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Liu Z, Sun H, Li Y, Bao Q, Huang Y. Metabolic regulation mechanism of melatonin for reducing cadmium accumulation and improving quality in rice. Food Chem 2024; 455:139857. [PMID: 38823141 DOI: 10.1016/j.foodchem.2024.139857] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Revised: 05/20/2024] [Accepted: 05/25/2024] [Indexed: 06/03/2024]
Abstract
Melatonin acts as a potential regulator of cadmium (Cd) tolerance in rice. However, its practical value in rice production remains unclear. To validate the hypothesis that melatonin affects Cd accumulation and rice quality, a series of experiments were conducted. The results showed that exogenous melatonin application was associated with reduced Cd accumulation (23-43%) in brown rice. Fourier transform infrared spectroscopy (FTIR) analysis showed that exogenous melatonin affected the rice protein secondary structure and starch short-range structure. Metabolomics based on LC-MS/MS revealed that exogenous melatonin altered the brown rice metabolic profile, decreased fatty acid metabolite content, but increased amino acid metabolite, citric acid, melatonin biosynthetic metabolite, and plant hormone contents. These findings indicate that exogenous melatonin can effectively reduced Cd accumulation and improve rice quality through metabolic network regulation, serving as an effective treatment for rice cultivated in Cd-contaminated soil.
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Affiliation(s)
- Zewei Liu
- Innovation Team of Heavy Metal Ecotoxicology and Pollution Remediation, Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin 300191, China
| | - Hongyu Sun
- Innovation Team of Heavy Metal Ecotoxicology and Pollution Remediation, Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin 300191, China
| | - Yan Li
- School of Energy and Environmental Sciences, Yunnan Normal University, Kunming 650500, China
| | - Qiongli Bao
- Innovation Team of Heavy Metal Ecotoxicology and Pollution Remediation, Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin 300191, China.
| | - Yizong Huang
- School of Energy and Environmental Sciences, Yunnan Normal University, Kunming 650500, China.
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Long Y, Wang C, Liu C, Li H, Pu A, Dong Z, Wei X, Wan X. Molecular mechanisms controlling grain size and weight and their biotechnological breeding applications in maize and other cereal crops. J Adv Res 2024; 62:27-46. [PMID: 37739122 PMCID: PMC11331183 DOI: 10.1016/j.jare.2023.09.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2023] [Revised: 09/03/2023] [Accepted: 09/18/2023] [Indexed: 09/24/2023] Open
Abstract
BACKGROUND Cereal crops are a primary energy source for humans. Grain size and weight affect both evolutionary fitness and grain yield of cereals. Although studies on gene mining and molecular mechanisms controlling grain size and weight are constantly emerging in cereal crops, only a few systematic reviews on the underlying molecular mechanisms and their breeding applications are available so far. AIM OF REVIEW This review provides a general state-of-the-art overview of molecular mechanisms and targeted strategies for improving grain size and weight of cereals as well as insights for future yield-improving biotechnology-assisted breeding. KEY SCIENTIFIC CONCEPTS OF REVIEW In this review, the evolution of research on grain size and weight over the last 20 years is traced based on a bibliometric analysis of 1158 publications and the main signaling pathways and transcriptional factors involved are summarized. In addition, the roles of post-transcriptional regulation and photosynthetic product accumulation affecting grain size and weight in maize and rice are outlined. State-of-the-art strategies for discovering novel genes related to grain size and weight in maize and other cereal crops as well as advanced breeding biotechnology strategies being used for improving yield including marker-assisted selection, genomic selection, transgenic breeding, and genome editing are also discussed.
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Affiliation(s)
- Yan Long
- Research Institute of Biology and Agriculture, University of Science and Technology Beijing, Beijing 100083, China; Industry Research Institute of Biotechnology Breeding, Yili Normal University, Yining 835000, China; Beijing Engineering Laboratory of Main Crop Bio-Tech Breeding, Beijing International Science and Technology Cooperation Base of Bio-Tech Breeding, Zhongzhi International Institute of Agricultural Biosciences, Beijing 100192, China
| | - Cheng Wang
- Research Institute of Biology and Agriculture, University of Science and Technology Beijing, Beijing 100083, China; Beijing Engineering Laboratory of Main Crop Bio-Tech Breeding, Beijing International Science and Technology Cooperation Base of Bio-Tech Breeding, Zhongzhi International Institute of Agricultural Biosciences, Beijing 100192, China
| | - Chang Liu
- Research Institute of Biology and Agriculture, University of Science and Technology Beijing, Beijing 100083, China; Beijing Engineering Laboratory of Main Crop Bio-Tech Breeding, Beijing International Science and Technology Cooperation Base of Bio-Tech Breeding, Zhongzhi International Institute of Agricultural Biosciences, Beijing 100192, China
| | - Huangai Li
- Research Institute of Biology and Agriculture, University of Science and Technology Beijing, Beijing 100083, China; Beijing Engineering Laboratory of Main Crop Bio-Tech Breeding, Beijing International Science and Technology Cooperation Base of Bio-Tech Breeding, Zhongzhi International Institute of Agricultural Biosciences, Beijing 100192, China
| | - Aqing Pu
- Research Institute of Biology and Agriculture, University of Science and Technology Beijing, Beijing 100083, China; Beijing Engineering Laboratory of Main Crop Bio-Tech Breeding, Beijing International Science and Technology Cooperation Base of Bio-Tech Breeding, Zhongzhi International Institute of Agricultural Biosciences, Beijing 100192, China
| | - Zhenying Dong
- Research Institute of Biology and Agriculture, University of Science and Technology Beijing, Beijing 100083, China; Industry Research Institute of Biotechnology Breeding, Yili Normal University, Yining 835000, China; Beijing Engineering Laboratory of Main Crop Bio-Tech Breeding, Beijing International Science and Technology Cooperation Base of Bio-Tech Breeding, Zhongzhi International Institute of Agricultural Biosciences, Beijing 100192, China
| | - Xun Wei
- Research Institute of Biology and Agriculture, University of Science and Technology Beijing, Beijing 100083, China; Industry Research Institute of Biotechnology Breeding, Yili Normal University, Yining 835000, China; Beijing Engineering Laboratory of Main Crop Bio-Tech Breeding, Beijing International Science and Technology Cooperation Base of Bio-Tech Breeding, Zhongzhi International Institute of Agricultural Biosciences, Beijing 100192, China
| | - Xiangyuan Wan
- Research Institute of Biology and Agriculture, University of Science and Technology Beijing, Beijing 100083, China; Industry Research Institute of Biotechnology Breeding, Yili Normal University, Yining 835000, China; Beijing Engineering Laboratory of Main Crop Bio-Tech Breeding, Beijing International Science and Technology Cooperation Base of Bio-Tech Breeding, Zhongzhi International Institute of Agricultural Biosciences, Beijing 100192, China.
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3
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Kim H, Lee N, Kim Y, Choi G. The phytochrome-interacting factor genes PIF1 and PIF4 are functionally diversified due to divergence of promoters and proteins. THE PLANT CELL 2024; 36:2778-2797. [PMID: 38593049 PMCID: PMC11289632 DOI: 10.1093/plcell/koae110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Revised: 03/19/2024] [Accepted: 03/23/2024] [Indexed: 04/11/2024]
Abstract
Phytochrome-interacting factors (PIFs) are basic helix-loop-helix transcription factors that regulate light responses downstream of phytochromes. In Arabidopsis (Arabidopsis thaliana), 8 PIFs (PIF1-8) regulate light responses, either redundantly or distinctively. Distinctive roles of PIFs may be attributed to differences in mRNA expression patterns governed by promoters or variations in molecular activities of proteins. However, elements responsible for the functional diversification of PIFs have yet to be determined. Here, we investigated the role of promoters and proteins in the functional diversification of PIF1 and PIF4 by analyzing transgenic lines expressing promoter-swapped PIF1 and PIF4, as well as chimeric PIF1 and PIF4 proteins. For seed germination, PIF1 promoter played a major role, conferring dominance to PIF1 gene with a minor contribution from PIF1 protein. Conversely, for hypocotyl elongation under red light, PIF4 protein was the major element conferring dominance to PIF4 gene with the minor contribution from PIF4 promoter. In contrast, both PIF4 promoter and PIF4 protein were required for the dominant role of PIF4 in promoting hypocotyl elongation at high ambient temperatures. Together, our results support that the functional diversification of PIF1 and PIF4 genes resulted from contributions of both promoters and proteins, with their relative importance varying depending on specific light responses.
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Affiliation(s)
- Hanim Kim
- Department of Biological Sciences, KAIST, Daejeon 34141, Republic of Korea
| | - Nayoung Lee
- Department of Biological Sciences, KAIST, Daejeon 34141, Republic of Korea
| | - Yeojae Kim
- Department of Biological Sciences, KAIST, Daejeon 34141, Republic of Korea
| | - Giltsu Choi
- Department of Biological Sciences, KAIST, Daejeon 34141, Republic of Korea
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4
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Han Y, Hu Q, Gong N, Yan H, Khan NU, Du Y, Sun H, Zhao Q, Peng W, Li Z, Zhang Z, Li J. Natural variation in MORE GRAINS 1 regulates grain number and grain weight in rice. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2024; 66:1440-1458. [PMID: 38780111 DOI: 10.1111/jipb.13674] [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: 11/14/2023] [Accepted: 04/14/2024] [Indexed: 05/25/2024]
Abstract
Grain yield is determined mainly by grain number and grain weight. In this study, we identified and characterized MORE GRAINS1 (MOG1), a gene associated with grain number and grain weight in rice (Oryza sativa L.), through map-based cloning. Overexpression of MOG1 increased grain yield by 18.6%-22.3% under field conditions. We determined that MOG1, a bHLH transcription factor, interacts with OsbHLH107 and directly activates the expression of LONELY GUY (LOG), which encodes a cytokinin-activating enzyme and the cell expansion gene EXPANSIN-LIKE1 (EXPLA1), positively regulating grain number per panicle and grain weight. Natural variations in the promoter and coding regions of MOG1 between Hap-LNW and Hap-HNW alleles resulted in changes in MOG1 expression level and transcriptional activation, leading to functional differences. Haplotype analysis revealed that Hap-HNW, which results in a greater number and heavier grains, has undergone strong selection but has been poorly utilized in modern lowland rice breeding. In summary, the MOG1-OsbHLH107 complex activates LOG and EXPLA1 expression to promote cell expansion and division of young panicles through the cytokinin pathway, thereby increasing grain number and grain weight. These findings suggest that Hap-HNW could be used in strategies to breed high-yielding temperate japonica lowland rice.
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Affiliation(s)
- Yingchun Han
- Henan Key Laboratory of Rice Molecular Breeding and High Efficiency Production, College of Agronomy, Henan Agricultural University, Zhengzhou, 450046, China
| | - Qianfeng Hu
- Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Nuo Gong
- Henan Key Laboratory of Rice Molecular Breeding and High Efficiency Production, College of Agronomy, Henan Agricultural University, Zhengzhou, 450046, China
| | - Huimin Yan
- Henan Key Laboratory of Rice Molecular Breeding and High Efficiency Production, College of Agronomy, Henan Agricultural University, Zhengzhou, 450046, China
| | - Najeeb Ullah Khan
- Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Yanxiu Du
- Henan Key Laboratory of Rice Molecular Breeding and High Efficiency Production, College of Agronomy, Henan Agricultural University, Zhengzhou, 450046, China
| | - Hongzheng Sun
- Henan Key Laboratory of Rice Molecular Breeding and High Efficiency Production, College of Agronomy, Henan Agricultural University, Zhengzhou, 450046, China
| | - Quanzhi Zhao
- Henan Key Laboratory of Rice Molecular Breeding and High Efficiency Production, College of Agronomy, Henan Agricultural University, Zhengzhou, 450046, China
- Rice Industrial Technology Research Institute, Guizhou University, Guiyang, 550025, China
| | - Wanxi Peng
- School of Forestry, Henan Agricultural University, Zhengzhou, 450046, China
| | - Zichao Li
- Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Zhanying Zhang
- Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Junzhou Li
- Henan Key Laboratory of Rice Molecular Breeding and High Efficiency Production, College of Agronomy, Henan Agricultural University, Zhengzhou, 450046, China
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5
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You J, Ye L, Wang D, Zhang Y, Xiao W, Wei M, Wu R, Liu J, He G, Zhao F, Zhang T. Mapping and candidate gene analysis of QTLs for grain shape in a rice chromosome segment substitution line Z485 and breeding of SSSLs. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2024; 44:39. [PMID: 38766512 PMCID: PMC11099003 DOI: 10.1007/s11032-024-01480-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2024] [Accepted: 05/10/2024] [Indexed: 05/22/2024]
Abstract
Grain shape is one of the most important factors that affects rice yield. Cloning novel grain shape genes and analyzing their genetic mechanisms are crucial for high yield breeding. In this study, a slender grain CSSL-Z485 with 3-segments substitution in the genetic background of Nipponbare was constructed in rice. Cytological analysis showed that the longer grain length of Z485 was related to the increase in glume cell numbers, while the narrower grain width was associated with the decrease in cell width. Three grain shape-related quantitative trait locus (QTLs), including qGL12, qGW12, and qRLW12, were identified through the F2 population constructed from a cross between Nipponbare and Z485. Furthermore, four single segment substitution lines (SSSLs, S1-S4) carrying the target QTLs were dissected from Z485 by MAS. Finally, three candidate genes of qGL12 for grain length and qGW12 for grain width located in S3 were confirmed by DNA sequencing, RT-qPCR, and protein structure prediction. Specifically, candidate gene 1 encodes a ubiquitin family protein, while candidate genes 2 and 3 encode zinc finger proteins. The results provide valuable germplasm resources for cloning novel grain shape genes and molecular breeding by design. Supplementary information The online version contains supplementary material available at 10.1007/s11032-024-01480-x.
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Affiliation(s)
- Jing You
- Key Laboratory of Crop Molecular Improvement, College of Agronomy and Biotechnology, Rice Research InstituteAcademy of Agricultural SciencesSouthwest University, Chongqing, 400715 China
| | - Li Ye
- Key Laboratory of Crop Molecular Improvement, College of Agronomy and Biotechnology, Rice Research InstituteAcademy of Agricultural SciencesSouthwest University, Chongqing, 400715 China
| | - Dachuan Wang
- Key Laboratory of Crop Molecular Improvement, College of Agronomy and Biotechnology, Rice Research InstituteAcademy of Agricultural SciencesSouthwest University, Chongqing, 400715 China
| | - Yi Zhang
- Key Laboratory of Crop Molecular Improvement, College of Agronomy and Biotechnology, Rice Research InstituteAcademy of Agricultural SciencesSouthwest University, Chongqing, 400715 China
| | - Wenwen Xiao
- Key Laboratory of Crop Molecular Improvement, College of Agronomy and Biotechnology, Rice Research InstituteAcademy of Agricultural SciencesSouthwest University, Chongqing, 400715 China
| | - Mi Wei
- Key Laboratory of Crop Molecular Improvement, College of Agronomy and Biotechnology, Rice Research InstituteAcademy of Agricultural SciencesSouthwest University, Chongqing, 400715 China
| | - Ruhui Wu
- Key Laboratory of Crop Molecular Improvement, College of Agronomy and Biotechnology, Rice Research InstituteAcademy of Agricultural SciencesSouthwest University, Chongqing, 400715 China
| | - Jinyan Liu
- Key Laboratory of Crop Molecular Improvement, College of Agronomy and Biotechnology, Rice Research InstituteAcademy of Agricultural SciencesSouthwest University, Chongqing, 400715 China
| | - Guanghua He
- Key Laboratory of Crop Molecular Improvement, College of Agronomy and Biotechnology, Rice Research InstituteAcademy of Agricultural SciencesSouthwest University, Chongqing, 400715 China
| | - Fangming Zhao
- Key Laboratory of Crop Molecular Improvement, College of Agronomy and Biotechnology, Rice Research InstituteAcademy of Agricultural SciencesSouthwest University, Chongqing, 400715 China
| | - Ting Zhang
- Key Laboratory of Crop Molecular Improvement, College of Agronomy and Biotechnology, Rice Research InstituteAcademy of Agricultural SciencesSouthwest University, Chongqing, 400715 China
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6
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Yan Y, Zhu X, Qi H, Zhang H, He J. Regulatory mechanism and molecular genetic dissection of rice ( Oryza sativa L.) grain size. Heliyon 2024; 10:e27139. [PMID: 38486732 PMCID: PMC10938125 DOI: 10.1016/j.heliyon.2024.e27139] [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: 10/25/2023] [Revised: 02/18/2024] [Accepted: 02/25/2024] [Indexed: 03/17/2024] Open
Abstract
With the sharp increase of the global population, adequate food supply is a great challenge. Grain size is an essential determinant of rice yield and quality. It is a typical quantitative trait controlled by multiple genes. In this paper, we summarized the quantitative trait loci (QTL) that have been molecularly characterized and provided a comprehensive summary of the regulation mechanism and genetic pathways of rice grain size. These pathways include the ubiquitin-proteasome system, G-protein, mitogen-activated protein kinase, phytohormone, transcriptional factors, abiotic stress. In addition, we discuss the possible application of advanced molecular biology methods and reasonable breeding strategies, and prospective on the development of high-yielding and high-quality rice varieties using molecular biology techniques.
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Affiliation(s)
- Yuntao Yan
- College of Agronomy, Hunan Agricultural University, Changsha 420128, China
| | - Xiaoya Zhu
- College of Agronomy, Hunan Agricultural University, Changsha 420128, China
| | - Hui Qi
- College of Agronomy, Hunan Agricultural University, Changsha 420128, China
- Hunan Institute of Nuclear Agricultural Science and Space Breeding, Hunan Academy of Agricultural Sciences, Changsha 410125, China
| | - Haiqing Zhang
- College of Agronomy, Hunan Agricultural University, Changsha 420128, China
| | - Jiwai He
- College of Agronomy, Hunan Agricultural University, Changsha 420128, China
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7
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Zhao T, Tang P, Liu C, Zuo R, Su S, Zhong Y, Li Y, Yang J. Multi-Omics Approach Reveals OsPIL1 as a Regulator Promotes Rice Growth, Grain Development, and Blast Resistance. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:1822-1843. [PMID: 38192056 DOI: 10.1021/acs.jafc.3c07330] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/10/2024]
Abstract
Rice (Oryza sativa) is a crucial crop, achieving high yield concurrent pathogen resistance remains a challenge. Transcription factors play roles in growth and abiotic tolerance. However, rice phytochrome-interacting factor-like 1 (OsPIL1) in pathogen resistance and agronomic traits remains unexplored. We generated OsPIL1 overexpressing (OsPIL1 OE) rice lines and evaluated their impact on growth, grain development, and resistance to Magnaporthe oryzae. Multiomics analysis (RNA-seq, metabolomics, and CUT&Tag) and RT-qPCR validated OsPIL1 target genes and key metabolites. In the results, OsPIL1 OE rice lines exhibited robust growth, longer grains, and enhanced resistance to M. oryzae without compromising growth. Integrative multiomics analysis revealed a coordinated regulatory network centered on OsPIL1, explaining these desirable traits. OsPIL1 likely acts as a positive regulator, targeting transcriptional elements or specific genes with direct functions in several biological programs. In particular, a range of key signaling genes (phosphatases, kinases, plant hormone genes, transcription factors), and metabolites (linolenic acid, vitamin E, trigonelline, d-glucose, serotonin, choline, genistein, riboflavin) contributed to enhanced rice growth, grain size, pathogen resistance, or a combination of these traits. These findings highlight OsPIL1's regulatory role in promoting important traits and provide insights into potential strategies for rice breeding.
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Affiliation(s)
- Tianqi Zhao
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming 650201, China
- Key Laboratory of Agro-Biodiversity and Pest Management of Ministry of Education, Yunnan Agricultural University, Kunming 650201, China
| | - Ping Tang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming 650201, China
- Key Laboratory of Agro-Biodiversity and Pest Management of Ministry of Education, Yunnan Agricultural University, Kunming 650201, China
| | - Chonglan Liu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming 650201, China
- Key Laboratory of Agro-Biodiversity and Pest Management of Ministry of Education, Yunnan Agricultural University, Kunming 650201, China
| | - Rubin Zuo
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming 650201, China
- Key Laboratory of Agro-Biodiversity and Pest Management of Ministry of Education, Yunnan Agricultural University, Kunming 650201, China
| | - Shunyu Su
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming 650201, China
- Key Laboratory of Agro-Biodiversity and Pest Management of Ministry of Education, Yunnan Agricultural University, Kunming 650201, China
| | - Yuanyuan Zhong
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming 650201, China
- Key Laboratory of Agro-Biodiversity and Pest Management of Ministry of Education, Yunnan Agricultural University, Kunming 650201, China
| | - Yongjie Li
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming 650201, China
- Key Laboratory of Agro-Biodiversity and Pest Management of Ministry of Education, Yunnan Agricultural University, Kunming 650201, China
| | - Jing Yang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming 650201, China
- Key Laboratory of Agro-Biodiversity and Pest Management of Ministry of Education, Yunnan Agricultural University, Kunming 650201, China
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8
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Sun Y, Li Q, Wu M, Wang Q, Zhang D, Gao Y. Rice PIFs: Critical regulators in rice development and stress response. PLANT MOLECULAR BIOLOGY 2024; 114:1. [PMID: 38177976 DOI: 10.1007/s11103-023-01406-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Accepted: 11/09/2023] [Indexed: 01/06/2024]
Abstract
Phytochrome-interacting factors (PIFs) belong to a subfamily of the basic helix-loop-helix (bHLH) family of transcription factors, which serve as a "hub" for development and growth of plants. They have the capability to regulate the expression of many downstream genes, integrate multiple signaling pathways, and act as a signaling center within the cell. In rice (Oryza sativa), the PIF family genes, known as OsPILs, play a crucial part in many different aspects. OsPILs play a crucial role in regulating various aspects of photomorphogenesis, skotomorphogenesis, plant growth, and development in rice. These vital processes include chlorophyll synthesis, plant gravitropism, plant height, flowering, and response to abiotic stress factors such as low temperature, drought, and high salt. Additionally, OsPILs are involved in controlling several important agronomic traits in rice. Some OsPILs members coordinate with each other to function. This review summarizes and prospects the latest research progress on the biological functions of OsPILs transcription factors and provides a reference for further exploring the functions and mechanism of OsPILs.
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Affiliation(s)
- Yixuan Sun
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/ Key Laboratory of Plant Functional Genomics of the Ministry of Education/ Jiangsu Key Laboratory of Crop Genetics and Physiology, Yangzhou University, Yangzhou, 225009, China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Joint International Research Laboratory of Agriculture and Agri-Product Safety of the Ministry of Education, Yangzhou University, Yangzhou, 225009, China
| | - Qian Li
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/ Key Laboratory of Plant Functional Genomics of the Ministry of Education/ Jiangsu Key Laboratory of Crop Genetics and Physiology, Yangzhou University, Yangzhou, 225009, China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Joint International Research Laboratory of Agriculture and Agri-Product Safety of the Ministry of Education, Yangzhou University, Yangzhou, 225009, China
| | - Meidi Wu
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/ Key Laboratory of Plant Functional Genomics of the Ministry of Education/ Jiangsu Key Laboratory of Crop Genetics and Physiology, Yangzhou University, Yangzhou, 225009, China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Joint International Research Laboratory of Agriculture and Agri-Product Safety of the Ministry of Education, Yangzhou University, Yangzhou, 225009, China
| | - Qingwen Wang
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/ Key Laboratory of Plant Functional Genomics of the Ministry of Education/ Jiangsu Key Laboratory of Crop Genetics and Physiology, Yangzhou University, Yangzhou, 225009, China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Joint International Research Laboratory of Agriculture and Agri-Product Safety of the Ministry of Education, Yangzhou University, Yangzhou, 225009, China
| | - Dongping Zhang
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/ Key Laboratory of Plant Functional Genomics of the Ministry of Education/ Jiangsu Key Laboratory of Crop Genetics and Physiology, Yangzhou University, Yangzhou, 225009, China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Joint International Research Laboratory of Agriculture and Agri-Product Safety of the Ministry of Education, Yangzhou University, Yangzhou, 225009, China
| | - Yong Gao
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/ Key Laboratory of Plant Functional Genomics of the Ministry of Education/ Jiangsu Key Laboratory of Crop Genetics and Physiology, Yangzhou University, Yangzhou, 225009, China.
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Joint International Research Laboratory of Agriculture and Agri-Product Safety of the Ministry of Education, Yangzhou University, Yangzhou, 225009, China.
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9
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Gasparis S, Miłoszewski MM. Genetic Basis of Grain Size and Weight in Rice, Wheat, and Barley. Int J Mol Sci 2023; 24:16921. [PMID: 38069243 PMCID: PMC10706642 DOI: 10.3390/ijms242316921] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Revised: 11/27/2023] [Accepted: 11/27/2023] [Indexed: 12/18/2023] Open
Abstract
Grain size is a key component of grain yield in cereals. It is a complex quantitative trait controlled by multiple genes. Grain size is determined via several factors in different plant development stages, beginning with early tillering, spikelet formation, and assimilates accumulation during the pre-anthesis phase, up to grain filling and maturation. Understanding the genetic and molecular mechanisms that control grain size is a prerequisite for improving grain yield potential. The last decade has brought significant progress in genomic studies of grain size control. Several genes underlying grain size and weight were identified and characterized in rice, which is a model plant for cereal crops. A molecular function analysis revealed most genes are involved in different cell signaling pathways, including phytohormone signaling, transcriptional regulation, ubiquitin-proteasome pathway, and other physiological processes. Compared to rice, the genetic background of grain size in other important cereal crops, such as wheat and barley, remains largely unexplored. However, the high level of conservation of genomic structure and sequences between closely related cereal crops should facilitate the identification of functional orthologs in other species. This review provides a comprehensive overview of the genetic and molecular bases of grain size and weight in wheat, barley, and rice, focusing on the latest discoveries in the field. We also present possibly the most updated list of experimentally validated genes that have a strong effect on grain size and discuss their molecular function.
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Affiliation(s)
- Sebastian Gasparis
- Plant Breeding and Acclimatization Institute—National Research Institute in Radzików, 05-870 Błonie, Poland;
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10
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Wang K, Li M, Zhang B, Chang Y, An S, Zhao W. Sugar starvation activates the OsSnRK1a-OsbHLH111/OsSGI1-OsTPP7 module to mediate growth inhibition of rice. PLANT BIOTECHNOLOGY JOURNAL 2023; 21:2033-2046. [PMID: 37384619 PMCID: PMC10502754 DOI: 10.1111/pbi.14110] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 05/29/2023] [Accepted: 06/15/2023] [Indexed: 07/01/2023]
Abstract
Sugar deficiency is the persistent challenge for plants during development. Trehalose-6-phosphate (T6P) is recognized as a key regulator in balancing plant sugar homeostasis. However, the underlying mechanisms by which sugar starvation limits plant development are unclear. Here, a basic helix-loop-helix (bHLH) transcription factor (OsbHLH111) was named starvation-associated growth inhibitor 1 (OsSGI1) and the focus is on the sugar shortage of rice. The transcript and protein levels of OsSGI1 were markedly increased during sugar starvation. The knockout mutants sgi1-1/2/3 exhibited increased grain size and promoted seed germination and vegetative growth, which were opposite to those of overexpression lines. The direct binding of OsSGI1 to sucrose non-fermenting-1 (SNF1)-related protein kinase 1a (OsSnRK1a) was enhanced during sugar shortage. Subsequently, OsSnRK1a-dependent phosphorylation of OsSGI1 enhanced the direct binding to the E-box of trehalose 6-phosphate phosphatase 7 (OsTPP7) promoter, thus rose the transcription inhibition on OsTPP7, then elevated trehalose 6-phosphate (Tre6P) content but decreased sucrose content. Meanwhile, OsSnRK1a degraded phosphorylated-OsSGI1 by proteasome pathway to prevent the cumulative toxicity of OsSGI1. Overall, we established the OsSGI1-OsTPP7-Tre6P loop with OsSnRK1a as center and OsSGI1 as forward, which is activated by sugar starvation to regulate sugar homeostasis and thus inhibits rice growth.
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Affiliation(s)
- Kun Wang
- College of Plant ProtectionHenan Agricultural UniversityZhengzhouHenanChina
- College of Biological SciencesChina Agricultural UniversityBeijingChina
| | - Mengqi Li
- College of Plant ProtectionHenan Agricultural UniversityZhengzhouHenanChina
| | - Bo Zhang
- College of Plant ProtectionHenan Agricultural UniversityZhengzhouHenanChina
| | - Yanpeng Chang
- College of Plant ProtectionHenan Agricultural UniversityZhengzhouHenanChina
| | - Shiheng An
- College of Plant ProtectionHenan Agricultural UniversityZhengzhouHenanChina
| | - Wenli Zhao
- College of Plant ProtectionHenan Agricultural UniversityZhengzhouHenanChina
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11
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Sharma A, Samtani H, Sahu K, Sharma AK, Khurana JP, Khurana P. Functions of Phytochrome-Interacting Factors (PIFs) in the regulation of plant growth and development: A comprehensive review. Int J Biol Macromol 2023:125234. [PMID: 37290549 DOI: 10.1016/j.ijbiomac.2023.125234] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 06/02/2023] [Accepted: 06/04/2023] [Indexed: 06/10/2023]
Abstract
Transcription factors play important roles in governing plant responses upon changes in their ambient conditions. Any fluctuation in the supply of critical requirements for plants, such as optimum light, temperature, and water leads to the reprogramming of gene-signaling pathways. At the same time, plants also evaluate and shift their metabolism according to the various stages of development. Phytochrome-Interacting Factors are one of the most important classes of transcription factors that regulate both developmental and external stimuli-based growth of plants. This review focuses on the identification of PIFs in various organisms, regulation of PIFs by various proteins, functions of PIFs of Arabidopsis in diverse developmental pathways such as seed germination, photomorphogenesis, flowering, senescence, seed and fruit development, and external stimuli-induced plant responses such as shade avoidance response, thermomorphogenesis, and various abiotic stress responses. Recent advances related to the functional characterization of PIFs of crops such as rice, maize, and tomato have also been incorporated in this review, to ascertain the potential of PIFs as key regulators to enhance the agronomic traits of these crops. Thus, an attempt has been made to provide a holistic view of the function of PIFs in various processes in plants.
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Affiliation(s)
- Aishwarye Sharma
- Department of Plant Molecular Biology, University of Delhi South Campus, Benito Juarez Road, New Delhi 110021, India
| | - Harsha Samtani
- Department of Plant Molecular Biology, University of Delhi South Campus, Benito Juarez Road, New Delhi 110021, India
| | - Karishma Sahu
- Department of Plant Molecular Biology, University of Delhi South Campus, Benito Juarez Road, New Delhi 110021, India
| | - Arun Kumar Sharma
- Department of Plant Molecular Biology, University of Delhi South Campus, Benito Juarez Road, New Delhi 110021, India
| | - Jitendra Paul Khurana
- Department of Plant Molecular Biology, University of Delhi South Campus, Benito Juarez Road, New Delhi 110021, India
| | - Paramjit Khurana
- Department of Plant Molecular Biology, University of Delhi South Campus, Benito Juarez Road, New Delhi 110021, India.
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12
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Yin Y, Yan Z, Guan J, Huo Y, Wang T, Li T, Cui Z, Ma W, Wang X, Chen W. Two interacting basic helix-loop-helix transcription factors control flowering time in rice. PLANT PHYSIOLOGY 2023; 192:205-221. [PMID: 36756926 PMCID: PMC10152653 DOI: 10.1093/plphys/kiad077] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 11/29/2022] [Accepted: 12/03/2022] [Indexed: 05/03/2023]
Abstract
Flowering time is one of the most important agronomic traits affecting the adaptation and yield of rice (Oryza sativa). Heading date 1 (Hd1) is a key factor in the photoperiodic control of flowering time. In this study, two basic helix-loop-helix (bHLH) transcription factors, Hd1 Binding Protein 1 (HBP1) and Partner of HBP1 (POH1) were identified as transcriptional regulators of Hd1. We generated knockout mutants of HBP1 and ectopically expressed transgenic lines of the two bHLH transcription factors and used these lines to investigate the roles of these two factors in regulating flowering time. HBP1 physically associated with POH1 forming homo- or heterodimers to perform their functions. Both HBP1 and POH1 bound directly to the cis-acting elements located in the promoter of Hd1 to activate its expression. CRISPR/Cas9-generated knockout mutations of HBP1, but not POH1 mutations, promoted earlier flowering time; conversely, HBP1 and POH1 overexpression delayed flowering time in rice under long-day and short-day conditions by activating the expression of Hd1 and suppressing the expression of Early heading date 1 (Ehd1), Heading date 3a (Hd3a), and Rice Flowering locus T 1 (RFT1), thus controlling flowering time in rice. Our findings revealed a mechanism for flowering time control through transcriptional regulation of Hd1 and laid theoretical and practical foundations for improving the growth period, adaptation, and yield of rice.
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Affiliation(s)
- Yanbin Yin
- Rice Research Institute, Shenyang Agricultural University, 120 Dongling Road, Shenhe District, Shenyang 110866, China
| | - Zhiqiang Yan
- Rice Research Institute, Shenyang Agricultural University, 120 Dongling Road, Shenhe District, Shenyang 110866, China
| | - Jianing Guan
- Rice Research Institute, Shenyang Agricultural University, 120 Dongling Road, Shenhe District, Shenyang 110866, China
| | - Yiqiong Huo
- Rice Research Institute, Shenyang Agricultural University, 120 Dongling Road, Shenhe District, Shenyang 110866, China
| | - Tianqiong Wang
- Rice Research Institute, Shenyang Agricultural University, 120 Dongling Road, Shenhe District, Shenyang 110866, China
| | - Tong Li
- Rice Research Institute, Shenyang Agricultural University, 120 Dongling Road, Shenhe District, Shenyang 110866, China
| | - Zhibo Cui
- Rice Research Institute, Shenyang Agricultural University, 120 Dongling Road, Shenhe District, Shenyang 110866, China
| | - Wenhong Ma
- Rice Research Institute, Shenyang Agricultural University, 120 Dongling Road, Shenhe District, Shenyang 110866, China
| | - Xiaoxue Wang
- Rice Research Institute, Shenyang Agricultural University, 120 Dongling Road, Shenhe District, Shenyang 110866, China
| | - Wenfu Chen
- Rice Research Institute, Shenyang Agricultural University, 120 Dongling Road, Shenhe District, Shenyang 110866, China
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13
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Yuan DP, Yang S, Feng L, Chu J, Dong H, Sun J, Chen H, Li Z, Yamamoto N, Zheng A, Li S, Yoon HC, Chen J, Ma D, Xuan YH. Red-light receptor phytochrome B inhibits BZR1-NAC028-CAD8B signaling to negatively regulate rice resistance to sheath blight. PLANT, CELL & ENVIRONMENT 2023; 46:1249-1263. [PMID: 36457051 DOI: 10.1111/pce.14502] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 11/01/2022] [Accepted: 11/10/2022] [Indexed: 06/17/2023]
Abstract
Phytochrome (Phy)-regulated light signalling plays important roles in plant growth, development, and stress responses. However, its function in rice defence against sheath blight disease (ShB) remains unclear. Here, we found that PhyB mutation or shade treatment promoted rice resistance to ShB, while resistance was reduced by PhyB overexpression. Further analysis showed that PhyB interacts with phytochrome-interacting factor-like 15 (PIL15), brassinazole resistant 1 (BZR1), and vascular plant one-zinc-finger 2 (VOZ2). Plants overexpressing PIL15 were more susceptible to ShB in contrast to bzr1-D-overexpressing plants compared with the wild-type, suggesting that PhyB may inhibit BZR1 to negatively regulate rice resistance to ShB. Although BZR1 is known to regulate brassinosteroid (BR) signalling, the observation that BR signalling negatively regulated resistance to ShB indicated an independent role for BZR1 in controlling rice resistance. It was also found that the BZR1 ligand NAC028 positively regulated resistance to ShB. RNA sequencing showed that cinnamyl alcohol dehydrogenase 8B (CAD8B), involved in lignin biosynthesis was upregulated in both bzr1-D- and NAC028-overexpressing plants compared with the wild-type. Yeast-one hybrid, ChIP, and transactivation assays demonstrated that BZR1 and NAC028 activate CAD8B directly. Taken together, the analyses demonstrated that PhyB-mediated light signalling inhibits the BZR1-NAC028-CAD8B pathway to regulate rice resistance to ShB.
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Affiliation(s)
- De Peng Yuan
- Department of Plant Pathology, College of Plant Protection, Shenyang Agricultural University, Shenyang, China
| | - Shuo Yang
- Department of Plant Pathology, College of Plant Protection, Shenyang Agricultural University, Shenyang, China
| | - Lu Feng
- Department of Plant Pathology, College of Plant Protection, Shenyang Agricultural University, Shenyang, China
| | - Jin Chu
- Laboratory of Rice Disease Research, Institution of Plant Protection, Liaoning Academy of Agricultural Sciences, Shenyang, China
| | - Hai Dong
- Laboratory of Rice Disease Research, Institution of Plant Protection, Liaoning Academy of Agricultural Sciences, Shenyang, China
| | - Jian Sun
- Rice Research Institute, College of Agronomy, Shenyang Agricultural University, Shenyang, China
| | - Huan Chen
- Department of Plant Pathology, College of Plant Protection, Shenyang Agricultural University, Shenyang, China
| | - Zhuo Li
- Department of Plant Pathology, College of Plant Protection, Shenyang Agricultural University, Shenyang, China
| | - Naoki Yamamoto
- Department of Plant Protection, Rice Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Aiping Zheng
- Department of Plant Protection, Rice Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Shuang Li
- Department of Biological Science, College of Life Science, Yan'an University, Yan'an, Shaanxi, China
| | | | - Jingsheng Chen
- College of Biology and Food Engineering, Chongqing Three Gorges University, Chongqing, China
| | - Dianrong Ma
- Rice Research Institute, College of Agronomy, Shenyang Agricultural University, Shenyang, China
| | - Yuan Hu Xuan
- Department of Plant Pathology, College of Plant Protection, Shenyang Agricultural University, Shenyang, China
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14
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Liu G, Zhang R, Li S, Ullah R, Yang F, Wang Z, Guo W, You M, Li B, Xie C, Wang L, Liu J, Ni Z, Sun Q, Liang R. TaMADS29 interacts with TaNF-YB1 to synergistically regulate early grain development in bread wheat. SCIENCE CHINA. LIFE SCIENCES 2023:10.1007/s11427-022-2286-0. [PMID: 36802319 DOI: 10.1007/s11427-022-2286-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2022] [Accepted: 01/18/2023] [Indexed: 02/23/2023]
Abstract
Grain development is a crucial determinant of yield and quality in bread wheat (Triticum aestivum L.). However, the regulatory mechanisms underlying wheat grain development remain elusive. Here we report how TaMADS29 interacts with TaNF-YB1 to synergistically regulate early grain development in bread wheat. The tamads29 mutants generated by CRISPR/Cas9 exhibited severe grain filling deficiency, coupled with excessive accumulation of reactive oxygen species (ROS) and abnormal programmed cell death that occurred in early developing grains, while overexpression of TaMADS29 increased grain width and 1,000-kernel weight. Further analysis revealed that TaMADS29 interacted directly with TaNF-YB1; null mutation in TaNF-YB1 caused grain developmental deficiency similar to tamads29 mutants. The regulatory complex composed of TaMADS29 and TaNF-YB1 exercises its possible function that inhibits the excessive accumulation of ROS by regulating the genes involved in chloroplast development and photosynthesis in early developing wheat grains and prevents nucellar projection degradation and endosperm cell death, facilitating transportation of nutrients into the endosperm and wholly filling of developing grains. Collectively, our work not only discloses the molecular mechanism of MADS-box and NF-Y TFs in facilitating bread wheat grain development, but also indicates that caryopsis chloroplast might be a central regulator of grain development rather than merely a photosynthesis organelle. More importantly, our work offers an innovative way to breed high-yield wheat cultivars by controlling the ROS level in developing grains.
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Affiliation(s)
- Guoyu Liu
- Frontiers Science Center for Molecular Design Breeding (MOE), State Key Laboratory for Agrobiotechnology, State Key Laboratory of Plant Physiology and Biochemistry, Key Laboratory of Crop Heterosis and Utilization (MOE), and Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Runqi Zhang
- Frontiers Science Center for Molecular Design Breeding (MOE), State Key Laboratory for Agrobiotechnology, State Key Laboratory of Plant Physiology and Biochemistry, Key Laboratory of Crop Heterosis and Utilization (MOE), and Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Sen Li
- Frontiers Science Center for Molecular Design Breeding (MOE), State Key Laboratory for Agrobiotechnology, State Key Laboratory of Plant Physiology and Biochemistry, Key Laboratory of Crop Heterosis and Utilization (MOE), and Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Rehmat Ullah
- Frontiers Science Center for Molecular Design Breeding (MOE), State Key Laboratory for Agrobiotechnology, State Key Laboratory of Plant Physiology and Biochemistry, Key Laboratory of Crop Heterosis and Utilization (MOE), and Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Fengping Yang
- Frontiers Science Center for Molecular Design Breeding (MOE), State Key Laboratory for Agrobiotechnology, State Key Laboratory of Plant Physiology and Biochemistry, Key Laboratory of Crop Heterosis and Utilization (MOE), and Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Zihao Wang
- Frontiers Science Center for Molecular Design Breeding (MOE), State Key Laboratory for Agrobiotechnology, State Key Laboratory of Plant Physiology and Biochemistry, Key Laboratory of Crop Heterosis and Utilization (MOE), and Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Weilong Guo
- Frontiers Science Center for Molecular Design Breeding (MOE), State Key Laboratory for Agrobiotechnology, State Key Laboratory of Plant Physiology and Biochemistry, Key Laboratory of Crop Heterosis and Utilization (MOE), and Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Mingshan You
- Frontiers Science Center for Molecular Design Breeding (MOE), State Key Laboratory for Agrobiotechnology, State Key Laboratory of Plant Physiology and Biochemistry, Key Laboratory of Crop Heterosis and Utilization (MOE), and Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Baoyun Li
- Frontiers Science Center for Molecular Design Breeding (MOE), State Key Laboratory for Agrobiotechnology, State Key Laboratory of Plant Physiology and Biochemistry, Key Laboratory of Crop Heterosis and Utilization (MOE), and Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Chaojie Xie
- Frontiers Science Center for Molecular Design Breeding (MOE), State Key Laboratory for Agrobiotechnology, State Key Laboratory of Plant Physiology and Biochemistry, Key Laboratory of Crop Heterosis and Utilization (MOE), and Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Liangsheng Wang
- Frontiers Science Center for Molecular Design Breeding (MOE), State Key Laboratory for Agrobiotechnology, State Key Laboratory of Plant Physiology and Biochemistry, Key Laboratory of Crop Heterosis and Utilization (MOE), and Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Jie Liu
- Frontiers Science Center for Molecular Design Breeding (MOE), State Key Laboratory for Agrobiotechnology, State Key Laboratory of Plant Physiology and Biochemistry, Key Laboratory of Crop Heterosis and Utilization (MOE), and Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Zhongfu Ni
- Frontiers Science Center for Molecular Design Breeding (MOE), State Key Laboratory for Agrobiotechnology, State Key Laboratory of Plant Physiology and Biochemistry, Key Laboratory of Crop Heterosis and Utilization (MOE), and Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Qixin Sun
- Frontiers Science Center for Molecular Design Breeding (MOE), State Key Laboratory for Agrobiotechnology, State Key Laboratory of Plant Physiology and Biochemistry, Key Laboratory of Crop Heterosis and Utilization (MOE), and Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Rongqi Liang
- Frontiers Science Center for Molecular Design Breeding (MOE), State Key Laboratory for Agrobiotechnology, State Key Laboratory of Plant Physiology and Biochemistry, Key Laboratory of Crop Heterosis and Utilization (MOE), and Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China.
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15
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Nie N, Huo J, Sun S, Zuo Z, Chen Y, Liu Q, He S, Gao S, Zhang H, Zhao N, Zhai H. Genome-Wide Characterization of the PIFs Family in Sweet Potato and Functional Identification of IbPIF3.1 under Drought and Fusarium Wilt Stresses. Int J Mol Sci 2023; 24:ijms24044092. [PMID: 36835500 PMCID: PMC9965949 DOI: 10.3390/ijms24044092] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Revised: 02/12/2023] [Accepted: 02/14/2023] [Indexed: 02/22/2023] Open
Abstract
Phytochrome-interacting factors (PIFs) are essential for plant growth, development, and defense responses. However, research on the PIFs in sweet potato has been insufficient to date. In this study, we identified PIF genes in the cultivated hexaploid sweet potato (Ipomoea batatas) and its two wild relatives, Ipomoea triloba, and Ipomoea trifida. Phylogenetic analysis revealed that IbPIFs could be divided into four groups, showing the closest relationship with tomato and potato. Subsequently, the PIFs protein properties, chromosome location, gene structure, and protein interaction network were systematically analyzed. RNA-Seq and qRT-PCR analyses showed that IbPIFs were mainly expressed in stem, as well as had different gene expression patterns in response to various stresses. Among them, the expression of IbPIF3.1 was strongly induced by salt, drought, H2O2, cold, heat, Fusarium oxysporum f. sp. batatas (Fob), and stem nematodes, indicating that IbPIF3.1 might play an important role in response to abiotic and biotic stresses in sweet potato. Further research revealed that overexpression of IbPIF3.1 significantly enhanced drought and Fusarium wilt tolerance in transgenic tobacco plants. This study provides new insights for understanding PIF-mediated stress responses and lays a foundation for future investigation of sweet potato PIFs.
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Affiliation(s)
- Nan Nie
- Key Laboratory of Sweet Potato Biology and Biotechnology, Ministry of Agriculture and Rural Affairs/Beijing Key Laboratory of Crop Genetic Improvement/Laboratory of Crop Heterosis and Utilization, Ministry of Education, College of Agronomy & Biotechnology, China Agricultural University, Beijing 100193, China
| | - Jinxi Huo
- Key Laboratory of Sweet Potato Biology and Biotechnology, Ministry of Agriculture and Rural Affairs/Beijing Key Laboratory of Crop Genetic Improvement/Laboratory of Crop Heterosis and Utilization, Ministry of Education, College of Agronomy & Biotechnology, China Agricultural University, Beijing 100193, China
- Institute of Sericulture and Tea, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Sifan Sun
- Key Laboratory of Sweet Potato Biology and Biotechnology, Ministry of Agriculture and Rural Affairs/Beijing Key Laboratory of Crop Genetic Improvement/Laboratory of Crop Heterosis and Utilization, Ministry of Education, College of Agronomy & Biotechnology, China Agricultural University, Beijing 100193, China
| | - Zhidan Zuo
- Key Laboratory of Sweet Potato Biology and Biotechnology, Ministry of Agriculture and Rural Affairs/Beijing Key Laboratory of Crop Genetic Improvement/Laboratory of Crop Heterosis and Utilization, Ministry of Education, College of Agronomy & Biotechnology, China Agricultural University, Beijing 100193, China
| | - Yanqi Chen
- Key Laboratory of Sweet Potato Biology and Biotechnology, Ministry of Agriculture and Rural Affairs/Beijing Key Laboratory of Crop Genetic Improvement/Laboratory of Crop Heterosis and Utilization, Ministry of Education, College of Agronomy & Biotechnology, China Agricultural University, Beijing 100193, China
| | - Qingchang Liu
- Key Laboratory of Sweet Potato Biology and Biotechnology, Ministry of Agriculture and Rural Affairs/Beijing Key Laboratory of Crop Genetic Improvement/Laboratory of Crop Heterosis and Utilization, Ministry of Education, College of Agronomy & Biotechnology, China Agricultural University, Beijing 100193, China
| | - Shaozhen He
- Key Laboratory of Sweet Potato Biology and Biotechnology, Ministry of Agriculture and Rural Affairs/Beijing Key Laboratory of Crop Genetic Improvement/Laboratory of Crop Heterosis and Utilization, Ministry of Education, College of Agronomy & Biotechnology, China Agricultural University, Beijing 100193, China
| | - Shaopei Gao
- Key Laboratory of Sweet Potato Biology and Biotechnology, Ministry of Agriculture and Rural Affairs/Beijing Key Laboratory of Crop Genetic Improvement/Laboratory of Crop Heterosis and Utilization, Ministry of Education, College of Agronomy & Biotechnology, China Agricultural University, Beijing 100193, China
| | - Huan Zhang
- Key Laboratory of Sweet Potato Biology and Biotechnology, Ministry of Agriculture and Rural Affairs/Beijing Key Laboratory of Crop Genetic Improvement/Laboratory of Crop Heterosis and Utilization, Ministry of Education, College of Agronomy & Biotechnology, China Agricultural University, Beijing 100193, China
| | - Ning Zhao
- Key Laboratory of Sweet Potato Biology and Biotechnology, Ministry of Agriculture and Rural Affairs/Beijing Key Laboratory of Crop Genetic Improvement/Laboratory of Crop Heterosis and Utilization, Ministry of Education, College of Agronomy & Biotechnology, China Agricultural University, Beijing 100193, China
| | - Hong Zhai
- Key Laboratory of Sweet Potato Biology and Biotechnology, Ministry of Agriculture and Rural Affairs/Beijing Key Laboratory of Crop Genetic Improvement/Laboratory of Crop Heterosis and Utilization, Ministry of Education, College of Agronomy & Biotechnology, China Agricultural University, Beijing 100193, China
- Correspondence: ; Tel.: +86-010-62732559
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16
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Molecular bases of rice grain size and quality for optimized productivity. Sci Bull (Beijing) 2023; 68:314-350. [PMID: 36710151 DOI: 10.1016/j.scib.2023.01.026] [Citation(s) in RCA: 55] [Impact Index Per Article: 55.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Revised: 12/30/2022] [Accepted: 01/16/2023] [Indexed: 01/19/2023]
Abstract
The accomplishment of further optimization of crop productivity in grain yield and quality is a great challenge. Grain size is one of the crucial determinants of rice yield and quality; all of these traits are typical quantitative traits controlled by multiple genes. Research advances have revealed several molecular and developmental pathways that govern these traits of agronomical importance. This review provides a comprehensive summary of these pathways, including those mediated by G-protein, the ubiquitin-proteasome system, mitogen-activated protein kinase, phytohormone, transcriptional regulators, and storage product biosynthesis and accumulation. We also generalize the excellent precedents for rice variety improvement of grain size and quality, which utilize newly developed gene editing and conventional gene pyramiding capabilities. In addition, we discuss the rational and accurate breeding strategies, with the aim of better applying molecular design to breed high-yield and superior-quality varieties.
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17
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Li P, Li Y, Bai S, Zhang Y, Zhao L. miR-4732-3p prevents lung cancer progression via inhibition of the TBX15/TNFSF11 axis. Epigenomics 2023; 15:195-207. [PMID: 37125501 DOI: 10.2217/epi-2023-0009] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/02/2023] Open
Abstract
Aim: Possible roles of miRNAs in cancer treatment have been highly studied. This study aimed to elucidate the role of miR-4732-3p in lung cancer. Methods: Bioinformatics analysis was conducted to predict miR-4732-3p-related mRNA targets in lung cancer. Following interaction determination between miR-4732-3p and TBX15 as well as between TBX15 and TNFSF11, their in vitro and in vivo roles were assayed. Results: miR-4732-3p negatively targeted TBX15, which upregulated TNFSF11 by enhancing the activity of the TNFSF11 promoter. Overexpression of miR-4732-3p or silencing of TBX15 or TNFSF11 inhibited the malignant phenotype of lung cancer cells and reduced tumorigenicity in vivo. Conclusion: Overall, this study highlighted the inhibitory role of miR-4732-3p in lung cancer progression through the TBX15/TNFSF11 axis.
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Affiliation(s)
- Pengfei Li
- Radiology Department, Harbin Medical University Cancer Hospital, Harbin, 150081, P. R. China
| | - Ying Li
- Department of Respiratory, Zaozhuang Cancer Hospital, Zaozhuang, 277500, P. R. China
| | - Shuping Bai
- The Second Department of Respiratory, Harbin Medical University Cancer Hospital, Harbin, 150081, P. R. China
| | - Yu Zhang
- The Second Department of Respiratory, Harbin Medical University Cancer Hospital, Harbin, 150081, P. R. China
| | - Ling Zhao
- The Second Department of Respiratory, Harbin Medical University Cancer Hospital, Harbin, 150081, P. R. China
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18
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Zuo ZF, Lee HY, Kang HG. Basic Helix-Loop-Helix Transcription Factors: Regulators for Plant Growth Development and Abiotic Stress Responses. Int J Mol Sci 2023; 24:ijms24021419. [PMID: 36674933 PMCID: PMC9867082 DOI: 10.3390/ijms24021419] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 12/30/2022] [Accepted: 01/04/2023] [Indexed: 01/12/2023] Open
Abstract
Plant basic helix-loop-helix (bHLH) transcription factors are involved in many physiological processes, and they play important roles in the abiotic stress responses. The literature related to genome sequences has increased, with genome-wide studies on the bHLH transcription factors in plants. Researchers have detailed the functionally characterized bHLH transcription factors from different aspects in the model plant Arabidopsis thaliana, such as iron homeostasis and abiotic stresses; however, other important economic crops, such as rice, have not been summarized and highlighted. The bHLH members in the same subfamily have similar functions; therefore, unraveling their regulatory mechanisms will help us to identify and understand the roles of some of the unknown bHLH transcription factors in the same subfamily. In this review, we summarize the available knowledge on functionally characterized bHLH transcription factors according to four categories: plant growth and development; metabolism synthesis; plant signaling, and abiotic stress responses. We also highlight the roles of the bHLH transcription factors in some economic crops, especially in rice, and discuss future research directions for possible genetic applications in crop breeding.
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19
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Luo X, Wei Y, Zheng Y, Wei L, Wu F, Cai Q, Xie H, Zhang J. Analysis of co-expression and gene regulatory networks associated with sterile lemma development in rice. BMC PLANT BIOLOGY 2023; 23:11. [PMID: 36604645 PMCID: PMC9817312 DOI: 10.1186/s12870-022-04012-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Accepted: 12/20/2022] [Indexed: 06/17/2023]
Abstract
BACKGROUND The sterile lemma is a unique organ of the rice (Oryza sativa L.) spikelet. However, the characteristics and origin of the rice sterile lemma have not been determined unequivocally, so it is important to elucidate the molecular mechanism of the development of the sterile lemma. RESULTS In the paper, we outline the regulatory mechanism of sterile lemma development by LONG STERILE LEMMA1 (G1), which has been identified as the gene controlling sterile lemma development. Based on the comprehensive analyses of transcriptome dynamics during sterile lemma development with G1 alleles between wild-type (WT) and mutant (MT) in rice, we obtained co-expression data and regulatory networks related to sterile lemma development. Co-transfection assays of rice protoplasts confirmed that G1 affects the expression of various phytohormone-related genes by regulating a number of critical transcription factors, such as OsLBD37 and OSH1. The hormone levels in sterile lemmas from WT and MT of rice supports the hypotheses that lower auxin, lower gibberellin, and higher cytokinin concentrations are required to maintain a normal phenotype of sterile lemmas. CONCLUSION The regulatory networks have considerable reference value, and some of the regulatory relationships exhibiting strong correlations are worthy of further study. Taken together, these work provided a detailed guide for further studies into the molecular mechanism of sterile lemma development.
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Affiliation(s)
- Xi Luo
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- Rice Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou, 350019, China
- Key Laboratory of Germplasm Innovation and Molecular Breeding of Hybrid Rice for South China, Ministry of Agriculture and Affairs P.R. China/Incubator of National Key Laboratory of Germplasm Innovation and Molecular Breeding between Fujian and Ministry of Sciences and Technology/Fuzhou Branch, National Rice Improvement Center of China/Fujian Engineering Laboratory of Crop Molecular Breeding/Fujian Key Laboratory of Rice Molecular Breeding, Fuzhou, 350003, China
| | - Yidong Wei
- Rice Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou, 350019, China
- Key Laboratory of Germplasm Innovation and Molecular Breeding of Hybrid Rice for South China, Ministry of Agriculture and Affairs P.R. China/Incubator of National Key Laboratory of Germplasm Innovation and Molecular Breeding between Fujian and Ministry of Sciences and Technology/Fuzhou Branch, National Rice Improvement Center of China/Fujian Engineering Laboratory of Crop Molecular Breeding/Fujian Key Laboratory of Rice Molecular Breeding, Fuzhou, 350003, China
| | - Yanmei Zheng
- Rice Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou, 350019, China
- Key Laboratory of Germplasm Innovation and Molecular Breeding of Hybrid Rice for South China, Ministry of Agriculture and Affairs P.R. China/Incubator of National Key Laboratory of Germplasm Innovation and Molecular Breeding between Fujian and Ministry of Sciences and Technology/Fuzhou Branch, National Rice Improvement Center of China/Fujian Engineering Laboratory of Crop Molecular Breeding/Fujian Key Laboratory of Rice Molecular Breeding, Fuzhou, 350003, China
| | - Linyan Wei
- Rice Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou, 350019, China
- Key Laboratory of Germplasm Innovation and Molecular Breeding of Hybrid Rice for South China, Ministry of Agriculture and Affairs P.R. China/Incubator of National Key Laboratory of Germplasm Innovation and Molecular Breeding between Fujian and Ministry of Sciences and Technology/Fuzhou Branch, National Rice Improvement Center of China/Fujian Engineering Laboratory of Crop Molecular Breeding/Fujian Key Laboratory of Rice Molecular Breeding, Fuzhou, 350003, China
| | - Fangxi Wu
- Rice Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou, 350019, China
- Key Laboratory of Germplasm Innovation and Molecular Breeding of Hybrid Rice for South China, Ministry of Agriculture and Affairs P.R. China/Incubator of National Key Laboratory of Germplasm Innovation and Molecular Breeding between Fujian and Ministry of Sciences and Technology/Fuzhou Branch, National Rice Improvement Center of China/Fujian Engineering Laboratory of Crop Molecular Breeding/Fujian Key Laboratory of Rice Molecular Breeding, Fuzhou, 350003, China
| | - Qiuhua Cai
- Rice Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou, 350019, China
- Key Laboratory of Germplasm Innovation and Molecular Breeding of Hybrid Rice for South China, Ministry of Agriculture and Affairs P.R. China/Incubator of National Key Laboratory of Germplasm Innovation and Molecular Breeding between Fujian and Ministry of Sciences and Technology/Fuzhou Branch, National Rice Improvement Center of China/Fujian Engineering Laboratory of Crop Molecular Breeding/Fujian Key Laboratory of Rice Molecular Breeding, Fuzhou, 350003, China
| | - Huaan Xie
- Rice Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou, 350019, China.
- Key Laboratory of Germplasm Innovation and Molecular Breeding of Hybrid Rice for South China, Ministry of Agriculture and Affairs P.R. China/Incubator of National Key Laboratory of Germplasm Innovation and Molecular Breeding between Fujian and Ministry of Sciences and Technology/Fuzhou Branch, National Rice Improvement Center of China/Fujian Engineering Laboratory of Crop Molecular Breeding/Fujian Key Laboratory of Rice Molecular Breeding, Fuzhou, 350003, China.
| | - Jianfu Zhang
- Rice Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou, 350019, China.
- Key Laboratory of Germplasm Innovation and Molecular Breeding of Hybrid Rice for South China, Ministry of Agriculture and Affairs P.R. China/Incubator of National Key Laboratory of Germplasm Innovation and Molecular Breeding between Fujian and Ministry of Sciences and Technology/Fuzhou Branch, National Rice Improvement Center of China/Fujian Engineering Laboratory of Crop Molecular Breeding/Fujian Key Laboratory of Rice Molecular Breeding, Fuzhou, 350003, China.
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Li F, Liu Y, Zhang X, Liu L, Yan Y, Ji X, Kong F, Zhao Y, Li J, Peng T, Sun H, Du Y, Zhao Q. Transcriptome and Metabolome Analyses Reveals the Pathway and Metabolites of Grain Quality Under Phytochrome B in Rice (Oryza sativa L.). RICE (NEW YORK, N.Y.) 2022; 15:52. [PMID: 36302917 PMCID: PMC9613846 DOI: 10.1186/s12284-022-00600-5] [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: 05/09/2022] [Accepted: 10/05/2022] [Indexed: 06/16/2023]
Abstract
BACKGROUND Grain size and chalkiness is a critical agronomic trait affecting rice yield and quality. The application of transcriptomics to rice has widened the understanding of complex molecular responsive mechanisms, differential gene expression, and regulatory pathways under varying conditions. Similarly, metabolomics has also contributed drastically for rice trait improvements. As master regulators of plant growth and development, phys influence seed germination, vegetative growth, photoperiodic flowering, shade avoidance responses. OsPHYB can regulate a variety of plant growth and development processes, but little is known about the roles of rice gene OsPHYB in modulating grain development. RESULTS In this study, rice phytochrome B (OsPHYB) was edited using CRISPR/Cas9 technology. We found that OsPHYB knockout increased rice grain size and chalkiness, and increased the contents of amylose, free fatty acids and soluble sugar, while the gel consistency and contents of proteins were reduced in mutant grains. Furthermore, OsPHYB is involved in the regulation of grain size and chalk formation by controlling cell division and complex starch grain morphology. Transcriptomic analysis revealed that loss of OsPHYB function affects multiple metabolic pathways, especially enhancement of glycolysis, fatty acid, oxidative phosphorylation, and antioxidant pathways, as well as differential expression of starch and phytohormone pathways. An analysis of grain metabolites showed an increase in the free fatty acids and lysophosphatidylcholine, whereas the amounts of sugars, alcohols, amino acids and derivatives, organic acids, phenolic acids, alkaloids, nucleotides and derivatives, and flavonoids decreased, which were significantly associated with grain size and chalk formation. CONCLUSIONS Our study reveals that, OsPHYB plays an important regulatory role in the growth and development of rice grains, especially grain size and chalkiness. Furthermore, OsPHYB regulates grain size and chalkiness formation by affecting gene metabolism interaction network. Thus, this study not only revealed that OsPHYB plays a vital role in regulating grain size and chalkiness of rice but reveal new functions and highlighted the importance and value of OsPHYB in rice grain development and provide a new strategy for yield and quality improvement in rice breeding.
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Affiliation(s)
- Fei Li
- Henan Key Laboratory of Rice Biology, Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, No. 15, Longzihu University Park, Zhengdong New Area, Zhengzhou, China
| | - Ye Liu
- Henan Key Laboratory of Rice Biology, Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, No. 15, Longzihu University Park, Zhengdong New Area, Zhengzhou, China
| | - Xiaohua Zhang
- Henan Key Laboratory of Rice Biology, Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, No. 15, Longzihu University Park, Zhengdong New Area, Zhengzhou, China
| | - Lingzhi Liu
- Henan Key Laboratory of Rice Biology, Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, No. 15, Longzihu University Park, Zhengdong New Area, Zhengzhou, China
| | - Yun Yan
- Henan Key Laboratory of Rice Biology, Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, No. 15, Longzihu University Park, Zhengdong New Area, Zhengzhou, China
| | - Xin Ji
- Henan Key Laboratory of Rice Biology, Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, No. 15, Longzihu University Park, Zhengdong New Area, Zhengzhou, China
| | - Fanshu Kong
- Henan Key Laboratory of Rice Biology, Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, No. 15, Longzihu University Park, Zhengdong New Area, Zhengzhou, China
| | - Yafan Zhao
- Henan Key Laboratory of Rice Biology, Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, No. 15, Longzihu University Park, Zhengdong New Area, Zhengzhou, China
| | - Junzhou Li
- Henan Key Laboratory of Rice Biology, Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, No. 15, Longzihu University Park, Zhengdong New Area, Zhengzhou, China
| | - Ting Peng
- Henan Key Laboratory of Rice Biology, Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, No. 15, Longzihu University Park, Zhengdong New Area, Zhengzhou, China
| | - Hongzheng Sun
- Henan Key Laboratory of Rice Biology, Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, No. 15, Longzihu University Park, Zhengdong New Area, Zhengzhou, China
| | - Yanxiu Du
- Henan Key Laboratory of Rice Biology, Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, No. 15, Longzihu University Park, Zhengdong New Area, Zhengzhou, China.
| | - Quanzhi Zhao
- Henan Key Laboratory of Rice Biology, Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, No. 15, Longzihu University Park, Zhengdong New Area, Zhengzhou, China.
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Li Q, Zhou L, Chen Y, Xiao N, Zhang D, Zhang M, Wang W, Zhang C, Zhang A, Li H, Chen J, Gao Y. Phytochrome interacting factor regulates stomatal aperture by coordinating red light and abscisic acid. THE PLANT CELL 2022; 34:4293-4312. [PMID: 35929789 PMCID: PMC9614506 DOI: 10.1093/plcell/koac244] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 08/01/2022] [Indexed: 06/10/2023]
Abstract
Stomata are crucial valves coordinating the fixation of carbon dioxide by photosynthesis and water loss through leaf transpiration. Phytochrome interacting factors (PIFs) are negative regulators of red light responses that belong to the basic helix-loop-helix family of transcription factors. Here, we show that the rice (Oryza sativa) PIF family gene OsPIL15 acts as a negative regulator of stomatal aperture to control transpiration in rice. OsPIL15 reduces stomatal aperture by activating rice ABSCISIC ACID INSENSITIVE 5 (OsABI5), which encodes a critical positive regulator of ABSCISIC ACID (ABA) signaling in rice. Moreover, OsPIL15 interacts with the NIGT1/HRS1/HHO family transcription factor rice HRS1 HOMOLOG 3 (OsHHO3) to possibly enhance the regulation of stomatal aperture. Notably, we discovered that the maize (Zea mays) PIF family genes ZmPIF1 and ZmPIF3, which are homologous to OsPIL15, are also involved in the regulation of stomatal aperture in maize, indicating that PIF-mediated regulation of stomatal aperture may be conserved in the plant lineage. Our findings explain the molecular mechanism by which PIFs play a role in red-light-mediated stomatal opening, and demonstrate that PIFs regulate stomatal aperture by coordinating the red light and ABA signaling pathways.
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Affiliation(s)
| | | | - Yanan Chen
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Jiangsu Key Laboratory of Crop Genetics and Physiology, Yangzhou University, Yangzhou 225009, China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Joint International Research Laboratory of Agriculture, Agri-Product Safety of the Ministry of Education, Yangzhou University, Yangzhou 225009, China
| | - Ning Xiao
- Institute of Agricultural Sciences for Lixiahe Region in Jiangsu, Yangzhou 225009, China
| | - Dongping Zhang
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Jiangsu Key Laboratory of Crop Genetics and Physiology, Yangzhou University, Yangzhou 225009, China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Joint International Research Laboratory of Agriculture, Agri-Product Safety of the Ministry of Education, Yangzhou University, Yangzhou 225009, China
| | - Mengjiao Zhang
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Jiangsu Key Laboratory of Crop Genetics and Physiology, Yangzhou University, Yangzhou 225009, China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Joint International Research Laboratory of Agriculture, Agri-Product Safety of the Ministry of Education, Yangzhou University, Yangzhou 225009, China
| | - Wenguo Wang
- Biogas Institute of Ministry of Agriculture and Rural Affairs, Chengdu 610041, China
| | - Changquan Zhang
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Jiangsu Key Laboratory of Crop Genetics and Physiology, Yangzhou University, Yangzhou 225009, China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Joint International Research Laboratory of Agriculture, Agri-Product Safety of the Ministry of Education, Yangzhou University, Yangzhou 225009, China
| | - Anning Zhang
- Shanghai Agrobiological Gene Center, Shanghai 201106, China
| | - Hua Li
- Hezhou Academy of Agricultural Sciences, Hezhou 542813, China
| | - Jianmin Chen
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Jiangsu Key Laboratory of Crop Genetics and Physiology, Yangzhou University, Yangzhou 225009, China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Joint International Research Laboratory of Agriculture, Agri-Product Safety of the Ministry of Education, Yangzhou University, Yangzhou 225009, China
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22
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Sun G, Yang L, Zhan W, Chen S, Song M, Wang L, Jiang L, Guo L, Wang K, Ye X, Gou M, Zheng X, Yang J, Yan Z. HFR1, a bHLH Transcriptional Regulator from Arabidopsis thaliana, Improves Grain Yield, Shade and Osmotic Stress Tolerances in Common Wheat. Int J Mol Sci 2022; 23:ijms231912057. [PMID: 36233359 PMCID: PMC9569703 DOI: 10.3390/ijms231912057] [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: 08/22/2022] [Revised: 09/30/2022] [Accepted: 10/04/2022] [Indexed: 11/16/2022] Open
Abstract
Common wheat, Triticum aestivum, is the most widely grown staple crop worldwide. To catch up with the increasing global population and cope with the changing climate, it is valuable to breed wheat cultivars that are tolerant to abiotic or shade stresses for density farming. Arabidopsis LONG HYPOCOTYL IN FAR-RED 1 (AtHFR1), a photomorphogenesis-promoting factor, is involved in multiple light-related signaling pathways and inhibits seedling etiolation and shade avoidance. We report that overexpression of AtHFR1 in wheat inhibits etiolation phenotypes under various light and shade conditions, leading to shortened plant height and increased spike number relative to non-transgenic plants in the field. Ectopic expression of AtHFR1 in wheat increases the transcript levels of TaCAB and TaCHS as observed previously in Arabidopsis, indicating that the AtHFR1 transgene can activate the light signal transduction pathway in wheat. AtHFR1 transgenic seedlings significantly exhibit tolerance to osmotic stress during seed germination compared to non-transgenic wheat. The AtHFR1 transgene represses transcription of TaFT1, TaCO1, and TaCO2, delaying development of the shoot apex and heading in wheat. Furthermore, the AtHFR1 transgene in wheat inhibits transcript levels of PHYTOCHROME-INTERACTING FACTOR 3-LIKEs (TaPIL13, TaPIL15-1B, and TaPIL15-1D), downregulating the target gene STAYGREEN (TaSGR), and thus delaying dark-induced leaf senescence. In the field, grain yields of three AtHFR1 transgenic lines were 18.2–48.1% higher than those of non-transgenic wheat. In summary, genetic modification of light signaling pathways using a photomorphogenesis-promoting factor has positive effects on grain yield due to changes in plant architecture and resource allocation and enhances tolerances to osmotic stress and shade avoidance response.
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Affiliation(s)
- Guanghua Sun
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu 611130, China
- State Key Laboratory of Wheat and Maize Crop Science, Center for Crop Genome Engineering, Longzi Lake Campus, College of Agronomy, Henan Agricultural University, Zhengzhou 450046, China
| | - Luhao Yang
- State Key Laboratory of Wheat and Maize Crop Science, Center for Crop Genome Engineering, Longzi Lake Campus, College of Agronomy, Henan Agricultural University, Zhengzhou 450046, China
| | - Weimin Zhan
- State Key Laboratory of Wheat and Maize Crop Science, Center for Crop Genome Engineering, Longzi Lake Campus, College of Agronomy, Henan Agricultural University, Zhengzhou 450046, China
| | - Shizhan Chen
- State Key Laboratory of Wheat and Maize Crop Science, Center for Crop Genome Engineering, Longzi Lake Campus, College of Agronomy, Henan Agricultural University, Zhengzhou 450046, China
| | - Meifang Song
- Institute of Radiation Technology, Beijing Academy of Science and Technology, Beijing 100875, China
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Lijian Wang
- State Key Laboratory of Wheat and Maize Crop Science, Center for Crop Genome Engineering, Longzi Lake Campus, College of Agronomy, Henan Agricultural University, Zhengzhou 450046, China
| | - Liangliang Jiang
- State Key Laboratory of Wheat and Maize Crop Science, Center for Crop Genome Engineering, Longzi Lake Campus, College of Agronomy, Henan Agricultural University, Zhengzhou 450046, China
| | - Lin Guo
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Ke Wang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Xingguo Ye
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Mingyue Gou
- State Key Laboratory of Wheat and Maize Crop Science, Center for Crop Genome Engineering, Longzi Lake Campus, College of Agronomy, Henan Agricultural University, Zhengzhou 450046, China
| | - Xu Zheng
- State Key Laboratory of Wheat and Maize Crop Science, Center for Crop Genome Engineering, Longzi Lake Campus, College of Agronomy, Henan Agricultural University, Zhengzhou 450046, China
| | - Jianping Yang
- State Key Laboratory of Wheat and Maize Crop Science, Center for Crop Genome Engineering, Longzi Lake Campus, College of Agronomy, Henan Agricultural University, Zhengzhou 450046, China
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
- Correspondence: (J.Y.); (Z.Y.)
| | - Zehong Yan
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu 611130, China
- Correspondence: (J.Y.); (Z.Y.)
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Ayalew H, Peiris S, Chiluwal A, Kumar R, Tiwari M, Ostmeyer T, Bean S, Jagadish SVK. Stable sorghum grain quality QTL were identified using SC35 × RTx430 mapping population. THE PLANT GENOME 2022; 15:e20227. [PMID: 35880472 DOI: 10.1002/tpg2.20227] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 04/18/2022] [Indexed: 06/15/2023]
Abstract
Understanding the genetic control and inheritance of grain quality traits is instrumental in facilitating end-use quality improvement. This study was conducted to identify and map quantitative trait loci (QTL) controlling protein, starch, and amylose content in grain sorghum [Sorghum bicolor (L.) Moench] grown under variable environmental conditions. A recombinant inbred line (RIL) population derived from a cross between RTx430 and SC35 was evaluated in six environments across Hays and Manhattan, KS. Significant variation was observed in genotype, environment, and genotype × environment interaction for all three quality traits. Unlike the RILs, the two parental lines did not show significant differences for these traits. However, significant transgressive segregation was observed for all traits resulting in phenotypic performance extending beyond the two parents. A total of seven protein, 10 starch, and 10 amylose content QTL were identified. Chromosomal regions and phenotypic variation (PVE) of QTL were variable across growing conditions. Quantitative trait loci hotspots for all three traits were detected on chromosomes 1 (115.2-119.2 cM) and 2 (118.2-127.4 cM). Candidate gene analysis indicated that these QTL hotspots were conditioned by several transcription factors, such as Cytochrome P450 and basic helix-loop-helix DNA binding protein, which regulate starch and protein accumulation in the grain. The identified genomic regions and underlying candidate genes provide a starting point for further validation and marker-assisted gene pyramiding to improve sorghum grain quality.
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Affiliation(s)
- Habtamu Ayalew
- Dep. of Agronomy, Kansas State Univ., Manhattan, KS, 66506, USA
| | - Shantha Peiris
- Grain Quality and Structure Research Unit, CGAHR, USDA-ARS, Manhattan, KS, 66502, USA
| | - Anuj Chiluwal
- Dep. of Agronomy, Kansas State Univ., Manhattan, KS, 66506, USA
| | - Ritesh Kumar
- Dep. of Agronomy, Kansas State Univ., Manhattan, KS, 66506, USA
| | - Manish Tiwari
- Dep. of Agronomy, Kansas State Univ., Manhattan, KS, 66506, USA
| | - Troy Ostmeyer
- Dep. of Agronomy, Kansas State Univ., Manhattan, KS, 66506, USA
| | - Scott Bean
- Grain Quality and Structure Research Unit, CGAHR, USDA-ARS, Manhattan, KS, 66502, USA
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24
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Guo X, Fu Y, Lee YJ, Chern M, Li M, Cheng M, Dong H, Yuan Z, Gui L, Yin J, Qing H, Zhang C, Pu Z, Liu Y, Li W, Li W, Qi P, Chen G, Jiang Q, Ma J, Chen X, Wei Y, Zheng Y, Wu Y, Liu B, Wang J. The PGS1 basic helix-loop-helix protein regulates Fl3 to impact seed growth and grain yield in cereals. PLANT BIOTECHNOLOGY JOURNAL 2022; 20:1311-1326. [PMID: 35315196 PMCID: PMC9241376 DOI: 10.1111/pbi.13809] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Accepted: 03/11/2022] [Indexed: 05/02/2023]
Abstract
Plant transcription factors (TFs), such as basic helix-loop-helix (bHLH) and AT-rich zinc-binding proteins (PLATZ), play critical roles in regulating the expression of developmental genes in cereals. We identified the bHLH protein TaPGS1 (T. aestivum Positive Regulator of Grain Size 1) specifically expressed in the seeds at 5-20 days post-anthesis in wheat. TaPGS1 was ectopically overexpressed (OE) in wheat and rice, leading to increased grain weight (up to 13.81% in wheat and 18.55% in rice lines) and grain size. Carbohydrate and total protein levels also increased. Scanning electron microscopy results indicated that the starch granules in the endosperm of TaPGS1 OE wheat and rice lines were smaller and tightly embedded in a proteinaceous matrix. Furthermore, TaPGS1 was bound directly to the E-box motif at the promoter of the PLATZ TF genes TaFl3 and OsFl3 and positively regulated their expression in wheat and rice. In rice, the OsFl3 CRISPR/Cas9 knockout lines showed reduced average thousand-grain weight, grain width, and grain length in rice. Our results reveal that TaPGS1 functions as a valuable trait-associated gene for improving cereal grain yield.
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Affiliation(s)
- Xiaojiang Guo
- Triticeae Research InstituteSichuan Agricultural UniversityChengduChina
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest ChinaSichuan Agricultural UniversityChengduChina
- Department of Plant BiologyUniversity of CaliforniaDavisCAUSA
| | - Yuxin Fu
- Triticeae Research InstituteSichuan Agricultural UniversityChengduChina
- National Key Laboratory of Plant Molecular GeneticsCAS Center for Excellence in Molecular Plant SciencesInstitute of Plant Physiology and EcologyShanghai Institutes for Biological SciencesChinese Academy of SciencesShanghaiChina
| | | | - Mawsheng Chern
- Department of Plant PathologyUniversity of CaliforniaDavisCAUSA
| | - Maolian Li
- Triticeae Research InstituteSichuan Agricultural UniversityChengduChina
| | - Mengping Cheng
- Triticeae Research InstituteSichuan Agricultural UniversityChengduChina
| | - Huixue Dong
- Triticeae Research InstituteSichuan Agricultural UniversityChengduChina
| | - Zhongwei Yuan
- Triticeae Research InstituteSichuan Agricultural UniversityChengduChina
| | - Lixuan Gui
- Triticeae Research InstituteSichuan Agricultural UniversityChengduChina
| | - Junjie Yin
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest ChinaSichuan Agricultural UniversityChengduChina
| | - Hai Qing
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest ChinaSichuan Agricultural UniversityChengduChina
| | - Chengbi Zhang
- Triticeae Research InstituteSichuan Agricultural UniversityChengduChina
| | - Zhien Pu
- Triticeae Research InstituteSichuan Agricultural UniversityChengduChina
| | - Yujiao Liu
- Triticeae Research InstituteSichuan Agricultural UniversityChengduChina
| | - Weitao Li
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest ChinaSichuan Agricultural UniversityChengduChina
| | - Wei Li
- Triticeae Research InstituteSichuan Agricultural UniversityChengduChina
| | - Pengfei Qi
- Triticeae Research InstituteSichuan Agricultural UniversityChengduChina
| | - Guoyue Chen
- Triticeae Research InstituteSichuan Agricultural UniversityChengduChina
| | - Qiantao Jiang
- Triticeae Research InstituteSichuan Agricultural UniversityChengduChina
| | - Jian Ma
- Triticeae Research InstituteSichuan Agricultural UniversityChengduChina
| | - Xuewei Chen
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest ChinaSichuan Agricultural UniversityChengduChina
| | - Yuming Wei
- Triticeae Research InstituteSichuan Agricultural UniversityChengduChina
- Ministry of Education Key Laboratory for Crop Genetic Resources and Improvement in Southwest ChinaSichuan Agricultural UniversityChengduChina
| | - Youliang Zheng
- Triticeae Research InstituteSichuan Agricultural UniversityChengduChina
- Ministry of Education Key Laboratory for Crop Genetic Resources and Improvement in Southwest ChinaSichuan Agricultural UniversityChengduChina
| | - Yongrui Wu
- National Key Laboratory of Plant Molecular GeneticsCAS Center for Excellence in Molecular Plant SciencesInstitute of Plant Physiology and EcologyShanghai Institutes for Biological SciencesChinese Academy of SciencesShanghaiChina
| | - Bo Liu
- Department of Plant BiologyUniversity of CaliforniaDavisCAUSA
| | - Jirui Wang
- Triticeae Research InstituteSichuan Agricultural UniversityChengduChina
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest ChinaSichuan Agricultural UniversityChengduChina
- Ministry of Education Key Laboratory for Crop Genetic Resources and Improvement in Southwest ChinaSichuan Agricultural UniversityChengduChina
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Du Y, Liu L, Zhang X, Li F, Kong F, Zhang J, Li J, Peng T, Sun H, Zhao Q. Regulation of OsPIL15 on rice quality. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2022; 42:39. [PMID: 37313503 PMCID: PMC10248670 DOI: 10.1007/s11032-022-01311-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Accepted: 06/16/2022] [Indexed: 06/15/2023]
Abstract
The phytochrome-interacting factor-like gene OsPIL15 negatively regulates grain size and 1000-grain weight, but its regulatory effect on rice quality traits is unknown. Here, knock-down, knock-out, and over-expression of OsPIL15 transgenic rice lines were used to investigate the effects of OsPIL15 on rice yield and quality traits. The results showed that knock-down or knock-out of OsPIL15 increased grain length and width, chalkiness, amylose content, glutenin and globulin content, and total protein content but reduced amylopectin content, total starch content, prolamin and albumin content, and gel consistency. Over-expression of OsPIL15 showed the opposite results, except for the reduction of prolamin content. Although OsPIL15 changed the grain size and weight, it had no effect on grain length/width ratio, brown rice rate, and milled rice rate. KEGG pathway enrichment analysis of differentially expressed genes between transgenic lines and wild type showed that OsPIL15 mainly regulated genes related to ribosome, metabolic pathways, and biosynthesis of secondary metabolites. Gene expression analysis showed that RNAi transgenic lines decreased OsCIN2 and OsSUS1 expression and increased OsGBSSI, OsSSI, OsAPGL2, and OsAPGL3 expression level, while over-expression of OsPIL15 increased OsCIN2, OsSUS1, OsSUS6, and OsSSI and decreased OsSSIIa, OsSSIIc, and OsAPGL2 expression level. These results revealed that OsPIL15 plays an important role in rice grain development. In addition to grain shape, OsPIL15 also regulates chalkiness, starch content, protein content, and gel consistency. Supplementary Information The online version contains supplementary material available at 10.1007/s11032-022-01311-x.
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Affiliation(s)
- Yanxiu Du
- Henan Key Laboratory of Rice Biology, Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, Zhengzhou, China
| | - Lingzhi Liu
- Henan Key Laboratory of Rice Biology, Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, Zhengzhou, China
| | - Xiaohua Zhang
- Henan Key Laboratory of Rice Biology, Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, Zhengzhou, China
| | - Fei Li
- Henan Key Laboratory of Rice Biology, Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, Zhengzhou, China
| | - Fanshu Kong
- Henan Key Laboratory of Rice Biology, Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, Zhengzhou, China
| | - Jing Zhang
- Henan Key Laboratory of Rice Biology, Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, Zhengzhou, China
| | - Junzhou Li
- Henan Key Laboratory of Rice Biology, Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, Zhengzhou, China
| | - Ting Peng
- Henan Key Laboratory of Rice Biology, Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, Zhengzhou, China
| | - Hongzheng Sun
- Henan Key Laboratory of Rice Biology, Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, Zhengzhou, China
| | - Quanzhi Zhao
- Henan Key Laboratory of Rice Biology, Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, Zhengzhou, China
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Cordeiro AM, Andrade L, Monteiro CC, Leitão G, Wigge PA, Saibo NJM. PHYTOCHROME-INTERACTING FACTORS: a promising tool to improve crop productivity. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:3881-3897. [PMID: 35429385 DOI: 10.1093/jxb/erac142] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Accepted: 04/14/2022] [Indexed: 06/14/2023]
Abstract
Light is a key determinant for plant growth, development, and ultimately yield. Phytochromes, red/far-red photoreceptors, play an important role in plant architecture, stress tolerance, and productivity. In the model plant Arabidopsis, it has been shown that PHYTOCHROME-INTERACTING FACTORS (PIFs; bHLH transcription factors) act as central hubs in the integration of external stimuli to regulate plant development. Recent studies have unveiled the importance of PIFs in crops. They are involved in the modulation of plant architecture and productivity through the regulation of cell division and elongation in response to different environmental cues. These studies show that different PIFs have overlapping but also distinct functions in the regulation of plant growth. Therefore, understanding the molecular mechanisms by which PIFs regulate plant development is crucial to improve crop productivity under both optimal and adverse environmental conditions. In this review, we discuss current knowledge of PIFs acting as integrators of light and other signals in different crops, with particular focus on the role of PIFs in responding to different environmental conditions and how this can be used to improve crop productivity.
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Affiliation(s)
- André M Cordeiro
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
| | - Luis Andrade
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
- Leibniz-Institut für Gemüse- und Zierpflanzenbau, Theodor-Echtermeyer-Weg 1, 14979 Großbeeren, Germany
| | - Catarina C Monteiro
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
| | - Guilherme Leitão
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
| | - Philip A Wigge
- Leibniz-Institut für Gemüse- und Zierpflanzenbau, Theodor-Echtermeyer-Weg 1, 14979 Großbeeren, Germany
- Institute of Biochemistry and Biology, University of Potsdam, 14476 Potsdam, Germany
| | - Nelson J M Saibo
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
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27
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Kumar J, Kumar A, Sen Gupta D, Kumar S, DePauw RM. Reverse genetic approaches for breeding nutrient-rich and climate-resilient cereal and food legume crops. Heredity (Edinb) 2022; 128:473-496. [PMID: 35249099 PMCID: PMC9178024 DOI: 10.1038/s41437-022-00513-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 02/10/2022] [Accepted: 02/10/2022] [Indexed: 12/21/2022] Open
Abstract
In the last decade, advancements in genomics tools and techniques have led to the discovery of many genes. Most of these genes still need to be characterized for their associated function and therefore, such genes remain underutilized for breeding the next generation of improved crop varieties. The recent developments in different reverse genetic approaches have made it possible to identify the function of genes controlling nutritional, biochemical, and metabolic traits imparting drought, heat, cold, salinity tolerance as well as diseases and insect-pests. This article focuses on reviewing the current status and prospects of using reverse genetic approaches to breed nutrient-rich and climate resilient cereal and food legume crops.
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Affiliation(s)
- Jitendra Kumar
- Division of Crop Improvement, ICAR-Indian Institute of Pulses Research, Kanpur, India.
| | - Ajay Kumar
- Department of Plant Sciences, North Dakota State University, Fargo, ND, 58108, USA
| | - Debjyoti Sen Gupta
- Division of Crop Improvement, ICAR-Indian Institute of Pulses Research, Kanpur, India
| | - Sachin Kumar
- Department of Genetics and Plant Breeding, Chaudhary Charan Singh University, Meerut, 250 004, India
| | - Ron M DePauw
- Advancing Wheat Technologies, 118 Strathcona Rd SW, Calgary, AB, T3H 1P3, Canada
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28
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Wu L, Jia B, Pei W, Wang L, Ma J, Wu M, Song J, Yang S, Xin Y, Huang L, Feng P, Zhang J, Yu J. Quantitative Trait Locus Analysis and Identification of Candidate Genes Affecting Seed Size and Shape in an Interspecific Backcross Inbred Line Population of Gossypium hirsutum × Gossypium barbadense. FRONTIERS IN PLANT SCIENCE 2022; 13:837984. [PMID: 35392518 PMCID: PMC8981304 DOI: 10.3389/fpls.2022.837984] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 01/31/2022] [Indexed: 06/14/2023]
Abstract
Seed size and shape are key agronomic traits affecting seedcotton yield and seed quality in cotton (Gossypium spp.). However, the genetic mechanisms that regulate the seed physical traits in cotton are largely unknown. In this study, an interspecific backcross inbred line (BIL) population of 250 BC1F7 lines, derived from the recurrent parent Upland CRI36 (Gossypium hirsutum) and Hai7124 (Gossypium barbadense), was used to investigate the genetic basis of cotton seed physical traits via quantitative trait locus (QTL) mapping and candidate gene identification. The BILs were tested in five environments, measuring eight seed size and shape-related traits, including 100-kernel weight, kernel length width and their ratio, kernel area, kernel girth, kernel diameter, and kernel roundness. Based on 7,709 single nucleotide polymorphic (SNP) markers, a total of 49 QTLs were detected and each explained 2.91-35.01% of the phenotypic variation, including nine stable QTLs mapped in at least three environments. Based on pathway enrichment, gene annotation, genome sequence, and expression analysis, five genes encoding starch synthase 4, transcription factor PIF7 and MYC4, ubiquitin-conjugating enzyme E27, and THO complex subunit 4A were identified as candidate genes that might be associated with seed size and shape. Our research provides valuable information to improve seed physical traits in cotton breeding.
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Affiliation(s)
- Luyao Wu
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, China
- State Key Laboratory of Cotton Biology, Key Laboratory of Cotton Genetic Improvement, Ministry of Agriculture, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, China
| | - Bing Jia
- State Key Laboratory of Cotton Biology, Key Laboratory of Cotton Genetic Improvement, Ministry of Agriculture, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, China
| | - Wenfeng Pei
- State Key Laboratory of Cotton Biology, Key Laboratory of Cotton Genetic Improvement, Ministry of Agriculture, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, China
| | - Li Wang
- State Key Laboratory of Cotton Biology, Key Laboratory of Cotton Genetic Improvement, Ministry of Agriculture, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, China
| | - Jianjiang Ma
- State Key Laboratory of Cotton Biology, Key Laboratory of Cotton Genetic Improvement, Ministry of Agriculture, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, China
| | - Man Wu
- State Key Laboratory of Cotton Biology, Key Laboratory of Cotton Genetic Improvement, Ministry of Agriculture, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, China
| | - Jikun Song
- State Key Laboratory of Cotton Biology, Key Laboratory of Cotton Genetic Improvement, Ministry of Agriculture, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, China
| | - Shuxian Yang
- State Key Laboratory of Cotton Biology, Key Laboratory of Cotton Genetic Improvement, Ministry of Agriculture, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, China
| | - Yue Xin
- State Key Laboratory of Cotton Biology, Key Laboratory of Cotton Genetic Improvement, Ministry of Agriculture, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, China
| | - Li Huang
- State Key Laboratory of Cotton Biology, Key Laboratory of Cotton Genetic Improvement, Ministry of Agriculture, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, China
| | - Pan Feng
- State Key Laboratory of Cotton Biology, Key Laboratory of Cotton Genetic Improvement, Ministry of Agriculture, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, China
| | - Jinfa Zhang
- Department of Plant and Environmental Sciences, New Mexico State University, Las Cruces, NM, United States
| | - Jiwen Yu
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, China
- State Key Laboratory of Cotton Biology, Key Laboratory of Cotton Genetic Improvement, Ministry of Agriculture, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, China
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29
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Singh A, Mathan J, Yadav A, K. Goyal A, Chaudhury A. Molecular and Transcriptional Regulation of Seed Development in Cereals: Present Status and Future Prospects. CEREAL GRAINS - VOLUME 1 2021. [DOI: 10.5772/intechopen.99318] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/19/2023]
Abstract
Cereals are a rich source of vitamins, minerals, carbohydrates, fats, oils and protein, making them the world’s most important source of nutrition. The influence of rising global population, as well as the emergence and spread of disease, has the major impact on cereal production. To meet the demand, there is a pressing need to increase cereal production. Optimal seed development is a key agronomical trait that contributes to crop yield. The seed development and maturation is a complex process that includes not only embryo and endosperm development, but also accompanied by huge physiological, biochemical, metabolic, molecular and transcriptional changes. This chapter discusses the growth of cereal seed and highlights the novel biological insights, with a focus on transgenic and new molecular breeding, as well as biotechnological intervention strategies that have improved crop yield in two major cereal crops, primarily wheat and rice, over the last 21 years (2000–2021).
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30
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OsPDCD5 negatively regulates plant architecture and grain yield in rice. Proc Natl Acad Sci U S A 2021; 118:2018799118. [PMID: 34266944 DOI: 10.1073/pnas.2018799118] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Plant architecture is an important agronomic trait that affects crop yield. Here, we report that a gene involved in programmed cell death, OsPDCD5, negatively regulates plant architecture and grain yield in rice. We used the CRISPR/Cas9 system to introduce loss-of-function mutations into OsPDCD5 in 11 rice cultivars. Targeted mutagenesis of OsPDCD5 enhanced grain yield and improved plant architecture by increasing plant height and optimizing panicle type and grain shape. Transcriptome analysis showed that OsPDCD5 knockout affected auxin biosynthesis, as well as the gibberellin and cytokinin biosynthesis and signaling pathways. OsPDCD5 interacted directly with OsAGAP, and OsAGAP positively regulated plant architecture and grain yield in rice. Collectively, these findings demonstrate that OsPDCD5 is a promising candidate gene for breeding super rice cultivars with increased yield potential and superior quality.
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31
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Chen K, Łyskowski A, Jaremko Ł, Jaremko M. Genetic and Molecular Factors Determining Grain Weight in Rice. FRONTIERS IN PLANT SCIENCE 2021; 12:605799. [PMID: 34322138 PMCID: PMC8313227 DOI: 10.3389/fpls.2021.605799] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2020] [Accepted: 06/22/2021] [Indexed: 05/06/2023]
Abstract
Grain weight is one of the major factors determining single plant yield production of rice and other cereal crops. Research has begun to reveal the regulatory mechanisms underlying grain weight as well as grain size, highlighting the importance of this research for plant molecular biology. The developmental trait of grain weight is affected by multiple molecular and genetic aspects that lead to dynamic changes in cell division, expansion and differentiation. Additionally, several important biological pathways contribute to grain weight, such as ubiquitination, phytohormones, G-proteins, photosynthesis, epigenetic modifications and microRNAs. Our review integrates early and more recent findings, and provides future perspectives for how a more complete understanding of grain weight can optimize strategies for improving yield production. It is surprising that the acquired wealth of knowledge has not revealed more insights into the underlying molecular mechanisms. To accelerating molecular breeding of rice and other cereals is becoming an emergent and critical task for agronomists. Lastly, we highlighted the importance of leveraging gene editing technologies as well as structural studies for future rice breeding applications.
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Affiliation(s)
- Ke Chen
- Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
- Guangdong Key Laboratory of New Technology in Rice Breeding, Guangzhou, China
| | - Andrzej Łyskowski
- Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
- Faculty of Chemistry, Rzeszow University of Technology, Rzeszow, Poland
| | - Łukasz Jaremko
- Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Mariusz Jaremko
- Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
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32
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Huang X, Hilscher J, Stoger E, Christou P, Zhu C. Modification of cereal plant architecture by genome editing to improve yields. PLANT CELL REPORTS 2021; 40:953-978. [PMID: 33559722 DOI: 10.1007/s00299-021-02668-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Accepted: 01/22/2021] [Indexed: 06/12/2023]
Abstract
We summarize recent genome editing studies that have focused on the examination (or reexamination) of plant architectural phenotypes in cereals and the modification of these traits for crop improvement. Plant architecture is defined as the three-dimensional organization of the entire plant. Shoot architecture refers to the structure and organization of the aboveground components of a plant, reflecting the developmental patterning of stems, branches, leaves and inflorescences/flowers. Root system architecture is essentially determined by four major shape parameters-growth, branching, surface area and angle. Interest in plant architecture has arisen from the profound impact of many architectural traits on agronomic performance, and the genetic and hormonal regulation of these traits which makes them sensitive to both selective breeding and agronomic practices. This is particularly important in staple crops, and a large body of literature has, therefore, accumulated on the control of architectural phenotypes in cereals, particularly rice due to its twin role as one of the world's most important food crops as well as a model organism in plant biology and biotechnology. These studies have revealed many of the molecular mechanisms involved in the regulation of tiller/axillary branching, stem height, leaf and flower development, root architecture and the grain characteristics that ultimately help to determine yield. The advent of genome editing has made it possible, for the first time, to introduce precise mutations into cereal crops to optimize their architecture and close in on the concept of the ideotype. In this review, we consider recent genome editing studies that have focused on the examination (or reexamination) of plant architectural phenotypes in cereals and the modification of these traits for crop improvement.
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Affiliation(s)
- Xin Huang
- Department of Plant Production and Forestry Science, University of Lleida-Agrotecnio Center, Av. Alcalde Rovira Roure, 191, 25198, Lleida, Spain
| | - Julia Hilscher
- Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences, Gregor-Mendel-Straße 33, 1180, Vienna, Austria
| | - Eva Stoger
- Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences, Gregor-Mendel-Straße 33, 1180, Vienna, Austria
| | - Paul Christou
- Department of Plant Production and Forestry Science, University of Lleida-Agrotecnio Center, Av. Alcalde Rovira Roure, 191, 25198, Lleida, Spain
- ICREA, Catalan Institute for Research and Advanced Studies, Passeig Lluís Companys 23, 08010, Barcelona, Spain
| | - Changfu Zhu
- Department of Plant Production and Forestry Science, University of Lleida-Agrotecnio Center, Av. Alcalde Rovira Roure, 191, 25198, Lleida, Spain.
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33
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Hoang QTN, Tripathi S, Cho JY, Choi DM, Shin AY, Kwon SY, Han YJ, Kim JI. Suppression of Phytochrome-Interacting Factors Enhances Photoresponses of Seedlings and Delays Flowering With Increased Plant Height in Brachypodium distachyon. FRONTIERS IN PLANT SCIENCE 2021; 12:756795. [PMID: 34650585 PMCID: PMC8505764 DOI: 10.3389/fpls.2021.756795] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Accepted: 09/07/2021] [Indexed: 05/05/2023]
Abstract
Phytochromes are red and far-red photoreceptors that regulate plant growth and development under ambient light conditions. During phytochrome-mediated photomorphogenesis, phytochrome-interacting factors (PIFs) are the most important signaling partners that regulate the expression of light-responsive genes. However, the function of PIFs in monocots has not been studied well. In this study, using RNA interference (RNAi), we investigated the functions of BdPIL1 and BdPIL3, two PIF-like genes identified in Brachypodium distachyon, which are closely related to Arabidopsis PIF1 and PIF3. The expression of their genes is light-inducible, and both BdPIL1 and BdPIL3 proteins interact with phytochromes in an active form-specific manner. Transgenic Brachypodium seedlings with the RNAi constructs of BdPIL1 and BdPIL3 showed decreased coleoptile lengths and increased leaf growth when exposed to both red and far-red light. In addition, the transgenic plants were taller with elongated internodes than wild-type Bd21-3 plant, exhibiting late flowering. Moreover, RNA-seq analysis revealed downregulation of many genes in the transgenic plants, especially those related to the regulation of cell number, floral induction, and chlorophyll biosynthesis, which were consistent with the phenotypes of increased plant height, delayed flowering, and pale green leaves. Furthermore, we demonstrated the DNA-binding ability of BdPIL1 and BdPIL3 to the putative target promoters and that the DNA-binding was inhibited in the presence of phytochromes. Therefore, this study determines a molecular mechanism underlying phytochrome-mediated PIF regulation in Brachypodium, i.e., sequestration, and also elucidates the functions of BdPIL1 and BdPIL3 in the growth and development of the monocot plant.
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Affiliation(s)
- Quyen T. N. Hoang
- Department of Integrative Food, Bioscience and Biotechnology, Chonnam National University, Gwangju, South Korea
| | - Sharanya Tripathi
- Department of Integrative Food, Bioscience and Biotechnology, Chonnam National University, Gwangju, South Korea
| | - Jae-Yong Cho
- Department of Integrative Food, Bioscience and Biotechnology, Chonnam National University, Gwangju, South Korea
| | - Da-Min Choi
- Department of Integrative Food, Bioscience and Biotechnology, Chonnam National University, Gwangju, South Korea
| | - Ah-Young Shin
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, South Korea
| | - Suk-Yoon Kwon
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, South Korea
| | - Yun-Jeong Han
- Kumho Life Science Laboratory, Chonnam National University, Gwangju, South Korea
| | - Jeong-Il Kim
- Department of Integrative Food, Bioscience and Biotechnology, Chonnam National University, Gwangju, South Korea
- Kumho Life Science Laboratory, Chonnam National University, Gwangju, South Korea
- *Correspondence: Jeong-Il Kim,
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34
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Parween S, Anonuevo JJ, Butardo VM, Misra G, Anacleto R, Llorente C, Kosik O, Romero MV, Bandonill EH, Mendioro MS, Lovegrove A, Fernie AR, Brotman Y, Sreenivasulu N. Balancing the double-edged sword effect of increased resistant starch content and its impact on rice texture: its genetics and molecular physiological mechanisms. PLANT BIOTECHNOLOGY JOURNAL 2020; 18:1763-1777. [PMID: 31945237 PMCID: PMC7336377 DOI: 10.1111/pbi.13339] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2019] [Revised: 12/15/2019] [Accepted: 01/05/2020] [Indexed: 05/07/2023]
Abstract
Resistant starch (RS) is the portion of starch that escapes gastrointestinal digestion and acts as a substrate for fermentation of probiotic bacteria in the gut. Aside from enhancing gut health, RS contributes to a lower glycemic index. A genome-wide association study coupled with targeted gene association studies was conducted utilizing a diverse panel of 281 resequenced Indica rice lines comprising of ~2.2 million single nucleotide polymorphisms. Low-to-intermediate RS phenotypic variations were identified in the rice diversity panel, resulting in novel associations of RS to several genes associated with amylopectin biosynthesis and degradation. Selected rice lines encoding superior alleles of SSIIa with medium RS and inferior alleles with low RS groups were subjected to detailed transcriptomic, metabolomic, non-starch dietary fibre (DF), starch structural and textural attributes. The gene regulatory networks highlighted the importance of a protein phosphatase alongside multiple genes of starch metabolism. Metabolomics analyses resulted in the identification of several metabolite hubs (carboxylic acid, sugars and polyamines) in the medium RS group. Among DF, mannose and galactose from the water-insoluble fraction were found to be highly associated with low and medium RS lines, respectively. Starch structural analyses revealed that a moderate increase in RS is also linked to an elevation of amylose 1 and amylose 2 fractions. Although rice lines with medium RS content negatively affected textural and viscosity properties in comparison to low RS, the textural property of medium RS lines was in the same acceptable range as IR64, a rice mega variety popular in Asia.
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Affiliation(s)
- Sabiha Parween
- International Rice Research InstituteMetro ManilaPhilippines
| | | | - Vito M. Butardo
- International Rice Research InstituteMetro ManilaPhilippines
- Present address:
Department of Chemistry and BiotechnologyFaculty of Science, Engineering and TechnologySwinburne University of TechnologyHawthornVictoriaAustralia
| | - Gopal Misra
- International Rice Research InstituteMetro ManilaPhilippines
| | - Roslen Anacleto
- International Rice Research InstituteMetro ManilaPhilippines
| | - Cindy Llorente
- International Rice Research InstituteMetro ManilaPhilippines
| | - Ondrej Kosik
- Department of Plant SciencesRothamsted ResearchHarpendenHertsUK
| | - Marissa V. Romero
- Philippine Rice Research InstituteMaligayaScience City of MuñozPhilippines
| | | | - Merlyn S. Mendioro
- Institute of Biological SciencesCollege of Arts and ScienceUniversity of PhilippinesLos BanosPhilippines
| | | | | | - Yariv Brotman
- Department of Life SciencesBen‐Gurion University of the NegevBeershebaIsrael
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35
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Xu L, You H, Zhang O, Xiang X. Genetic Effects of Soluble Starch Synthase IV-2 and It with ADPglucose Pyrophorylase Large Unit and Pullulanase on Rice Qualities. RICE (NEW YORK, N.Y.) 2020; 13:46. [PMID: 32661799 PMCID: PMC7359214 DOI: 10.1186/s12284-020-00409-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Accepted: 07/06/2020] [Indexed: 05/27/2023]
Abstract
BACKGROUND Rice amylose content and amylopectin structure corporately determine rice eating and cooking qualities (ECQs). Soluble starch synthase (SS) IV-2 is a member of the soluble starch synthesis gene family but with unknown effects on ECQs. RESULTS In this study, three populations derived from a cross of two parents who possess the same major genes of starch bio-synthesis were employed to investigate the influence of SSIV-2 and its combined effects with ADPglucose pyrophorylase large unit (AGPlar) and Pullulanase (PUL) on ECQs. The results illustrated that the polymorphism of SSIV-2 alleles significantly affected gel consistency (GC), gelatinization temperature (GT), percent of retrogradation (PR) and three crucial rapid viscosity analysis (RVA) profile parameters: peak viscosity (PKV), breakdown viscosity (BDV) and setback viscosity (SBV). And SSIV-2 allele derived from CG173R had better quality traits with lower GT, SBV and PR. Moreover, its interaction with AGPlar was responsible for the variations of GC, apparent amylose content (AAC), GT, PR and all RVA parameters except for pasting temperature (PaT) and peak time (PeT), in terms of GC, PKV and CSV, AGPlar derived from CG173R had an epistatic effect on SSIV-2; additionally, interaction of SSIV-2 and PUL mainly affected GC, AAC, PKV, CPV, CSV and SBV. I-C and C-1 (I, allele of AGPlar from Guangzhan 63S; C, allele of SSIV-2 from CG173R; 1, allele of PUL from Guangzhan 63S) combinations had better ECQs. CONCLUSIONS SSIV-2 alleles significantly affect rice quality, especially the parameters relevant to gelatinized and thermal characteristics of starch (GC, PR, GT, PKV, BDV and SBV) under the same major genes (Waxy and SSII-3) background. It indicates that SSIV-2 functions elongation of starch chain. These findings suggest that the effects of SSIV-2 and its interaction with AGPlar and PUL are vital for rice quality breeding with the same major genes.
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Affiliation(s)
- Liang Xu
- Lab of Plant Molecular Genetics and Breeding, Southwest University of Science and Technology, 59 Qinglong Road, Mianyang, 621010, China
| | - Hui You
- Lab of Plant Molecular Genetics and Breeding, Southwest University of Science and Technology, 59 Qinglong Road, Mianyang, 621010, China
| | - Ouling Zhang
- Lab of Plant Molecular Genetics and Breeding, Southwest University of Science and Technology, 59 Qinglong Road, Mianyang, 621010, China
| | - Xunchao Xiang
- Lab of Plant Molecular Genetics and Breeding, Southwest University of Science and Technology, 59 Qinglong Road, Mianyang, 621010, China.
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Watt C, Zhou G, McFawn LA, Li C. Fine mapping qGL2H, a major locus controlling grain length in barley (Hordeum vulgare L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2020; 133:2095-2103. [PMID: 32193568 DOI: 10.1007/s00122-00020-03579-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Accepted: 03/12/2020] [Indexed: 05/23/2023]
Abstract
A major grain length QTL on chromosome 2H was fine mapped to a 140.9 Kb region containing three genes. Increasing yield is an important target for barley breeding programs. One approach to increase yield is by enhancing individual grain weights through the regulation of grain size. Fine mapping major grain size-related quantitative trait loci is necessary for future marker-assisted selection strategies, yet studies of this nature are limited in barley. In the present study, we utilised a doubled haploid population derived from two Australian malt barley varieties, Vlamingh and Buloke, coupled with extensive genotypic and phenotypic data from three independent environments. A major grain length locus identified on chromosome 2H designated qGL2H was fine mapped to a 140.9 Kb interval. qGL2H was able to account for 25.4% of the phenotypic variation for grain length and 10.2% for grain yield. Underlying qGL2H were three high-confidence predicted genes. One of these genes encodes a MYB transcription factor and represents a promising candidate for further genetic research.
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Affiliation(s)
- Calum Watt
- Western Barley Genetic Alliance, Murdoch University, Murdoch, WA, Australia
- Western Australian State Agricultural Biotechnology Centre, Murdoch University, Murdoch, WA, Australia
| | - Gaofeng Zhou
- Western Barley Genetic Alliance, Murdoch University, Murdoch, WA, Australia
- Western Australian State Agricultural Biotechnology Centre, Murdoch University, Murdoch, WA, Australia
| | - Lee-Anne McFawn
- Western Barley Genetic Alliance, Murdoch University, Murdoch, WA, Australia
- Department of Primary Industry and Regional Development, South Perth, WA, Australia
| | - Chengdao Li
- Western Barley Genetic Alliance, Murdoch University, Murdoch, WA, Australia.
- Western Australian State Agricultural Biotechnology Centre, Murdoch University, Murdoch, WA, Australia.
- Department of Primary Industry and Regional Development, South Perth, WA, Australia.
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Watt C, Zhou G, McFawn LA, Li C. Fine mapping qGL2H, a major locus controlling grain length in barley (Hordeum vulgare L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2020; 133:2095-2103. [PMID: 32193568 PMCID: PMC7311499 DOI: 10.1007/s00122-020-03579-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Accepted: 03/12/2020] [Indexed: 05/08/2023]
Abstract
A major grain length QTL on chromosome 2H was fine mapped to a 140.9 Kb region containing three genes. Increasing yield is an important target for barley breeding programs. One approach to increase yield is by enhancing individual grain weights through the regulation of grain size. Fine mapping major grain size-related quantitative trait loci is necessary for future marker-assisted selection strategies, yet studies of this nature are limited in barley. In the present study, we utilised a doubled haploid population derived from two Australian malt barley varieties, Vlamingh and Buloke, coupled with extensive genotypic and phenotypic data from three independent environments. A major grain length locus identified on chromosome 2H designated qGL2H was fine mapped to a 140.9 Kb interval. qGL2H was able to account for 25.4% of the phenotypic variation for grain length and 10.2% for grain yield. Underlying qGL2H were three high-confidence predicted genes. One of these genes encodes a MYB transcription factor and represents a promising candidate for further genetic research.
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Affiliation(s)
- Calum Watt
- Western Barley Genetic Alliance, Murdoch University, Murdoch, WA, Australia
- Western Australian State Agricultural Biotechnology Centre, Murdoch University, Murdoch, WA, Australia
| | - Gaofeng Zhou
- Western Barley Genetic Alliance, Murdoch University, Murdoch, WA, Australia
- Western Australian State Agricultural Biotechnology Centre, Murdoch University, Murdoch, WA, Australia
| | - Lee-Anne McFawn
- Western Barley Genetic Alliance, Murdoch University, Murdoch, WA, Australia
- Department of Primary Industry and Regional Development, South Perth, WA, Australia
| | - Chengdao Li
- Western Barley Genetic Alliance, Murdoch University, Murdoch, WA, Australia.
- Western Australian State Agricultural Biotechnology Centre, Murdoch University, Murdoch, WA, Australia.
- Department of Primary Industry and Regional Development, South Perth, WA, Australia.
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Sun W, Xu XH, Li Y, Xie L, He Y, Li W, Lu X, Sun H, Xie X. OsmiR530 acts downstream of OsPIL15 to regulate grain yield in rice. THE NEW PHYTOLOGIST 2020; 226:823-837. [PMID: 31883119 PMCID: PMC7187366 DOI: 10.1111/nph.16399] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Accepted: 12/15/2019] [Indexed: 05/03/2023]
Abstract
MicroRNAs (miRNAs) are a class of small noncoding RNAs that play important roles in plant growth and development as well as in stress responses. However, little is known about their regulatory functions affecting rice grain yield. We functionally characterized a novel miRNA in rice, OsmiR530, its target OsPL3, and its upstream regulator phytochrome-interacting factor-like 15 (OsPIL15). Their effects on rice yield were dissected comprehensively. We determined that OsmiR530 negatively regulates grain yield. Blocking OsmiR530 increases grain yield, whereas OsmiR530 overexpression significantly decreases grain size and panicle branching, leading to yield loss. Additionally, OsPL3, which encodes a PLUS3 domain-containing protein, is targeted directly by OsmiR530. Knocking out OsPL3 decreases the grain yield. In-depth analyses indicated that OsPIL15 activates OsMIR530 expression by directly binding to the G-box elements in the promoter. Analyses of genetic variations suggested that the OsMIR530 locus has likely been subjected to artificial selection during rice breeding. The results presented herein reveal a novel OsPIL15-OsmiR530 module controlling rice grain yield, thus providing researchers with a new target for the breeding of high-yielding rice.
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Affiliation(s)
- Wei Sun
- Shandong Rice Engineering Technology Research CenterShandong Rice Research InstituteShandong Academy of Agricultural SciencesJinan250100China
| | - Xiao Hui Xu
- Shandong Key Laboratory of Plant VirologyInstitute of Plant ProtectionShandong Academy of Agricultural SciencesJinan250100China
| | - Yaping Li
- Shandong Rice Engineering Technology Research CenterShandong Rice Research InstituteShandong Academy of Agricultural SciencesJinan250100China
| | - Lixia Xie
- Shandong Rice Engineering Technology Research CenterShandong Rice Research InstituteShandong Academy of Agricultural SciencesJinan250100China
| | - Yanan He
- Shandong Rice Engineering Technology Research CenterShandong Rice Research InstituteShandong Academy of Agricultural SciencesJinan250100China
| | - Wen Li
- Shandong Rice Engineering Technology Research CenterShandong Rice Research InstituteShandong Academy of Agricultural SciencesJinan250100China
| | - Xingbo Lu
- Shandong Key Laboratory of Plant VirologyInstitute of Plant ProtectionShandong Academy of Agricultural SciencesJinan250100China
| | - Hongwei Sun
- Shandong Key Laboratory of Plant VirologyInstitute of Plant ProtectionShandong Academy of Agricultural SciencesJinan250100China
| | - Xianzhi Xie
- Shandong Rice Engineering Technology Research CenterShandong Rice Research InstituteShandong Academy of Agricultural SciencesJinan250100China
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OsINV3 and Its Homolog, OsINV2, Control Grain Size in Rice. Int J Mol Sci 2020; 21:ijms21062199. [PMID: 32209971 PMCID: PMC7139340 DOI: 10.3390/ijms21062199] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Revised: 03/16/2020] [Accepted: 03/21/2020] [Indexed: 01/31/2023] Open
Abstract
Vacuolar invertase is involved in sugar metabolism and plays a crucial role in plant growth and development, thus regulating seed size. However, information linking vacuolar invertase and seed size in rice is limited. Here we characterized a small grain mutant sg2 (grain size on chromosome 2) that showed a reduced in grain size and 1000-grain weight compared to the wild type. Map-based cloning and genetic complementation showed that OsINV3 is responsible for the observed phenotype. Loss-of-function of OsINV3 resulted in grains of smaller size when compared to the wild type, while overexpression showed increased grain size. We also obtained a T-DNA insertion mutant of OsINV2, which is a homolog of OsINV3 and generated double knockout (KO) mutants of OsINV2 and OsINV3 using CRISPR/Cas9. Genetic data showed that OsINV2, that has no effect on grain size by itself, reduces grain length and width in the absence of OsINV3. Altered sugar content with increased sucrose and decreased hexose levels, as well as changes vacuolar invertase activities and starch constitution in INV3KO, INV2KO, INV3KOINV2KO mutants indicate that OsINV2 and OsINV3 affect sucrose metabolism in sink organs. In summary, we identified OsINV3 as a positive regulator of grain size in rice, and while OsINV2 has no function on grain size by itself. In the absence of OsINV3, it is possible to detect a role of OsINV2 in the regulation of grain size. Both OsINV3 and OsINV2 are involved in sucrose metabolism, and thus regulate grain size. Our findings increase our understanding of the role of OsINV3 and its homolog, OsINV2, in grain size development and also suggest a potential strategy to improve grain yield in rice.
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Oh J, Park E, Song K, Bae G, Choi G. PHYTOCHROME INTERACTING FACTOR8 Inhibits Phytochrome A-Mediated Far-Red Light Responses in Arabidopsis. THE PLANT CELL 2020; 32:186-205. [PMID: 31732705 PMCID: PMC6961613 DOI: 10.1105/tpc.19.00515] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Revised: 10/25/2019] [Accepted: 11/14/2019] [Indexed: 05/04/2023]
Abstract
PHYTOCHROME INTERACTING FACTORs (PIFs) are a group of basic helix-loop-helix (bHLH) transcription factors that repress plant light responses. PIF8 is one of the less-characterized Arabidopsis (Arabidopsis thaliana) PIFs, whose putative orthologs are conserved in other plant species. PIF8 possesses a bHLH motif and an active phytochrome B motif but not an active phytochrome A motif. Consistent with this motif composition, PIF8 binds to G-box elements and interacts with the Pfr form of phyB but only very weakly, if at all, with that of phyA. PIF8 differs, however, from other PIFs in its protein accumulation pattern and functional roles in different light conditions. First, PIF8 inhibits phyA-induced seed germination, suppression of hypocotyl elongation, and randomization of hypocotyl growth orientation in far-red light, but it does not inhibit phyB-induced red light responses. Second, PIF8 protein accumulates more in far-red light than in darkness or red light. This is distinct from the pattern observed with PIF3, which accumulates more in darkness. This PIF8 accumulation pattern requires degradation of PIF8 by CONSTITUTIVE PHOTOMORPHOGENIC1 (COP1) in darkness, inhibition of COP1 by phyA in far-red light, and promotion of PIF8 degradation by phyB in red light. Together, our results indicate that PIF8 is a genuine PIF that represses phyA-mediated light responses.
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Affiliation(s)
- Jeonghwa Oh
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Korea
| | - Eunae Park
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Korea
| | - Kijong Song
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Korea
| | - Gabyong Bae
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Korea
| | - Giltsu Choi
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Korea
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Watt C, Zhou G, Li C. Harnessing Transcription Factors as Potential Tools to Enhance Grain Size Under Stressful Abiotic Conditions in Cereal Crops. FRONTIERS IN PLANT SCIENCE 2020; 11:1273. [PMID: 33013947 PMCID: PMC7461896 DOI: 10.3389/fpls.2020.01273] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Accepted: 08/05/2020] [Indexed: 05/07/2023]
Abstract
Predicted climate change is widely cited to significantly reduce yields of the major cereal crop species in a period where demand is rapidly rising due to a growing global population. This requires exhaustive research to develop genetic resources in order to address the expected production deficiencies which will largely be driven by abiotic stress. Modification of multiple genes is an approach that can address the predicted challenges; however, it is time-consuming and costly to modify multiple genes simultaneously. Transcription factors represent a group of proteins regulating multiple genes simultaneously and are therefore promising targets to concurrently improve multiple traits concurrently, such as abiotic stress tolerance and grain size (a contributor to yield). Many studies have identified the complex role that transcription factors of multiple families have contributed toward abiotic stress tolerance or grain size, although research addressing both simultaneously is in its infancy despite its potential significance for cereal crop improvement. Here we discuss the potential role that transcription factors may contribute toward improving cereal crop productivity under adverse environmental conditions and offer research objectives that need to be addressed before the modification of transcription factors becomes routinely used to positively manipulate multiple target traits.
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Molecular mechanisms underlying phytochrome-controlled morphogenesis in plants. Nat Commun 2019; 10:5219. [PMID: 31745087 PMCID: PMC6864062 DOI: 10.1038/s41467-019-13045-0] [Citation(s) in RCA: 200] [Impact Index Per Article: 40.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Accepted: 10/17/2019] [Indexed: 11/08/2022] Open
Abstract
Phytochromes are bilin-binding photosensory receptors which control development over a broad range of environmental conditions and throughout the whole plant life cycle. Light-induced conformational changes enable phytochromes to interact with signaling partners, in particular transcription factors or proteins that regulate them, resulting in large-scale transcriptional reprograming. Phytochromes also regulate promoter usage, mRNA splicing and translation through less defined routes. In this review we summarize our current understanding of plant phytochrome signaling, emphasizing recent work performed in Arabidopsis. We compare and contrast phytochrome responses and signaling mechanisms among land plants and highlight open questions in phytochrome research.
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