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Yu Z, Cui B, Xiao J, Jiao W, Wang H, Wang Z, Sun L, Song Q, Yuan J, Wang X. Dosage effect genes modulate grain development in synthesized Triticum durum-Haynaldia villosa allohexaploid. J Genet Genomics 2024:S1673-8527(24)00081-X. [PMID: 38670432 DOI: 10.1016/j.jgg.2024.04.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2023] [Revised: 04/15/2024] [Accepted: 04/15/2024] [Indexed: 04/28/2024]
Abstract
Polyploidization in plants often leads to increased cell size and grain size, which may be affected by the increased genome dosage and transcription abundance. The synthesized Triticum durum (AABB)-Haynaldia villosa (VV) amphiploid (AABBVV) has significantly increased grain size, especially grain length, than the tetraploid and diploid parents. To investigate how polyploidization affects grain development at the transcriptional level, we perform transcriptome analysis using the immature seeds of T. durum, H. villosa, and the amphiploid. The dosage effect genes are contributed more by differentially expressed genes from genome V of H. villosa. The dosage effect genes overrepresent grain development-related genes. Interestingly, the vernalization gene TaVRN1 is among the positive dosage effect genes in the T. durum‒H. villosa and T. turgidum‒Ae. tauschii amphiploids. The expression levels of TaVRN1 homologs are positively correlated with the grain size and weight. The TaVRN1-B1 or TaVRN1-D1 mutation shows delayed florescence, decreased cell size, grain size, and grain yield. These data indicate that dosage effect genes could be one of the important explanations for increased grain size by regulating grain development. The identification and functional validation of dosage effect genes may facilitate the finding of valuable genes for improving wheat yield.
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Affiliation(s)
- Zhongyu Yu
- State Key Lab of Crop Genetics & Germplasm Enhancement and Utilization, Cytogenetics Institute, Nanjing Agricultural University/JCIC-MCP/Zhongshan Biological Breeding Laboratory, Nanjing, Jiangsu 210095, China
| | - Baofeng Cui
- State Key Lab of Crop Genetics & Germplasm Enhancement and Utilization, Cytogenetics Institute, Nanjing Agricultural University/JCIC-MCP/Zhongshan Biological Breeding Laboratory, Nanjing, Jiangsu 210095, China
| | - Jin Xiao
- State Key Lab of Crop Genetics & Germplasm Enhancement and Utilization, Cytogenetics Institute, Nanjing Agricultural University/JCIC-MCP/Zhongshan Biological Breeding Laboratory, Nanjing, Jiangsu 210095, China
| | - Wu Jiao
- State Key Lab of Crop Genetics & Germplasm Enhancement and Utilization, Cytogenetics Institute, Nanjing Agricultural University/JCIC-MCP/Zhongshan Biological Breeding Laboratory, Nanjing, Jiangsu 210095, China
| | - Haiyan Wang
- State Key Lab of Crop Genetics & Germplasm Enhancement and Utilization, Cytogenetics Institute, Nanjing Agricultural University/JCIC-MCP/Zhongshan Biological Breeding Laboratory, Nanjing, Jiangsu 210095, China
| | - Zongkuan Wang
- State Key Lab of Crop Genetics & Germplasm Enhancement and Utilization, Cytogenetics Institute, Nanjing Agricultural University/JCIC-MCP/Zhongshan Biological Breeding Laboratory, Nanjing, Jiangsu 210095, China
| | - Li Sun
- State Key Lab of Crop Genetics & Germplasm Enhancement and Utilization, Cytogenetics Institute, Nanjing Agricultural University/JCIC-MCP/Zhongshan Biological Breeding Laboratory, Nanjing, Jiangsu 210095, China
| | - Qingxin Song
- State Key Lab of Crop Genetics & Germplasm Enhancement and Utilization, Cytogenetics Institute, Nanjing Agricultural University/JCIC-MCP/Zhongshan Biological Breeding Laboratory, Nanjing, Jiangsu 210095, China
| | - Jingya Yuan
- State Key Lab of Crop Genetics & Germplasm Enhancement and Utilization, Cytogenetics Institute, Nanjing Agricultural University/JCIC-MCP/Zhongshan Biological Breeding Laboratory, Nanjing, Jiangsu 210095, China.
| | - Xiue Wang
- State Key Lab of Crop Genetics & Germplasm Enhancement and Utilization, Cytogenetics Institute, Nanjing Agricultural University/JCIC-MCP/Zhongshan Biological Breeding Laboratory, Nanjing, Jiangsu 210095, China.
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Tao B, Ma Y, Wang L, He C, Chen J, Ge X, Zhao L, Wen J, Yi B, Tu J, Fu T, Shen J. Developmental pleiotropy of SDP1 from seedling to mature stages in B. napus. PLANT MOLECULAR BIOLOGY 2024; 114:49. [PMID: 38642182 DOI: 10.1007/s11103-024-01447-8] [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: 12/22/2023] [Accepted: 03/25/2024] [Indexed: 04/22/2024]
Abstract
Rapeseed, an important oil crop, relies on robust seedling emergence for optimal yields. Seedling emergence in the field is vulnerable to various factors, among which inadequate self-supply of energy is crucial to limiting seedling growth in early stage. SUGAR-DEPENDENT1 (SDP1) initiates triacylglycerol (TAG) degradation, yet its detailed function has not been determined in B. napus. Here, we focused on the effects of plant growth during whole growth stages and energy mobilization during seedling establishment by mutation in BnSDP1. Protein sequence alignment and haplotypic analysis revealed the conservation of SDP1 among species, with a favorable haplotype enhancing oil content. Investigation of agronomic traits indicated bnsdp1 had a minor impact on vegetative growth and no obvious developmental defects when compared with wild type (WT) across growth stages. The seed oil content was improved by 2.0-2.37% in bnsdp1 lines, with slight reductions in silique length and seed number per silique. Furthermore, bnsdp1 resulted in lower seedling emergence, characterized by a shrunken hypocotyl and poor photosynthetic capacity in the early stages. Additionally, impaired seedling growth, especially in yellow seedlings, was not fully rescued in medium supplemented with exogenous sucrose. The limited lipid turnover in bnsdp1 was accompanied by induced amino acid degradation and PPDK-dependent gluconeogenesis pathway. Analysis of the metabolites in cotyledons revealed active amino acid metabolism and suppressed lipid degradation, consistent with the RNA-seq results. Finally, we proposed strategies for applying BnSDP1 in molecular breeding. Our study provides theoretical guidance for understanding trade-off between oil accumulation and seedling energy mobilization in B. napus.
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Affiliation(s)
- Baolong Tao
- Huazhong Agricultural University, National Key Laboratory of Crop Genetic Improvement/National Engineering Research Center of Rapeseed, Wuhan, 430070, China
| | - Yina Ma
- Huazhong Agricultural University, National Key Laboratory of Crop Genetic Improvement/National Engineering Research Center of Rapeseed, Wuhan, 430070, China
| | - Liqin Wang
- Huazhong Agricultural University, National Key Laboratory of Crop Genetic Improvement/National Engineering Research Center of Rapeseed, Wuhan, 430070, China
| | - Chao He
- Huazhong Agricultural University, National Key Laboratory of Crop Genetic Improvement/National Engineering Research Center of Rapeseed, Wuhan, 430070, China
| | - Junlin Chen
- Huazhong Agricultural University, National Key Laboratory of Crop Genetic Improvement/National Engineering Research Center of Rapeseed, Wuhan, 430070, China
| | - Xiaoyu Ge
- Huazhong Agricultural University, National Key Laboratory of Crop Genetic Improvement/National Engineering Research Center of Rapeseed, Wuhan, 430070, China
| | - Lun Zhao
- Huazhong Agricultural University, National Key Laboratory of Crop Genetic Improvement/National Engineering Research Center of Rapeseed, Wuhan, 430070, China
| | - Jing Wen
- Huazhong Agricultural University, National Key Laboratory of Crop Genetic Improvement/National Engineering Research Center of Rapeseed, Wuhan, 430070, China
| | - Bin Yi
- Huazhong Agricultural University, National Key Laboratory of Crop Genetic Improvement/National Engineering Research Center of Rapeseed, Wuhan, 430070, China
| | - Jinxing Tu
- Huazhong Agricultural University, National Key Laboratory of Crop Genetic Improvement/National Engineering Research Center of Rapeseed, Wuhan, 430070, China
| | - Tingdong Fu
- Huazhong Agricultural University, National Key Laboratory of Crop Genetic Improvement/National Engineering Research Center of Rapeseed, Wuhan, 430070, China
| | - Jinxiong Shen
- Huazhong Agricultural University, National Key Laboratory of Crop Genetic Improvement/National Engineering Research Center of Rapeseed, Wuhan, 430070, China.
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Wang X, Feng S, Luo J, Song S, Lin J, Tian Y, Xu T, Ma J. The Role of FveAFB5 in Auxin-Mediated Responses and Growth in Strawberries. PLANTS (BASEL, SWITZERLAND) 2024; 13:1142. [PMID: 38674551 PMCID: PMC11055006 DOI: 10.3390/plants13081142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Revised: 04/16/2024] [Accepted: 04/17/2024] [Indexed: 04/28/2024]
Abstract
Auxin is a crucial hormone that regulates various aspects of plant growth and development. It exerts its effects through multiple signaling pathways, including the TIR1/AFB-based transcriptional regulation in the nucleus. However, the specific role of auxin receptors in determining developmental features in the strawberry (Fragaria vesca) remains unclear. Our research has identified FveAFB5, a potential auxin receptor, as a key player in the development and auxin responses of woodland strawberry diploid variety Hawaii 4. FveAFB5 positively influences lateral root development, plant height, and fruit development, while negatively regulating shoot branching. Moreover, the mutation of FveAFB5 confers strong resistance to the auxinic herbicide picloram, compared to dicamba and quinclorac. Transcriptome analysis suggests that FveAFB5 may initiate auxin and abscisic acid signaling to inhibit growth in response to picloram. Therefore, FveAFB5 likely acts as an auxin receptor involved in regulating multiple processes related to strawberry growth and development.
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Affiliation(s)
- Xuhui Wang
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China;
- Plant Synthetic Biology Center, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (S.F.); (J.L.); (S.S.); (J.L.); (Y.T.)
| | - Shuo Feng
- Plant Synthetic Biology Center, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (S.F.); (J.L.); (S.S.); (J.L.); (Y.T.)
| | - Jiangshan Luo
- Plant Synthetic Biology Center, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (S.F.); (J.L.); (S.S.); (J.L.); (Y.T.)
| | - Shikui Song
- Plant Synthetic Biology Center, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (S.F.); (J.L.); (S.S.); (J.L.); (Y.T.)
| | - Juncheng Lin
- Plant Synthetic Biology Center, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (S.F.); (J.L.); (S.S.); (J.L.); (Y.T.)
| | - Yunhe Tian
- Plant Synthetic Biology Center, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (S.F.); (J.L.); (S.S.); (J.L.); (Y.T.)
| | - Tongda Xu
- Plant Synthetic Biology Center, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (S.F.); (J.L.); (S.S.); (J.L.); (Y.T.)
| | - Jun Ma
- Plant Synthetic Biology Center, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (S.F.); (J.L.); (S.S.); (J.L.); (Y.T.)
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Wang H, Fang J, Li X, Sun P, Gao H, Ren Y, Liu Y, Feng Z, Dong L. Epigenetic Regulation of CYP72A385-Mediated Metabolic Resistance to Novel Auxin Herbicide Florpyrauxifen-benzyl in Echinochloa crus-galli (L.) P. Beauv. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024. [PMID: 38600742 DOI: 10.1021/acs.jafc.4c00804] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/12/2024]
Abstract
Weed's metabolic resistance to herbicides has undermined the sustainability of herbicides and global food security. Notably, we identified an Echinochloa crus-galli (L.) P. Beauv population (R) that evolved resistance to the never-used florpyrauxifen-benzyl, in which florpyrauxifen-benzyl was metabolized faster than the susceptible E. crus-galli population (S). RNA-seq identified potential metabolism-related genes, EcCYP72A385 and EcCYP85A1, whose expression in yeast exhibited the capacity to degrade florpyrauxifen-benzyl. Region-2 in the EcCYP72A385 promoter showed significant demethylation after florpyrauxifen-benzyl treatment in the R population. DNA methyltransferase inhibitors induce EcCYP72A385 overexpression in the S population and endow it with tolerance to florpyrauxifen-benzyl. Moreover, methyltransferase-like 7A (EcMETTL7A) was overexpressed in the S population and specifically bound to the EcCYP72A385 promoter. Transgenic EcCYP72A385 in Arabidopsis and Oryza sativa L. exhibited resistance to florpyrauxifen-benzyl, whereas EcMETTL7A transgenic plants were sensitive. Overall, EcCYP72A385 is the principal functional gene for conferring resistance to florpyrauxifen-benzyl and is regulated by EcMETTL7A in E. crus-galli.
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Affiliation(s)
- Hao Wang
- College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
- Key Laboratory of Integrated Pest Management on Crops in East China, Ministry of Agriculture and Rural Affairs, Nanjing Agricultural University, Nanjing 210095, China
| | - Jiapeng Fang
- College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
- Shanghai Academy of Agricultural Sciences, Shanghai 201403, China
| | - Xiaoxu Li
- College of Plant Protection, Shandong Agricultural University, Tai'an 271018, China
| | - Penglei Sun
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Haitao Gao
- College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
- Key Laboratory of Integrated Pest Management on Crops in East China, Ministry of Agriculture and Rural Affairs, Nanjing Agricultural University, Nanjing 210095, China
| | - Yanrong Ren
- College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
- Key Laboratory of Integrated Pest Management on Crops in East China, Ministry of Agriculture and Rural Affairs, Nanjing Agricultural University, Nanjing 210095, China
| | - Ying Liu
- College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
- Key Laboratory of Integrated Pest Management on Crops in East China, Ministry of Agriculture and Rural Affairs, Nanjing Agricultural University, Nanjing 210095, China
| | - Zhike Feng
- College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
- Key Laboratory of Integrated Pest Management on Crops in East China, Ministry of Agriculture and Rural Affairs, Nanjing Agricultural University, Nanjing 210095, China
| | - Liyao Dong
- College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
- Key Laboratory of Integrated Pest Management on Crops in East China, Ministry of Agriculture and Rural Affairs, Nanjing Agricultural University, Nanjing 210095, China
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Yang X, Wang M, Zhou Q, Xu X, Li Y, Hou X, Xiao D, Liu T. BcABF1 Plays a Role in the Feedback Regulation of Abscisic Acid Signaling via the Direct Activation of BcPYL4 Expression in Pakchoi. Int J Mol Sci 2024; 25:3877. [PMID: 38612692 PMCID: PMC11011251 DOI: 10.3390/ijms25073877] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2024] [Revised: 03/18/2024] [Accepted: 03/21/2024] [Indexed: 04/14/2024] Open
Abstract
Abscisic acid-responsive element-binding factor 1 (ABF1), a key transcription factor in the ABA signal transduction process, regulates the expression of downstream ABA-responsive genes and is involved in modulating plant responses to abiotic stress and developmental processes. However, there is currently limited research on the feedback regulation of ABF1 in ABA signaling. This study delves into the function of BcABF1 in Pakchoi. We observed a marked increase in BcABF1 expression in leaves upon ABA induction. The overexpression of BcABF1 not only spurred Arabidopsis growth but also augmented the levels of endogenous IAA. Furthermore, BcABF1 overexpression in Arabidopsis significantly decreased leaf water loss and enhanced the expression of genes associated with drought tolerance in the ABA pathway. Intriguingly, we found that BcABF1 can directly activate BcPYL4 expression, a critical receptor in the ABA pathway. Similar to BcABF1, the overexpression of BcPYL4 in Arabidopsis also reduces leaf water loss and promotes the expression of drought and other ABA-responsive genes. Finally, our findings suggested a novel feedback regulation mechanism within the ABA signaling pathway, wherein BcABF1 positively amplifies the ABA signal by directly binding to and activating the BcPYL4 promoter.
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Affiliation(s)
- Xiaoxue Yang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (East China), State Key Laboratory of Crop Genetics & Germplasm Enhancement, Ministry of Agriculture and Rural Affairs of China, Engineering Research Center of Germplasm Enhancement and Utilization of Horticultural Crops, Ministry of Education of China, Nanjing Agricultural University, Nanjing 210095, China; (X.Y.); (M.W.); (Q.Z.); (X.X.); (Y.L.); (X.H.)
| | - Meiyun Wang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (East China), State Key Laboratory of Crop Genetics & Germplasm Enhancement, Ministry of Agriculture and Rural Affairs of China, Engineering Research Center of Germplasm Enhancement and Utilization of Horticultural Crops, Ministry of Education of China, Nanjing Agricultural University, Nanjing 210095, China; (X.Y.); (M.W.); (Q.Z.); (X.X.); (Y.L.); (X.H.)
| | - Qian Zhou
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (East China), State Key Laboratory of Crop Genetics & Germplasm Enhancement, Ministry of Agriculture and Rural Affairs of China, Engineering Research Center of Germplasm Enhancement and Utilization of Horticultural Crops, Ministry of Education of China, Nanjing Agricultural University, Nanjing 210095, China; (X.Y.); (M.W.); (Q.Z.); (X.X.); (Y.L.); (X.H.)
| | - Xinfeng Xu
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (East China), State Key Laboratory of Crop Genetics & Germplasm Enhancement, Ministry of Agriculture and Rural Affairs of China, Engineering Research Center of Germplasm Enhancement and Utilization of Horticultural Crops, Ministry of Education of China, Nanjing Agricultural University, Nanjing 210095, China; (X.Y.); (M.W.); (Q.Z.); (X.X.); (Y.L.); (X.H.)
| | - Ying Li
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (East China), State Key Laboratory of Crop Genetics & Germplasm Enhancement, Ministry of Agriculture and Rural Affairs of China, Engineering Research Center of Germplasm Enhancement and Utilization of Horticultural Crops, Ministry of Education of China, Nanjing Agricultural University, Nanjing 210095, China; (X.Y.); (M.W.); (Q.Z.); (X.X.); (Y.L.); (X.H.)
| | - Xilin Hou
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (East China), State Key Laboratory of Crop Genetics & Germplasm Enhancement, Ministry of Agriculture and Rural Affairs of China, Engineering Research Center of Germplasm Enhancement and Utilization of Horticultural Crops, Ministry of Education of China, Nanjing Agricultural University, Nanjing 210095, China; (X.Y.); (M.W.); (Q.Z.); (X.X.); (Y.L.); (X.H.)
| | - Dong Xiao
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (East China), State Key Laboratory of Crop Genetics & Germplasm Enhancement, Ministry of Agriculture and Rural Affairs of China, Engineering Research Center of Germplasm Enhancement and Utilization of Horticultural Crops, Ministry of Education of China, Nanjing Agricultural University, Nanjing 210095, China; (X.Y.); (M.W.); (Q.Z.); (X.X.); (Y.L.); (X.H.)
| | - Tongkun Liu
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (East China), State Key Laboratory of Crop Genetics & Germplasm Enhancement, Ministry of Agriculture and Rural Affairs of China, Engineering Research Center of Germplasm Enhancement and Utilization of Horticultural Crops, Ministry of Education of China, Nanjing Agricultural University, Nanjing 210095, China; (X.Y.); (M.W.); (Q.Z.); (X.X.); (Y.L.); (X.H.)
- Sanya Research Institute, Nanjing Agricultural University, Nanjing 210095, China
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Wu D, Cao Y, Wang D, Zong G, Han K, Zhang W, Qi Y, Xu G, Zhang Y. Auxin receptor OsTIR1 mediates auxin signaling during seed filling in rice. PLANT PHYSIOLOGY 2024; 194:2434-2448. [PMID: 38214208 DOI: 10.1093/plphys/kiae013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Revised: 11/28/2023] [Accepted: 11/28/2023] [Indexed: 01/13/2024]
Abstract
Cereal endosperm represents the most important source of the world's food. Nevertheless, the molecular mechanisms behind sugar import into rice (Oryza sativa) endosperm and their relationship with auxin signaling are poorly understood. Here, we report that auxin transport inhibitor response 1 (TIR1) plays an essential role in rice grain yield and quality via modulating sugar transport into endosperm. The fluctuations of OsTIR1 transcripts parallel to the early stage of grain expansion among those of the 5 TIR1/AFB (auxin-signaling F-box) auxin co-receptor proteins. OsTIR1 is abundantly expressed in ovular vascular trace, nucellar projection, nucellar epidermis, aleurone layer cells, and endosperm, providing a potential path for sugar into the endosperm. Compared to wild-type (WT) plants, starch accumulation is repressed by mutation of OsTIR1 and improved by overexpression of the gene, ultimately leading to reduced grain yield and quality in tir1 mutants but improvement in overexpression lines. Of the rice AUXIN RESPONSE FACTOR (ARF) genes, only the OsARF25 transcript is repressed in tir1 mutants and enhanced by overexpression of OsTIR1; its highest transcript is recorded at 10 d after fertilization, consistent with OsTIR1 expression. Also, OsARF25 can bind the promoter of the sugar transporter OsSWEET11 (SWEET, sugars will eventually be exported transporter) in vivo and in vitro. arf25 and arf25/sweet11 mutants exhibit reduced starch content and seed size (relative to the WTs), similar to tir1 mutants. Our data reveal that OsTIR1 mediates sugar import into endosperm via the auxin signaling component OsARF25 interacting with sugar transporter OsSWEET11. The results of this study are of great significance to further clarify the regulatory mechanism of auxin signaling on grain development in rice.
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Affiliation(s)
- Daxia Wu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
- College of Resource and Environment, Anhui Science and Technology University, Fengyang 233100, China
| | - Yanan Cao
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Daojian Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Guoxinan Zong
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Kunxu Han
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Wei Zhang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Yanhua Qi
- Key Laboratory of Herbage & Endemic Crop Biology of Ministry of Education, Inner Mongolia Key Laboratory of Herbage & Endemic Crop Biotechnology, School of Life Sciences, Inner Mongolia University, Hohhot 010000, China
| | - Guohua Xu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
- Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing 210095, China
| | - Yali Zhang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
- Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing 210095, China
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Chen Z, Zhou W, Guo X, Ling S, Li W, Wang X, Yao J. Heat Stress Responsive Aux/IAA Protein, OsIAA29 Regulates Grain Filling Through OsARF17 Mediated Auxin Signaling Pathway. RICE (NEW YORK, N.Y.) 2024; 17:16. [PMID: 38374238 PMCID: PMC10876508 DOI: 10.1186/s12284-024-00694-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Accepted: 02/13/2024] [Indexed: 02/21/2024]
Abstract
High temperature during grain filling considerably reduces yield and quality in rice, but its molecular mechanisms are not fully understood. We investigated the functions of a seed preferentially expressed Aux/IAA gene, OsIAA29, under high temperature-stress in grain filling using CRISPR/Cas9, RNAi, and overexpression. We observed that the osiaa29 had a higher percentage of shrunken and chalkiness seed, as well as lower 1000-grain weight than ZH11 under high temperature. Meanwhile, the expression of OsIAA29 was induced and the IAA content was remarkably reduced in the ZH11 seeds under high temperature. In addition, OsIAA29 may enhance the transcriptional activation activity of OsARF17 through competition with OsIAA21 binding to OsARF17. Finally, chromatin immunoprecipitation quantitative real-time PCR (ChIP-qPCR) results proved that OsARF17 regulated expression of several starch and protein synthesis related genes (like OsPDIL1-1, OsSS1, OsNAC20, OsSBE1, and OsC2H2). Therefore, OsIAA29 regulates seed development in high temperature through competition with OsIAA21 in the binding to OsARF17, mediating auxin signaling pathway in rice. This study provides a theoretical basis and gene resources for auxin signaling and effective molecular design breeding.
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Affiliation(s)
- Zhanghao Chen
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Wei Zhou
- College of Life Sciences, Xinyang Normal University, Xinyang, 464000, China
| | - Xianyu Guo
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Sheng Ling
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Wang Li
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Xin Wang
- Key Laboratory of Molecular Biology and Genetic Engineering of Jiangxi Province, School of Life Sciences, Nanchang University, Nanchang, 330031, China.
| | - Jialing Yao
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China.
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8
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Wang X, Wang T, Yu P, Li Y, Lv X. NO enhances the adaptability to high-salt environments by regulating osmotic balance, antioxidant defense, and ion homeostasis in eelgrass based on transcriptome and metabolome analysis. FRONTIERS IN PLANT SCIENCE 2024; 15:1343154. [PMID: 38384762 PMCID: PMC10880190 DOI: 10.3389/fpls.2024.1343154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Accepted: 01/09/2024] [Indexed: 02/23/2024]
Abstract
Introduction Eelgrass is a typical marine angiosperm that exhibits strong adaptability to high-salt environments. Previous studies have shown that various growth and physiological indicators were significantly affected after the nitrate reductase (NR) pathway for nitric oxide (NO) synthesis in eelgrass was blocked. Methods To analyze the molecular mechanism of NO on the adaptability to high-salt environment in eelgrass, we treated eelgrass with artificial seawater (control group) and artificial seawater with 1 mM/L Na2WO4 (experimental group). Based on transcriptomics and metabolomics, we explored the molecular mechanism of NO affecting the salt tolerance of eelgrass. Results We obtained 326, 368, and 859 differentially expressed genes (DEGs) by transcriptome sequencing in eelgrass roots, stems, and leaves, respectively. Meanwhile, we obtained 63, 52, and 36 differentially accumulated metabolites (DAMs) by metabolomics in roots, stems, and leaves, respectively. Finally, through the combined analysis of transcriptome and metabolome, we found that the NO regulatory mechanism of roots and leaves of eelgrass is similar to that of terrestrial plants, while the regulatory mechanism of stems has similar and unique features. Discussion NO in eelgrass roots regulates osmotic balance and antioxidant defense by affecting genes in transmembrane transport and jasmonic acid-related pathways to improve the adaptability of eelgrass to high-salt environments. NO in eelgrass leaves regulates the downstream antioxidant defense system by affecting the signal transduction of plant hormones. NO in the stems of eelgrass regulates ion homeostasis by affecting genes related to ion homeostasis to enhance the adaptability of eelgrass to high-salt environments. Differently, after the NO synthesis was inhibited, the glyoxylate and dicarboxylate metabolism, as well as the tricarboxylic acid (TCA) cycle, was regulated by glucose metabolism as a complementary effect to cope with the high-salt environment in the stems of eelgrass. These are studies on the regulatory mechanism of NO in eelgrass, providing a theoretical basis for the study of the salt tolerance mechanism of marine plants and the improvement of terrestrial crop traits. The key genes discovered in this study can be applied to increase salt tolerance in terrestrial crops through cloning and molecular breeding methods in the future.
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Affiliation(s)
- Xianyan Wang
- Marine College, Shandong University, Weihai, China
| | | | - Pei Yu
- Shandong University-Australian National University (SDU-ANU) Joint Science College, Shandong University, Weihai, China
| | - Yuchun Li
- Marine College, Shandong University, Weihai, China
| | - Xinfang Lv
- Marine College, Shandong University, Weihai, China
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Zhang Z, Qu J, Lu M, Zhao X, Xu Y, Wang L, Liu Z, Shi Y, Liu C, Li Y, Wang C, Xu M, Nan Z, Cao Q, Pan J, Liu W, Li X, Sun Q, Wang W. The maize transcription factor CCT regulates drought tolerance by interacting with Fra a 1, E3 ligase WIPF2, and auxin response factor Aux/IAA8. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:103-122. [PMID: 37725963 DOI: 10.1093/jxb/erad372] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Accepted: 09/18/2023] [Indexed: 09/21/2023]
Abstract
Plants are commonly exposed to abiotic stressors, which can affect their growth, productivity, and quality. Previously, the maize transcription factor ZmCCT was shown to be involved in the photoperiod response, delayed flowering, and quantitative resistance to Gibberella stalk rot. In this study, we demonstrate that ZmCCT can regulate plant responses to drought. ZmCCT physically interacted with ZmFra a 1, ZmWIPF2, and ZmAux/IAA8, which localized to the cell membrane, cytoplasm, and nucleus, respectively, both in vitro and in vivo in a yeast two-hybrid screen in response to abiotic stress. Notably, ZmCCT recruits ZmWIPF2 to the nucleus, which has strong E3 self-ubiquitination activity dependent on its RING-H2 finger domain in vitro. When treated with higher indole-3-acetic acid/abscisic acid ratios, the height and root length of Y331-ΔTE maize plants increased. Y331-ΔTE plants exhibited increased responses to exogenously applied auxin or ABA compared to Y331 plants, indicating that ZmCCT may be a negative regulator of ABA signalling in maize. In vivo, ZmCCT promoted indole-3-acetic acid biosynthesis in ZmCCT-overexpressing Arabidopsis. RNA-sequencing and DNA affinity purification-sequencing analyses showed that ZmCCT can regulate the expression of ZmRD17, ZmAFP3, ZmPP2C, and ZmARR16 under drought. Our findings provide a detailed overview of the molecular mechanism controlling ZmCCT functions and highlight that ZmCCT has multiple roles in promoting abiotic stress tolerance.
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Affiliation(s)
- Zhaoheng Zhang
- Beijing Key Laboratory of New Technology in Agricultural Application, National Demonstration Center for Experimental Plant Production Education, College of Plant Science and Technology, Beijing University of Agriculture, Beijing, China
| | - Jiayue Qu
- Beijing Key Laboratory of New Technology in Agricultural Application, National Demonstration Center for Experimental Plant Production Education, College of Plant Science and Technology, Beijing University of Agriculture, Beijing, China
| | - Min Lu
- Beijing Key Laboratory of New Technology in Agricultural Application, National Demonstration Center for Experimental Plant Production Education, College of Plant Science and Technology, Beijing University of Agriculture, Beijing, China
| | - Xinyu Zhao
- Beijing Key Laboratory of New Technology in Agricultural Application, National Demonstration Center for Experimental Plant Production Education, College of Plant Science and Technology, Beijing University of Agriculture, Beijing, China
| | - Yang Xu
- Beijing Key Laboratory of New Technology in Agricultural Application, National Demonstration Center for Experimental Plant Production Education, College of Plant Science and Technology, Beijing University of Agriculture, Beijing, China
| | - Li Wang
- Beijing Key Laboratory of New Technology in Agricultural Application, National Demonstration Center for Experimental Plant Production Education, College of Plant Science and Technology, Beijing University of Agriculture, Beijing, China
| | - Zhongjia Liu
- Beijing Key Laboratory of New Technology in Agricultural Application, National Demonstration Center for Experimental Plant Production Education, College of Plant Science and Technology, Beijing University of Agriculture, Beijing, China
| | - Yingying Shi
- Beijing Key Laboratory of New Technology in Agricultural Application, National Demonstration Center for Experimental Plant Production Education, College of Plant Science and Technology, Beijing University of Agriculture, Beijing, China
| | - Chaotian Liu
- Beijing Key Laboratory of New Technology in Agricultural Application, National Demonstration Center for Experimental Plant Production Education, College of Plant Science and Technology, Beijing University of Agriculture, Beijing, China
| | - Yipu Li
- State Key Laboratory of Plant Physiology and Biochemistry, College of Agronomy and Biotechnology, National Maize Improvement Center, Center for Crop Functional Genomics and Molecular Breeding, China Agricultural University, Beijing, China
- Agricultural College, Inner Mongolia Agricultural University, Hohhot, China
| | - Chao Wang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Agronomy and Biotechnology, National Maize Improvement Center, Center for Crop Functional Genomics and Molecular Breeding, China Agricultural University, Beijing, China
| | - Mingliang Xu
- State Key Laboratory of Plant Physiology and Biochemistry, College of Agronomy and Biotechnology, National Maize Improvement Center, Center for Crop Functional Genomics and Molecular Breeding, China Agricultural University, Beijing, China
| | - Zhangjie Nan
- Beijing Key Laboratory of New Technology in Agricultural Application, National Demonstration Center for Experimental Plant Production Education, College of Plant Science and Technology, Beijing University of Agriculture, Beijing, China
| | - Qingqin Cao
- Beijing Key Laboratory of New Technology in Agricultural Application, National Demonstration Center for Experimental Plant Production Education, College of Plant Science and Technology, Beijing University of Agriculture, Beijing, China
| | - Jinbao Pan
- Beijing Key Laboratory of New Technology in Agricultural Application, National Demonstration Center for Experimental Plant Production Education, College of Plant Science and Technology, Beijing University of Agriculture, Beijing, China
| | - Wende Liu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xinrui Li
- Beijing Key Laboratory of New Technology in Agricultural Application, National Demonstration Center for Experimental Plant Production Education, College of Plant Science and Technology, Beijing University of Agriculture, Beijing, China
| | - Qingpeng Sun
- Beijing Key Laboratory of New Technology in Agricultural Application, National Demonstration Center for Experimental Plant Production Education, College of Plant Science and Technology, Beijing University of Agriculture, Beijing, China
| | - Weixiang Wang
- Beijing Key Laboratory of New Technology in Agricultural Application, National Demonstration Center for Experimental Plant Production Education, College of Plant Science and Technology, Beijing University of Agriculture, Beijing, China
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Wakeman A, Bennett T. Auxins and grass shoot architecture: how the most important hormone makes the most important plants. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:6975-6988. [PMID: 37474124 PMCID: PMC10690731 DOI: 10.1093/jxb/erad288] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2023] [Accepted: 07/19/2023] [Indexed: 07/22/2023]
Abstract
Cereals are a group of grasses cultivated by humans for their grain. It is from these cereal grains that the majority of all calories consumed by humans are derived. The production of these grains is the result of the development of a series of hierarchical reproductive structures that form the distinct shoot architecture of the grasses. Being spatiotemporally complex, the coordination of grass shoot development is tightly controlled by a network of genes and signals, including the key phytohormone auxin. Hormonal manipulation has therefore been identified as a promising potential approach to increasing cereal crop yields and therefore ultimately global food security. Recent work translating the substantial body of auxin research from model plants into cereal crop species is revealing the contribution of auxin biosynthesis, transport, and signalling to the development of grass shoot architecture. This review discusses this still-maturing knowledge base and examines the possibility that changes in auxin biology could have been a causative agent in the evolution of differences in shoot architecture between key grass species, or could underpin the future selective breeding of cereal crops.
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Affiliation(s)
- Alex Wakeman
- School of Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Tom Bennett
- School of Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
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11
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Zhou Z, Liu J, Meng W, Sun Z, Tan Y, Liu Y, Tan M, Wang B, Yang J. Integrated Analysis of Transcriptome and Metabolome Reveals Molecular Mechanisms of Rice with Different Salinity Tolerances. PLANTS (BASEL, SWITZERLAND) 2023; 12:3359. [PMID: 37836098 PMCID: PMC10574619 DOI: 10.3390/plants12193359] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 09/08/2023] [Accepted: 09/20/2023] [Indexed: 10/15/2023]
Abstract
Rice is a crucial global food crop, but it lacks a natural tolerance to high salt levels, resulting in significant yield reductions. To gain a comprehensive understanding of the molecular mechanisms underlying rice's salt tolerance, further research is required. In this study, the transcriptomic and metabolomic differences between the salt-tolerant rice variety Lianjian5 (TLJIAN) and the salt-sensitive rice variety Huajing5 (HJING) were examined. Transcriptome analysis revealed 1518 differentially expressed genes (DEGs), including 46 previously reported salt-tolerance-related genes. Notably, most of the differentially expressed transcription factors, such as NAC, WRKY, MYB, and EREBP, were upregulated in the salt-tolerant rice. Metabolome analysis identified 42 differentially accumulated metabolites (DAMs) that were upregulated in TLJIAN, including flavonoids, pyrocatechol, lignans, lipids, and trehalose-6-phosphate, whereas the majority of organic acids were downregulated in TLJIAN. The interaction network of 29 differentially expressed transporter genes and 19 upregulated metabolites showed a positive correlation between the upregulated calcium/cation exchange protein genes (OsCCX2 and CCX5_Ath) and ABC transporter gene AB2E_Ath with multiple upregulated DAMs in the salt-tolerant rice variety. Similarly, in the interaction network of differentially expressed transcription factors and 19 upregulated metabolites in TLJIAN, 6 NACs, 13 AP2/ERFs, and the upregulated WRKY transcription factors were positively correlated with 3 flavonoids, 3 lignans, and the lipid oleamide. These results suggested that the combined effects of differentially expressed transcription factors, transporter genes, and DAMs contribute to the enhancement of salt tolerance in TLJIAN. Moreover, this study provides a valuable gene-metabolite network reference for understanding the salt tolerance mechanism in rice.
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Affiliation(s)
- Zhenling Zhou
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Jiangsu Key Laboratory of Crop Cultivation and Physiology, Agricultural College, Yangzhou University, Yangzhou 225009, China;
- Lianyungang Academy of Agricultural Sciences, Lianyungang 222000, China; (Z.S.); (Y.T.); (Y.L.)
| | - Juan Liu
- College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China; (J.L.); (W.M.); (M.T.)
| | - Wenna Meng
- College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China; (J.L.); (W.M.); (M.T.)
| | - Zhiguang Sun
- Lianyungang Academy of Agricultural Sciences, Lianyungang 222000, China; (Z.S.); (Y.T.); (Y.L.)
| | - Yiluo Tan
- Lianyungang Academy of Agricultural Sciences, Lianyungang 222000, China; (Z.S.); (Y.T.); (Y.L.)
| | - Yan Liu
- Lianyungang Academy of Agricultural Sciences, Lianyungang 222000, China; (Z.S.); (Y.T.); (Y.L.)
| | - Mingpu Tan
- College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China; (J.L.); (W.M.); (M.T.)
| | - Baoxiang Wang
- Lianyungang Academy of Agricultural Sciences, Lianyungang 222000, China; (Z.S.); (Y.T.); (Y.L.)
| | - Jianchang Yang
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Jiangsu Key Laboratory of Crop Cultivation and Physiology, Agricultural College, Yangzhou University, Yangzhou 225009, China;
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12
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Shaheen N, Ahmad S, Alghamdi SS, Rehman HM, Javed MA, Tabassum J, Shao G. CRISPR-Cas System, a Possible "Savior" of Rice Threatened by Climate Change: An Updated Review. RICE (NEW YORK, N.Y.) 2023; 16:39. [PMID: 37688677 PMCID: PMC10492775 DOI: 10.1186/s12284-023-00652-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Accepted: 08/04/2023] [Indexed: 09/11/2023]
Abstract
Climate change has significantly affected agriculture production, particularly the rice crop that is consumed by almost half of the world's population and contributes significantly to global food security. Rice is vulnerable to several abiotic and biotic stresses such as drought, heat, salinity, heavy metals, rice blast, and bacterial blight that cause huge yield losses in rice, thus threatening food security worldwide. In this regard, several plant breeding and biotechnological techniques have been used to raise such rice varieties that could tackle climate changes. Nowadays, gene editing (GE) technology has revolutionized crop improvement. Among GE technology, CRISPR/Cas (Clustered Regularly Interspaced Short Palindromic Repeats/CRISPR-associated protein) system has emerged as one of the most convenient, robust, cost-effective, and less labor-intensive system due to which it has got more popularity among plant researchers, especially rice breeders and geneticists. Since 2013 (the year of first application of CRISPR/Cas-based GE system in rice), several trait-specific climate-resilient rice lines have been developed using CRISPR/Cas-based GE tools. Earlier, several reports have been published confirming the successful application of GE tools for rice improvement. However, this review particularly aims to provide an updated and well-synthesized brief discussion based on the recent studies (from 2020 to present) on the applications of GE tools, particularly CRISPR-based systems for developing CRISPR rice to tackle the current alarming situation of climate change, worldwide. Moreover, potential limitations and technical bottlenecks in the development of CRISPR rice, and prospects are also discussed.
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Affiliation(s)
- Nabeel Shaheen
- Seed Center and Plant Genetic Resources Bank, Ministry of Environment, Water & Agriculture, Riyadh, 14712, Saudi Arabia
| | - Shakeel Ahmad
- Seed Center and Plant Genetic Resources Bank, Ministry of Environment, Water & Agriculture, Riyadh, 14712, Saudi Arabia.
| | - Salem S Alghamdi
- Plant Production Department, College of Food and Agriculture Sciences, King Saud University, Riyadh, Saudi Arabia
| | - Hafiz Mamoon Rehman
- Centre for Agricultural Biochemistry and Biotechnology (CABB), University of Agriculture Faisalabad, Faisalabad, 38000, Pakistan
| | - Muhammad Arshad Javed
- Department of Plant Breeding and Genetics, Faculty of Agricultural Sciences, University of the Punjab, Lahore, 54590, Pakistan
| | - Javaria Tabassum
- Department of Plant Breeding and Genetics, Faculty of Agricultural Sciences, University of the Punjab, Lahore, 54590, Pakistan
| | - Gaoneng Shao
- State Key Laboratory of Rice Biology and China National Center for Rice Improvement, National Rice Research Institute, 310006, Hangzhou, China.
- Zhejiang Lab, 310006, Hangzhou, China.
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13
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Wang J, Xue L, Zhang X, Hou Y, Zheng K, Fu D, Dong W. A New Function of MbIAA19 Identified to Modulate Malus Plants Dwarfing Growth. PLANTS (BASEL, SWITZERLAND) 2023; 12:3097. [PMID: 37687343 PMCID: PMC10490418 DOI: 10.3390/plants12173097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 08/05/2023] [Accepted: 08/21/2023] [Indexed: 09/10/2023]
Abstract
The primary determinants of apple (Malus) tree architecture include plant height and internode length, which are the significant criteria for evaluating apple dwarf rootstocks. Plant height and internode length are predominantly governed by phytohormones. In this study, we aimed to assess the mechanisms underlying dwarfism in a mutant of Malus baccata. M. baccata dwarf mutant (Dwf) was previously obtained through natural mutation. It has considerably reduced plant height and internode length. A comparative transcriptome analysis of wild-type (WT) and Dwf mutant was performed to identify and annotate the differentially expressed genes responsible for the Dwf phenotype using RNA-seq and GO and KEGG pathway enrichment analyses. Multiple DEGs involved in hormone signaling pathways, particularly auxin signaling pathways, were identified. Moreover, the levels of endogenous indole-3-acetic acid (IAA) were lower in Dwf mutant than in WT. The Aux/IAA transcription factor gene MbIAA19 was downregulated in Dwf mutant due to a single nucleotide sequence change in its promoter. Genetic transformation assay demonstrated strong association between MbIAA19 and the dwarf phenotype. RNAi-IAA19 lines clearly exhibited reduced plant height, internode length, and endogenous IAA levels. Our study revealed that MbIAA19 plays a role in the regulation of dwarfism and endogenous IAA levels in M. baccata.
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Affiliation(s)
| | | | | | | | | | | | - Wenxuan Dong
- College of Horticulture, Shenyang Agricultural University, Shenyang 110866, China; (J.W.); (L.X.); (X.Z.); (Y.H.); (K.Z.); (D.F.)
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14
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Liu Y, Liu Y, He Y, Yan Y, Yu X, Ali M, Pan C, Lu G. Cytokinin-inducible response regulator SlRR6 controls plant height through gibberellin and auxin pathways in tomato. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:4471-4488. [PMID: 37115725 DOI: 10.1093/jxb/erad159] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Accepted: 04/27/2023] [Indexed: 06/19/2023]
Abstract
Plant height is a key agronomic trait regulated by several phytohormones such as gibberellins (GAs) and auxin. However, little is known about how cytokinin (CK) participates in this process. Here, we report that SlRR6, a type-A response regulator in the CK signaling pathway, positively regulates plant height in tomato. SlRR6 was induced by exogenous kinetin and GA3, but inhibited by indole-3-acetic acid (IAA). Knock out of SlRR6 reduced tomato plant height through shortening internode length, while overexpression of SlRR6 caused taller plants due to increased internode number. Cytological observation of longitudinal stems showed that both knock out and overexpression of SlRR6 generated larger cells, but significantly reduced cell numbers in each internode. Further studies demonstrated that overexpression of SlRR6 enhanced GA accumulation and lowered IAA content, along with expression changes in GA- and IAA-related genes. Exogenous paclobutrazol and IAA treatments restored the increased plant height phenotype in SlRR6-overexpressing lines. Yeast two-hybrid, bimolecular fluorescence complementation, and co-immunoprecipitation assays showed that SlRR6 interacts with a small auxin up RNA protein, SlSAUR58. Moreover, SlSAUR58-overexpressing plants were dwarf with decreased internode length. Overall, our findings establish SlRR6 as a vital component in the CK signaling, GA, and IAA regulatory network that controls plant height.
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Affiliation(s)
- Yue Liu
- Department of Horticulture, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Yichen Liu
- Department of Horticulture, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Yanjun He
- Institute of Vegetable Science, Zhejiang Academy of Agricultural Sciences, Hangzhou 310022, China
| | - Yanqiu Yan
- Department of Horticulture, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Xiaolin Yu
- Department of Horticulture, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Muhammad Ali
- Department of Horticulture, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Changtian Pan
- Department of Horticulture, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Gang Lu
- Department of Horticulture, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
- Key Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Ministry of Agricultural, Zhejiang University, Hangzhou 310058, China
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15
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Peng S, Liu Y, Xu Y, Zhao J, Gao P, Liu Q, Yan S, Xiao Y, Zuo SM, Kang H. Genome-Wide Association Study Identifies a Plant-Height-Associated Gene OsPG3 in a Population of Commercial Rice Varieties. Int J Mol Sci 2023; 24:11454. [PMID: 37511211 PMCID: PMC10380248 DOI: 10.3390/ijms241411454] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 07/05/2023] [Accepted: 07/11/2023] [Indexed: 07/30/2023] Open
Abstract
Plant height is one of the most crucial components of plant structure. However, due to its complexity, the genetic architecture of rice plant height has not been fully elucidated. In this study, we performed a genome-wide association study (GWAS) to determine rice plant height using 178 commercial rice varieties and identified 37 loci associated with rice plant height (LAPH). Among these loci, in LAPH2, we identified a polygalacturonase gene, OsPG3, which was genetically and functionally associated with rice plant height. The rice plant exhibits a super dwarf phenotype when the knockout of the OsPG3 gene occurs via CRISPR-Cas9 gene-editing technology. RNA-Seq analysis indicated that OsPG3 modulates the expression of genes involved in phytohormone metabolism and cell-wall-biosynthesis pathways. Our findings suggest that OsPG3 plays a vital role in controlling rice plant height by regulating cell wall biosynthesis. Given that rice architecture is one of the most critical phenotypes in rice breeding, OsPG3 has potential in rice's molecular design breeding toward an ideal plant height.
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Affiliation(s)
- Shasha Peng
- College of Agronomy, Hunan Agricultural University, Changsha 410128, China
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Yanchen Liu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Yuchen Xu
- College of Agronomy, Hunan Agricultural University, Changsha 410128, China
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Jianhua Zhao
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Zhongshan Biological Breeding Laboratory/Key Laboratory of Plant Functional Genomics of the Ministry of Education, Agricultural College of Yangzhou University, Yangzhou 225009, China
| | - Peng Gao
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Zhongshan Biological Breeding Laboratory/Key Laboratory of Plant Functional Genomics of the Ministry of Education, Agricultural College of Yangzhou University, Yangzhou 225009, China
| | - Qi Liu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Shuangyong Yan
- Tianjin Key Laboratory of Crop Genetic Breeding, Tianjin Crop Research Institute, Tianjin Academy of Agriculture Sciences, Tianjin 300112, China
| | - Yinghui Xiao
- College of Agronomy, Hunan Agricultural University, Changsha 410128, China
| | - Shi-Min Zuo
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Zhongshan Biological Breeding Laboratory/Key Laboratory of Plant Functional Genomics of the Ministry of Education, Agricultural College of Yangzhou University, Yangzhou 225009, China
| | - Houxiang Kang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
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Guo F, Wang H, Lian G, Cai G, Liu W, Zhang H, Li D, Zhou C, Han N, Zhu M, Su Y, Seo PJ, Xu L, Bian H. Initiation of scutellum-derived callus is regulated by an embryo-like developmental pathway in rice. Commun Biol 2023; 6:457. [PMID: 37100819 PMCID: PMC10130139 DOI: 10.1038/s42003-023-04835-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Accepted: 04/12/2023] [Indexed: 04/28/2023] Open
Abstract
In rice (Oryza sativa) tissue culture, callus can be induced from the scutellum in embryo or from the vasculature of non-embryonic organs such as leaves, nodes, or roots. Here we show that the auxin signaling pathway triggers cell division in the epidermis of the scutellum to form an embryo-like structure, which leads to callus formation. Our transcriptome data show that embryo-, stem cell-, and auxin-related genes are upregulated during scutellum-derived callus initiation. Among those genes, the embryo-specific gene OsLEC1 is activated by auxin and involved in scutellum-derived callus initiation. However, OsLEC1 is not required for vasculature-derived callus initiation from roots. In addition, OsIAA11 and OsCRL1, which are involved in root development, are required for vasculature-derived callus formation but not for scutellum-derived callus formation. Overall, our data indicate that scutellum-derived callus initiation is regulated by an embryo-like development program, and this is different from vasculature-derived callus initiation which borrows a root development program.
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Affiliation(s)
- Fu Guo
- Institute of Genetic and Regenerative Biology, Key Laboratory for Cell and Gene Engineering of Zhejiang Province, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
- Hainan Institute, Zhejiang University, Yazhou Bay Science and Technology City, Sanya, 572025, China
- Yazhou Bay Seed Laboratory, Yazhou Bay Science and Technology City, Yazhou District, Sanya, 572025, China
| | - Hua Wang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai, 200032, China
| | - Guiwei Lian
- Institute of Genetic and Regenerative Biology, Key Laboratory for Cell and Gene Engineering of Zhejiang Province, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Gui Cai
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai, 200032, China
- University of the Chinese Academy of Sciences, 19A Yuquan Road, Beijing, 100049, China
| | - Wu Liu
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai, 200032, China
| | - Haidao Zhang
- Institute of Genetic and Regenerative Biology, Key Laboratory for Cell and Gene Engineering of Zhejiang Province, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
- Institute of Cell Biology, School of Biological Sciences, The University of Edinburgh, Edinburgh, UK
| | - Dandan Li
- Hainan Institute, Zhejiang University, Yazhou Bay Science and Technology City, Sanya, 572025, China
| | - Chun Zhou
- Institute of Genetic and Regenerative Biology, Key Laboratory for Cell and Gene Engineering of Zhejiang Province, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Ning Han
- Institute of Genetic and Regenerative Biology, Key Laboratory for Cell and Gene Engineering of Zhejiang Province, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Muyuan Zhu
- Institute of Genetic and Regenerative Biology, Key Laboratory for Cell and Gene Engineering of Zhejiang Province, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Yinghua Su
- State Key Laboratory of Crop Biology, Shandong Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, Shandong, 271018, China
| | - Pil Joon Seo
- Department of Chemistry, Seoul National University, Seoul, 08826, Korea
- Plant Genomics and Breeding Institute, Seoul National University, Seoul, 08826, Korea
| | - Lin Xu
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai, 200032, China.
| | - Hongwu Bian
- Institute of Genetic and Regenerative Biology, Key Laboratory for Cell and Gene Engineering of Zhejiang Province, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China.
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17
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Ma F, Zhang F, Zhu Y, Lan D, Yan P, Wang Y, Hu Z, Zhang X, Hu J, Niu F, Liu M, He S, Cui J, Yuan X, Yan Y, Wu S, Cao L, Bian H, Yang J, Li Z, Luo X. Auxin signaling module OsSK41-OsIAA10-OsARF regulates grain yield traits in rice. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2023. [PMID: 36939166 DOI: 10.1111/jipb.13484] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Accepted: 03/20/2023] [Indexed: 06/18/2023]
Abstract
Auxin is an important phytohormone in plants, and auxin signaling pathways in rice play key roles in regulating its growth, development, and productivity. To investigate how rice grain yield traits are regulated by auxin signaling pathways and to facilitate their application in rice improvement, we validated the functional relationships among regulatory genes such as OsIAA10, OsSK41, and OsARF21 that are involved in one of the auxin (OsIAA10) signaling pathways. We assessed the phenotypic effects of these genes on several grain yield traits across two environments using knockout and/or overexpression transgenic lines. Based on the results, we constructed a model that showed how grain yield traits were regulated by OsIAA10 and OsTIR1, OsAFB2, and OsSK41 and OsmiR393 in the OsSK41-OsIAA10-OsARF module and by OsARF21 in the transcriptional regulation of downstream auxin response genes in the OsSK41-OsIAA10-OsARF module. The population genomic analyses revealed rich genetic diversity and the presence of major functional alleles at most of these loci in rice populations. The strong differentiation of many major alleles between Xian/indica and Geng/japonica subspecies and/or among modern varieties and landraces suggested that they contributed to improved productivity during evolution and breeding. We identified several important aspects associated with the genetic and molecular bases of rice grain and yield traits that were regulated by auxin signaling pathways. We also suggested rice auxin response factor (OsARF) activators as candidate target genes for improving specific target traits by overexpression and/or editing subspecies-specific alleles and by searching and pyramiding the 'best' gene allelic combinations at multiple regulatory genes in auxin signaling pathways in rice breeding programs.
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Affiliation(s)
- Fuying Ma
- State Key Laboratory of Genetic Engineering and MOE Engineering Research Center of Gene Technology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Fan Zhang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- College of Agronomy, Anhui Agricultural University, Hefei, 230036, China
| | - Yu Zhu
- State Key Laboratory of Genetic Engineering and MOE Engineering Research Center of Gene Technology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Dengyong Lan
- State Key Laboratory of Genetic Engineering and MOE Engineering Research Center of Gene Technology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Peiwen Yan
- State Key Laboratory of Genetic Engineering and MOE Engineering Research Center of Gene Technology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Ying Wang
- State Key Laboratory of Genetic Engineering and MOE Engineering Research Center of Gene Technology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Zejun Hu
- Institute of Crop Breeding and Cultivation, Shanghai Academy of Agricultural Sciences, Shanghai, 201403, China
| | - Xinwei Zhang
- State Key Laboratory of Genetic Engineering and MOE Engineering Research Center of Gene Technology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Jian Hu
- State Key Laboratory of Genetic Engineering and MOE Engineering Research Center of Gene Technology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Fuan Niu
- State Key Laboratory of Genetic Engineering and MOE Engineering Research Center of Gene Technology, School of Life Sciences, Fudan University, Shanghai, 200438, China
- Institute of Crop Breeding and Cultivation, Shanghai Academy of Agricultural Sciences, Shanghai, 201403, China
| | - Mingyu Liu
- State Key Laboratory of Genetic Engineering and MOE Engineering Research Center of Gene Technology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Shicong He
- State Key Laboratory of Genetic Engineering and MOE Engineering Research Center of Gene Technology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Jinhao Cui
- State Key Laboratory of Genetic Engineering and MOE Engineering Research Center of Gene Technology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Xinyu Yuan
- State Key Laboratory of Genetic Engineering and MOE Engineering Research Center of Gene Technology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Ying Yan
- Institute of Crop Breeding and Cultivation, Shanghai Academy of Agricultural Sciences, Shanghai, 201403, China
| | - Shujun Wu
- Institute of Crop Breeding and Cultivation, Shanghai Academy of Agricultural Sciences, Shanghai, 201403, China
| | - Liming Cao
- Institute of Crop Breeding and Cultivation, Shanghai Academy of Agricultural Sciences, Shanghai, 201403, China
| | - Hongwu Bian
- Institute of Genetics and Regenerative Biology, Key Laboratory for Cell and Gene Engineering of Zhejiang Province, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Jinshui Yang
- State Key Laboratory of Genetic Engineering and MOE Engineering Research Center of Gene Technology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Zhikang Li
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- College of Agronomy, Anhui Agricultural University, Hefei, 230036, China
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518100, China
| | - Xiaojin Luo
- State Key Laboratory of Genetic Engineering and MOE Engineering Research Center of Gene Technology, School of Life Sciences, Fudan University, Shanghai, 200438, China
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18
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Li L, Chen X. Auxin regulation on crop: from mechanisms to opportunities in soybean breeding. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2023; 43:16. [PMID: 37313296 PMCID: PMC10248601 DOI: 10.1007/s11032-023-01361-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Accepted: 02/10/2023] [Indexed: 06/15/2023]
Abstract
Breeding crop varieties with high yield and ideal plant architecture is a desirable goal of agricultural science. The success of "Green Revolution" in cereal crops provides opportunities to incorporate phytohormones in crop breeding. Auxin is a critical phytohormone to determine nearly all the aspects of plant development. Despite the current knowledge regarding auxin biosynthesis, auxin transport and auxin signaling have been well characterized in model Arabidopsis (Arabidopsis thaliana) plants, how auxin regulates crop architecture is far from being understood, and the introduction of auxin biology in crop breeding stays in the theoretical stage. Here, we give an overview on molecular mechanisms of auxin biology in Arabidopsis, and mainly summarize auxin contributions for crop plant development. Furthermore, we propose potential opportunities to integrate auxin biology in soybean (Glycine max) breeding.
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Affiliation(s)
- Linfang Li
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002 Fujian China
- Haixia Institute of Science and Technology, Horticultural Plant Biology and Metabolomics Center, Fujian Agriculture and Forestry University, Fuzhou, 350002 Fujian China
| | - Xu Chen
- Haixia Institute of Science and Technology, Horticultural Plant Biology and Metabolomics Center, Fujian Agriculture and Forestry University, Fuzhou, 350002 Fujian China
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19
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Le L, Guo W, Du D, Zhang X, Wang W, Yu J, Wang H, Qiao H, Zhang C, Pu L. A spatiotemporal transcriptomic network dynamically modulates stalk development in maize. PLANT BIOTECHNOLOGY JOURNAL 2022; 20:2313-2331. [PMID: 36070002 PMCID: PMC9674325 DOI: 10.1111/pbi.13909] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 04/19/2022] [Accepted: 08/12/2022] [Indexed: 06/15/2023]
Abstract
Maize (Zea mays) is an important cereal crop with suitable stalk formation which is beneficial for acquiring an ideal agronomic trait to resist lodging and higher planting density. The elongation pattern of stalks arises from the variable growth of individual internodes driven by cell division and cell expansion comprising the maize stalk. However, the spatiotemporal dynamics and regulatory network of the maize stalk development and differentiation process remain unclear. Here, we report spatiotemporally resolved transcriptomes using all internodes of the whole stalks from developing maize at the elongation and maturation stages. We identified four distinct groups corresponding to four developmental zones and nine specific clusters with diverse spatiotemporal expression patterns among individual internodes of the stalk. Through weighted gene coexpression network analysis, we constructed transcriptional regulatory networks at a fine spatiotemporal resolution and uncovered key modules and candidate genes involved in internode maintenance, elongation, and division that determine stalk length and thickness in maize. Further CRISPR/Cas9-mediated knockout validated the function of a cytochrome P450 gene, ZmD1, in the regulation of stalk length and thickness as predicted by the WGCN. Collectively, these results provide insights into the high genetic complexity of stalk development and the potentially valuable resources with ideal stalk lengths and widths for genetic improvements in maize.
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Affiliation(s)
- Liang Le
- Biotechnology Research InstituteChinese Academy of Agricultural SciencesBeijingChina
- National Nanfan Research Institute (Sanya)Chinese Academy of Agricultural SciencesSanyaChina
| | - Weijun Guo
- Biotechnology Research InstituteChinese Academy of Agricultural SciencesBeijingChina
| | - Danyao Du
- Biotechnology Research InstituteChinese Academy of Agricultural SciencesBeijingChina
| | - Xiaoyuan Zhang
- Biotechnology Research InstituteChinese Academy of Agricultural SciencesBeijingChina
| | - Weixuan Wang
- Biotechnology Research InstituteChinese Academy of Agricultural SciencesBeijingChina
| | - Jia Yu
- Biotechnology Research InstituteChinese Academy of Agricultural SciencesBeijingChina
| | - Huan Wang
- Biotechnology Research InstituteChinese Academy of Agricultural SciencesBeijingChina
| | - Hong Qiao
- Institute for Cellular and Molecular Biology, The University of Texas at AustinAustinTXUSA
- Department of Molecular BiosciencesThe University of Texas at AustinAustinTXUSA
| | - Chunyi Zhang
- Biotechnology Research InstituteChinese Academy of Agricultural SciencesBeijingChina
- Sanya InstituteHainan Academy of Agricultural SciencesSanyaChina
| | - Li Pu
- Biotechnology Research InstituteChinese Academy of Agricultural SciencesBeijingChina
- National Nanfan Research Institute (Sanya)Chinese Academy of Agricultural SciencesSanyaChina
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20
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Du W, Lu Y, Li Q, Luo S, Shen S, Li N, Chen X. TIR1/AFB proteins: Active players in abiotic and biotic stress signaling. FRONTIERS IN PLANT SCIENCE 2022; 13:1083409. [PMID: 36523629 PMCID: PMC9745157 DOI: 10.3389/fpls.2022.1083409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Accepted: 11/16/2022] [Indexed: 06/17/2023]
Abstract
The TIR1/AFB family of proteins is a group of functionally diverse auxin receptors that are only found in plants. TIR1/AFB family members are characterized by a conserved N-terminal F-box domain followed by 18 leucine-rich repeats. In the past few decades, extensive research has been conducted on the role of these proteins in regulating plant development, metabolism, and responses to abiotic and biotic stress. In this review, we focus on TIR1/AFB proteins that play crucial roles in plant responses to diverse abiotic and biotic stress. We highlight studies that have shed light on the mechanisms by which TIR1/AFB proteins are regulated at the transcriptional and post-transcriptional as well as the downstream in abiotic or biotic stress pathways regulated by the TIR1/AFB family.
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Affiliation(s)
- Wenchao Du
- Key Laboratory for Vegetable Germplasm Enhancement and Utilization of Hebei, Collaborative Innovation Center of Vegetable Industry in Hebei, College of Horticulture, Hebei Agricultural University, Baoding, China
| | - Yang Lu
- Hebei University Characteristic sericulture Application Technology Research and Development Center, Institute of Sericulture, Chengde Medical University, Chengde, China
| | - Qiang Li
- Key Laboratory for Vegetable Germplasm Enhancement and Utilization of Hebei, Collaborative Innovation Center of Vegetable Industry in Hebei, College of Horticulture, Hebei Agricultural University, Baoding, China
| | - Shuangxia Luo
- Key Laboratory for Vegetable Germplasm Enhancement and Utilization of Hebei, Collaborative Innovation Center of Vegetable Industry in Hebei, College of Horticulture, Hebei Agricultural University, Baoding, China
| | - Shuxing Shen
- Key Laboratory for Vegetable Germplasm Enhancement and Utilization of Hebei, Collaborative Innovation Center of Vegetable Industry in Hebei, College of Horticulture, Hebei Agricultural University, Baoding, China
| | - Na Li
- Key Laboratory for Vegetable Germplasm Enhancement and Utilization of Hebei, Collaborative Innovation Center of Vegetable Industry in Hebei, College of Horticulture, Hebei Agricultural University, Baoding, China
| | - Xueping Chen
- Key Laboratory for Vegetable Germplasm Enhancement and Utilization of Hebei, Collaborative Innovation Center of Vegetable Industry in Hebei, College of Horticulture, Hebei Agricultural University, Baoding, China
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21
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Wang H, Han X, Fu X, Sun X, Chen H, Wei X, Cui S, Liu Y, Guo W, Li X, Xing J, Zhang Y. Overexpression of TaLBD16-4D alters plant architecture and heading date in transgenic wheat. FRONTIERS IN PLANT SCIENCE 2022; 13:911993. [PMID: 36212357 PMCID: PMC9533090 DOI: 10.3389/fpls.2022.911993] [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: 04/03/2022] [Accepted: 09/02/2022] [Indexed: 06/16/2023]
Abstract
Lateral organ boundaries domain (LBD) proteins, a class of plant-specific transcription factors with a special domain of lateral organ boundaries (LOB), play essential roles in plant growth and development. However, there is little known about the functions of these genes in wheat to date. Our previous study demonstrated that TaLBD16-4D is conducive to increasing lateral root number in wheat. In the present work, we further examined important agronomical traits of the aerial part of transgenic wheat overexpressing TaLBD16-4D. Interestingly, it was revealed that overexpressing TaLBD16-4D could lead to early heading and multiple alterations of plant architecture, including decreased plant height, increased flag leaf size and stem diameter, reduced spike length and tillering number, improved spike density and grain width, and decreased grain length. Moreover, auxin-responsive experiments demonstrated that the expression of TaLBD16-4D in wild-type (WT) wheat plants showed a significant upregulation through 2,4-D treatment. TaLBD16-4D-overexpression lines displayed a hyposensitivity to 2,4-D treatment and reduced shoot gravitropic response. The expressions of a set of auxin-responsive genes were markedly different between WT and transgenic plants. In addition, overexpressing TaLBD16-4D affected the transcript levels of flowering-related genes (TaGI, TaCO1, TaHd1, TaVRN1, TaVRN2, and TaFT1). Notably, the expression of TaGI, TaCO1, TaHd1, TaVRN1, and TaFT1 displayed significant upregulation under IAA treatment. Collectively, our observations indicated that overexpressing TaLBD16-4D could affect aerial architecture and heading time possibly though participating in the auxin pathway.
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Affiliation(s)
- Huifang Wang
- Shandong Provincial Key Laboratory of Dryland Farming Technology, Qingdao Agricultural University, Qingdao, China
| | - Xiaofan Han
- Shandong Provincial Key Laboratory of Dryland Farming Technology, Qingdao Agricultural University, Qingdao, China
| | - Xiaofeng Fu
- Shandong Provincial Key Laboratory of Dryland Farming Technology, Qingdao Agricultural University, Qingdao, China
| | - Xinling Sun
- Shandong Provincial Key Laboratory of Dryland Farming Technology, Qingdao Agricultural University, Qingdao, China
| | - Hailong Chen
- Shandong Provincial Key Laboratory of Dryland Farming Technology, Qingdao Agricultural University, Qingdao, China
| | - Xirui Wei
- Shandong Provincial Key Laboratory of Dryland Farming Technology, Qingdao Agricultural University, Qingdao, China
| | - Shubin Cui
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, China
| | - Yiguo Liu
- Shandong Provincial Key Laboratory of Dryland Farming Technology, Qingdao Agricultural University, Qingdao, China
| | - Weiwei Guo
- Shandong Provincial Key Laboratory of Dryland Farming Technology, Qingdao Agricultural University, Qingdao, China
| | - Ximei Li
- Shandong Provincial Key Laboratory of Dryland Farming Technology, Qingdao Agricultural University, Qingdao, China
| | - Jiewen Xing
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, China
| | - Yumei Zhang
- Shandong Provincial Key Laboratory of Dryland Farming Technology, Qingdao Agricultural University, Qingdao, China
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22
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Xu Z, Wang R, Kong K, Begum N, Almakas A, Liu J, Li H, Liu B, Zhao T, Zhao T. An APETALA2/ethylene responsive factor transcription factor GmCRF4a regulates plant height and auxin biosynthesis in soybean. FRONTIERS IN PLANT SCIENCE 2022; 13:983650. [PMID: 36147224 PMCID: PMC9485679 DOI: 10.3389/fpls.2022.983650] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 08/17/2022] [Indexed: 06/01/2023]
Abstract
Plant height is one of the key agronomic traits affecting soybean yield. The cytokinin response factors (CRFs), as a branch of the APETALA2/ethylene responsive factor (AP2/ERF) super gene family, have been reported to play important roles in regulating plant growth and development. However, their functions in soybean remain unknown. This study characterized a soybean CRF gene named GmCRF4a by comparing the performance of the homozygous Gmcrf4a-1 mutant, GmCRF4a overexpression (OX) and co-silencing (CS) lines. Phenotypic analysis showed that overexpression of GmCRF4a resulted in taller hypocotyls and epicotyls, more main stem nodes, and higher plant height. While down-regulation of GmCRF4a conferred shorter hypocotyls and epicotyls, as well as a reduction in plant height. The histological analysis results demonstrated that GmCRF4a promotes epicotyl elongation primarily by increasing cell length. Furthermore, GmCRF4a is required for the expression of GmYUCs genes to elevate endogenous auxin levels, which may subsequently enhance stem elongation. Taken together, these observations describe a novel regulatory mechanism in soybean, and provide the basis for elucidating the function of GmCRF4a in auxin biosynthesis pathway and plant heigh regulation in plants.
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Affiliation(s)
- Zhiyong Xu
- National Center for Soybean Improvement, Key Laboratory of Biology and Genetics and Breeding for Soybean, Ministry of Agriculture and Rural Affairs, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Ruikai Wang
- National Center for Soybean Improvement, Key Laboratory of Biology and Genetics and Breeding for Soybean, Ministry of Agriculture and Rural Affairs, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
| | - Keke Kong
- National Center for Soybean Improvement, Key Laboratory of Biology and Genetics and Breeding for Soybean, Ministry of Agriculture and Rural Affairs, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
| | - Naheeda Begum
- National Center for Soybean Improvement, Key Laboratory of Biology and Genetics and Breeding for Soybean, Ministry of Agriculture and Rural Affairs, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
| | - Aisha Almakas
- National Center for Soybean Improvement, Key Laboratory of Biology and Genetics and Breeding for Soybean, Ministry of Agriculture and Rural Affairs, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
| | - Jun Liu
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Hongyu Li
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Bin Liu
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Tuanjie Zhao
- National Center for Soybean Improvement, Key Laboratory of Biology and Genetics and Breeding for Soybean, Ministry of Agriculture and Rural Affairs, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
| | - Tao Zhao
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
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23
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Jiang J, Zhu H, Li N, Batley J, Wang Y. The miR393-Target Module Regulates Plant Development and Responses to Biotic and Abiotic Stresses. Int J Mol Sci 2022; 23:ijms23169477. [PMID: 36012740 PMCID: PMC9409142 DOI: 10.3390/ijms23169477] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 08/18/2022] [Accepted: 08/19/2022] [Indexed: 11/16/2022] Open
Abstract
MicroRNAs (miRNAs), a class of endogenous small RNAs, are broadly involved in plant development, morphogenesis and responses to various environmental stresses, through manipulating the cleavage, translational expression, or DNA methylation of target mRNAs. miR393 is a conserved miRNA family present in many plants, which mainly targets genes encoding the transport inhibitor response1 (TIR1)/auxin signaling F-box (AFB) auxin receptors, and thus greatly affects the auxin signal perception, Aux/IAA degradation, and related gene expression. This review introduces the advances made on the miR393/target module regulating plant development and the plant’s responses to biotic and abiotic stresses. This module is valuable for genetic manipulation of optimized conditions for crop growth and development and would also be helpful in improving crop yield through molecular breeding.
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Affiliation(s)
- Jinjin Jiang
- Jiangsu Provincial Key Laboratory of Crop Genetics and Physiology, Yangzhou University, Yangzhou 225009, China
| | - Haotian Zhu
- Jiangsu Provincial Key Laboratory of Crop Genetics and Physiology, Yangzhou University, Yangzhou 225009, China
| | - Na Li
- Jiangsu Provincial Key Laboratory of Crop Genetics and Physiology, Yangzhou University, Yangzhou 225009, China
| | - Jacqueline Batley
- School of Biological Sciences, University of Western Australia, Perth, WA 6009, Australia
- Correspondence: (J.B.); (Y.W.)
| | - Youping Wang
- Jiangsu Provincial Key Laboratory of Crop Genetics and Physiology, Yangzhou University, Yangzhou 225009, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, The Ministry of Education of China, Yangzhou University, Yangzhou 225009, China
- Correspondence: (J.B.); (Y.W.)
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24
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Liu M, Huang L, Zhang Y, Yan Z, Wang N. Overexpression of PdeGATA3 results in a dwarf phenotype in poplar by promoting the expression of PdeSTM and altering the content of gibberellins. TREE PHYSIOLOGY 2022; 42:tpac086. [PMID: 35980326 DOI: 10.1093/treephys/tpac086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Revised: 06/09/2022] [Accepted: 07/12/2022] [Indexed: 06/15/2023]
Abstract
In previous studies, GA20 oxidase (GA20ox) has been identified to be an important enzyme in the biosynthesis of GA, and SHOOTMERISTEMLESS (STM) can repress the expression of GA20ox. In this study, the GATA transcription factor PdeGATA3 was identified in the poplar line NL895, and its overexpression (OE) transgenic lines showed a dwarf phenotype. RNA sequencing (RNA-Seq) analysis suggested that OE PdeGATA3 could promote the expression of PdeSTM and repress the expression of PdeGA20ox. Therefore, we hypothesized that PdeGATA3 would directly promote the expression of PdeSTM and that PdeSTM would repress the expression of PdeGA20ox. Four experiments, a dual-luciferase reporter assay, GUS transient coexpression assay, yeast one-hybrid assay and electrophoretic mobility shift assay, were conducted and verified that PdeGATA3 could promote the expression of PdeSTM by binding GATA-Boxes in its promoter. OE PdeSTM in poplar resulted in a dwarf phenotype and repressed the expression of PdeGA20ox. GA measurement of the OE PdeSTM and PdeGATA3 lines showed that GA3 and GA4 contents were significantly lower than those in the wild type (WT). Accordingly, we put forward a regulation model involving plant height regulation by PdeGATA3, PdeSTM and PdeGA20ox.
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Affiliation(s)
- Meifeng Liu
- College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Liyu Huang
- College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Yan Zhang
- College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Zhaogui Yan
- College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Nian Wang
- College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
- Hubei Engineering Technology Research Center for Forestry Information, Huazhong Agricultural University, Wuhan 430070, China
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25
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Luo L, Zhu M, Jia L, Xie Y, Wang Z, Xuan W. Ammonium transporters cooperatively regulate rice crown root formation responding to ammonium nitrogen. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:3671-3685. [PMID: 35176162 DOI: 10.1093/jxb/erac059] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Accepted: 02/16/2022] [Indexed: 06/14/2023]
Abstract
Crown roots (CRs) are major components of the rice root system. They form at the basal node of the shoot, and their development is greatly influenced by environmental factors. Ammonium nitrogen is known to impact plant root development through ammonium transporters (AMTs), but it remains unclear whether ammonium and AMTs play roles in rice CR formation. In this study, we revealed a significant role of ammonium, rather than nitrate, in regulating rice CR development. High ammonium supply increases CR formation but inhibits CR elongation. Genetic evidence showed that ammonium regulation of CR development relies on ammonium uptake mediated jointly by ammonium transporters OsAMT1;1, OsAMT1;2; OsAMT1;3, and OsAMT2;1, but not on root acidification which was the result of ammonium uptake. OsAMTs are also needed for glutamine-induced CR formation. Furthermore, we showed that polar auxin transport dependent on the PIN auxin efflux carriers acts downstream of ammonium uptake and assimilation to activate local auxin signaling at CR primordia, in turn promoting CR formation. Taken together, our results highlight a critical role for OsAMTs in cooperatively regulating CR formation through regulating auxin transport under nitrogen-rich conditions.
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Affiliation(s)
- Long Luo
- MOA Key Laboratory of Plant Nutrition and Fertilization in Lower-Middle Reaches of the Yangtze River and State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Ming Zhu
- MOA Key Laboratory of Plant Nutrition and Fertilization in Lower-Middle Reaches of the Yangtze River and State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Letian Jia
- MOA Key Laboratory of Plant Nutrition and Fertilization in Lower-Middle Reaches of the Yangtze River and State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Yuanming Xie
- MOA Key Laboratory of Plant Nutrition and Fertilization in Lower-Middle Reaches of the Yangtze River and State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Ziniu Wang
- MOA Key Laboratory of Plant Nutrition and Fertilization in Lower-Middle Reaches of the Yangtze River and State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Wei Xuan
- MOA Key Laboratory of Plant Nutrition and Fertilization in Lower-Middle Reaches of the Yangtze River and State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
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Guo F, Zhang P, Wu Y, Lian G, Yang Z, Liu W, Buerte B, Zhou C, Zhang W, Li D, Han N, Tong Z, Zhu M, Xu L, Chen M, Bian H. Rice LEAFY COTYLEDON1 Hinders Embryo Greening During the Seed Development. FRONTIERS IN PLANT SCIENCE 2022; 13:887980. [PMID: 35620685 PMCID: PMC9128838 DOI: 10.3389/fpls.2022.887980] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 04/14/2022] [Indexed: 06/15/2023]
Abstract
LEAFY COTYLEDON1 (LEC1) is the central regulator of seed development in Arabidopsis, while its function in monocots is largely elusive. We generated Oslec1 mutants using CRISPR/Cas9 technology. Oslec1 mutant seeds lost desiccation tolerance and triggered embryo greening at the early development stage. Transcriptome analysis demonstrated that Oslec1 mutation altered diverse hormonal pathways and stress response in seed maturation, and promoted a series of photosynthesis-related genes. Further, genome-wide identification of OsLEC1-binding sites demonstrated that OsLEC1 bound to genes involved in photosynthesis, photomorphogenesis, as well as abscisic acid (ABA) and gibberellin (GA) pathways, involved in seed maturation. We illustrated an OsLEC1-regulating gene network during seed development, including the interconnection between photosynthesis and ABA/GA biosynthesis/signaling. Our findings suggested that OsLEC1 acts as not only a central regulator of seed maturation but also an inhibitor of embryo greening during rice seed development. This study would provide new understanding for the OsLEC1 regulatory mechanisms on photosynthesis in the monocot seed development.
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Affiliation(s)
- Fu Guo
- College of Life Sciences, Zhejiang University, Hangzhou, China
- Hainan Institute, Zhejiang University, Yazhou Bay Science and Technology City, Sanya, China
| | - Peijing Zhang
- College of Life Sciences, Zhejiang University, Hangzhou, China
- Liangzhu Laboratory, Zhejiang University Medical Centre, Hangzhou, China
| | - Yan Wu
- College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Guiwei Lian
- College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Zhengfei Yang
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
- College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Wu Liu
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - B. Buerte
- College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Chun Zhou
- College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Wenqian Zhang
- College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Dandan Li
- Hainan Institute, Zhejiang University, Yazhou Bay Science and Technology City, Sanya, China
| | - Ning Han
- College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Zaikang Tong
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an, China
| | - Muyuan Zhu
- College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Lin Xu
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Ming Chen
- College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Hongwu Bian
- College of Life Sciences, Zhejiang University, Hangzhou, China
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27
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Kořínková N, Fontana IM, Nguyen TD, Pouramini P, Bergougnoux V, Hensel G. Enhancing cereal productivity by genetic modification of root architecture. Biotechnol J 2022; 17:e2100505. [PMID: 35537849 DOI: 10.1002/biot.202100505] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 04/03/2022] [Accepted: 04/23/2022] [Indexed: 11/06/2022]
Abstract
Food security is one of the main topics of today's agriculture, primarily due to increasingly challenging environmental conditions. As most of humankind has a daily intake of cereal grains, current breeding programs focus on these crop plants. Customised endonucleases have been included in the breeders' toolbox after successfully demonstrating their use. Due to technological restrictions, the main focus of the new technology was on above-ground plant organs. In contrast, the essential below ground components were given only limited attention. In the present review, the knowledge of the root system architecture in cereals and the role of phytohormones during their establishment is summarized, and the underlying molecular mechanisms are outlined. The review summarizes how the use of CRISPR-based genome editing methodology can improve the root system architecture to enhance crop production genetically. Finally, future research directions involving this knowledge and technical advances are suggested. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Nikola Kořínková
- Centre of Region Haná for Biotechnological and Agricultural Research, Czech Advanced Technology and Research Institute, Palacký University Olomouc, Olomouc, CZ-78371.,Faculty of Science, Palacký University Olomouc, Olomouc, CZ-78371
| | - Irene M Fontana
- Leibniz Institute of Plant Genetics and Crop Plant Research, Plant Reproductive Biology, D-06466 Seeland OT, Gatersleben
| | - Thu D Nguyen
- Centre of Region Haná for Biotechnological and Agricultural Research, Czech Advanced Technology and Research Institute, Palacký University Olomouc, Olomouc, CZ-78371.,Faculty of Science, Palacký University Olomouc, Olomouc, CZ-78371
| | - Pouneh Pouramini
- Leibniz Institute of Plant Genetics and Crop Plant Research, Plant Reproductive Biology, D-06466 Seeland OT, Gatersleben
| | - Véronique Bergougnoux
- Centre of Region Haná for Biotechnological and Agricultural Research, Czech Advanced Technology and Research Institute, Palacký University Olomouc, Olomouc, CZ-78371
| | - Goetz Hensel
- Centre of Region Haná for Biotechnological and Agricultural Research, Czech Advanced Technology and Research Institute, Palacký University Olomouc, Olomouc, CZ-78371.,Centre for Plant Genome Engineering, Institute of Plant Biochemistry, Heinrich-Heine-University, D-40225, Dusseldorf
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28
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Hao Z, Ma S, Liang L, Feng T, Xiong M, Lian S, Zhu J, Chen Y, Meng L, Li M. Candidate Genes and Pathways in Rice Co-Responding to Drought and Salt Identified by gcHap Network. Int J Mol Sci 2022; 23:ijms23074016. [PMID: 35409377 PMCID: PMC8999833 DOI: 10.3390/ijms23074016] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2022] [Revised: 03/26/2022] [Accepted: 04/01/2022] [Indexed: 01/24/2023] Open
Abstract
Drought and salinity stresses are significant abiotic factors that limit rice yield. Exploring the co-response mechanism to drought and salt stress will be conducive to future rice breeding. A total of 1748 drought and salt co-responsive genes were screened, most of which are enriched in plant hormone signal transduction, protein processing in the endoplasmic reticulum, and the MAPK signaling pathways. We performed gene-coding sequence haplotype (gcHap) network analysis on nine important genes out of the total amount, which showed significant differences between the Xian/indica and Geng/japonica population. These genes were combined with related pathways, resulting in an interesting mechanistic draft called the ‘gcHap-network pathway’. Meanwhile, we collected a lot of drought and salt breeding varieties, especially the introgression lines (ILs) with HHZ as the parent, which contained the above-mentioned nine genes. This might imply that these ILs have the potential to improve the tolerance to drought and salt. In this paper, we focus on the relationship of drought and salt co-response gene gcHaps and their related pathways using a novel angle. The haplotype network will be helpful to explore the desired haplotypes that can be implemented in haplotype-based breeding programs.
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Affiliation(s)
- Zhiqi Hao
- College of Agronomy, Anhui Agricultural University, Hefei 230036, China; (Z.H.); (S.M.); (L.L.); (T.F.); (M.X.); (S.L.); (J.Z.); (Y.C.)
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Sai Ma
- College of Agronomy, Anhui Agricultural University, Hefei 230036, China; (Z.H.); (S.M.); (L.L.); (T.F.); (M.X.); (S.L.); (J.Z.); (Y.C.)
| | - Lunping Liang
- College of Agronomy, Anhui Agricultural University, Hefei 230036, China; (Z.H.); (S.M.); (L.L.); (T.F.); (M.X.); (S.L.); (J.Z.); (Y.C.)
| | - Ting Feng
- College of Agronomy, Anhui Agricultural University, Hefei 230036, China; (Z.H.); (S.M.); (L.L.); (T.F.); (M.X.); (S.L.); (J.Z.); (Y.C.)
| | - Mengyuan Xiong
- College of Agronomy, Anhui Agricultural University, Hefei 230036, China; (Z.H.); (S.M.); (L.L.); (T.F.); (M.X.); (S.L.); (J.Z.); (Y.C.)
| | - Shangshu Lian
- College of Agronomy, Anhui Agricultural University, Hefei 230036, China; (Z.H.); (S.M.); (L.L.); (T.F.); (M.X.); (S.L.); (J.Z.); (Y.C.)
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Jingyan Zhu
- College of Agronomy, Anhui Agricultural University, Hefei 230036, China; (Z.H.); (S.M.); (L.L.); (T.F.); (M.X.); (S.L.); (J.Z.); (Y.C.)
| | - Yanjun Chen
- College of Agronomy, Anhui Agricultural University, Hefei 230036, China; (Z.H.); (S.M.); (L.L.); (T.F.); (M.X.); (S.L.); (J.Z.); (Y.C.)
| | - Lijun Meng
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
- Correspondence: (L.M.); (M.L.)
| | - Min Li
- College of Agronomy, Anhui Agricultural University, Hefei 230036, China; (Z.H.); (S.M.); (L.L.); (T.F.); (M.X.); (S.L.); (J.Z.); (Y.C.)
- Correspondence: (L.M.); (M.L.)
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Wang C, Han B. Twenty years of rice genomics research: From sequencing and functional genomics to quantitative genomics. MOLECULAR PLANT 2022; 15:593-619. [PMID: 35331914 DOI: 10.1016/j.molp.2022.03.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Revised: 03/04/2022] [Accepted: 03/18/2022] [Indexed: 06/14/2023]
Abstract
Since the completion of the rice genome sequencing project in 2005, we have entered the era of rice genomics, which is still in its ascendancy. Rice genomics studies can be classified into three stages: structural genomics, functional genomics, and quantitative genomics. Structural genomics refers primarily to genome sequencing for the construction of a complete map of rice genome sequence. This is fundamental for rice genetics and molecular biology research. Functional genomics aims to decode the functions of rice genes. Quantitative genomics is large-scale sequence- and statistics-based research to define the quantitative traits and genetic features of rice populations. Rice genomics has been a transformative influence on rice biological research and contributes significantly to rice breeding, making rice a good model plant for studying crop sciences.
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Affiliation(s)
- Changsheng Wang
- National Center for Gene Research, State Key Laboratory of Plant Molecular Genetics, Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200233, China.
| | - Bin Han
- National Center for Gene Research, State Key Laboratory of Plant Molecular Genetics, Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200233, China.
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B B, Zeng Z, Zhou C, Lian G, Guo F, Wang J, Han N, Zhu M, Bian H. Identification of New ATG8s-Binding Proteins with Canonical LC3-Interacting Region in Autophagosomes of Barley Callus. PLANT & CELL PHYSIOLOGY 2022:pcac015. [PMID: 35134996 DOI: 10.1093/pcp/pcac015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Accepted: 02/02/2022] [Indexed: 06/14/2023]
Abstract
Autophagy is essential to maintain cellular homeostasis for normal cell growth and development. In selective autophagy, ATG8 plays a crucial role in cargo target recognition by binding to various adaptors and receptors with the ATG8-interacting motif, also known as the LC3-interacting region (LIR). However, the process of autophagy in the callus, as a proliferating cell type, is largely unknown. In this study, we overexpressed green fluorescent protein (GFP)-ATG8a and GFP-ATG8b transgenic barley callus and checked their autophagic activities. We identified five new ATG8 candidate interactors containing the canonical LIR motif by using immunoprecipitation coupled with mass spectrometry: RPP3, COPE, NCLN, RAE1, and CTSL. The binding activities between these candidate interactors and ATG8 were further demonstrated in the punctate structure. Notably, RPP3 was colocalized in ATG8-labeled autophagosomes under tunicamycin-induced ER stress. GST pull-down assays showed that the interaction between RPP3 and ATG8 could be prevented by mutating the LIRs region of RPP3 or the LIR docking site (LDS) of ATG8, suggesting that RPP3 directly interacted with ATG8 in an LIR-dependent manner via the LDS. Our findings would provide the basis for further investigations on novel receptors and functions of autophagy in plants, especially in the physiological state of cell de-differentiation.
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31
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A New RING Finger Protein, PLANT ARCHITECTURE and GRAIN NUMBER 1, Affects Plant Architecture and Grain Yield in Rice. Int J Mol Sci 2022; 23:ijms23020824. [PMID: 35055011 PMCID: PMC8777624 DOI: 10.3390/ijms23020824] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 01/09/2022] [Accepted: 01/10/2022] [Indexed: 12/21/2022] Open
Abstract
Developing methods for increasing the biomass and improving the plant architecture is important for crop improvement. We herein describe a gene belonging to the RING_Ubox (RING (Really Interesting New Gene) finger domain and U-box domain) superfamily, PLANT ARCHITECTURE and GRAIN NUMBER 1 (PAGN1), which regulates the number of grains per panicle, the plant height, and the number of tillers. We used the CRISPR/Cas9 system to introduce loss-of-function mutations to OsPAGN1. Compared with the control plants, the resulting pagn1 mutant plants had a higher grain yield because of increases in the plant height and in the number of tillers and grains per panicle. Thus, OsPAGN1 may be useful for the genetic improvement of plant architecture and yield. An examination of evolutionary relationships revealed that OsPAGN1 is highly conserved in rice. We demonstrated that OsPAGN1 can interact directly with OsCNR10 (CELL NUMBER REGULATOR10), which negatively regulates the number of rice grains per panicle. A transcriptome analysis indicated that silencing OsPAGN1 affects the levels of active cytokinins in rice. Therefore, our findings have clarified the OsPAGN1 functions related to rice growth and grain development.
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32
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Chen DG, Zhou XQ, Chen K, Chen PL, Guo J, Liu CG, Chen YD. Fine-mapping and candidate gene analysis of a major locus controlling leaf thickness in rice ( Oryza sativa L.). MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2022; 42:6. [PMID: 35103045 PMCID: PMC8792131 DOI: 10.1007/s11032-022-01275-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2021] [Accepted: 01/13/2022] [Indexed: 05/16/2023]
Abstract
UNLABELLED Leaf thickness is an important trait in rice (Oryza sativa L.). It affects both photosynthesis and sink-resource efficiency. However, compared to leaf length and length width, reports seldom focused on leaf thickness due to the complicated measurement and minor difference. To identify the quantitative trait loci (QTL) and explore the genetic mechanism regulating the natural variation of leaf thickness, we crossed a high leaf thickness variety Aixiuzhan (AXZ) to a thin leaf thickness variety Yangdao No.6 (YD 6) and evaluated 585 F2 individuals. We further use bulked sergeant analysis with whole-genome resequencing (BSA-seq) to identify five genomic regions, including chromosomes 1, 6, 9, 10, and 12. These regions represented significant allele frequency differentiation between thick and thin leaf thickness among the mixed pool offspring. Moreover, we conducted a linkage mapping using 276 individuals derived from the F2 population. We fine-mapped and confirmed that chromosome 9 contributed the primary explanation of phenotypic variance. We fine-mapped the candidate regions and confirmed that the chromosome 9 region contributed to flag leaf thickness in rice. We observed the virtual cellular slices and found that the bundle sheath cells in YD 6 flag leaf veins are fewer than AXZ. We analyzed the potential regions on chromosome 9 and narrowed the QTL candidate intervals in the 928-kb region. Candidate genes of this major QTL were listed as potentially controlled leaf thickness. These results provide promising evidence that cloning leaf thickness is associated with yield production in rice. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s11032-022-01275-y.
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Affiliation(s)
- Da-gang Chen
- Rice Research Institute, Guangdong Rice Engineering Laboratory, Guangdong Key Laboratory of New Technology in Rice Breeding, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640 People’s Republic of China
| | - Xin-qiao Zhou
- Rice Research Institute, Guangdong Rice Engineering Laboratory, Guangdong Key Laboratory of New Technology in Rice Breeding, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640 People’s Republic of China
| | - Ke Chen
- Rice Research Institute, Guangdong Rice Engineering Laboratory, Guangdong Key Laboratory of New Technology in Rice Breeding, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640 People’s Republic of China
| | - Ping-li Chen
- Rice Research Institute, Guangdong Rice Engineering Laboratory, Guangdong Key Laboratory of New Technology in Rice Breeding, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640 People’s Republic of China
| | - Jie Guo
- Rice Research Institute, Guangdong Rice Engineering Laboratory, Guangdong Key Laboratory of New Technology in Rice Breeding, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640 People’s Republic of China
| | - Chuan-guang Liu
- Rice Research Institute, Guangdong Rice Engineering Laboratory, Guangdong Key Laboratory of New Technology in Rice Breeding, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640 People’s Republic of China
| | - You-ding Chen
- Rice Research Institute, Guangdong Rice Engineering Laboratory, Guangdong Key Laboratory of New Technology in Rice Breeding, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640 People’s Republic of China
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Rice functional genomics: decades' efforts and roads ahead. SCIENCE CHINA. LIFE SCIENCES 2021; 65:33-92. [PMID: 34881420 DOI: 10.1007/s11427-021-2024-0] [Citation(s) in RCA: 92] [Impact Index Per Article: 30.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 11/01/2021] [Indexed: 12/16/2022]
Abstract
Rice (Oryza sativa L.) is one of the most important crops in the world. Since the completion of rice reference genome sequences, tremendous progress has been achieved in understanding the molecular mechanisms on various rice traits and dissecting the underlying regulatory networks. In this review, we summarize the research progress of rice biology over past decades, including omics, genome-wide association study, phytohormone action, nutrient use, biotic and abiotic responses, photoperiodic flowering, and reproductive development (fertility and sterility). For the roads ahead, cutting-edge technologies such as new genomics methods, high-throughput phenotyping platforms, precise genome-editing tools, environmental microbiome optimization, and synthetic methods will further extend our understanding of unsolved molecular biology questions in rice, and facilitate integrations of the knowledge for agricultural applications.
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Wang H, Sun X, Yu J, Li J, Dong L. The phytotoxicity mechanism of florpyrauxifen-benzyl to Echinochloa crus-galli (L.) P. Beauv and weed control effect. PESTICIDE BIOCHEMISTRY AND PHYSIOLOGY 2021; 179:104978. [PMID: 34802528 DOI: 10.1016/j.pestbp.2021.104978] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Revised: 09/28/2021] [Accepted: 10/11/2021] [Indexed: 06/13/2023]
Abstract
Weeds infest rice causing high yield losses, leading to the increasing use of herbicides for weed control. However, many weeds have evolved resistance to common commercial herbicides, including penoxsulam, metamifop and quinclorac. This study investigated the weed control effect and the phytotoxicity mechanism of florpyrauxifen-benzyl, a novel synthetic auxin herbicide registered for weed management in rice fields in China. The greenhouse study showed that florpyrauxifen-benzyl was highly efficient (GR50 < 6 and GR90 < 15 g a.i ha-1) at controlling 10 weed species commonly found in rice fields, including penoxsulam- and quinclorac- resistant(R) biotypes of Echinochloa Beauv. and bensulfuron-methyl-R biotype of Ammannia arenaria. The typical plant hormone content showed that following florpyrauxifen-benzyl treatment, indole-3-acetic acid (IAA) production changed only slightly at 12 h, while abscisic acid (ABA) production increased with time in the treated group, whose content was significantly higher than that of the control. Besides, ethylene biosynthesis was stimulated by florpyrauxifen-benzyl, ethylene production, 1-aminocyclopropane-1-carboxylic acid (ACC) content, and 1-aminocyclopropane-1-carboxylate synthase (ACS) and 1-aminocyclopropane-1-carboxylate oxidase (ACO) activities, which evidently increased in the treated group, and ethylene peaked at 36 h. For the antioxidant enzyme activities and malondialdehyde (MDA) content in the treated group, results showed that MDA content continuously increased with time and was greater than that in the untreated group at 48 h and 72 h, superoxide dismutase (SOD) activity changed with exposure time and was significantly higher in the treatment group than the control at 48 h. A similar phenomenon was observed in peroxidase (POD) activity, which reached a peak at 48 h, and no distinct difference in catalase (CAT) activity was observed among groups except for the higher activity in the treated groups than control at 36 h and 48 h. Our results showed that that the stimulation ethylene biosynthesis and accumulation of ABA and reactive oxygen species (ROS) play important roles in the phytotoxicity mechanism of florpyrauxifen-benzyl in plants. Our findings demonstrate the potential of florpyrauxifen-benzyl to provide an alternative weed management strategy for rice fields.
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Affiliation(s)
- Hao Wang
- Key Laboratory of Integrated Pest Management on Crops in East China, Ministry of Agriculture, Nanjing Agricultural University, 210095 Nanjing, China; State & Local Joint Engineering Research Center of Green Pesticide Invention and Application, Nanjing Agricultural University, 210095 Nanjing, China
| | - Xutao Sun
- Key Laboratory of Integrated Pest Management on Crops in East China, Ministry of Agriculture, Nanjing Agricultural University, 210095 Nanjing, China; State & Local Joint Engineering Research Center of Green Pesticide Invention and Application, Nanjing Agricultural University, 210095 Nanjing, China
| | - Jiaxing Yu
- Key Laboratory of Integrated Pest Management on Crops in East China, Ministry of Agriculture, Nanjing Agricultural University, 210095 Nanjing, China; State & Local Joint Engineering Research Center of Green Pesticide Invention and Application, Nanjing Agricultural University, 210095 Nanjing, China
| | - Jun Li
- Key Laboratory of Integrated Pest Management on Crops in East China, Ministry of Agriculture, Nanjing Agricultural University, 210095 Nanjing, China; State & Local Joint Engineering Research Center of Green Pesticide Invention and Application, Nanjing Agricultural University, 210095 Nanjing, China
| | - Liyao Dong
- Key Laboratory of Integrated Pest Management on Crops in East China, Ministry of Agriculture, Nanjing Agricultural University, 210095 Nanjing, China; State & Local Joint Engineering Research Center of Green Pesticide Invention and Application, Nanjing Agricultural University, 210095 Nanjing, China.
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The Lotus japonicus AFB6 Gene Is Involved in the Auxin Dependent Root Developmental Program. Int J Mol Sci 2021; 22:ijms22168495. [PMID: 34445201 PMCID: PMC8395167 DOI: 10.3390/ijms22168495] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Revised: 07/30/2021] [Accepted: 08/03/2021] [Indexed: 11/16/2022] Open
Abstract
Auxin is essential for root development, and its regulatory action is exerted at different steps from perception of the hormone up to transcriptional regulation of target genes. In legume plants there is an overlap between the developmental programs governing lateral root and N2-fixing nodule organogenesis, the latter induced as the result of the symbiotic interaction with rhizobia. Here we report the characterization of a member of the L. japonicus TIR1/AFB auxin receptor family, LjAFB6. A preferential expression of the LjAFB6 gene in the aerial portion of L. japonicus plants was observed. Significant regulation of the expression was not observed during the symbiotic interaction with Mesorhizobium loti and the nodule organogenesis process. In roots, the LjAFB6 expression was induced in response to nitrate supply and was mainly localized in the meristematic regions of both primary and lateral roots. The phenotypic analyses conducted on two independent null mutants indicated a specialized role in the control of primary and lateral root elongation processes in response to auxin, whereas no involvement in the nodulation process was found. We also report the involvement of LjAFB6 in the hypocotyl elongation process and in the control of the expression profile of an auxin-responsive gene.
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