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Gupta MK, Vadde R. Next-generation development and application of codon model in evolution. Front Genet 2023; 14:1091575. [PMID: 36777719 PMCID: PMC9911445 DOI: 10.3389/fgene.2023.1091575] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Accepted: 01/17/2023] [Indexed: 01/28/2023] Open
Abstract
To date, numerous nucleotide, amino acid, and codon substitution models have been developed to estimate the evolutionary history of any sequence/organism in a more comprehensive way. Out of these three, the codon substitution model is the most powerful. These models have been utilized extensively to detect selective pressure on a protein, codon usage bias, ancestral reconstruction and phylogenetic reconstruction. However, due to more computational demanding, in comparison to nucleotide and amino acid substitution models, only a few studies have employed the codon substitution model to understand the heterogeneity of the evolutionary process in a genome-scale analysis. Hence, there is always a question of how to develop more robust but less computationally demanding codon substitution models to get more accurate results. In this review article, the authors attempted to understand the basis of the development of different types of codon-substitution models and how this information can be utilized to develop more robust but less computationally demanding codon substitution models. The codon substitution model enables to detect selection regime under which any gene or gene region is evolving, codon usage bias in any organism or tissue-specific region and phylogenetic relationship between different lineages more accurately than nucleotide and amino acid substitution models. Thus, in the near future, these codon models can be utilized in the field of conservation, breeding and medicine.
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Lu Y, Chuan M, Wang H, Chen R, Tao T, Zhou Y, Xu Y, Li P, Yao Y, Xu C, Yang Z. Genetic and molecular factors in determining grain number per panicle of rice. FRONTIERS IN PLANT SCIENCE 2022; 13:964246. [PMID: 35991390 PMCID: PMC9386260 DOI: 10.3389/fpls.2022.964246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Accepted: 07/15/2022] [Indexed: 06/15/2023]
Abstract
It was suggested that the most effective way to improve rice grain yield is to increase the grain number per panicle (GN) through the breeding practice in recent decades. GN is a representative quantitative trait affected by multiple genetic and environmental factors. Understanding the mechanisms controlling GN has become an important research field in rice biotechnology and breeding. The regulation of rice GN is coordinately controlled by panicle architecture and branch differentiation, and many GN-associated genes showed pleiotropic effect in regulating tillering, grain size, flowering time, and other domestication-related traits. It is also revealed that GN determination is closely related to vascular development and the metabolism of some phytohormones. In this review, we summarize the recent findings in rice GN determination and discuss the genetic and molecular mechanisms of GN regulators.
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Affiliation(s)
- Yue Lu
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, College of Agriculture, Yangzhou University, Yangzhou, China
- Jiangsu Key Laboratory of Crop Genetics and Physiology, Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, China
| | - Mingli Chuan
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, College of Agriculture, Yangzhou University, Yangzhou, China
- Jiangsu Key Laboratory of Crop Genetics and Physiology, Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, China
| | - Hanyao Wang
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, College of Agriculture, Yangzhou University, Yangzhou, China
| | - Rujia Chen
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, College of Agriculture, Yangzhou University, Yangzhou, China
| | - Tianyun Tao
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, College of Agriculture, Yangzhou University, Yangzhou, China
| | - Yong Zhou
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, College of Agriculture, Yangzhou University, Yangzhou, China
- Jiangsu Key Laboratory of Crop Genetics and Physiology, Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of the Ministry of Education, Yangzhou University, Yangzhou, China
| | - Yang Xu
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, College of Agriculture, Yangzhou University, Yangzhou, China
- Jiangsu Key Laboratory of Crop Genetics and Physiology, Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, China
| | - Pengcheng Li
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, College of Agriculture, Yangzhou University, Yangzhou, China
| | - Youli Yao
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, College of Agriculture, Yangzhou University, Yangzhou, China
- Jiangsu Key Laboratory of Crop Genetics and Physiology, Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, China
| | - Chenwu Xu
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, College of Agriculture, Yangzhou University, Yangzhou, China
- Jiangsu Key Laboratory of Crop Genetics and Physiology, Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of the Ministry of Education, Yangzhou University, Yangzhou, China
| | - Zefeng Yang
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, College of Agriculture, Yangzhou University, Yangzhou, China
- Jiangsu Key Laboratory of Crop Genetics and Physiology, Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of the Ministry of Education, Yangzhou University, Yangzhou, China
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Arora K, Sen S. Cytokinin Oxygenase/Dehydrogenase Inhibitors: An Emerging Tool in Stress Biotechnology Employed for Crop Improvement. Front Genet 2022; 13:877510. [PMID: 35401687 PMCID: PMC8987495 DOI: 10.3389/fgene.2022.877510] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Accepted: 03/04/2022] [Indexed: 12/02/2022] Open
Abstract
In order to meet the global challenges of food security, one of the foremost solutions lies in enhancing the crop productivity. This can be attained by considering key plant hormones such as cytokinins as agrochemicals as cytokinins in particular are known to control the essential processes of the plants. Even though, it has already been established since 1980s that the enzyme, cytokinin oxidase/dehydrogenase (CKO/CKX) deactivates cytokinins; the potential applications of manipulating these enzymes have mostly been speculated to have a high potential in the biotechnology industry and spreads to agriculture, horticulture and agroforestry. The enzyme is critical in maintaining a balanced level of cytokinins in plants. However, it is yet to be fully established that inhibiting this enzyme can be the constant source of improvement in the productivity of plants, even though success has been obtained in some economically important plant species. Furthermore, the impact efficiency of this enzyme may vary from plant to plant, which needs to be evaluated employing tissue culture and other extrinsic applications. This review intends to cover the relevant studies addressing any biological activity of this enzyme in the current context and any associated biotechnological applications specific to enhanced grain yield, abiotic stress tolerance, delayed senescence and in vitro organogenesis among various plants and not only cereals. Moreover, our study will identify the present gaps in research with respect to many important food crops, which will be useful for researchers who are actively involved in providing a foundation for a variety of genetically improved plants achieved through this manner. In addition to this, other ways of engineering the amount of cytokinin levels appropriate for signaling also needs to be analyzed in order to extend the benefits of cytokinin biology to other crops too. The application of these inhibitors can be considered among the best alternates as well as addition to genetically modified plants for overcoming the gaps in crop demand.
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Affiliation(s)
- Kavita Arora
- Department of Botany, National P.G. College, Lucknow, India
- *Correspondence: Kavita Arora, ; Sangeeta Sen,
| | - Sangeeta Sen
- Bangalore, India
- *Correspondence: Kavita Arora, ; Sangeeta Sen,
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Li T, Zou H, Zhang J, Ding H, Li C, Chen X, Li Y, Feng W, Kageyama K. High-efficiency and high-fidelity ssDNA circularisation via the pairing of five 3′-terminal bases to assist LR-LAMP for the genotyping of single-nucleotide polymorphisms. Analyst 2022; 147:3993-3999. [DOI: 10.1039/d2an01042a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A high-fidelity ssDNA circularisation via the pairing of five 3′-terminal bases was developed to assist LR-LAMP for genotyping of SNPs.
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Affiliation(s)
- Taiwen Li
- Key Laboratory of Agricultural Microbiology, College of Agriculture, Guiyang 550025, China
| | - Huayan Zou
- Key Laboratory of Agricultural Microbiology, College of Agriculture, Guiyang 550025, China
| | - Jing Zhang
- Key Laboratory of Agricultural Microbiology, College of Agriculture, Guiyang 550025, China
| | - Haixia Ding
- Key Laboratory of Agricultural Microbiology, College of Agriculture, Guiyang 550025, China
| | - Cheng Li
- Key Laboratory of Agricultural Microbiology, College of Agriculture, Guiyang 550025, China
| | - Xiangru Chen
- Key Laboratory of Agricultural Microbiology, College of Agriculture, Guiyang 550025, China
| | - Yunzhou Li
- Key Laboratory of Agricultural Microbiology, College of Agriculture, Guiyang 550025, China
| | - Wenzhuo Feng
- Key Laboratory of Agricultural Microbiology, College of Agriculture, Guiyang 550025, China
| | - Koji Kageyama
- River Basin Research Center, Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan
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Gupta MK, Gouda G, Donde R, Vadde R, Behera L. Novel cytokinin oxidase/dehydrogenase inhibitors for enhancing grain yield in crop plants and potential applications in the biotechnology industry. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:153-156. [PMID: 33529340 DOI: 10.1093/jxb/eraa445] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
This article comments on:Nisler J, Kopečný D, Pěkná Z, Končitíková R, Koprna R, Murvanidze N, Werbrouck SPO, Havlíček L, De Diego N, Wimmer Z, Briozzo P, Moréra S, Zalabák D, Spíchal L, Strnad M. 2021. Diphenylurea-derived cytokinin oxidase/dehydrogenase inhibitors for biotechnology and agriculture. Journal of Experimental Botany 72, 355–370.
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Affiliation(s)
- Manoj Kumar Gupta
- ICAR-National Rice Research Institute, Cuttack, Odisha, India
- Department of Biotechnology & Bioinformatics, Yogi Vemana University, Kadapa, Andhra Pradesh, India
| | - Gayatri Gouda
- ICAR-National Rice Research Institute, Cuttack, Odisha, India
| | - Ravindra Donde
- ICAR-National Rice Research Institute, Cuttack, Odisha, India
| | - Ramakrishna Vadde
- Department of Biotechnology & Bioinformatics, Yogi Vemana University, Kadapa, Andhra Pradesh, India
| | - Lambodar Behera
- ICAR-National Rice Research Institute, Cuttack, Odisha, India
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Gupta MK, Gouda G, Donde R, Vadde R, Behera L. In silico characterization of the impact of mutation (LEU112PRO) on the structure and function of carotenoid cleavage dioxygenase 8 in Oryza sativa. PHYTOCHEMISTRY 2020; 175:112365. [PMID: 32247721 DOI: 10.1016/j.phytochem.2020.112365] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2020] [Revised: 03/22/2020] [Accepted: 03/23/2020] [Indexed: 06/11/2023]
Abstract
Mutation (p.LEU112PRO) in "carotenoid cleavage dioxygenase 8" (CCD8) protein increases tiller formation in rice plants by cross-talking with auxin and cytokinins. However, owing to the nonexistence of a "three-dimension" structure of CCD8, detail information about its structure and function remain elusive until date. Hence, in the present study, computational approaches were adopted to predict "three-dimensional" (3D) structure of CCD8 protein through comparative modeling techniques and to study the effect of mutation (p.LEU112PRO) on its function as well as architecture through "molecular dynamics" simulation studies. The obtained result reveals that wild-type CCD8 protein is made up of 10 α-helix and 25 β-strands while mutant CCD8 is made up of 11 α-helix and 24 β-strands. Further, molecular docking studies reveals that the wild-type has a better binding affinity with auxin and cytokinin in comparison to mutant. Subsequent molecular dynamics simulation of these four complexes, separately, reveals that the movement of both wild-type as well as mutant CCD8 get reduced after binding with auxin, which in turn prevent auxin transport out of the bud and increases tiller number. However, when cytokinin binds with wild-type and mutant CCD8, it inhibits and enhance CCD8 activity, respectively. As cytokinin positively regulates tiller number formation, enhance activity of mutant CCD8 after binding with cytokinin might be the main reason for more tiller number in mutant than wild-type plant. In the near future, mutant CCD8 along with auxin and cytokinin may be utilized for increasing grain yield in rice plants.
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Affiliation(s)
- Manoj Kumar Gupta
- Department of Biotechnology & Bioinformatics, Yogi Vemana University, Kadapa, 516005, Andhra Pradesh, India
| | - Gayatri Gouda
- ICAR-National Rice Research Institute, Cuttack, Odisha, 753 006, India
| | - Ravindra Donde
- ICAR-National Rice Research Institute, Cuttack, Odisha, 753 006, India
| | - Ramakrishna Vadde
- Department of Biotechnology & Bioinformatics, Yogi Vemana University, Kadapa, 516005, Andhra Pradesh, India
| | - Lambodar Behera
- ICAR-National Rice Research Institute, Cuttack, Odisha, 753 006, India.
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