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Gawande ND, Bhalla H, Watts A, Shelake RM, Sankaranarayanan S. Application of genome editing in plant reproductive biology: recent advances and challenges. PLANT REPRODUCTION 2024:10.1007/s00497-024-00506-w. [PMID: 38954018 DOI: 10.1007/s00497-024-00506-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2024] [Accepted: 06/21/2024] [Indexed: 07/04/2024]
Abstract
KEY MESSAGE This comprehensive review underscores the application of genome editing in plant reproductive biology, including recent advances and challenges associated with it. Genome editing (GE) is a powerful technology that has the potential to accelerate crop improvement by enabling efficient, precise, and rapid engineering of plant genomes. Over the last decade, this technology has rapidly evolved from the use of meganucleases (homing endonucleases), zinc-finger nucleases, transcription activator-like effector nucleases to the use of clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein (CRISPR/Cas), which has emerged as a popular GE tool in recent times and has been extensively used in several organisms, including plants. GE has been successfully employed in several crops to improve plant reproductive traits. Improving crop reproductive traits is essential for crop yields and securing the world's food supplies. In this review, we discuss the application of GE in various aspects of plant reproductive biology, including its potential application in haploid induction, apomixis, parthenocarpy, development of male sterile lines, and the regulation of self-incompatibility. We also discuss current challenges and future prospects of this technology for crop improvement, focusing on plant reproduction.
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Affiliation(s)
- Nilesh D Gawande
- Department of Biological Sciences and Engineering, Indian Institute of Technology Gandhinagar, Palaj, Gujarat, 382355, India
| | - Hemal Bhalla
- Department of Biological Sciences and Engineering, Indian Institute of Technology Gandhinagar, Palaj, Gujarat, 382355, India
| | - Anshul Watts
- ICAR-National Institute for Plant Biotechnology, New Delhi, India
| | - Rahul Mahadev Shelake
- Division of Applied Life Science (BK21 Four Program), Plant Molecular and Biotechnology Research Center, Gyeongsang National University, Jinju, 52828, Korea
| | - Subramanian Sankaranarayanan
- Department of Biological Sciences and Engineering, Indian Institute of Technology Gandhinagar, Palaj, Gujarat, 382355, India.
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Rengasamy B, Manna M, Thajuddin NB, Sathiyabama M, Sinha AK. Breeding rice for yield improvement through CRISPR/Cas9 genome editing method: current technologies and examples. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2024; 30:185-198. [PMID: 38623165 PMCID: PMC11016042 DOI: 10.1007/s12298-024-01423-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Revised: 01/23/2024] [Accepted: 02/27/2024] [Indexed: 04/17/2024]
Abstract
The impending climate change is threatening the rice productivity of the Asian subcontinent as instances of crop failures due to adverse abiotic and biotic stress factors are becoming common occurrences. CRISPR-Cas9 mediated genome editing offers a potential solution for improving rice yield as well as its stress adaptation. This technology allows modification of plant's genetic elements and is not dependent on foreign DNA/gene insertion for incorporating a particular trait. In this review, we have discussed various CRISPR-Cas9 mediated genome editing tools for gene knockout, gene knock-in, simultaneously disrupting multiple genes by multiplexing, base editing and prime editing the genes. The review here also presents how these genome editing technologies have been employed to improve rice productivity by directly targeting the yield related genes or by indirectly manipulating various abiotic and biotic stress responsive genes. Lately, many countries treat genome-edited crops as non-GMOs because of the absence of foreign DNA in the final product. Thus, genome edited rice plants with improved yield attributes and stress resilience are expected to be accepted by the public and solve food crisis of a major portion of the globe. Supplementary Information The online version contains supplementary material available at 10.1007/s12298-024-01423-y.
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Affiliation(s)
- Balakrishnan Rengasamy
- Department of Botany, Bharathidasan University, Tiruchirappalli, Tamil Nadu 620024 India
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067 India
| | - Mrinalini Manna
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067 India
| | - Nargis Begum Thajuddin
- P. G. and Research Department of Biotechnology, Jamal Mohamed College, Affiliated to Bharathidasan University, Tiruchirappalli, Tamil Nadu 620024 India
| | | | - Alok Krishna Sinha
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067 India
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Ahmar S, Hensel G, Gruszka D. CRISPR/Cas9-mediated genome editing techniques and new breeding strategies in cereals - current status, improvements, and perspectives. Biotechnol Adv 2023; 69:108248. [PMID: 37666372 DOI: 10.1016/j.biotechadv.2023.108248] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 08/29/2023] [Accepted: 08/31/2023] [Indexed: 09/06/2023]
Abstract
Cereal crops, including triticeae species (barley, wheat, rye), as well as edible cereals (wheat, corn, rice, oat, rye, sorghum), are significant suppliers for human consumption, livestock feed, and breweries. Over the past half-century, modern varieties of cereal crops with increased yields have contributed to global food security. However, presently cultivated elite crop varieties were developed mainly for optimal environmental conditions. Thus, it has become evident that taking into account the ongoing climate changes, currently a priority should be given to developing new stress-tolerant cereal cultivars. It is necessary to enhance the accuracy of methods and time required to generate new cereal cultivars with the desired features to adapt to climate change and keep up with the world population expansion. The CRISPR/Cas9 system has been developed as a powerful and versatile genome editing tool to achieve desirable traits, such as developing high-yielding, stress-tolerant, and disease-resistant transgene-free lines in major cereals. Despite recent advances, the CRISPR/Cas9 application in cereals faces several challenges, including a significant amount of time required to develop transgene-free lines, laboriousness, and a limited number of genotypes that may be used for the transformation and in vitro regeneration. Additionally, developing elite lines through genome editing has been restricted in many countries, especially Europe and New Zealand, due to a lack of flexibility in GMO regulations. This review provides a comprehensive update to researchers interested in improving cereals using gene-editing technologies, such as CRISPR/Cas9. We will review some critical and recent studies on crop improvements and their contributing factors to superior cereals through gene-editing technologies.
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Affiliation(s)
- Sunny Ahmar
- Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia, Katowice, Poland
| | - Goetz Hensel
- Centre for Plant Genome Engineering, Institute of Plant Biochemistry, Heinrich-Heine-University, Duesseldorf, Germany; Centre of Region Haná for Biotechnological and Agricultural Research, Czech Advanced Technology and Research Institute, Palacký University Olomouc, Olomouc, Czech Republic
| | - Damian Gruszka
- Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia, Katowice, Poland.
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Matinvafa MA, Makani S, Parsasharif N, Zahed MA, Movahed E, Ghiasvand S. CRISPR-Cas technology secures sustainability through its applications: a review in green biotechnology. 3 Biotech 2023; 13:383. [PMID: 37920190 PMCID: PMC10618153 DOI: 10.1007/s13205-023-03786-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Accepted: 09/09/2023] [Indexed: 11/04/2023] Open
Abstract
The CRISPR-Cas system's applications in biotechnology offer a promising avenue for addressing pressing global challenges, such as climate change, environmental pollution, the energy crisis, and the food crisis, thereby advancing sustainability. The ever-growing demand for food due to the projected population of around 9.6 billion by 2050 requires innovation in agriculture. CRISPR-Cas technology emerges as a powerful solution, enhancing crop varieties, optimizing yields, and improving resilience to stressors. It offers multiple gene editing, base editing, and prime editing, surpassing conventional methods. CRISPR-Cas introduces disease and herbicide resistance, high-yielding, drought-tolerant, and water-efficient crops to address rising water utilization and to improve the efficiency of agricultural practices which promise food sustainability and revolutionize agriculture for the benefit of future generations. The application of CRISPR-Cas technology extends beyond agriculture to address environmental challenges. With the adverse impacts of climate change and pollution endangering ecosystems, there is a growing need for sustainable solutions. The technology's potential in carbon capture and reduction through bio-sequestration is a pivotal strategy for combating climate change. Genomic advancements allow for the development of genetically modified organisms, optimizing biofuel and biomaterial production, and contributing to a renewable and sustainable energy future. This study reviews the multifaceted applications of CRISPR-Cas technology in the agricultural and environmental fields and emphasizes its potential to secure a sustainable future.
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Affiliation(s)
- Mohammad Ali Matinvafa
- Department of Biotechnology & Environment, Faculty of Chemical Engineering, Amirkabir University of Technology (Tehran Polytechnic), Tehran, Iran
| | - Shadi Makani
- Faculty of Biological Sciences, Kharazmi University, Tehran, 14911 - 15719 Iran
| | - Negin Parsasharif
- Faculty of Veterinary Medicine, Karaj Branch, Islamic Azad University, Karaj, Iran
| | - Mohammad Ali Zahed
- Faculty of Biological Sciences, Kharazmi University, Tehran, 14911 - 15719 Iran
| | - Elaheh Movahed
- Wadsworth Center, New York State Department of Health, Albany, NY USA
| | - Saeedeh Ghiasvand
- Department of Biology, Faculty of Basic Science, Malayer University, Malayer, Hamedan, Iran
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5
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Qing D, Chen W, Huang S, Li J, Pan Y, Zhou W, Liang Q, Yuan J, Gan D, Chen L, Chen L, Huang J, Zhou Y, Dai G, Deng G. Editing of rice (Oryza sativa L.) OsMKK3 gene using CRISPR/Cas9 decreases grain length by modulating the expression of photosystem components. Proteomics 2023; 23:e2200538. [PMID: 37376803 DOI: 10.1002/pmic.202200538] [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] [Received: 12/19/2022] [Revised: 06/14/2023] [Accepted: 06/15/2023] [Indexed: 06/29/2023]
Abstract
Grain size is one of the most important agronomic traits for grain yield determination in rice. To better understand the proteins that are regulated by the grain size regulatory gene OsMKK3, this gene was knocked out using the CRISPR/Cas9 system, and tandem mass tag (TMT) labeling combined with liquid chromatograph-tandem mass spectrometry analysis was performed to study the regulation of proteins in the panicle. Quantitative proteomic screening revealed a total of 106 differentially expressed proteins (DEPs) via comparison of the OsMKK3 mutant line to the wild-type YexiangB, including 15 and 91 up-regulated and down-regulated DEPs, respectively. Pathway analysis revealed that DEPs were enriched in metabolic pathways, biosynthesis of secondary metabolites, phenylpropanoid biosynthesis, and photosynthesis. Strong interactions were detected among seven down-regulated proteins related to photosystem components in the protein-protein interaction network, and photosynthetic rate was decreased in mutant plants. The results of the liquid chromatography-parallel reaction monitoring/mass spectromery analysis and western blot analysis were consistent with the results of the proteomic analysis, and the results of the quantitative reverse transcription polymerase chain reaction analysis revealed that the expression levels of most candidate genes were consistent with protein levels. Overall, OsMKK3 controls grain size by regulating the protein content in cells. Our findings provide new candidate genes that will aid the study of grain size regulatory mechanisms associated with the mitogen-activated protein kinase (MAPK) signaling pathway.
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Affiliation(s)
- Dongjin Qing
- Guangxi Academy of Agricultural Sciences/Guangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Nanning, China
| | - Weiwei Chen
- Guangxi Academy of Agricultural Sciences/Guangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Nanning, China
| | - Suosheng Huang
- Guangxi Academy of Agricultural Sciences, Plant Protection Research Institute, Nanning, China
| | - Jingcheng Li
- Guangxi Academy of Agricultural Sciences/Guangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Nanning, China
| | - Yinghua Pan
- Guangxi Academy of Agricultural Sciences/Guangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Nanning, China
| | - Weiyong Zhou
- Guangxi Academy of Agricultural Sciences/Guangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Nanning, China
| | - Qiongyue Liang
- Guangxi Academy of Agricultural Sciences/Guangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Nanning, China
| | - Jinghua Yuan
- Guangxi Academy of Agricultural Sciences/Guangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Nanning, China
| | - Dongmei Gan
- Guangxi Academy of Agricultural Sciences/Guangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Nanning, China
| | - Li Chen
- Guangxi Academy of Agricultural Sciences/Guangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Nanning, China
| | - Lei Chen
- Guangxi Academy of Agricultural Sciences/Guangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Nanning, China
| | - Juan Huang
- Guangxi Academy of Agricultural Sciences/Guangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Nanning, China
| | - Yan Zhou
- Key Laboratory of Chemistry and Engineering of Forest Products, School of Chemistry and Chemical Engineering, Guangxi Minzu University, Nanning, China
| | - Gaoxing Dai
- Guangxi Academy of Agricultural Sciences/Guangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Nanning, China
| | - Guofu Deng
- Guangxi Academy of Agricultural Sciences/Guangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Nanning, China
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6
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Yang J, Fang Y, Wu H, Zhao N, Guo X, Mackon E, Peng H, Huang S, He Y, Qin B, Liu Y, Liu F, Chen S, Li R. Improvement of resistance to rice blast and bacterial leaf streak by CRISPR/Cas9-mediated mutagenesis of Pi21 and OsSULTR3;6 in rice ( Oryza sativa L.). FRONTIERS IN PLANT SCIENCE 2023; 14:1209384. [PMID: 37528980 PMCID: PMC10389665 DOI: 10.3389/fpls.2023.1209384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Accepted: 06/27/2023] [Indexed: 08/03/2023]
Abstract
Rice (Oryza sativa L.) is a staple food in many countries around the world, particularly in China. The production of rice is seriously affected by the bacterial leaf streak and rice blast, which can reduce rice yield or even cause it to fail to be harvested. In this study, susceptible material 58B was edited by CRISPR/Cas9, targeting a target of the Pi21 gene and a target of the effector-binding element (EBE) of the OsSULTR3;6 gene, and the mutants 58b were obtained by Agrobacterium-mediated method. The editing efficiency of the two targets in the T0 generation was higher than 90.09%, the homozygous mutants were successfully selected in the T0 generation, and the homozygous mutation rate of each target was higher than 26.67%. The expression of the edited pi21 and EBE of Ossultr3;6 was significantly reduced, and the expression of defense responsive genes was significantly upregulated after infected with rice blast. The lesion areas of rice blast and bacterial leaf streak were significantly reduced in 58b, and the resistance of both was effectively improved. Furthermore, the gene editing events did not affect the agronomic traits of rice. In this study, the resistance of 58b to rice blast and bacterial leaf streak was improved simultaneously. This study provides a reference for using Clustered Regularly Interspaced Short Palindromic Repeats/Cas9 (CRISPR/Cas9) to accelerate the improvement of rice varieties and the development of new materials for rice breeding.
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Affiliation(s)
- Jinlian Yang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning, China
| | - Yaoyu Fang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning, China
| | - Hu Wu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning, China
| | - Neng Zhao
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning, China
| | - Xinying Guo
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning, China
| | - Enerand Mackon
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning, China
| | - Haowen Peng
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning, China
| | - Sheng Huang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, Nanning, China
| | - Yongqiang He
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning, China
| | - Baoxiang Qin
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning, China
| | - Yaoguang Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agricultural Bioresources, South China Agricultural University, Guangzhou, China
| | - Fang Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning, China
| | - Shengwu Chen
- Guangxi Lvhai Seed Co., Ltd, Marketing Department, Nanning, China
| | - Rongbai Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning, China
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7
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Mijiti M, Maimaiti A, Chen X, Tuersun M, Dilixiati M, Dilixiati Y, Zhu G, Wu H, Li Y, Turhon M, Abulaiti A, Maimaitiaili N, Yiming N, Kasimu M, Wang Y. CRISPR-cas9 screening identified lethal genes enriched in Hippo kinase pathway and of predictive significance in primary low-grade glioma. Mol Med 2023; 29:64. [PMID: 37183261 PMCID: PMC10183247 DOI: 10.1186/s10020-023-00652-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 04/14/2023] [Indexed: 05/16/2023] Open
Abstract
BACKGROUND Low-grade gliomas (LGG) are a type of brain tumor that can be lethal, and it is essential to identify genes that are correlated with patient prognosis. In this study, we aimed to use CRISPR-cas9 screening data to identify key signaling pathways and develop a genetic signature associated with high-risk, low-grade glioma patients. METHODS The study used CRISPR-cas9 screening data to identify essential genes correlated with cell survival in LGG. We used RNA-seq data to identify differentially expressed genes (DEGs) related to cell viability. Moreover, we used the least absolute shrinkage and selection operator (LASSO) method to construct a genetic signature for predicting overall survival in patients. We performed enrichment analysis to identify pathways mediated by DEGs, overlapping genes, and genes shared in the Weighted correlation network analysis (WGCNA). Finally, the study used western blot, qRT-PCR, and IHC to detect the expression of hub genes from signature in clinical samples. RESULTS The study identified 145 overexpressed oncogenes in low-grade gliomas using the TCGA database. These genes were intersected with lethal genes identified in the CRISPR-cas9 screening data from Depmap database, which are enriched in Hippo pathways. A total of 19 genes were used to construct a genetic signature, and the Hippo signaling pathway was found to be the predominantly enriched pathway. The signature effectively distinguished between low- and high-risk patients, with high-risk patients showing a shorter overall survival duration. Differences in hub gene expression were found in different clinical samples, with the protein and mRNA expression of REP65 being significantly up-regulated in tumor cells. The study suggests that the Hippo signaling pathway may be a critical regulator of viability and tumor proliferation and therefore is an innovative new target for treating cancerous brain tumors, including low-grade gliomas. CONCLUSION Our study identified a novel genetic signature associated with high-risk, LGG patients. We found that the Hippo signaling pathway was significantly enriched in this signature, indicating that it may be a critical regulator of tumor viability and proliferation in LGG. Targeting the Hippo pathway could be an innovative new strategy for treating LGG.
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Affiliation(s)
- Maimaitili Mijiti
- Department of Neurosurgery, Neurosurgery Centre, The First Affiliated Hospital of Xinjiang Medical University, Xinjiang, 830054, Urumqi, China
| | - Aierpati Maimaiti
- Department of Neurosurgery, Neurosurgery Centre, The First Affiliated Hospital of Xinjiang Medical University, Xinjiang, 830054, Urumqi, China
| | - Xiaoqing Chen
- The First Affiliated Hospital of Xinjiang Medical University, Urumqi, 830054, Xinjiang, China
| | - Maidina Tuersun
- Xinjiang Medical University, Urumqi, 830011, Xinjiang, China
| | | | | | - Guohua Zhu
- Department of Neurosurgery, Neurosurgery Centre, The First Affiliated Hospital of Xinjiang Medical University, Xinjiang, 830054, Urumqi, China
| | - Hao Wu
- Department of Neurosurgery, Neurosurgery Centre, The First Affiliated Hospital of Xinjiang Medical University, Xinjiang, 830054, Urumqi, China
| | - Yandong Li
- Department of Neurosurgery, Neurosurgery Centre, The First Affiliated Hospital of Xinjiang Medical University, Xinjiang, 830054, Urumqi, China
| | - Mirzat Turhon
- Department of Neurointerventional Surgery, Beijing Neurosurgical Institute, Capital Medical University, Beijing, 100070, China
- Department of Neurointerventional Surgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, 100070, China
| | - Aimitaji Abulaiti
- Department of Neurosurgery, Neurosurgery Centre, The First Affiliated Hospital of Xinjiang Medical University, Xinjiang, 830054, Urumqi, China
| | | | - Nadire Yiming
- Xinjiang Medical University, Urumqi, 830011, Xinjiang, China
| | - Maimaitijiang Kasimu
- Department of Neurosurgery, Neurosurgery Centre, The First Affiliated Hospital of Xinjiang Medical University, Xinjiang, 830054, Urumqi, China.
| | - Yongxin Wang
- Department of Neurosurgery, Neurosurgery Centre, The First Affiliated Hospital of Xinjiang Medical University, Xinjiang, 830054, Urumqi, China.
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Qing D, Zhou Y, Pan Y, Yang X, Li J, Zhou W, Liang H, Chen W, Chen L, Lu C, Dai G, Deng G. TMT-based quantitative proteomic analysis of indica rice cultivars reveals that novel components of the signaling pathways might play a role in grain length regulation. J Proteomics 2023; 270:104745. [PMID: 36220543 DOI: 10.1016/j.jprot.2022.104745] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 09/22/2022] [Accepted: 09/27/2022] [Indexed: 11/06/2022]
Abstract
Grain length is one of the most important rice grain appearance components. To better understand the protein regulated by grain length in indica rice, the tandem mass tag (TMT) labeling combined with LC-MS/MS analysis was used for quantitative identification of differentially regulated proteins by comparing six long-grain cultivars (MeiB, LongfengB, YexiangB, FengtianB, WantaiB, and DingxiangB) to the short-grain cultivar BoB, respectively. A total of 6622 proteins were detected for quantitative analysis by comparing protein content of six long-grain cultivars to the short-grain cultivar, and 715 proteins were significantly regulated, consisting of 336 uniquely over-accumulated proteins and 355 uniquely down-accumulated proteins. KEGG pathway analysis revealed that most of accumulated proteins are involved in metabolic pathways, biosynthesis of secondary metabolites and phenylpropanoid biosynthesis. Four down-accumulated proteins maybe involved in the signaling pathways for grain length regulation. LC-PRM/MS quantitative analysis was used to analyze 10 differentially expressed proteins. The results were almost consistent with the TMT quantitative analysis. qRT-PCR analysis results showed that the transcription level was not always parallel to the protein content. This study identified many novel grain length accumulated proteins through the quantitative proteomics approach, providing candidate genes for further study of grain size regulatory mechanisms. SIGNIFICANCE: Rice grain length is one of the most important characteristics influencing appearance and yield. Six long-grain cultivars (MeiB, LongfengB, YexiangB, FengtianB, WantaiB, and DingxiangB obtained in Guangxi province of China from the 2000s to 2020s) and one short-grain cultivar (BoB obtained in Guangxi province of China in 1980s) were used for comparative analyses. Totally, 715 differentially expressed proteins (DEPs) were identified using TMT-base proteomic analysis. The numbers of DEPs increased as the grain length increased. 4 DEPs may be related to rice's signaling pathways for grain size regulation. A total of 85 DEPs regulated in at least four long-grain cultivars compared with the short-grain cultivar BoB, and 7 proteins were over-accumulated, and 3 proteins were down-accumulated in six long-grain cultivars. These findings provide valuable information to better understand the mechanisms of protein regulation by grain length in rice.
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Affiliation(s)
- Dongjin Qing
- Rice Research Institute, Guangxi Academy of Agricultural Sciences, Guangxi Key Laboratory of Rice Genetics and Breeding, Nanning 530007, China
| | - Yan Zhou
- School of Chemistry and Chemical Engineering, Guangxi Minzu University, Nanning 530006, China; Key Laboratory of Chemistry and Engineering of Forest Products, State Ethnic Affairs Commission, Nanning 530006, China; Key Laboratory of Guangxi Colleges, Universities for Food Safety and Pharmaceutical Analytical Chemistry, Nanning 530006, China
| | - Yinghua Pan
- Rice Research Institute, Guangxi Academy of Agricultural Sciences, Guangxi Key Laboratory of Rice Genetics and Breeding, Nanning 530007, China
| | - Xinghai Yang
- Rice Research Institute, Guangxi Academy of Agricultural Sciences, Guangxi Key Laboratory of Rice Genetics and Breeding, Nanning 530007, China
| | - Jingcheng Li
- Rice Research Institute, Guangxi Academy of Agricultural Sciences, Guangxi Key Laboratory of Rice Genetics and Breeding, Nanning 530007, China
| | - Weiyong Zhou
- Rice Research Institute, Guangxi Academy of Agricultural Sciences, Guangxi Key Laboratory of Rice Genetics and Breeding, Nanning 530007, China
| | - Haifu Liang
- Rice Research Institute, Guangxi Academy of Agricultural Sciences, Guangxi Key Laboratory of Rice Genetics and Breeding, Nanning 530007, China
| | - Weiwei Chen
- Rice Research Institute, Guangxi Academy of Agricultural Sciences, Guangxi Key Laboratory of Rice Genetics and Breeding, Nanning 530007, China
| | - Lei Chen
- Rice Research Institute, Guangxi Academy of Agricultural Sciences, Guangxi Key Laboratory of Rice Genetics and Breeding, Nanning 530007, China
| | - Chunju Lu
- Rice Research Institute, Guangxi Academy of Agricultural Sciences, Guangxi Key Laboratory of Rice Genetics and Breeding, Nanning 530007, China
| | - Gaoxing Dai
- Rice Research Institute, Guangxi Academy of Agricultural Sciences, Guangxi Key Laboratory of Rice Genetics and Breeding, Nanning 530007, China.
| | - Guofu Deng
- Rice Research Institute, Guangxi Academy of Agricultural Sciences, Guangxi Key Laboratory of Rice Genetics and Breeding, Nanning 530007, China.
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9
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Zhao N, Yuan R, Usman B, Qin J, Yang J, Peng L, Mackon E, Liu F, Qin B, Li R. Detection of QTLs Regulating Six Agronomic Traits of Rice Based on Chromosome Segment Substitution Lines of Common Wild Rice ( Oryza rufipogon Griff.) and Mapping of qPH1.1 and qLMC6.1. Biomolecules 2022; 12:biom12121850. [PMID: 36551278 PMCID: PMC9775987 DOI: 10.3390/biom12121850] [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: 11/16/2022] [Revised: 12/06/2022] [Accepted: 12/07/2022] [Indexed: 12/14/2022] Open
Abstract
Wild rice is a primary source of genes that can be utilized to generate rice cultivars with advantageous traits. Chromosome segment substitution lines (CSSLs) are consisting of a set of consecutive and overlapping donor chromosome segments in a recipient's genetic background. CSSLs are an ideal genetic population for mapping quantitative traits loci (QTLs). In this study, 59 CSSLs from the common wild rice (Oryza rufipogon Griff.) accession DP15 under the indica rice cultivar (O. sativa L. ssp. indica) variety 93-11 background were constructed through multiple backcrosses and marker-assisted selection (MAS). Through high-throughput whole genome re-sequencing (WGRS) of parental lines, 12,565 mapped InDels were identified and designed for polymorphic molecular markers. The 59 CSSLs library covered 91.72% of the genome of common wild rice accession DP15. The DP15-CSSLs displayed variation in six economic traits including grain length (GL), grain width (GW), thousand-grain weight (TGW), grain length-width ratio (GLWR), plant height (PH), and leaf margin color (LMC), which were finally attributed to 22 QTLs. A homozygous CSSL line and a purple leave margin CSSL line were selected to construct two secondary genetic populations for the QTLs mapping. Thus, the PH-controlling QTL qPH1.1 was mapped to a region of 4.31-Mb on chromosome 1, and the LMC-controlling QTL qLMC6.1 was mapped to a region of 370-kb on chromosome 6. Taken together, these identified novel QTLs/genes from common wild rice can potentially promote theoretical knowledge and genetic applications to rice breeders worldwide.
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Affiliation(s)
- Neng Zhao
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning 530004, China
| | - Ruizhi Yuan
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning 530004, China
| | - Babar Usman
- Graduate School of Green-Bio Science and Crop Biotech Institute, Kyung Hee University, Yongin 17104, Republic of Korea
| | - Jiaming Qin
- Maize Research Institute, Guangxi Academy of Agricultural Science, Nanning 530007, China
| | - Jinlian Yang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning 530004, China
| | - Liyun Peng
- State Key Laboratory of Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Science and Technology, Guangxi University, Nanning 530005, China
| | - Enerand Mackon
- State Key Laboratory of Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Science and Technology, Guangxi University, Nanning 530005, China
| | - Fang Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning 530004, China
| | - Baoxiang Qin
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning 530004, China
| | - Rongbai Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning 530004, China
- Correspondence:
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10
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Transgenic Improvement for Biotic Resistance of Crops. Int J Mol Sci 2022; 23:ijms232214370. [PMID: 36430848 PMCID: PMC9697442 DOI: 10.3390/ijms232214370] [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: 10/25/2022] [Revised: 11/15/2022] [Accepted: 11/17/2022] [Indexed: 11/22/2022] Open
Abstract
Biotic constraints, including pathogenic fungi, viruses and bacteria, herbivory insects, as well as parasitic nematodes, cause significant yield loss and quality deterioration of crops. The effect of conventional management of these biotic constraints is limited. The advances in transgenic technologies provide a direct and directional approach to improve crops for biotic resistance. More than a hundred transgenic events and hundreds of cultivars resistant to herbivory insects, pathogenic viruses, and fungi have been developed by the heterologous expression of exogenous genes and RNAi, authorized for cultivation and market, and resulted in a significant reduction in yield loss and quality deterioration. However, the exploration of transgenic improvement for resistance to bacteria and nematodes by overexpression of endogenous genes and RNAi remains at the testing stage. Recent advances in RNAi and CRISPR/Cas technologies open up possibilities to improve the resistance of crops to pathogenic bacteria and plant parasitic nematodes, as well as other biotic constraints.
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11
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Kumar D, Yadav A, Ahmad R, Dwivedi UN, Yadav K. CRISPR-Based Genome Editing for Nutrient Enrichment in Crops: A Promising Approach Toward Global Food Security. Front Genet 2022; 13:932859. [PMID: 35910203 PMCID: PMC9329789 DOI: 10.3389/fgene.2022.932859] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Accepted: 06/08/2022] [Indexed: 12/21/2022] Open
Abstract
The global malnutrition burden imparts long-term developmental, economic, social, and medical consequences to individuals, communities, and countries. The current developments in biotechnology have infused biofortification in several food crops to fight malnutrition. However, these methods are not sustainable and suffer from several limitations, which are being solved by the CRISPR-Cas-based system of genome editing. The pin-pointed approach of CRISPR-based genome editing has made it a top-notch method due to targeted gene editing, thus making it free from ethical issues faced by transgenic crops. The CRISPR-Cas genome-editing tool has been extensively used in crop improvement programs due to its more straightforward design, low methodology cost, high efficiency, good reproducibility, and quick cycle. The system is now being utilized in the biofortification of cereal crops such as rice, wheat, barley, and maize, including vegetable crops such as potato and tomato. The CRISPR-Cas-based crop genome editing has been utilized in imparting/producing qualitative enhancement in aroma, shelf life, sweetness, and quantitative improvement in starch, protein, gamma-aminobutyric acid (GABA), oleic acid, anthocyanin, phytic acid, gluten, and steroidal glycoalkaloid contents. Some varieties have even been modified to become disease and stress-resistant. Thus, the present review critically discusses CRISPR-Cas genome editing-based biofortification of crops for imparting nutraceutical properties.
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Affiliation(s)
- Dileep Kumar
- Department of Biochemistry, University of Lucknow, Lucknow, India
| | - Anurag Yadav
- Department of Microbiology, College of Basic Science and Humanities, Sardarkrushinagar Dantiwada Agriculture University, Banaskantha, India
| | - Rumana Ahmad
- Department of Biochemistry, Era Medical University and Hospital, Lucknow, India
| | | | - Kusum Yadav
- Department of Biochemistry, University of Lucknow, Lucknow, India
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12
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Yu H, Yang Q, Fu F, Li W. Three strategies of transgenic manipulation for crop improvement. FRONTIERS IN PLANT SCIENCE 2022; 13:948518. [PMID: 35937379 PMCID: PMC9354092 DOI: 10.3389/fpls.2022.948518] [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: 05/19/2022] [Accepted: 06/27/2022] [Indexed: 06/15/2023]
Abstract
Heterologous expression of exogenous genes, overexpression of endogenous genes, and suppressed expression of undesirable genes are the three strategies of transgenic manipulation for crop improvement. Up to 2020, most (227) of the singular transgenic events (265) of crops approved for commercial release worldwide have been developed by the first strategy. Thirty-eight of them have been transformed by synthetic sequences transcribing antisense or double-stranded RNAs and three by mutated copies for suppressed expression of undesirable genes (the third strategy). By the first and the third strategies, hundreds of transgenic events and thousands of varieties with significant improvement of resistance to herbicides and pesticides, as well as nutritional quality, have been developed and approved for commercial release. Their application has significantly decreased the use of synthetic pesticides and the cost of crop production and increased the yield of crops and the benefits to farmers. However, almost all the events overexpressing endogenous genes remain at the testing stage, except one for fertility restoration and another for pyramiding herbicide tolerance. The novel functions conferred by the heterologously expressing exogenous genes under the control of constitutive promoters are usually absent in the recipient crops themselves or perform in different pathways. However, the endogenous proteins encoded by the overexpressing endogenous genes are regulated in complex networks with functionally redundant and replaceable pathways and are difficult to confer the desirable phenotypes significantly. It is concluded that heterologous expression of exogenous genes and suppressed expression by RNA interference and clustered regularly interspaced short palindromic repeats-cas (CRISPR/Cas) of undesirable genes are superior to the overexpression of endogenous genes for transgenic improvement of crops.
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Affiliation(s)
| | | | - Fengling Fu
- Maize Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Wanchen Li
- Maize Research Institute, Sichuan Agricultural University, Chengdu, China
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13
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Riaz A, Kanwal F, Ahmad I, Ahmad S, Farooq A, Madsen CK, Brinch-Pedersen H, Bekalu ZE, Dai F, Zhang G, Alqudah AM. New Hope for Genome Editing in Cultivated Grasses: CRISPR Variants and Application. Front Genet 2022; 13:866121. [PMID: 35923689 PMCID: PMC9340155 DOI: 10.3389/fgene.2022.866121] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Accepted: 06/23/2022] [Indexed: 12/24/2022] Open
Abstract
With the advent of Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) and CRISPR-associated protein (Cas) mediated genome editing, crop improvement has progressed significantly in recent years. In this genome editing tool, CRISPR-associated Cas nucleases are restricted to their target of DNA by their preferred protospacer adjacent motifs (PAMs). A number of CRISPR-Cas variants have been developed e.g. CRISPR-Cas9, -Cas12a and -Cas12b, with different PAM requirements. In this mini-review, we briefly explain the components of the CRISPR-based genome editing tool for crop improvement. Moreover, we intend to highlight the information on the latest development and breakthrough in CRISPR technology, with a focus on a comparison of major variants (CRISPR-Cas9, -Cas12a, and -Cas12b) to the newly developed CRISPR-SpRY that have nearly PAM-less genome editing ability. Additionally, we briefly explain the application of CRISPR technology in the improvement of cultivated grasses with regard to biotic and abiotic stress tolerance as well as improving the quality and yield.
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Affiliation(s)
- Asad Riaz
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Farah Kanwal
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Iqrar Ahmad
- Centre for Advanced Studies in Agriculture and Food Security, University of Agriculture Faisalabad, Faisalabad, Pakistan
| | - Shakeel Ahmad
- Centre for Advanced Studies in Agriculture and Food Security, University of Agriculture Faisalabad, Faisalabad, Pakistan
| | - Ayesha Farooq
- Centre for Advanced Studies in Agriculture and Food Security, University of Agriculture Faisalabad, Faisalabad, Pakistan
| | - Claus Krogh Madsen
- Department of Agroecology, Research Center Flakkebjerg, Aarhus University, Slagelse, Denmark
| | - Henrik Brinch-Pedersen
- Department of Agroecology, Research Center Flakkebjerg, Aarhus University, Slagelse, Denmark
| | - Zelalem Eshetu Bekalu
- Department of Agroecology, Research Center Flakkebjerg, Aarhus University, Slagelse, Denmark
| | - Fei Dai
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Guoping Zhang
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
- *Correspondence: Guoping Zhang, ; Ahmad M. Alqudah, ,
| | - Ahmad M. Alqudah
- Department of Agroecology, Research Center Flakkebjerg, Aarhus University, Slagelse, Denmark
- *Correspondence: Guoping Zhang, ; Ahmad M. Alqudah, ,
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14
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Viviani A, Spada M, Giordani T, Fambrini M, Pugliesi C. Origin of the genome editing systems: application for crop improvement. Biologia (Bratisl) 2022. [DOI: 10.1007/s11756-022-01142-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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15
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Abdullah M, Okemo P, Furtado A, Henry R. Potential of Genome Editing to Capture Diversity From Australian Wild Rice Relatives. Front Genome Ed 2022; 4:875243. [PMID: 35572739 PMCID: PMC9091330 DOI: 10.3389/fgeed.2022.875243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Accepted: 03/25/2022] [Indexed: 11/13/2022] Open
Abstract
Rice, a staple food worldwide and a model crop, could benefit from the introduction of novel genetics from wild relatives. Wild rice in the AA genome group closely related to domesticated rice is found across the tropical world. Due to their locality outside the range of domesticated rice, Australian wild rice populations are a potential source of unique traits for rice breeding. These rice species provide a diverse gene pool for improvement that could be utilized for desirable traits such as stress resistance, disease tolerance, and nutritional qualities. However, they remain poorly characterized. The CRISPR/Cas system has revolutionized gene editing and has improved our understanding of gene functions. Coupled with the increasing availability of genomic information on the species, genes in Australian wild rice could be modified through genome editing technologies to produce new domesticates. Alternatively, beneficial alleles from these rice species could be incorporated into cultivated rice to improve critical traits. Here, we summarize the beneficial traits in Australian wild rice, the available genomic information and the potential of gene editing to discover and understand the functions of novel alleles. Moreover, we discuss the potential domestication of these wild rice species for health and economic benefits to rice production globally.
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Affiliation(s)
- Muhammad Abdullah
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, QLD, Australia
- ARC Centre for Plant Success in Nature and Agriculture, University of Queensland, Brisbane, QLD, Australia
| | - Pauline Okemo
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, QLD, Australia
- ARC Centre for Plant Success in Nature and Agriculture, University of Queensland, Brisbane, QLD, Australia
| | - Agnelo Furtado
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, QLD, Australia
| | - Robert Henry
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, QLD, Australia
- ARC Centre for Plant Success in Nature and Agriculture, University of Queensland, Brisbane, QLD, Australia
- *Correspondence: Robert Henry,
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16
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CRISPR-Based Genome Editing: Advancements and Opportunities for Rice Improvement. Int J Mol Sci 2022; 23:ijms23084454. [PMID: 35457271 PMCID: PMC9027422 DOI: 10.3390/ijms23084454] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 04/08/2022] [Accepted: 04/08/2022] [Indexed: 01/27/2023] Open
Abstract
To increase the potentiality of crop production for future food security, new technologies for plant breeding are required, including genome editing technology—being one of the most promising. Genome editing with the CRISPR/Cas system has attracted researchers in the last decade as a safer and easier tool for genome editing in a variety of living organisms including rice. Genome editing has transformed agriculture by reducing biotic and abiotic stresses and increasing yield. Recently, genome editing technologies have been developed quickly in order to avoid the challenges that genetically modified crops face. Developing transgenic-free edited plants without introducing foreign DNA has received regulatory approval in a number of countries. Several ongoing efforts from various countries are rapidly expanding to adopt the innovations. This review covers the mechanisms of CRISPR/Cas9, comparisons of CRISPR/Cas9 with other gene-editing technologies—including newly emerged Cas variants—and focuses on CRISPR/Cas9-targeted genes for rice crop improvement. We have further highlighted CRISPR/Cas9 vector construction model design and different bioinformatics tools for target site selection.
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17
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Naik BJ, Shimoga G, Kim SC, Manjulatha M, Subramanyam Reddy C, Palem RR, Kumar M, Kim SY, Lee SH. CRISPR/Cas9 and Nanotechnology Pertinence in Agricultural Crop Refinement. FRONTIERS IN PLANT SCIENCE 2022; 13:843575. [PMID: 35463432 PMCID: PMC9024397 DOI: 10.3389/fpls.2022.843575] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/26/2021] [Accepted: 02/07/2022] [Indexed: 05/08/2023]
Abstract
The CRISPR/Cas9 (Clustered Regularly Interspaced Short Palindromic Repeats/CRISPR-associated protein 9) method is a versatile technique that can be applied in crop refinement. Currently, the main reasons for declining agricultural yield are global warming, low rainfall, biotic and abiotic stresses, in addition to soil fertility issues caused by the use of harmful chemicals as fertilizers/additives. The declining yields can lead to inadequate supply of nutritional food as per global demand. Grains and horticultural crops including fruits, vegetables, and ornamental plants are crucial in sustaining human life. Genomic editing using CRISPR/Cas9 and nanotechnology has numerous advantages in crop development. Improving crop production using transgenic-free CRISPR/Cas9 technology and produced fertilizers, pesticides, and boosters for plants by adopting nanotechnology-based protocols can essentially overcome the universal food scarcity. This review briefly gives an overview on the potential applications of CRISPR/Cas9 and nanotechnology-based methods in developing the cultivation of major agricultural crops. In addition, the limitations and major challenges of genome editing in grains, vegetables, and fruits have been discussed in detail by emphasizing its applications in crop refinement strategy.
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Affiliation(s)
- Banavath Jayanna Naik
- Research Institute of Climate Change and Agriculture, National Institute of Horticultural and Herbal Science, Rural Development Administration (RDA), Jeju, South Korea
| | - Ganesh Shimoga
- Interaction Laboratory, Future Convergence Engineering, Advanced Technology Research Center, Korea University of Technology and Education, Cheonan-si, South Korea
| | - Seong-Cheol Kim
- Research Institute of Climate Change and Agriculture, National Institute of Horticultural and Herbal Science, Rural Development Administration (RDA), Jeju, South Korea
| | | | | | | | - Manu Kumar
- Department of Life Science, College of Life Science and Biotechnology, Dongguk University, Seoul, South Korea
| | - Sang-Youn Kim
- Interaction Laboratory, Future Convergence Engineering, Advanced Technology Research Center, Korea University of Technology and Education, Cheonan-si, South Korea
| | - Soo-Hong Lee
- Department of Medical Biotechnology, Dongguk University, Seoul, South Korea
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18
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PSD-93 up-regulates the synaptic activity of corticotropin-releasing hormone neurons in the paraventricular nucleus in depression. Acta Neuropathol 2021; 142:1045-1064. [PMID: 34536123 DOI: 10.1007/s00401-021-02371-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 09/07/2021] [Accepted: 09/10/2021] [Indexed: 12/28/2022]
Abstract
Since the discovery of ketamine anti-depressant effects in last decade, it has effectively revitalized interest in investigating excitatory synapses hypothesis in the pathogenesis of depression. In the present study, we aimed to reveal the excitatory synaptic regulation of corticotropin-releasing hormone (CRH) neuron in the hypothalamus, which is the driving force in hypothalamic-pituitary-adrenal (HPA) axis regulation. This study constitutes the first observation of an increased density of PSD-93-CRH co-localized neurons in the hypothalamic paraventricular nucleus (PVN) of patients with major depression. PSD-93 overexpression in CRH neurons in the PVN induced depression-like behaviors in mice, accompanied by increased serum corticosterone level. PSD-93 knockdown relieved the depression-like phenotypes in a lipopolysaccharide (LPS)-induced depression model. Electrophysiological data showed that PSD-93 overexpression increased CRH neurons synaptic activity, while PSD-93 knockdown decreased CRH neurons synaptic activity. Furthermore, we found that LPS induced increased the release of glutamate from microglia to CRH neurons resulted in depression-like behaviors using fiber photometry recordings. Together, these results show that PSD-93 is involved in the pathogenesis of depression via increasing the synaptic activity of CRH neurons in the PVN, leading to the hyperactivity of the HPA axis that underlies depression-like behaviors.
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19
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Rasheed A, Gill RA, Hassan MU, Mahmood A, Qari S, Zaman QU, Ilyas M, Aamer M, Batool M, Li H, Wu Z. A Critical Review: Recent Advancements in the Use of CRISPR/Cas9 Technology to Enhance Crops and Alleviate Global Food Crises. Curr Issues Mol Biol 2021; 43:1950-1976. [PMID: 34889892 PMCID: PMC8929161 DOI: 10.3390/cimb43030135] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 11/04/2021] [Accepted: 11/05/2021] [Indexed: 12/22/2022] Open
Abstract
Genome editing (GE) has revolutionized the biological sciences by creating a novel approach for manipulating the genomes of living organisms. Many tools have been developed in recent years to enable the editing of complex genomes. Therefore, a reliable and rapid approach for increasing yield and tolerance to various environmental stresses is necessary to sustain agricultural crop production for global food security. This critical review elaborates the GE tools used for crop improvement. These tools include mega-nucleases (MNs), such as zinc-finger nucleases (ZFNs), and transcriptional activator-like effector nucleases (TALENs), and clustered regularly interspaced short palindromic repeats (CRISPR). Specifically, this review addresses the latest advancements in the role of CRISPR/Cas9 for genome manipulation for major crop improvement, including yield and quality development of biotic stress- and abiotic stress-tolerant crops. Implementation of this technique will lead to the production of non-transgene crops with preferred characteristics that can result in enhanced yield capacity under various environmental stresses. The CRISPR/Cas9 technique can be combined with current and potential breeding methods (e.g., speed breeding and omics-assisted breeding) to enhance agricultural productivity to ensure food security. We have also discussed the challenges and limitations of CRISPR/Cas9. This information will be useful to plant breeders and researchers in the thorough investigation of the use of CRISPR/Cas9 to boost crops by targeting the gene of interest.
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Affiliation(s)
- Adnan Rasheed
- Key Laboratory of Crops Physiology, Ecology and Genetic Breeding, Ministry of Education/College of Agronomy, Jiangxi Agricultural University, Nanchang 330045, China; (A.R.); (H.L.)
| | - Rafaqat Ali Gill
- Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China; (R.A.G.); (Q.U.Z.)
| | - Muhammad Umair Hassan
- Research Center on Ecological Sciences, Jiangxi Agricultural University, Nanchang 330045, China; (M.U.H.); (M.A.)
| | - Athar Mahmood
- Department of Agronomy, University of Agriculture, Faisalabad 38040, Pakistan;
| | - Sameer Qari
- Biology Department, (Genetics and Molecular Biology Central Laboratory), Aljumum University College, Umm Al-Qura University, Makkah 24382, Saudi Arabia;
| | - Qamar U. Zaman
- Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China; (R.A.G.); (Q.U.Z.)
| | - Muhammad Ilyas
- University College of Dera Murad Jamali, Nasirabad 80700, Balochistan, Pakistan;
| | - Muhammad Aamer
- Research Center on Ecological Sciences, Jiangxi Agricultural University, Nanchang 330045, China; (M.U.H.); (M.A.)
| | - Maria Batool
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China;
| | - Huijie Li
- Key Laboratory of Crops Physiology, Ecology and Genetic Breeding, Ministry of Education/College of Agronomy, Jiangxi Agricultural University, Nanchang 330045, China; (A.R.); (H.L.)
- College of Humanity and Public Administration, Jiangxi Agricultural University, Nanchang 330045, China
| | - Ziming Wu
- Key Laboratory of Crops Physiology, Ecology and Genetic Breeding, Ministry of Education/College of Agronomy, Jiangxi Agricultural University, Nanchang 330045, China; (A.R.); (H.L.)
- Correspondence:
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20
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Zheng S, Ye C, Lu J, Liufu J, Lin L, Dong Z, Li J, Zhuang C. Improving the Rice Photosynthetic Efficiency and Yield by Editing OsHXK1 via CRISPR/Cas9 System. Int J Mol Sci 2021; 22:ijms22179554. [PMID: 34502462 PMCID: PMC8430575 DOI: 10.3390/ijms22179554] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 08/29/2021] [Accepted: 08/30/2021] [Indexed: 01/19/2023] Open
Abstract
Rice (Oryza sativa L.) is an important food crop species in China. Cultivating high-yielding rice varieties that have a high photosynthetic efficiency is an important goal of rice breeding in China. In recent years, due to the continual innovation of molecular breeding methods, many excellent genes have been applied in rice breeding, which is highly important for increasing rice yields. In this paper, the hexokinase gene OsHXK1 was knocked out via the CRISPR/Cas9 gene-editing method in the indica rice varieties Huanghuazhan, Meixiangzhan, and Wushansimiao, and OsHXK1-CRISPR/Cas9 lines were obtained. According to the results of a phenotypic analysis and agronomic trait statistics, the OsHXK1-CRISPR/Cas9 plants presented increased light saturation points, stomatal conductance, light tolerance, photosynthetic products, and rice yields. Moreover, transcriptome analysis showed that the expression of photosynthesis-related genes significantly increased. Taken together, our results revealed that knocking out OsHXK1 via the CRISPR/Cas9 gene-editing method could effectively lead to the cultivation of high-photosynthetic efficiency and high-yielding rice varieties. They also revealed the important roles of OsHXK1 in the regulation of rice yield and photosynthesis.
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Affiliation(s)
- Shaoyan Zheng
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China; (S.Z.); (C.Y.); (J.L.); (J.L.); (L.L.); (Z.D.); (J.L.)
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou 510642, China
| | - Chanjuan Ye
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China; (S.Z.); (C.Y.); (J.L.); (J.L.); (L.L.); (Z.D.); (J.L.)
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou 510642, China
| | - Jingqin Lu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China; (S.Z.); (C.Y.); (J.L.); (J.L.); (L.L.); (Z.D.); (J.L.)
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou 510642, China
| | - Jiamin Liufu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China; (S.Z.); (C.Y.); (J.L.); (J.L.); (L.L.); (Z.D.); (J.L.)
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou 510642, China
| | - Lin Lin
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China; (S.Z.); (C.Y.); (J.L.); (J.L.); (L.L.); (Z.D.); (J.L.)
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou 510642, China
| | - Zequn Dong
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China; (S.Z.); (C.Y.); (J.L.); (J.L.); (L.L.); (Z.D.); (J.L.)
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou 510642, China
| | - Jing Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China; (S.Z.); (C.Y.); (J.L.); (J.L.); (L.L.); (Z.D.); (J.L.)
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou 510642, China
| | - Chuxiong Zhuang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China; (S.Z.); (C.Y.); (J.L.); (J.L.); (L.L.); (Z.D.); (J.L.)
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou 510642, China
- Correspondence:
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21
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Genome-Wide Analysis Identified a Set of Conserved lncRNAs Associated with Domestication-Related Traits in Rice. Int J Mol Sci 2021; 22:ijms22094742. [PMID: 33947059 PMCID: PMC8124408 DOI: 10.3390/ijms22094742] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Revised: 04/25/2021] [Accepted: 04/27/2021] [Indexed: 12/12/2022] Open
Abstract
Crop domestication, which gives rise to a number of desirable agronomic traits, represents a typical model system of plant evolution. Numerous genomic evidence has proven that noncoding RNAs such as microRNAs and phasiRNAs, as well as protein-coding genes, are selected during crop domestication. However, limited data shows plant long noncoding RNAs (lncRNAs) are also involved in this biological process. In this study, we performed strand-specific RNA sequencing of cultivated rice Oryza sativa ssp. japonica and O. sativa ssp. indica, and their wild progenitor O. rufipogon. We identified a total of 8528 lncRNAs, including 4072 lncRNAs in O. rufipogon, 2091 lncRNAs in japonica rice, and 2365 lncRNAs in indica rice. The lncRNAs expressed in wild rice were revealed to be shorter in length and had fewer exon numbers when compared with lncRNAs from cultivated rice. We also identified a number of conserved lncRNAs in the wild and cultivated rice. The functional study demonstrated that several of these conserved lncRNAs are associated with domestication-related traits in rice. Our findings revealed the feature and conservation of lncRNAs during rice domestication and will further promote functional studies of lncRNAs in rice.
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Usman B, Zhao N, Nawaz G, Qin B, Liu F, Liu Y, Li R. CRISPR/Cas9 Guided Mutagenesis of Grain Size 3 Confers Increased Rice ( Oryza sativa L.) Grain Length by Regulating Cysteine Proteinase Inhibitor and Ubiquitin-Related Proteins. Int J Mol Sci 2021; 22:ijms22063225. [PMID: 33810044 PMCID: PMC8004693 DOI: 10.3390/ijms22063225] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 03/19/2021] [Accepted: 03/20/2021] [Indexed: 12/21/2022] Open
Abstract
Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)/CRISPR-associated protein (Cas9)-mediated genome editing has become an important way for molecular breeding in crop plants. To promote rice breeding, we edited the Grain Size 3 (GS3) gene for obtaining valuable and stable long-grain rice mutants. Furthermore, isobaric tags for the relative and absolute quantitation (iTRAQ)-based proteomic method were applied to determine the proteome-wide changes in the GS3 mutants compared with wild type (WT). Two target sites were designed to construct the vector, and the Agrobacterium-mediated method was used for rice transformation. Specific mutations were successfully introduced, and the grain length (GL) and 1000-grain weight (GWT) of the mutants were increased by 31.39% and 27.15%, respectively, compared with WT. The iTRAQ-based proteomic analysis revealed that a total of 31 proteins were differentially expressed in the GS3 mutants, including 20 up-regulated and 11 down-regulated proteins. Results showed that differentially expressed proteins (DEPs) were mainly related to cysteine synthase, cysteine proteinase inhibitor, vacuolar protein sorting-associated, ubiquitin, and DNA ligase. Furthermore, functional analysis revealed that DEPs were mostly enriched in cellular process, metabolic process, binding, transmembrane, structural, and catalytic activities. Pathway enrichment analysis revealed that DEPs were mainly involved in lipid metabolism and oxylipin biosynthesis. The protein-to-protein interaction (PPI) network found that proteins related to DNA damage-binding, ubiquitin-40S ribosomal, and cysteine proteinase inhibitor showed a higher degree of interaction. The homozygous mutant lines featured by stable inheritance and long-grain phenotype were obtained using the CRISPR/Cas9 system. This study provides a convenient and effective way of improving grain yield, which could significantly accelerate the breeding process of long-grain japonica parents and promote the development of high-yielding rice.
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Affiliation(s)
- Babar Usman
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning 530004, China; (B.U.); (N.Z.); (G.N.); (B.Q.); (F.L.)
| | - Neng Zhao
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning 530004, China; (B.U.); (N.Z.); (G.N.); (B.Q.); (F.L.)
| | - Gul Nawaz
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning 530004, China; (B.U.); (N.Z.); (G.N.); (B.Q.); (F.L.)
| | - Baoxiang Qin
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning 530004, China; (B.U.); (N.Z.); (G.N.); (B.Q.); (F.L.)
| | - Fang Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning 530004, China; (B.U.); (N.Z.); (G.N.); (B.Q.); (F.L.)
| | - Yaoguang Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agricultural Bioresources, South China Agricultural University, Guangzhou 510642, China
- Correspondence: (Y.L.); (R.L.); Tel.: +86-20-8528-1908 (Y.L.); +86-136-0009-4135 (R.L.)
| | - Rongbai Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning 530004, China; (B.U.); (N.Z.); (G.N.); (B.Q.); (F.L.)
- Correspondence: (Y.L.); (R.L.); Tel.: +86-20-8528-1908 (Y.L.); +86-136-0009-4135 (R.L.)
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