation in CYP96B4, plays an important role in the fine-tuning of plant growth. PLoS One 2014; 9:e88068. [PMID: 24498428 PMCID: PMC3912173 DOI: 10.1371/journal.pone.0088068] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2013] [Accepted: 01/06/2014] [Indexed: 12/02/2022] Open
Abstract
Plant cytochrome P450 has diverse roles in developmental processes and in the response to environmental cues. Here, we characterized the rice (Oryza sativa L ssp. indica cultivar 3037) semi-dwarf mutant sd37, in which the gene CYP96B4 (Cytochrome P450 96B subfamily) was identified and confirmed as the target by map-based cloning and a complementation test. A point mutation in the SRS2 domain of CYP96B4 resulted in a threonine to lysine substitution in the sd37 mutant. Examination of the subcellular localization of the protein revealed that SD37 was ER-localized protein. And SD37 was predominantly expressed in the shoot apical meristem and developing leaf and root maturation zone but not in the root apical meristem. The sd37 leaves, panicles, and seeds were smaller than those of the wild type. Histological analysis further revealed that a decrease in cell number in the mutant, specifically in the shoots, was the main cause of the dwarf phenotype. Microarray analysis demonstrated that the expression of several cell division-related genes was disturbed in the sd37 mutant. In addition, mutation or strongly overexpression of SD37 results in dwarf plants but moderate overexpression increases plant height. These data suggest that CYP96B4 may be an important regulator of plant growth that affects plant height in rice.
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Affiliation(s)
- Jie Zhang
- State Key Laboratory of Plant Genomics, National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
- National Engineering Research Center for Vegetables, Beijing Academy of Agriculture and Forestry Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Beijing, China
| | - Xiaoqiang Liu
- State Key Laboratory of Plant Genomics, National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Shuyu Li
- State Key Laboratory of Plant Genomics, National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Zhukuan Cheng
- State Key Laboratory of Plant Genomics, National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Chuanyou Li
- State Key Laboratory of Plant Genomics, National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
- * E-mail:
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Hori K, Ogiso-Tanaka E, Matsubara K, Yamanouchi U, Ebana K, Yano M. Hd16, a gene for casein kinase I, is involved in the control of rice flowering time by modulating the day-length response. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2013; 76:36-46. [PMID: 23789941 PMCID: PMC4223384 DOI: 10.1111/tpj.12268] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2013] [Revised: 05/29/2013] [Accepted: 06/17/2013] [Indexed: 05/02/2023]
Abstract
The alteration of photoperiod sensitivity has let breeders diversify flowering time in Oryza sativa (rice) and develop cultivars adjusted to a range of growing season periods. Map-based cloning revealed that the rice flowering-time quantitative trait locus (QTL) Heading date 16 (Hd16) encodes a casein kinase-I protein. One non-synonymous substitution in Hd16 resulted in decreased photoperiod sensitivity in rice, and this substitution occurred naturally in an old rice cultivar. By using near-isogenic lines with functional or deficient alleles of several rice flowering-time genes, we observed significant digenetic interactions between Hd16 and four other flowering-time genes (Ghd7, Hd1, DTH8 and Hd2). In a near-isogenic line with the weak-photoperiod-sensitivity allele of Hd16, transcription levels of Ehd1, Hd3a, and RFT1 increased under long-day conditions, and transcription levels of Hd3a and RFT1 decreased under short-day conditions. Expression analysis under continuous light and dark conditions showed that Hd16 was not likely to be associated with circadian clock regulation. Biochemical characterization indicated that the functional Hd16 recombinant protein specifically phosphorylated Ghd7. These results demonstrate that Hd16 acts as an inhibitor in the rice flowering pathway by enhancing the photoperiod response as a result of the phosphorylation of Ghd7.
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Affiliation(s)
| | | | - Kazuki Matsubara
- Institute of Crop Sciences, National Agriculture and Food Organization2-1-18 Kannondai, Tsukuba, Ibaraki, 305-8518, Japan
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Tan MK, Koval J, Ghalayini A. Novel genetic variants of GA-insensitive Rht-1 genes in hexaploid wheat and their potential agronomic value. PLoS One 2013; 8:e69690. [PMID: 23894524 PMCID: PMC3716649 DOI: 10.1371/journal.pone.0069690] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2012] [Accepted: 06/13/2013] [Indexed: 01/01/2023] Open
Abstract
This study has found numerous novel genetic variants of GA-insensitive dwarfing genes with potential agricultural value for crop improvement. The cultivar, Spica is a tall genotype and possesses the wild-type genes of Rht-A1a, Rht-B1a and Rht-D1a. The cultivar Quarrion possesses a null mutant in the DELLA motif in each of the 3 genomes. This is a first report of a null mutant of Rht-A1. In addition, novel null mutants which differ from reported null alleles of Rht-B1b, Rht-B1e and Rht-D1b have been found in Quarrion, Carnamah and Whistler. The accession, Aus1408 has an allele of Rht-B1 with a mutation in the conserved ‘TVHYNP’ N-terminal signal binding domain with possible implications on its sensitivity to GA. Mutations in the conserved C-terminal GRAS domain of Rht-A1 alleles with possible effects on expression have been found in WW1842, Quarrion and Drysdale. Genetic variants with putative spliceosomal introns in the GRAS domain have been found in all accessions except Spica. Genome-specific cis-sequences about 124 bp upstream of the start codon of the Rht-1 gene have been identified for each of the three genomes.
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Affiliation(s)
- Mui-Keng Tan
- Elizabeth Macarthur Agricultural Institute, New South Wales (NSW) Department of Primary Industries, Menangle, New South Wales, Australia.
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Chandler PM, Harding CA. 'Overgrowth' mutants in barley and wheat: new alleles and phenotypes of the 'Green Revolution' DELLA gene. JOURNAL OF EXPERIMENTAL BOTANY 2013; 64:1603-13. [PMID: 23382550 PMCID: PMC3617830 DOI: 10.1093/jxb/ert022] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
A suppressor screen using dwarf mutants of barley (Hordeum vulgare L.) led to the isolation of 'overgrowth' derivatives, which retained the original dwarfing gene but grew at a faster rate because of a new mutation. The new mutations were in the Slender1 (Sln1) gene (11/13 cases), which encodes the DELLA protein central to gibberellin (GA) signalling, showed 100% genetic linkage to Sln1 (1/13), or were in the Spindly1 (Spy1) gene (1/13), which encodes another protein involved in GA signalling. The overgrowth mutants were characterized by increased GA signalling, although the extent still depended on the background GA biosynthesis capacity, GA receptor function, and DELLA activity. A comparison between two GA responses, α-amylase production and leaf growth rate, revealed degrees of specificity for both the overgrowth allele and the GA response under consideration. Many overgrowth mutants were also isolated in a dwarf line of bread wheat (Triticum aestivum L.) and 19 new alleles were identified in the Rht-B1 gene, one of the 'Green Revolution' semi-dwarfing genes and the orthologue of Sln1. The sites of amino acid substitutions in the DELLA proteins of both species provide insight into DELLA function, and included examples where identical but independent substitutions were observed. In both species, the starting lines were too dwarfed to be directly useful in breeding programmes, but new overgrowth derivatives with semidwarf heights have now been characterized. The variation they exhibit in GA-influenced traits identifies novel alleles with perfect markers that are of potential use in breeding.
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