1
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Bravo-Vázquez LA, Méndez-García A, Chamu-García V, Rodríguez AL, Bandyopadhyay A, Paul S. The applications of CRISPR/Cas-mediated microRNA and lncRNA editing in plant biology: shaping the future of plant non-coding RNA research. PLANTA 2023; 259:32. [PMID: 38153530 DOI: 10.1007/s00425-023-04303-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2023] [Accepted: 11/25/2023] [Indexed: 12/29/2023]
Abstract
MAIN CONCLUSION CRISPR/Cas technology has greatly facilitated plant non-coding RNA (ncRNA) biology research, establishing itself as a promising tool for ncRNA functional characterization and ncRNA-mediated plant improvement. Throughout the last decade, the promising genome editing tool clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated proteins (Cas; CRISPR/Cas) has allowed unprecedented advances in the field of plant functional genomics and crop improvement. Even though CRISPR/Cas-mediated genome editing system has been widely used to elucidate the biological significance of a number of plant protein-coding genes, this technology has been barely applied in the functional analysis of those non-coding RNAs (ncRNAs) that modulate gene expression, such as microRNAs (miRNAs) and long non-coding RNAs (lncRNAs). Nevertheless, compelling findings indicate that CRISPR/Cas-based ncRNA editing has remarkable potential for deciphering the biological roles of ncRNAs in plants, as well as for plant breeding. For instance, it has been demonstrated that CRISPR/Cas tool could overcome the challenges associated with other approaches employed in functional genomic studies (e.g., incomplete knockdown and off-target activity). Thus, in this review article, we discuss the current status and progress of CRISPR/Cas-mediated ncRNA editing in plant science in order to provide novel prospects for further assessment and validation of the biological activities of plant ncRNAs and to enhance the development of ncRNA-centered protocols for crop improvement.
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Affiliation(s)
- Luis Alberto Bravo-Vázquez
- Tecnologico de Monterrey, School of Engineering and Sciences, Campus Querétaro, Av. Epigmenio González, No. 500 Fracc. San Pablo, 76130, Querétaro, Mexico
| | - Andrea Méndez-García
- Tecnologico de Monterrey, School of Engineering and Sciences, Campus Querétaro, Av. Epigmenio González, No. 500 Fracc. San Pablo, 76130, Querétaro, Mexico
| | - Verenice Chamu-García
- Tecnologico de Monterrey, School of Engineering and Sciences, Campus Puebla, Atlixcáyotl 5718, Reserva Territorial Atlixcáyotl, 72453, Puebla, Mexico
| | - Alma L Rodríguez
- Tecnologico de Monterrey, School of Engineering and Sciences, Campus Querétaro, Av. Epigmenio González, No. 500 Fracc. San Pablo, 76130, Querétaro, Mexico
| | - Anindya Bandyopadhyay
- International Rice Research Institute, 4031, Manila, Philippines.
- Reliance Industries Ltd., Navi Mumbai, Maharashtra, 400701, India.
| | - Sujay Paul
- Tecnologico de Monterrey, School of Engineering and Sciences, Campus Querétaro, Av. Epigmenio González, No. 500 Fracc. San Pablo, 76130, Querétaro, Mexico.
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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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3
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Yadav B, Majhi A, Phagna K, Meena MK, Ram H. Negative regulators of grain yield and mineral contents in rice: potential targets for CRISPR-Cas9-mediated genome editing. Funct Integr Genomics 2023; 23:317. [PMID: 37837547 DOI: 10.1007/s10142-023-01244-4] [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: 07/31/2023] [Revised: 09/27/2023] [Accepted: 09/29/2023] [Indexed: 10/16/2023]
Abstract
Rice is a major global staple food crop, and improving its grain yield and nutritional quality has been a major thrust research area since last decades. Yield and nutritional quality are complex traits which are controlled by multiple signaling pathways. Sincere efforts during past decades of research have identified several key genetic and molecular regulators that governed these complex traits. The advent of clustered regularly interspaced short palindromic repeats (CRISPR)-CRISPR-associated protein 9 (Cas9)-mediated gene knockout approaches has accelerated the development of improved varieties; however, finding out target gene with negative regulatory function in particular trait without giving any pleiotropic effect remains a challenge. Here, we have reviewed past and recent literature and identified important negative regulators of grain yield and mineral contents which could be potential targets for CRISPR-Cas9-mediated gene knockout. Additionally, we have also compiled a list of microRNAs (miRNAs), which target positive regulators of grain yield, plant stress tolerance, and grain mineral contents. Knocking out these miRNAs could help to increase expression of such positive regulators and thus improve the plant trait. The knowledge presented in this review would help to further accelerate the CRISPR-Cas9-mediated trait improvement in rice.
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Affiliation(s)
- Banita Yadav
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Ashis Majhi
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Kanika Phagna
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Mukesh Kumar Meena
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India.
| | - Hasthi Ram
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India.
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4
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Li Z, Zhou T, Zhu K, Wang W, Zhang W, Zhang H, Liu L, Zhang Z, Wang Z, Wang B, Xu D, Gu J, Yang J. Effects of Salt Stress on Grain Yield and Quality Parameters in Rice Cultivars with Differing Salt Tolerance. PLANTS (BASEL, SWITZERLAND) 2023; 12:3243. [PMID: 37765407 PMCID: PMC10538069 DOI: 10.3390/plants12183243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 09/09/2023] [Accepted: 09/11/2023] [Indexed: 09/29/2023]
Abstract
Rice yield and grain quality are highly sensitive to salinity stress. Salt-tolerant/susceptible rice cultivars respond to salinity differently. To explore the variation in grain yield and quality to moderate/severe salinity stress, five rice cultivars differing in degrees of salt tolerance, including three salt-tolerant rice cultivars (Lianjian 5, Lianjian 6, and Lianjian 7) and two salt-susceptible rice cultivars (Wuyunjing 30 and Lianjing 7) were examined. Grain yield was significantly decreased under salinity stress, while the extent of yield loss was lesser in salt-tolerant rice cultivars due to the relatively higher grain filling ratio and grain weight. The milling quality continued to increase with increasing levels. There were genotypic differences in the responses of appearance quality to mild salinity. The appearance quality was first increased and then decreased with increasing levels of salinity stress in salt-tolerant rice but continued to decrease in salt-susceptible rice. Under severe salinity stress, the protein accumulation was increased and the starch content was decreased; the content of short branched-chain of amylopectin was decreased; the crystallinity and stability of the starch were increased, and the gelatinization temperature was increased. These changes resulted in the deterioration of cooking and eating quality of rice under severe salinity-stressed environments. However, salt-tolerant and salt-susceptible rice cultivars responded differently to moderate salinity stress in cooking and eating quality and in the physicochemical properties of the starch. For salt-tolerant rice cultivars, the chain length of amylopectin was decreased, the degrees of order of the starch structure were decreased, and pasting properties and thermal properties were increased significantly, whereas for salt-susceptible rice cultivars, cooking and eating quality was deteriorated under moderate salinity stress. In conclusion, the selection of salt-tolerant rice cultivars can effectively maintain the rice production at a relatively high level while simultaneously enhancing grain quality in moderate salinity-stressed environments. Our results demonstrate specific salinity responses among the rice genotypes and the planting of salt-tolerant rice under moderate soil salinity is a solution to ensure rice production in China.
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Affiliation(s)
- Zhikang Li
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Jiangsu Key Laboratory of Crop Cultivation and Physiology, Agricultural College, Yangzhou University, Yangzhou 225009, China (K.Z.); (W.W.); (W.Z.); (H.Z.); (L.L.); (Z.Z.)
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225009, China
| | - Tianyang Zhou
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Jiangsu Key Laboratory of Crop Cultivation and Physiology, Agricultural College, Yangzhou University, Yangzhou 225009, China (K.Z.); (W.W.); (W.Z.); (H.Z.); (L.L.); (Z.Z.)
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225009, China
| | - Kuanyu Zhu
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Jiangsu Key Laboratory of Crop Cultivation and Physiology, Agricultural College, Yangzhou University, Yangzhou 225009, China (K.Z.); (W.W.); (W.Z.); (H.Z.); (L.L.); (Z.Z.)
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225009, China
| | - Weilu Wang
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Jiangsu Key Laboratory of Crop Cultivation and Physiology, Agricultural College, Yangzhou University, Yangzhou 225009, China (K.Z.); (W.W.); (W.Z.); (H.Z.); (L.L.); (Z.Z.)
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225009, China
| | - Weiyang Zhang
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Jiangsu Key Laboratory of Crop Cultivation and Physiology, Agricultural College, Yangzhou University, Yangzhou 225009, China (K.Z.); (W.W.); (W.Z.); (H.Z.); (L.L.); (Z.Z.)
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225009, China
| | - Hao Zhang
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Jiangsu Key Laboratory of Crop Cultivation and Physiology, Agricultural College, Yangzhou University, Yangzhou 225009, China (K.Z.); (W.W.); (W.Z.); (H.Z.); (L.L.); (Z.Z.)
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225009, China
| | - Lijun Liu
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Jiangsu Key Laboratory of Crop Cultivation and Physiology, Agricultural College, Yangzhou University, Yangzhou 225009, China (K.Z.); (W.W.); (W.Z.); (H.Z.); (L.L.); (Z.Z.)
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225009, China
| | - Zujian Zhang
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Jiangsu Key Laboratory of Crop Cultivation and Physiology, Agricultural College, Yangzhou University, Yangzhou 225009, China (K.Z.); (W.W.); (W.Z.); (H.Z.); (L.L.); (Z.Z.)
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225009, China
| | - Zhiqin Wang
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Jiangsu Key Laboratory of Crop Cultivation and Physiology, Agricultural College, Yangzhou University, Yangzhou 225009, China (K.Z.); (W.W.); (W.Z.); (H.Z.); (L.L.); (Z.Z.)
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225009, China
| | - Baoxiang Wang
- Lianyungang Academy of Agricultural Science, Lianyungang 222000, China
| | - Dayong Xu
- Lianyungang Academy of Agricultural Science, Lianyungang 222000, China
| | - Junfei Gu
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Jiangsu Key Laboratory of Crop Cultivation and Physiology, Agricultural College, Yangzhou University, Yangzhou 225009, China (K.Z.); (W.W.); (W.Z.); (H.Z.); (L.L.); (Z.Z.)
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225009, China
| | - Jianchang Yang
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Jiangsu Key Laboratory of Crop Cultivation and Physiology, Agricultural College, Yangzhou University, Yangzhou 225009, China (K.Z.); (W.W.); (W.Z.); (H.Z.); (L.L.); (Z.Z.)
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225009, China
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Shaheen N, Ahmad S, Alghamdi SS, Rehman HM, Javed MA, Tabassum J, Shao G. CRISPR-Cas System, a Possible "Savior" of Rice Threatened by Climate Change: An Updated Review. RICE (NEW YORK, N.Y.) 2023; 16:39. [PMID: 37688677 PMCID: PMC10492775 DOI: 10.1186/s12284-023-00652-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Accepted: 08/04/2023] [Indexed: 09/11/2023]
Abstract
Climate change has significantly affected agriculture production, particularly the rice crop that is consumed by almost half of the world's population and contributes significantly to global food security. Rice is vulnerable to several abiotic and biotic stresses such as drought, heat, salinity, heavy metals, rice blast, and bacterial blight that cause huge yield losses in rice, thus threatening food security worldwide. In this regard, several plant breeding and biotechnological techniques have been used to raise such rice varieties that could tackle climate changes. Nowadays, gene editing (GE) technology has revolutionized crop improvement. Among GE technology, CRISPR/Cas (Clustered Regularly Interspaced Short Palindromic Repeats/CRISPR-associated protein) system has emerged as one of the most convenient, robust, cost-effective, and less labor-intensive system due to which it has got more popularity among plant researchers, especially rice breeders and geneticists. Since 2013 (the year of first application of CRISPR/Cas-based GE system in rice), several trait-specific climate-resilient rice lines have been developed using CRISPR/Cas-based GE tools. Earlier, several reports have been published confirming the successful application of GE tools for rice improvement. However, this review particularly aims to provide an updated and well-synthesized brief discussion based on the recent studies (from 2020 to present) on the applications of GE tools, particularly CRISPR-based systems for developing CRISPR rice to tackle the current alarming situation of climate change, worldwide. Moreover, potential limitations and technical bottlenecks in the development of CRISPR rice, and prospects are also discussed.
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Affiliation(s)
- Nabeel Shaheen
- Seed Center and Plant Genetic Resources Bank, Ministry of Environment, Water & Agriculture, Riyadh, 14712, Saudi Arabia
| | - Shakeel Ahmad
- Seed Center and Plant Genetic Resources Bank, Ministry of Environment, Water & Agriculture, Riyadh, 14712, Saudi Arabia.
| | - Salem S Alghamdi
- Plant Production Department, College of Food and Agriculture Sciences, King Saud University, Riyadh, Saudi Arabia
| | - Hafiz Mamoon Rehman
- Centre for Agricultural Biochemistry and Biotechnology (CABB), University of Agriculture Faisalabad, Faisalabad, 38000, Pakistan
| | - Muhammad Arshad Javed
- Department of Plant Breeding and Genetics, Faculty of Agricultural Sciences, University of the Punjab, Lahore, 54590, Pakistan
| | - Javaria Tabassum
- Department of Plant Breeding and Genetics, Faculty of Agricultural Sciences, University of the Punjab, Lahore, 54590, Pakistan
| | - Gaoneng Shao
- State Key Laboratory of Rice Biology and China National Center for Rice Improvement, National Rice Research Institute, 310006, Hangzhou, China.
- Zhejiang Lab, 310006, Hangzhou, China.
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6
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Kobayashi K, Wang X, Wang W. Genetically Modified Rice Is Associated with Hunger, Health, and Climate Resilience. Foods 2023; 12:2776. [PMID: 37509868 PMCID: PMC10379675 DOI: 10.3390/foods12142776] [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: 06/24/2023] [Revised: 07/14/2023] [Accepted: 07/19/2023] [Indexed: 07/30/2023] Open
Abstract
While nearly one in nine people in the world deals with hunger, one in eight has obesity, and all face the threat of climate change. The production of rice, an important cereal crop and staple food for most of the world's population, faces challenges due to climate change, the increasing global population, and the simultaneous prevalence of hunger and obesity worldwide. These issues could be addressed at least in part by genetically modified rice. Genetic engineering has greatly developed over the century. Genetically modified rice has been approved by the ISAAA's GM approval database as safe for human consumption. The aim behind the development of this rice is to improve the crop yield, nutritional value, and food safety of rice grains. This review article provides a summary of the research data on genetically modified rice and its potential role in improving the double burden of malnutrition, primarily through increasing nutritional quality as well as grain size and yield. It also reviews the potential health benefits of certain bioactive components generated in genetically modified rice. Furthermore, this article discusses potential solutions to these challenges, including the use of genetically modified crops and the identification of quantitative trait loci involved in grain weight and nutritional quality. Specifically, a quantitative trait locus called grain weight on chromosome 6 has been identified, which was amplified by the Kasa allele, resulting in a substantial increase in grain weight and brown grain. An overexpressing a specific gene in rice, Oryza sativa plasma membrane H+-ATPase1, was observed to improve the absorption and assimilation of ammonium in the roots, as well as enhance stomatal opening and photosynthesis rate in the leaves under light exposure. Cloning research has also enabled the identification of several underlying quantitative trait loci involved in grain weight and nutritional quality. Finally, this article discusses the increasing threats of climate change such as methane-nitrous oxide emissions and global warming, and how they may be significantly improved by genetically modified rice through modifying a water-management technique. Taken together, this comprehensive review will be of particular importance to the field of bioactive components of cereal grains and food industries trying to produce high-quality functional cereal foods through genetic engineering.
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Affiliation(s)
- Kaori Kobayashi
- Department of Food Nutrition Dietetics and Health, Kansas State University, Manhattan, KS 66506, USA
| | - Xiaohui Wang
- College of Agronomy, Sichuan Agricultural University, Chengdu 611130, China
| | - Weiqun Wang
- Department of Food Nutrition Dietetics and Health, Kansas State University, Manhattan, KS 66506, USA
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Han WK, Tang FX, Gao HL, Wang Y, Yu N, Jiang JJ, Liu ZW. Co-CRISPR: A valuable toolkit for mutation enrichment in the gene editing of Spodoptera frugiperda. INSECT SCIENCE 2023; 30:625-636. [PMID: 36169087 DOI: 10.1111/1744-7917.13122] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 08/28/2022] [Accepted: 09/05/2022] [Indexed: 06/15/2023]
Abstract
The CRISPR/Cas9 system has been successfully applied in dozens of diverse species; although the screening of successful CRISPR/Cas9 editing events remains particularly laborious, especially for those that occur at relatively low frequency. Recently, a co-CRISPR strategy was proved to enrich the desired CRISPR events. Here, the co-CRISPR strategy was developed in the Fall armyworm, Spodoptera frugiperda, with kynurenine 3-monooxygenase gene (kmo) as a marker. The kmo mosaics induced by single-guide RNAs (sgRNAs)/Cas9 displayed the darker green color phenotype in larvae, compared with wild type (brown), and mosaic-eye adults were significantly acquired from the mosaic larvae group. In the kmo knockout strain, no significant difference was observed in larval development and adult reproduction. Acetylcholinesterase 2 (ace2) and Wnt1 were selected as target genes to construct the co-CRISPR strategy using kmo marker. By co-injection of kmo and ace2 sgRNAs, the mutant efficiency of ace2 was significantly increased in the kmo mosaic (larvae or adults) groups. Similarly, more malformed pupae with Wnt1 mutations were observed in the darker green larvae group. Taken together, these results demonstrated that kmo was a suitable visible marker gene for the application and extension of co-CRISPR strategy in Fall armyworm. Using darker green color in larvae or mosaic-eye in adults from kmo knockout as a marker, the mutant efficiency of a target gene could be enriched in a Fall armyworm group consisting of marked individuals. The co-CRISPR strategy is helpful for gene function studies by the knockout technique with no or lethal phenotypes.
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Affiliation(s)
- Wei-Kang Han
- Key Laboratory of Integrated Management of Crop Diseases and Pests (Ministry of Education), College of Plant Protection, Nanjing Agricultural University, Nanjing, China
| | - Feng-Xian Tang
- Key Laboratory of Integrated Management of Crop Diseases and Pests (Ministry of Education), College of Plant Protection, Nanjing Agricultural University, Nanjing, China
| | - Hao-Li Gao
- Key Laboratory of Integrated Management of Crop Diseases and Pests (Ministry of Education), College of Plant Protection, Nanjing Agricultural University, Nanjing, China
| | - Yan Wang
- Key Laboratory of Integrated Management of Crop Diseases and Pests (Ministry of Education), College of Plant Protection, Nanjing Agricultural University, Nanjing, China
| | - Na Yu
- Key Laboratory of Integrated Management of Crop Diseases and Pests (Ministry of Education), College of Plant Protection, Nanjing Agricultural University, Nanjing, China
| | - Jian-Jun Jiang
- Plant Protection Research Institute, Guangxi Academy of Agricultural Science, Guangxi Key Laboratory of Biology for Crop Diseases and Insect Pests, Nanning, China
| | - Ze-Wen Liu
- Key Laboratory of Integrated Management of Crop Diseases and Pests (Ministry of Education), College of Plant Protection, Nanjing Agricultural University, Nanjing, China
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Mackon E, Mackon GCJDE, Guo Y, Ma Y, Yao Y, Liu P. Development and Application of CRISPR/Cas9 to Improve Anthocyanin Pigmentation in Plants: Opportunities and Perspectives. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2023:111746. [PMID: 37230190 DOI: 10.1016/j.plantsci.2023.111746] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 04/22/2023] [Accepted: 05/21/2023] [Indexed: 05/27/2023]
Abstract
Since its discovery in 2012, the novel technology of clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated protein 9 (Cas9) has greatly contributed to revolutionizing molecular biology. It has been demonstrated to be an effective approach for identifying gene function and improving some important traits. Anthocyanins are secondary metabolites responsible for a wide spectrum of aesthetic coloration in various plant organs and are beneficial for health. As such, increasing anthocyanin content in plants, especially the edible tissue and organs, is always a main goal for plant breeding. Recently, CRISPR/Cas9 technology has been highly desired to enhance the amount of anthocyanin in vegetables, fruits, cereals, and other attractive plants with more precision. Here we reviewed the recent knowledge concerning CRISPR/Cas9-mediated anthocyanin enhancement in plants. In addition, we addressed the future avenues of promising potential target genes that could be helpful for achieving the same goal using CRISPR/Cas9 in several plants. Thus, molecular biologists, genetic engineers, agricultural scientists, plant geneticists, and physiologists may benefit from CRISPR technology to boost the biosynthesis and accumulation of anthocyanins in fresh fruits, vegetables, grains, roots, and ornamental plants.
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Affiliation(s)
- Enerand Mackon
- State Key Laboratory of Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Science and Technology, Guangxi University.
| | | | - Yongqiang Guo
- State Key Laboratory of Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning 530005, P.R. China.
| | - Yafei Ma
- State Key Laboratory of Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning 530005, P.R. China.
| | - Yuhang Yao
- State Key Laboratory of Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning 530005, P.R. China.
| | - Piqing Liu
- State Key Laboratory of Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning 530005, P.R. China.
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9
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Wu H, He Q, Wang Q. Advances in Rice Seed Shattering. Int J Mol Sci 2023; 24:ijms24108889. [PMID: 37240235 DOI: 10.3390/ijms24108889] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2023] [Revised: 05/15/2023] [Accepted: 05/16/2023] [Indexed: 05/28/2023] Open
Abstract
Seed shattering is an important trait that wild rice uses to adapt to the natural environment and maintain population reproduction, and weedy rice also uses it to compete with the rice crop. The loss of shattering is a key event in rice domestication. The degree of shattering is not only one of the main reasons for rice yield reduction but also affects its adaptability to modern mechanical harvesting methods. Therefore, it is important to cultivate rice varieties with a moderate shattering degree. In this paper, the research progress on rice seed shattering in recent years is reviewed, including the physiological basis, morphological and anatomical characteristics of rice seed shattering, inheritance and QTL/gene mapping of rice seed shattering, the molecular mechanism regulating rice seed shattering, the application of seed-shattering genes, and the relationship between seed-shattering genes and domestication.
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Affiliation(s)
- Hao Wu
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Qi He
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Quan Wang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
- College of Agricultural Sciences, Nankai University, Tianjin 300071, China
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Shi T, Gao Y, Xu A, Wang R, Lyu M, Sun Y, Chen L, Liu Y, Luo R, Wang H, Liu J. A fast breeding strategy creates fragrance- and anthocyanin-enriched rice lines by marker-free gene-editing and hybridization. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2023; 43:23. [PMID: 37313528 PMCID: PMC10248702 DOI: 10.1007/s11032-023-01369-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Accepted: 03/06/2023] [Indexed: 06/15/2023]
Abstract
As rice is a staple food for nearly half of the world's population, rice varieties with excellent agronomic traits as well as high flavor and nutritional quality such as fragrant rice and purple rice are naturally favored by the market. In the current study, we adopt a fast breeding strategy to improve the aroma and anthocyanin content in the excellent rice inbred line, F25. The strategy skillfully used the advantages of obtaining editing pure lines in T0 generation of CRISPR/Cas9 editing system and easy observation of purple character and grain shape, integrated the subsequent screening of non-transgenic lines, and the elimination of undesirable edited variants from gene-editing and cross-breeding at the same time as the separation of the progeny from the purple cross, thus expediting the breeding process. Compared with conventional breeding strategies, this strategy saves about 6-8 generations and reduces breeding costs. Firstly, we edited the OsBADH2 gene associated with rice flavor using an Agrobacterium-mediated CRISPR/Cas9 system to improve the aroma of F25. In the T0 generation, a homozygous OsBADH2-edited F25 line (F25B) containing more of the scented substance 2-AP was obtained. Then, we crossed F25B (♀) with a purple rice inbred line, P351 (♂), with high anthocyanin enrichment to improve the anthocyanin content of F25. After nearly 2.5 years of screening and identification over five generations, the undesirable variation characteristics caused by gene-editing and hybridization and the transgenic components were screened out. Finally, the improved F25 line with highly stable aroma component, 2-AP, increased anthocyanin content and no exogenous transgenic components were obtained. This study not only provides high-quality aromatic anthocyanin rice lines that meet the market demand, but also offers a reference for the comprehensive use of CRISPR/Cas9 editing technology, hybridization, and marker-assisted selection to accelerate multi-trait improvement and breeding process. Supplementary Information The online version contains supplementary material available at 10.1007/s11032-023-01369-1.
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Affiliation(s)
- Tiantian Shi
- National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Institute of Crop Sciences, Chinese Academy of Agriculture Sciences (CAAS), Beijing, 100081 China
| | - Ying Gao
- National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Institute of Crop Sciences, Chinese Academy of Agriculture Sciences (CAAS), Beijing, 100081 China
| | - Andi Xu
- National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Institute of Crop Sciences, Chinese Academy of Agriculture Sciences (CAAS), Beijing, 100081 China
| | - Rui Wang
- National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Institute of Crop Sciences, Chinese Academy of Agriculture Sciences (CAAS), Beijing, 100081 China
| | - Mingjie Lyu
- Institute of Germplasm Resources and Biotechnology, Tianjin Academy of Agricultural Sciences, Tianjin, 300112 China
| | - Yinglu Sun
- National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Institute of Crop Sciences, Chinese Academy of Agriculture Sciences (CAAS), Beijing, 100081 China
| | - Luoying Chen
- National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Institute of Crop Sciences, Chinese Academy of Agriculture Sciences (CAAS), Beijing, 100081 China
- Tianjin Agricultural University, Tianjin, 300392 China
| | - Yuanhang Liu
- National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Institute of Crop Sciences, Chinese Academy of Agriculture Sciences (CAAS), Beijing, 100081 China
| | - Rong Luo
- National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Institute of Crop Sciences, Chinese Academy of Agriculture Sciences (CAAS), Beijing, 100081 China
| | - Huan Wang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081 China
- Chengdu National Agricultural Science and Technology Center, Chengdu, 610213 Sichuan China
| | - Jun Liu
- National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Institute of Crop Sciences, Chinese Academy of Agriculture Sciences (CAAS), Beijing, 100081 China
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Krishna TPA, Maharajan T, Ceasar SA. The Role of Membrane Transporters in the Biofortification of Zinc and Iron in Plants. Biol Trace Elem Res 2023; 201:464-478. [PMID: 35182385 DOI: 10.1007/s12011-022-03159-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Accepted: 02/11/2022] [Indexed: 01/11/2023]
Abstract
Over three billion people suffer from various health issues due to the low supply of zinc (Zn) and iron (Fe) in their food. Low supply of micronutrients is the main cause of malnutrition and biofortification could help to solve this issue. Understanding the molecular mechanisms of biofortification is challenging. The membrane transporters are involved in the uptake, transport, storage, and redistribution of Zn and Fe in plants. These transporters are also involved in biofortification and help to load the Zn and Fe into the endosperm of the seeds. Very little knowledge is available on the role and functions of membrane transporters involved in seed biofortification. Understanding the mechanism and role of membrane transporters could be helpful to improve biofortification. In this review, we provide the details on membrane transporters involved in the uptake, transport, storage, and redistribution of Zn and Fe. We also discuss available information on transporters involved in seed biofortification. This review will help plant breeders and molecular biologists understand the importance and implications of membrane transporters for seed biofortification.
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Affiliation(s)
- T P Ajeesh Krishna
- Department of Biosciences, Rajagiri College of Social Sciences, Kochi, 683104, Kerala, India
| | - T Maharajan
- Department of Biosciences, Rajagiri College of Social Sciences, Kochi, 683104, Kerala, India
| | - S Antony Ceasar
- Department of Biosciences, Rajagiri College of Social Sciences, Kochi, 683104, Kerala, India.
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Imran M, Shafiq S, Tang X. CRISPR-Cas9-mediated editing of BADH2 gene triggered fragrance revolution in rice. PHYSIOLOGIA PLANTARUM 2023; 175:e13871. [PMID: 36748269 DOI: 10.1111/ppl.13871] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2022] [Revised: 12/26/2022] [Accepted: 02/01/2023] [Indexed: 06/18/2023]
Abstract
Fragrance is one of the most important quality traits for breeding in rice. The natural aroma substance 2-acetyl-1-pyrroline (2-AP) is a key fragrance compound among over 200 volatiles identified in fragrant rice. In addition to rice, there are other plant species that contain a germplasm that naturally produces a fragrant aroma. These other plant species all have lower activity levels of the enzyme BETAINE ALDEHYDE DEHYDROGENASE 2 (BADH2). Therefore, improving fragrance efficiency has been a focus of intensive research. Recent studies have engineered BADH2 gene, which is responsible for fragrance trait in non-fragrant cultivars of rice, using CRISPR-Cas9. Although engineering rice BADH2 can be useful for upregulating 2-AP, there are still a lot of restrictions on how it can be applied in practice. In this review article, we discuss the recent developments in BADH2 editing and propose potential future strategies to effectively target BADH2 for transcriptional regulation, with the goal of producing a better fragrance.
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Affiliation(s)
- Muhammad Imran
- Department of Crop Science and Technology, College of Agriculture, South China Agricultural University, Guangzhou, China
- Scientific Observing and Experimental Station of Crop Cultivation in South China, Ministry of Agriculture, Guangzhou, China
- Yingdong College of Biology and Agriculture, Shaoguan University, Shaoguan, China
| | - Sarfraz Shafiq
- Department of Anatomy and Cell Biology, University of Western Ontario, London, Ontario, Canada
| | - Xiangru Tang
- Department of Crop Science and Technology, College of Agriculture, South China Agricultural University, Guangzhou, China
- Scientific Observing and Experimental Station of Crop Cultivation in South China, Ministry of Agriculture, Guangzhou, China
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Cheng C, Kan J, Li S, Jiang C, He X, Shen H, Xu R, Li B, Feng Z, Yang P. Mutation of barley HvPDIL5-1 improves resistance to yellow mosaic virus disease without growth or yield penalties. FRONTIERS IN PLANT SCIENCE 2022; 13:1018379. [PMID: 36275526 PMCID: PMC9583009 DOI: 10.3389/fpls.2022.1018379] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2022] [Accepted: 09/20/2022] [Indexed: 06/15/2023]
Abstract
The soil-borne yellow mosaic virus disease, which is caused by the bymoviruses barley yellow mosaic virus (BaYMV) and/or barley mild mosaic virus (BaMMV), seriously threatens winter barley production in Europe and East Asia. Both viruses are transmitted by the soil-borne plasmodiophorid Polymyxa graminis and are difficult to eliminate through chemical or physical measures in the field, making breeding for resistant cultivars the optimal strategy for disease control. The resistance locus rym1/11 was cloned encoding the host factor gene Protein Disulfide Isomerase Like 5-1 (PDIL5-1), whose loss-of-function variants confer broad-spectrum resistance to multiple strains of BaMMV/BaYMV. Most resistance-conferring variants have been identified in six-rowed barley landraces/historic cultivars, and their introgression into modern two-rowed malting cultivars is difficult because PDIL5-1 is located in a peri-centromeric region with suppressed recombination. In this study, we used CRISPR/Cas9 genome editing to modify PDIL5-1 in the BaYMV/BaMMV-susceptible elite malting barley cv. 'Golden Promise' and obtained the mutants pdil5-1-a and pdil5-1-b. PDIL5-1 in the pdil5-1-a mutant encodes a protein lacking a cysteine residue, and pdil5-1-b contains a protein-coding frameshift. Both mutants were completely resistant to BaYMV. The knockout mutant pdil5-1-b showed complete BaMMV resistance, while pdil5-1-a showed decreased viral accumulation but no disease symptoms if compared to 'Golden Promise'. Both PDIL5-1 edited lines, as well as the previously produced EMS-induced pdil5-1 mutant '10253-1-5' in the elite malting barley cv. 'Barke' background, displayed no growth or yield penalties in garden experiments or bymovirus-free field trials. Line '10253-1-5' showed improved resistance and yield performance compared to the wild-type and its sibling line when grown in infectious fields. Therefore, genome editing of the host factor gene PDIL5-1 could facilitate the breeding of barley varieties with resistance to bymoviruses.
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Affiliation(s)
- Chunyuan Cheng
- College of Agronomy, Qingdao Agricultural University, Qingdao, China
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jinhong Kan
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Shanshan Li
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
- College of Agronomy, Sichuan Agricultural University, Chengdu, China
| | - Congcong Jiang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xiaoyan He
- College of Agronomy, Qingdao Agricultural University, Qingdao, China
| | - Huiquan Shen
- Institute of Agricultural Science in Jiangsu Coastal Areas, Yancheng, China
| | - Rugen Xu
- College of Agronomy, Yangzhou University, Yangzhou, China
| | - Boqun Li
- Special Crops Institute, Chongqing Academy of Agricultural Sciences, Chongqing, China
| | - Zongyun Feng
- College of Agronomy, Sichuan Agricultural University, Chengdu, China
| | - Ping Yang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
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Sultana S, Faruque M, Islam MR. Rice grain quality parameters and determination tools: a review on the current developments and future prospects. INTERNATIONAL JOURNAL OF FOOD PROPERTIES 2022. [DOI: 10.1080/10942912.2022.2071295] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Sharmin Sultana
- IRRI-PPP Grain Quality Testing Laboratory, International Rice Research Institute, Los Baños, Bangladesh
| | - Muhiuddin Faruque
- IRRI-PPP Grain Quality Testing Laboratory, International Rice Research Institute, Los Baños, Bangladesh
| | - Md Rafiqul Islam
- IRRI-PPP Grain Quality Testing Laboratory, International Rice Research Institute, Los Baños, Bangladesh
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Zang Y, Gong Q, Xu Y, Liu H, Bai H, Li N, Du L, Ye X, Lan C, Wang K. Production of Conjoined Transgenic and Edited Barley and Wheat Plants for Nud Genes Using the CRISPR/SpCas9 System. Front Genet 2022; 13:873850. [PMID: 35601488 PMCID: PMC9117629 DOI: 10.3389/fgene.2022.873850] [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: 02/11/2022] [Accepted: 03/29/2022] [Indexed: 11/13/2022] Open
Abstract
The Nudum (Nud) gene controls the caryopsis type of cereal crops by regulating lipid biosynthetic pathways. Based on the HvNud sequence and its homologous gene sequences in wheat, a conserved sgRNA was designed to obtain the mutants from the barley variety “Vlamingh” and the wheat variety “Fielder” via Agrobacterium-mediated transformation. A total of 19 and 118 transgenic plants were obtained, and 11 and 61 mutant plants were identified in T0 transgenic plants in barley and wheat after PCR-RE detection, and the editing efficiencies of the targeted gene were 57.9 and 51.7% in barley and wheat, respectively. The grain shape of the barley mutants was naked. Five different combinations of mutations for wheat TaNud genes were identified in the T0 generation, and their homozygous-edited plants were obtained in the T1 generation. Interestingly, the conjoined plants in which one plant has different genotypes were first identified. The different tillers in an individual T0 plant showed independent transgenic or mutant events in both barley and wheat, and the different genotypes can stably inherit into T1 generation, indicating that the T0 transgenic plants were the conjoined type. In addition, we did not find any off-target mutations in both barley and wheat. A candidate method for detecting putative-edited wheat plants was suggested to avoid losing mutations in this investigation. This study provides not only materials for studying the function of the Nud gene in barley and wheat but also a system for detecting the mutants in wheat.
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Affiliation(s)
- Yiming Zang
- College of Plant Science & Technology, Huazhong Agricultural University, Wuhan, China
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Qiang Gong
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yanhao Xu
- Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement, Food Crops Institute, Hubei Academy of Agricultural Sciences, Wuhan, China
| | - Huiyun Liu
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Hao Bai
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Na Li
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Lipu Du
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xingguo Ye
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Caixia Lan
- College of Plant Science & Technology, Huazhong Agricultural University, Wuhan, China
- *Correspondence: Caixia Lan, ; Ke Wang,
| | - Ke Wang
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
- *Correspondence: Caixia Lan, ; Ke Wang,
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Mir TUG, Wani AK, Akhtar N, Shukla S. CRISPR/Cas9: Regulations and challenges for law enforcement to combat its dual-use. Forensic Sci Int 2022; 334:111274. [DOI: 10.1016/j.forsciint.2022.111274] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 02/19/2022] [Accepted: 03/13/2022] [Indexed: 12/15/2022]
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17
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Saeed F, Chaudhry UK, Bakhsh A, Raza A, Saeed Y, Bohra A, Varshney RK. Moving Beyond DNA Sequence to Improve Plant Stress Responses. Front Genet 2022; 13:874648. [PMID: 35518351 PMCID: PMC9061961 DOI: 10.3389/fgene.2022.874648] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2022] [Accepted: 03/31/2022] [Indexed: 01/25/2023] Open
Abstract
Plants offer a habitat for a range of interactions to occur among different stress factors. Epigenetics has become the most promising functional genomics tool, with huge potential for improving plant adaptation to biotic and abiotic stresses. Advances in plant molecular biology have dramatically changed our understanding of the molecular mechanisms that control these interactions, and plant epigenetics has attracted great interest in this context. Accumulating literature substantiates the crucial role of epigenetics in the diversity of plant responses that can be harnessed to accelerate the progress of crop improvement. However, harnessing epigenetics to its full potential will require a thorough understanding of the epigenetic modifications and assessing the functional relevance of these variants. The modern technologies of profiling and engineering plants at genome-wide scale provide new horizons to elucidate how epigenetic modifications occur in plants in response to stress conditions. This review summarizes recent progress on understanding the epigenetic regulation of plant stress responses, methods to detect genome-wide epigenetic modifications, and disentangling their contributions to plant phenotypes from other sources of variations. Key epigenetic mechanisms underlying stress memory are highlighted. Linking plant response with the patterns of epigenetic variations would help devise breeding strategies for improving crop performance under stressed scenarios.
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Affiliation(s)
- Faisal Saeed
- Department of Agricultural Genetic Engineering, Faculty of Agricultural Sciences and Technologies, Nigde Omer Halisdemir University, Nigde, Turkey
| | - Usman Khalid Chaudhry
- Department of Agricultural Genetic Engineering, Faculty of Agricultural Sciences and Technologies, Nigde Omer Halisdemir University, Nigde, Turkey
| | - Allah Bakhsh
- Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Ali Raza
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Oil Crops Research Institute, Center of Legume Crop Genetics and Systems Biology/College of Agriculture, Fujian Agriculture and Forestry University (FAFU), Fuzhou, China
| | - Yasir Saeed
- Department of Plant Pathology, Faculty of Agriculture, University of Agriculture, Faisalabad, Pakistan
| | - Abhishek Bohra
- State Agricultural Biotechnology Centre, Centre for Crop and Food Innovation, Murdoch University, Murdoch, WA, Australia
| | - Rajeev K. Varshney
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Oil Crops Research Institute, Center of Legume Crop Genetics and Systems Biology/College of Agriculture, Fujian Agriculture and Forestry University (FAFU), Fuzhou, China
- State Agricultural Biotechnology Centre, Centre for Crop and Food Innovation, Murdoch University, Murdoch, WA, Australia
- Center of Excellence in Genomics & Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
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18
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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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Hori K, Okunishi T, Nakamura K, Iijima K, Hagimoto M, Hayakawa K, Shu K, Ikka T, Yamashita H, Yamasaki M, Takeuchi Y, Koyama S, Tsujii Y, Kayano T, Ishii T, Kumamaru T, Kawagoe Y, Yamamoto T. Genetic Background Negates Improvements in Rice Flour Characteristics and Food Processing Properties Caused by a Mutant Allele of the PDIL1-1 Seed Storage Protein Gene. RICE (NEW YORK, N.Y.) 2022; 15:13. [PMID: 35247122 PMCID: PMC8898210 DOI: 10.1186/s12284-022-00560-w] [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: 12/14/2021] [Accepted: 02/08/2022] [Indexed: 05/18/2023]
Abstract
Phenotypic differences among breeding lines that introduce the same superior gene allele can be a barrier to effective development of cultivars with desirable traits in some crop species. For example, a deficient mutation of the Protein Disulfide Isomerase Like 1-1 (PDIL1-1) gene can cause accumulation of glutelin seed storage protein precursors in rice endosperm, and improves rice flour characteristics and food processing properties. However, the gene must be expressed to be useful. A deficient mutant allele of PDIL1-1 was introduced into two rice cultivars with different genetic backgrounds (Koshihikari and Oonari). The grain components, agronomic traits, and rice flour and food processing properties of the resulting lines were evaluated. The two breeding lines had similar seed storage protein accumulation, amylose content, and low-molecular-weight metabolites. However, only the Koshihikari breeding line had high flour quality and was highly suitable for rice bread, noodles, and sponge cake, evidence of the formation of high-molecular-weight protein complexes in the endosperm. Transcriptome analysis revealed that mRNA levels of fourteen PDI, Ero1, and BiP genes were increased in the Koshihikari breeding line, whereas this change was not observed in the Oonari breeding line. We elucidated part of the molecular basis of the phenotypic differences between two breeding lines possessing the same mutant allele in different genetic backgrounds. The results suggest that certain genetic backgrounds can negate the beneficial effect of the PDIL1-1 mutant allele. Better understanding of the molecular basis for such interactions may accelerate future breeding of novel rice cultivars to meet the strong demand for gluten-free foods.
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Affiliation(s)
- Kiyosumi Hori
- National Agricultural and Food Research Organization (NARO), Tsukuba, 305-8518, Japan.
- National Institute of Agrobiological Sciences, Tsukuba, 305-8602, Japan.
| | - Tomoya Okunishi
- National Agricultural and Food Research Organization (NARO), Tsukuba, 305-8518, Japan
| | - Kenji Nakamura
- Cereal Science Research Center of Tsukuba, Nisshin Flour Milling Inc, Tsukuba, 300-2611, Japan
| | - Ken Iijima
- National Agricultural and Food Research Organization (NARO), Tsukuba, 305-8518, Japan
- National Institute of Agrobiological Sciences, Tsukuba, 305-8602, Japan
| | - Masahiro Hagimoto
- Cereal Science Research Center of Tsukuba, Nisshin Flour Milling Inc, Tsukuba, 300-2611, Japan
| | - Katsuyuki Hayakawa
- Cereal Science Research Center of Tsukuba, Nisshin Flour Milling Inc, Tsukuba, 300-2611, Japan
| | - Koka Shu
- National Agricultural and Food Research Organization (NARO), Tsukuba, 305-8518, Japan
- National Institute of Agrobiological Sciences, Tsukuba, 305-8602, Japan
| | - Takashi Ikka
- National Institute of Agrobiological Sciences, Tsukuba, 305-8602, Japan
- Faculty of Agriculture, Shizuoka University, Shizuoka, 422-8529, Japan
| | - Hiroto Yamashita
- National Agricultural and Food Research Organization (NARO), Tsukuba, 305-8518, Japan
- Faculty of Agriculture, Shizuoka University, Shizuoka, 422-8529, Japan
| | - Masanori Yamasaki
- Food Resources Education and Research Center, Kobe University, Kasai, 675-2103, Japan
| | - Yoshinobu Takeuchi
- National Agricultural and Food Research Organization (NARO), Tsukuba, 305-8518, Japan
| | - Shota Koyama
- Department of Agricultural Chemistry, Tokyo University of Agriculture, Tokyo, 156-8502, Japan
| | - Yoshimasa Tsujii
- Department of Agricultural Chemistry, Tokyo University of Agriculture, Tokyo, 156-8502, Japan
| | - Toshiaki Kayano
- National Institute of Agrobiological Sciences, Tsukuba, 305-8602, Japan
| | - Takuro Ishii
- National Agricultural and Food Research Organization (NARO), Tsukuba, 305-8518, Japan
| | | | - Yasushi Kawagoe
- National Institute of Agrobiological Sciences, Tsukuba, 305-8602, Japan
| | - Toshio Yamamoto
- National Agricultural and Food Research Organization (NARO), Tsukuba, 305-8518, Japan
- National Institute of Agrobiological Sciences, Tsukuba, 305-8602, Japan
- Institute of Plant Science and Resources, Okayama University, Kurashiki, 710-0046, Japan
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20
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Park JR, Kim EG, Jang YH, Jan R, Farooq M, Ubaidillah M, Kim KM. Applications of CRISPR/Cas9 as New Strategies for Short Breeding to Drought Gene in Rice. FRONTIERS IN PLANT SCIENCE 2022; 13:850441. [PMID: 35283882 PMCID: PMC8908215 DOI: 10.3389/fpls.2022.850441] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Accepted: 02/02/2022] [Indexed: 05/25/2023]
Abstract
Recent unpredictable climate change is the main reason for the decline in rice yield. In particular, drought stress is a major constraint in reducing yield and quality for rice at rainfed agriculture areas, such as Asia and South America. CRISPR/Cas9 provides an effective solution for gene function study and molecular breeding due to specific editing of targeted genome sequences. In addition, CRISPR/Cas9 application can significantly reduce the time required to develop new cultivars with improved traits compared to conventional complex and time-consuming breeding. Here, drought-induced gene Oryza sativa Senescence-associated protein (OsSAP) was edited by CRISPR/Cas9. To investigate the possible role of OsSAP in drought stress, genome-editing plants were subjected to drought stress until the soil moisture content reached 20%, and the reactive oxygen species (ROS) scavenging efficiency of genome-editing plants were decreased. When the genome-editing plants were subjected to drought stress, survival rate, shoot length, root length, content of chlorophyll number of tiller, and 1,000-grain weight decreased, and more H2O2 and O2 - were detected in leaves. In addition, expression levels of several critical stress-related transcription factors were decreased in the OsSAP genome-editing plant. These results suggest that OsSAP function as a positive regulator during drought stress response in rice. We analyzed the expression of OsSAP and Cas9 in T0 and T1 plants as well as T2 seeds. As the course of generation advancement progressed, Cas9 expression remained stable or weakened but the OsSAP expression was continuously removed from the T0 plant. The coefficient of variation (CV) in both T1 plants and T2 seeds was lower than 5%. Overall, our results suggest that CRISPR/Cas9 could be a novel and important tool for efficiently generating specific and inheritable targeted genome editing in rice, with short breeding cycles.
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Affiliation(s)
- Jae-Ryoung Park
- Division of Plant Biosciences, School of Applied Biosciences, College of Agriculture and Life Science, Kyungpook National University, Daegu, South Korea
- Crop Breeding Division, National Institute of Crop Science, Rural Development Administration, Wanju, South Korea
| | - Eun-Gyeong Kim
- Division of Plant Biosciences, School of Applied Biosciences, College of Agriculture and Life Science, Kyungpook National University, Daegu, South Korea
| | - Yoon-Hee Jang
- Division of Plant Biosciences, School of Applied Biosciences, College of Agriculture and Life Science, Kyungpook National University, Daegu, South Korea
| | - Rahmatullah Jan
- Division of Plant Biosciences, School of Applied Biosciences, College of Agriculture and Life Science, Kyungpook National University, Daegu, South Korea
| | - Muhammad Farooq
- Division of Plant Biosciences, School of Applied Biosciences, College of Agriculture and Life Science, Kyungpook National University, Daegu, South Korea
| | - Mohammad Ubaidillah
- Department of Agronomy, Faculty of Agriculture, Jember University, Jember, Indonesia
| | - Kyung-Min Kim
- Division of Plant Biosciences, School of Applied Biosciences, College of Agriculture and Life Science, Kyungpook National University, Daegu, South Korea
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Sharma SK, Gupta OP, Pathaw N, Sharma D, Maibam A, Sharma P, Sanasam J, Karkute SG, Kumar S, Bhattacharjee B. CRISPR-Cas-Led Revolution in Diagnosis and Management of Emerging Plant Viruses: New Avenues Toward Food and Nutritional Security. Front Nutr 2022; 8:751512. [PMID: 34977113 PMCID: PMC8716883 DOI: 10.3389/fnut.2021.751512] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2021] [Accepted: 10/31/2021] [Indexed: 12/14/2022] Open
Abstract
Plant viruses pose a serious threat to agricultural production systems worldwide. The world's population is expected to reach the 10-billion mark by 2057. Under the scenario of declining cultivable land and challenges posed by rapidly emerging and re-emerging plant pathogens, conventional strategies could not accomplish the target of keeping pace with increasing global food demand. Gene-editing techniques have recently come up as promising options to enable precise changes in genomes with greater efficiency to achieve the target of higher crop productivity. Of genome engineering tools, clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated (Cas) proteins have gained much popularity, owing to their simplicity, reproducibility, and applicability in a wide range of species. Also, the application of different Cas proteins, such as Cas12a, Cas13a, and Cas9 nucleases, has enabled the development of more robust strategies for the engineering of antiviral mechanisms in many plant species. Recent studies have revealed the use of various CRISPR-Cas systems to either directly target a viral gene or modify a host genome to develop viral resistance in plants. This review provides a comprehensive record of the use of the CRISPR-Cas system in the development of antiviral resistance in plants and discusses its applications in the overall enhancement of productivity and nutritional landscape of cultivated plant species. Furthermore, the utility of this technique for the detection of various plant viruses could enable affordable and precise in-field or on-site detection. The futuristic potential of CRISPR-Cas technologies and possible challenges with their use and application are highlighted. Finally, the future of CRISPR-Cas in sustainable management of viral diseases, and its practical utility and regulatory guidelines in different parts of the globe are discussed systematically.
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Affiliation(s)
| | - Om Prakash Gupta
- Division of Quality & Basic Science, ICAR-Indian Institute of Wheat and Barley Research, Karnal, India
| | - Neeta Pathaw
- ICAR Research Complex for NEH Region, Manipur Centre, Imphal, India
| | - Devender Sharma
- Crop Improvement Division, ICAR-Vivekananda Parvatiya Krishi Anusandhan Sansthan, Almora, India
| | - Albert Maibam
- ICAR Research Complex for NEH Region, Manipur Centre, Imphal, India
| | - Parul Sharma
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, India
| | - Jyotsana Sanasam
- ICAR Research Complex for NEH Region, Manipur Centre, Imphal, India
| | - Suhas Gorakh Karkute
- Division of Crop Improvement, ICAR-Indian Institute of Vegetable Research, Varanasi, India
| | - Sandeep Kumar
- Department of Plant Pathology, Odisha University of Agriculture & Technology, Bhubaneswar, India
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Liu X, Ding Q, Wang W, Pan Y, Tan C, Qiu Y, Chen Y, Li H, Li Y, Ye N, Xu N, Wu X, Ye R, Liu J, Ma C. Targeted Deletion of the First Intron of the Wx b Allele via CRISPR/Cas9 Significantly Increases Grain Amylose Content in Rice. RICE (NEW YORK, N.Y.) 2022; 15:1. [PMID: 34982277 PMCID: PMC8727654 DOI: 10.1186/s12284-021-00548-y] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2021] [Accepted: 12/28/2021] [Indexed: 05/29/2023]
Abstract
BACKGROUND The rice Waxy (Wx) gene plays a major role in seed amylose synthesis and consequently controls grain amylose content. Wx gene expression is highly regulated at the post-transcriptional level. In particular, the GT/TT polymorphism at the 5'splicing site of its 1st intron greatly affects this intron's splicing efficiency and defines two predominant Wx alleles, Wxa and Wxb. Wxa rice often harbours intermediate to high amylose contents, whereas Wxb rice exhibits low to intermediate amylose contents. By deleting the Wx 1st intron using CRISPR/Cas9 technology, we generate a completely novel Wx allele and further investigate how intron removal affects Wx gene expression and rice grain amylose content. RESULTS CRISPR/Cas9-mediated targeted deletion of the Wx 1st intron was performed on 4 rice inbred lines: KY131 (Wxb), X32 (Wxb), X35 (Wxa) and X55 (Wxlv). Deletion of the 1st intron occurred in 8.6-11.8% of the primary transformants of these 4 inbred lines. Compared to wild-type plants, amylose content was significantly increased from 13.0% to approximately 24.0% in KY131 and X32 mutant lines, which both carried the Wxb allele. However, no significant difference in amylose content was observed between wild-type plants and X35 and X55 mutant lines, which carried the Wxa and Wxlv alleles, respectively. Wx gene expression analysis of wild-type plants and mutants yielded results that were highly consistent with amylose content results. KY131 and X32 mutants accumulated increased levels of steady mRNA transcripts compared with wild-type plants, whereas steady mRNA levels were not altered in X35 and X55 mutants compared with wild-type plants. Grain quality, including appearance quality and eating and cooking quality, which are tightly associated with amylose content, was also assessed in wild-type and mutant plants, and data were presented and analysed. CONCLUSIONS This study presents a novel and rapid strategy to increase amylose content in inbred rice carrying a Wxb allele. Our data strongly suggest that the 1st intron of the Wx gene regulates Wx gene expression mainly at the post-transcriptional level in rice. This finding is in contrast to a previous hypothesis suggesting that it influences Wx gene transcription. In addition, removal of the first intron generates a completely novel Wx allele. Further studies on this new Wx allele will provide invaluable insights into the regulation of Wx gene expression, which will help researchers engineer new Wx alleles to facilitate the breeding of rice cultivars with better eating and cooking quality.
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Affiliation(s)
- Xingdan Liu
- College of Agronomy, Hunan Agricultural University, Changsha, 410128, China
| | - Qi Ding
- Life Science and Technology Center, China National Seed Group Co., LTD, Wuhan, 430206, Hubei, China
- State Key Laboratory of Crop Breeding Technology Innovation and Integration, China National Seed Group Co., LTD, Wuhan, 430206, Hubei, China
| | - Wenshu Wang
- Life Science and Technology Center, China National Seed Group Co., LTD, Wuhan, 430206, Hubei, China
| | - Yanling Pan
- Life Science and Technology Center, China National Seed Group Co., LTD, Wuhan, 430206, Hubei, China
| | - Chao Tan
- Life Science and Technology Center, China National Seed Group Co., LTD, Wuhan, 430206, Hubei, China
| | - Yingbo Qiu
- Life Science and Technology Center, China National Seed Group Co., LTD, Wuhan, 430206, Hubei, China
| | - Ya Chen
- Life Science and Technology Center, China National Seed Group Co., LTD, Wuhan, 430206, Hubei, China
| | - Hongjing Li
- Life Science and Technology Center, China National Seed Group Co., LTD, Wuhan, 430206, Hubei, China
| | - Yinlong Li
- Life Science and Technology Center, China National Seed Group Co., LTD, Wuhan, 430206, Hubei, China
| | - Naizhong Ye
- Life Science and Technology Center, China National Seed Group Co., LTD, Wuhan, 430206, Hubei, China
| | - Nian Xu
- Life Science and Technology Center, China National Seed Group Co., LTD, Wuhan, 430206, Hubei, China
| | - Xiao Wu
- Life Science and Technology Center, China National Seed Group Co., LTD, Wuhan, 430206, Hubei, China
- State Key Laboratory of Crop Breeding Technology Innovation and Integration, China National Seed Group Co., LTD, Wuhan, 430206, Hubei, China
| | - Rongjian Ye
- Life Science and Technology Center, China National Seed Group Co., LTD, Wuhan, 430206, Hubei, China
- State Key Laboratory of Crop Breeding Technology Innovation and Integration, China National Seed Group Co., LTD, Wuhan, 430206, Hubei, China
| | - Jianfeng Liu
- College of Agronomy, Hunan Agricultural University, Changsha, 410128, China.
- Life Science and Technology Center, China National Seed Group Co., LTD, Wuhan, 430206, Hubei, China.
- State Key Laboratory of Crop Breeding Technology Innovation and Integration, China National Seed Group Co., LTD, Wuhan, 430206, Hubei, China.
| | - Chonglie Ma
- Life Science and Technology Center, China National Seed Group Co., LTD, Wuhan, 430206, Hubei, China.
- State Key Laboratory of Crop Breeding Technology Innovation and Integration, China National Seed Group Co., LTD, Wuhan, 430206, Hubei, China.
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23
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Hui S, Li H, Mawia AM, Zhou L, Cai J, Ahmad S, Lai C, Wang J, Jiao G, Xie L, Shao G, Sheng Z, Tang S, Wang J, Wei X, Hu S, Hu P. Production of aromatic three-line hybrid rice using novel alleles of BADH2. PLANT BIOTECHNOLOGY JOURNAL 2022; 20:59-74. [PMID: 34465003 PMCID: PMC8710899 DOI: 10.1111/pbi.13695] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 07/20/2021] [Accepted: 08/19/2021] [Indexed: 05/15/2023]
Abstract
Aroma is a key grain quality trait that directly influences the market price of rice globally. Loss of function of betaine aldehyde dehydrogenase 2 (OsBADH2) affects the biosynthesis of 2-acetyl-1-pyrroline (2-AP), which is responsible for aroma in fragrant rice. The current study was aimed at creating new alleles of BADH2 using CRISPR/Cas9 gene editing technology under the genetic background of the japonica Ningjing 1 (NJ1) and indica Huang Huazhan (HHZ) varieties. Sensory evaluation and analysis using headspace solid-phase microextraction gas chromatography-mass spectrometry (HS-SPME-GC-MS) showed that the grains of the four homozygous T1 lines with new alleles of BADH2 (nj1-cr BADH2 -1, nj1-cr BADH2 -2, hhz-cr BADH2 -1 and hhz-cr BADH2 -2) produced moderate fragrance and had significantly increased 2-AP content compared with wild-types. Moreover, there were no significant differences in the amylose content and gelatinization temperature among the four lines with new alleles of BADH2 to the wild-types. Thereafter, we crossed the HHZ background new alleles of BADH2 with CMS line Taonong 1A (TN1A) to produce a three-line hybrid variety B-Tao-You-Xiangzhan (BTYXZ) with increased grain aroma. The 2-AP content in grains of the improved BTYXZ-1 and BTYXZ-2 reached at 26.16 and 18.74 μg/kg, and the gel consistency of BTYXZ-1 and BTYXZ-2 increased significantly by 9.1% and 6.5%, respectively, compared with the wild-type Tao-You-Xiangzhan (TYXZ). However, the γ-aminobutyric acid (GABA) content in the improved three-line hybrid rice BTYXZ-1 (5.6 mg/100 g) and BTYXZ-2 (10.7 mg/100 g) was significantly lower than that of the TYXZ. These results demonstrated that CRISPR/Cas9 gene editing technology could be successfully utilized in improving aroma in non-fragrant japonica and indica varieties. In addition, the newly developed BADH2 alleles provided important genetic resources for grain aroma improvement in three-line hybrid rice.
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Affiliation(s)
- Suozhen Hui
- State Key Laboratory of Rice BiologyChina National Center for Rice ImprovementChina National Rice Research InstituteHangzhouChina
| | - Huijuan Li
- State Key Laboratory of Rice BiologyChina National Center for Rice ImprovementChina National Rice Research InstituteHangzhouChina
| | - Amos Musyoki Mawia
- State Key Laboratory of Rice BiologyChina National Center for Rice ImprovementChina National Rice Research InstituteHangzhouChina
| | - Liang Zhou
- State Key Laboratory of Rice BiologyChina National Center for Rice ImprovementChina National Rice Research InstituteHangzhouChina
| | - Jinyang Cai
- Jiaxing Academy of Agricultural SciencesJiaxingChina
| | - Shakeel Ahmad
- State Key Laboratory of Rice BiologyChina National Center for Rice ImprovementChina National Rice Research InstituteHangzhouChina
| | - Changkai Lai
- State Key Laboratory of Rice BiologyChina National Center for Rice ImprovementChina National Rice Research InstituteHangzhouChina
| | - Jingxin Wang
- State Key Laboratory of Rice BiologyChina National Center for Rice ImprovementChina National Rice Research InstituteHangzhouChina
| | - Guiai Jiao
- State Key Laboratory of Rice BiologyChina National Center for Rice ImprovementChina National Rice Research InstituteHangzhouChina
| | - Lihong Xie
- State Key Laboratory of Rice BiologyChina National Center for Rice ImprovementChina National Rice Research InstituteHangzhouChina
| | - Gaoneng Shao
- State Key Laboratory of Rice BiologyChina National Center for Rice ImprovementChina National Rice Research InstituteHangzhouChina
| | - Zhonghua Sheng
- State Key Laboratory of Rice BiologyChina National Center for Rice ImprovementChina National Rice Research InstituteHangzhouChina
| | - Shaoqing Tang
- State Key Laboratory of Rice BiologyChina National Center for Rice ImprovementChina National Rice Research InstituteHangzhouChina
| | | | - Xiangjin Wei
- State Key Laboratory of Rice BiologyChina National Center for Rice ImprovementChina National Rice Research InstituteHangzhouChina
| | - Shikai Hu
- State Key Laboratory of Rice BiologyChina National Center for Rice ImprovementChina National Rice Research InstituteHangzhouChina
| | - Peisong Hu
- State Key Laboratory of Rice BiologyChina National Center for Rice ImprovementChina National Rice Research InstituteHangzhouChina
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24
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Zuo ZW, Zhang ZH, Huang DR, Fan YY, Yu SB, Zhuang JY, Zhu YJ. Control of Thousand-Grain Weight by OsMADS56 in Rice. Int J Mol Sci 2021; 23:ijms23010125. [PMID: 35008551 PMCID: PMC8745348 DOI: 10.3390/ijms23010125] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Revised: 12/20/2021] [Accepted: 12/22/2021] [Indexed: 11/16/2022] Open
Abstract
Grain weight and size are important traits determining grain yield and influencing grain quality in rice. In a previous study, a quantitative trait locus controlling thousand-grain weight (TGW) in rice, qTGW10-20.8, was mapped in a 70.7 kb region on chromosome 10. Validation of the candidate gene for qTGW10-20.8, OsMADS56 encoding a MADS-box transcription factor, was performed in this study. In a near-isogenic line (NIL) population segregated only at the OsMADS56 locus, NILs carrying the OsMADS56 allele of IRBB52 were 1.9% and 2.9% lower in TGW than NILs carrying the OsMADS56 allele of Teqing in 2018 and 2020, respectively. Using OsMADS56 knock-out mutants and overexpression transgenic plants, OsMADS56 was validated as the causal gene for qTGW10-20.8. Compared with the recipients, the TGW of the knock-out mutants was reduced by 6.0-15.0%. In these populations, decreased grain weight and size were associated with a reduction in the expression of OsMADS56. In transgenic populations of OsMADS56 driven by a strong constitutive promoter, grain weight and size of the positive plants were significantly higher than those of the negative plants. Haplotype analysis showed that the Teqing-type allele of OsMADS56 is the major type presented in cultivated rice and used in variety improvement. Cloning of OsMADS56 provides a new gene resource to improve grain weight and size through molecular design breeding.
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Affiliation(s)
- Zi-Wei Zuo
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, China; (Z.-W.Z.); (Z.-H.Z.); (D.-R.H.); (Y.-Y.F.)
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China;
| | - Zhen-Hua Zhang
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, China; (Z.-W.Z.); (Z.-H.Z.); (D.-R.H.); (Y.-Y.F.)
| | - De-Run Huang
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, China; (Z.-W.Z.); (Z.-H.Z.); (D.-R.H.); (Y.-Y.F.)
| | - Ye-Yang Fan
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, China; (Z.-W.Z.); (Z.-H.Z.); (D.-R.H.); (Y.-Y.F.)
| | - Si-Bin Yu
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China;
| | - Jie-Yun Zhuang
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, China; (Z.-W.Z.); (Z.-H.Z.); (D.-R.H.); (Y.-Y.F.)
- Correspondence: (J.-Y.Z.); (Y.-J.Z.); Tel.: +86-571-6337-0369 (J.-Y.Z.); +86-571-6337-0364 (Y.-J.Z.)
| | - Yu-Jun Zhu
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, China; (Z.-W.Z.); (Z.-H.Z.); (D.-R.H.); (Y.-Y.F.)
- Correspondence: (J.-Y.Z.); (Y.-J.Z.); Tel.: +86-571-6337-0369 (J.-Y.Z.); +86-571-6337-0364 (Y.-J.Z.)
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25
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Xi M, Wu W, Xu Y, Zhou Y, Chen G, Ji Y, Sun X. Grain chalkiness traits is affected by the synthesis and dynamic accumulation of the storage protein in rice. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2021; 101:6125-6133. [PMID: 33905122 DOI: 10.1002/jsfa.11269] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Revised: 03/28/2021] [Accepted: 04/27/2021] [Indexed: 05/02/2023]
Abstract
BACKGROUOND Grain chalkiness lowers the market value of rice. Alleviating grain chalkiness is the most challenging issue in many rice-producing areas of the world. Nitrogen (N) metabolism has received increasing attention as a result of its relationship with grain chalkiness, although little information is available on the mechanism of N-induced grain chalk. RESULTS A highly chalky rice variety OM052 was used to explore the protein synthesis and its accumulation in the grain exposed to N topdressing (N+) at the panicle initiation stage and a control (N-). The results showed that chalky kernels were stimulated by the N+ treatment and more prone to occur on the top and primary rachis. The grain protein content was increased because of the increased average and maximum rates of protein accumulation during grain filling, which was related to the enhanced activities of glutamine synthetase, glutamate synthase, glutamic oxalo-acetic transaminase and glutamate pyruvate transaminase under the N+ treatment. The activities of these enzymes at 15 days after flowering (DAF) were notably positively correlated with grain chalky traits and protein content. CONCLUSION N topdressing regulates the synthesis and accumulation of the protein by affecting the key enzymes, especially at 15 DAF, which is attributed to grain chalkiness in rice. © 2021 Society of Chemical Industry.
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Affiliation(s)
- Min Xi
- Rice Research Institute, Anhui Academy of Agricultural Sciences, Hefei, China
| | - Wenge Wu
- Rice Research Institute, Anhui Academy of Agricultural Sciences, Hefei, China
| | - Youzun Xu
- Rice Research Institute, Anhui Academy of Agricultural Sciences, Hefei, China
| | - Yongjin Zhou
- Rice Research Institute, Anhui Academy of Agricultural Sciences, Hefei, China
| | - Gang Chen
- Rice Research Institute, Anhui Academy of Agricultural Sciences, Hefei, China
| | - Yalan Ji
- Rice Research Institute, Anhui Academy of Agricultural Sciences, Hefei, China
| | - Xueyuan Sun
- Rice Research Institute, Anhui Academy of Agricultural Sciences, Hefei, China
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26
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Fiaz S, Sheng Z, Zeb A, Barman HN, Shar T, Ali U, Tang S. Analysis of genomic regions for crude protein and fractions of protein using a recombinant inbred population in Rice ( Oryza sativa L.). JOURNAL OF TAIBAH UNIVERSITY FOR SCIENCE 2021. [DOI: 10.1080/16583655.2021.1991733] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Sajid Fiaz
- State Key Laboratory of Rice Biology, China National Centre for Rice Improvement, China National Rice Research Institute, Hangzhou, People’s Republic of China
- Department of Plant Breeding and Genetics, University of Haripur, Haripur, Pakistan
| | - Zhonghua Sheng
- State Key Laboratory of Rice Biology, China National Centre for Rice Improvement, China National Rice Research Institute, Hangzhou, People’s Republic of China
| | - Aqib Zeb
- State Key Laboratory of Rice Biology, China National Centre for Rice Improvement, China National Rice Research Institute, Hangzhou, People’s Republic of China
| | - Hirendra Nath Barman
- State Key Laboratory of Rice Biology, China National Centre for Rice Improvement, China National Rice Research Institute, Hangzhou, People’s Republic of China
| | - Tahmina Shar
- State Key Laboratory of Rice Biology, China National Centre for Rice Improvement, China National Rice Research Institute, Hangzhou, People’s Republic of China
| | - Umed Ali
- State Key Laboratory of Rice Biology, China National Centre for Rice Improvement, China National Rice Research Institute, Hangzhou, People’s Republic of China
| | - Shaoqing Tang
- State Key Laboratory of Rice Biology, China National Centre for Rice Improvement, China National Rice Research Institute, Hangzhou, People’s Republic of China
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27
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Shahzad R, Jamil S, Ahmad S, Nisar A, Khan S, Amina Z, Kanwal S, Aslam HMU, Gill RA, Zhou W. Biofortification of Cereals and Pulses Using New Breeding Techniques: Current and Future Perspectives. Front Nutr 2021; 8:721728. [PMID: 34692743 PMCID: PMC8528959 DOI: 10.3389/fnut.2021.721728] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Accepted: 08/23/2021] [Indexed: 12/25/2022] Open
Abstract
Cereals and pulses are consumed as a staple food in low-income countries for the fulfillment of daily dietary requirements and as a source of micronutrients. However, they are failing to offer balanced nutrition due to deficiencies of some essential compounds, macronutrients, and micronutrients, i.e., cereals are deficient in iron, zinc, some essential amino acids, and quality proteins. Meanwhile, the pulses are rich in anti-nutrient compounds that restrict the bioavailability of micronutrients. As a result, the population is suffering from malnutrition and resultantly different diseases, i.e., anemia, beriberi, pellagra, night blindness, rickets, and scurvy are common in the society. These facts highlight the need for the biofortification of cereals and pulses for the provision of balanced diets to masses and reduction of malnutrition. Biofortification of crops may be achieved through conventional approaches or new breeding techniques (NBTs). Conventional approaches for biofortification cover mineral fertilization through foliar or soil application, microbe-mediated enhanced uptake of nutrients, and conventional crossing of plants to obtain the desired combination of genes for balanced nutrient uptake and bioavailability. Whereas, NBTs rely on gene silencing, gene editing, overexpression, and gene transfer from other species for the acquisition of balanced nutritional profiles in mutant plants. Thus, we have highlighted the significance of conventional and NBTs for the biofortification of cereals and pulses. Current and future perspectives and opportunities are also discussed. Further, the regulatory aspects of newly developed biofortified transgenic and/or non-transgenic crop varieties via NBTs are also presented.
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Affiliation(s)
- Rahil Shahzad
- Agricultural Biotechnology Research Institute, Ayub Agricultural Research Institute, Faisalabad, Pakistan
| | - Shakra Jamil
- Agricultural Biotechnology Research Institute, Ayub Agricultural Research Institute, Faisalabad, Pakistan
| | - Shakeel Ahmad
- Maize Research Station, Ayub Agricultural Research Institute, Faisalabad, Pakistan
| | - Amina Nisar
- Department of Plant Breeding and Genetics, University of Agriculture, Faisalabad, Pakistan
| | - Sipper Khan
- Tropics and Subtropics Group, Institute of Agricultural Engineering, University of Hohenheim, Stuttgart, Germany
| | - Zarmaha Amina
- Tropics and Subtropics Group, Institute of Agricultural Engineering, University of Hohenheim, Stuttgart, Germany
| | - Shamsa Kanwal
- Agricultural Biotechnology Research Institute, Ayub Agricultural Research Institute, Faisalabad, Pakistan
| | | | - Rafaqat Ali Gill
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Weijun Zhou
- Key Laboratory of Spectroscopy Sensing, The Ministry of Agriculture and Rural Affairs, Institute of Crop Science, Zhejiang University, Hangzhou, China
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28
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Kavi Kishor PB, Anil Kumar S, Naravula J, Hima Kumari P, Kummari D, Guddimalli R, Edupuganti S, Karumanchi AR, Venkatachalam P, Suravajhala P, Polavarapu R. Improvement of small seed for big nutritional feed. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2021; 27:2433-2446. [PMID: 34566283 PMCID: PMC8455807 DOI: 10.1007/s12298-021-01071-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2021] [Revised: 08/04/2021] [Accepted: 09/11/2021] [Indexed: 05/14/2023]
Abstract
Exploding global population, rapid urbanization, salinization of soils, decreasing arable land availability, groundwater resources, and dynamic climatic conditions pose impending damage to our food security by reducing the grain quality and quantity. This issue is further compounded in arid and semi-arid regions due to the shortage of irrigation water and erratic rainfalls. Millets are gluten (a family of proteins)-free and cultivated all over the globe for human consumption, fuel, feed, and fodder. They provide nutritional security for the under- and malnourished. With the deployment of strategies like foliar spray, traditional/marker-assisted breeding, identification of candidate genes for the translocation of important minerals, and genome-editing technologies, it is now tenable to biofortify important millets. Since the bioavailability of iron and zinc has been proven in human trials, the challenge is to make such grains accessible. This review encompasses nutritional benefits, progress made, challenges being encountered, and prospects of enriching millet crops with essential minerals.
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Affiliation(s)
- P. B. Kavi Kishor
- Department of Biotechnology, Vignan’s Foundation for Science, Technology and Research, Vadlamudi, Guntur, Andhra Pradesh 522 213 India
| | - S. Anil Kumar
- Department of Biotechnology, Vignan’s Foundation for Science, Technology and Research, Vadlamudi, Guntur, Andhra Pradesh 522 213 India
- Bioclues.Org, Hyderabad, India
| | - Jalaja Naravula
- Department of Biotechnology, Vignan’s Foundation for Science, Technology and Research, Vadlamudi, Guntur, Andhra Pradesh 522 213 India
| | | | - Divya Kummari
- Department of Genetics, Osmania University, Hyderabad, Telangana, 500 007 India
| | | | - Sujatha Edupuganti
- Department of Botany, Osmania University, Hyderabad, Telangana, 500 007 India
| | - Appa Rao Karumanchi
- Department of Biotechnology, Acharya Nagarjuna University, Guntur, Andhra Pradesh, 522 508 India
| | | | - Prashanth Suravajhala
- Bioclues.Org, Hyderabad, India
- Amrita School of Biotechnology, Amrita University, Amritapuri, 690 525, Clappana, Kerala, India
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29
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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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Exploration of Epigenetics for Improvement of Drought and Other Stress Resistance in Crops: A Review. PLANTS 2021; 10:plants10061226. [PMID: 34208642 PMCID: PMC8235456 DOI: 10.3390/plants10061226] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Revised: 06/09/2021] [Accepted: 06/11/2021] [Indexed: 01/01/2023]
Abstract
Crop plants often have challenges of biotic and abiotic stresses, and they adapt sophisticated ways to acclimate and cope with these through the expression of specific genes. Changes in chromatin, histone, and DNA mostly serve the purpose of combating challenges and ensuring the survival of plants in stressful environments. Epigenetic changes, due to environmental stress, enable plants to remember a past stress event in order to deal with such challenges in the future. This heritable memory, called "plant stress memory", enables plants to respond against stresses in a better and efficient way, not only for the current plant in prevailing situations but also for future generations. Development of stress resistance in plants for increasing the yield potential and stability has always been a traditional objective of breeders for crop improvement through integrated breeding approaches. The application of epigenetics for improvements in complex traits in tetraploid and some other field crops has been unclear. An improved understanding of epigenetics and stress memory applications will contribute to the development of strategies to incorporate them into breeding for complex agronomic traits. The insight in the application of novel plant breeding techniques (NPBTs) has opened a new plethora of options among plant scientists to develop germplasms for stress tolerance. This review summarizes and discusses plant stress memory at the intergenerational and transgenerational levels, mechanisms involved in stress memory, exploitation of induced and natural epigenetic changes, and genome editing technologies with their future possible applications, in the breeding of crops for abiotic stress tolerance to increase the yield for zero hunger goals achievement on a sustainable basis in the changing climatic era.
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Mubarik MS, Wang X, Khan SH, Ahmad A, Khan Z, Amjid MW, Razzaq MK, Ali Z, Azhar MT. Engineering broad-spectrum resistance to cotton leaf curl disease by CRISPR-Cas9 based multiplex editing in plants. GM CROPS & FOOD 2021; 12:647-658. [PMID: 34124996 PMCID: PMC9208622 DOI: 10.1080/21645698.2021.1938488] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Advances in genome editing technologies have tremendous potential to address the limitations of classical resistance breeding. CRISPR-Cas9 based gene editing has been applied successfully in plants to tolerate virus infections. In this study, we successfully tested CRISPR-Cas9 system to counteract cotton leaf curl disease (CLCuD) caused by whitefly transmitted cotton leaf curl viruses (CLCuVs). We also analyzed the ability of CLCuV to escape the Cas9 endonuclease activity. Targeting overlapping genes of most prevalent CLCuVs with three gRNAs resulted in virus interference, as validated by low virus titer. Furthermore, multiplex CRISPR-Cas9 construct simultaneously targeting six genes of CLCuV, was found more effective to interfere with virus proliferation compared to targeting single region individually. Additionally, transgenic N. benthamiana plants expressing multiple gRNAs simultaneously showed enhanced tolerance against CLCuV infection when compared to wild-type plants. T7 Endonuclease-I (T7EI) assay, showing indels in the CLCuV genome, confirmed the occurrence of double strand breaks (DSBs) in DNA at target sequence induced by Cas9 endonuclease. We observed that targeting CLCuV genome at multiple sites simultaneously resulted in better interference, also with inefficient recovery of altered virus molecules. Next, we tested multiplex construct in cotton to interfere CLCuV infection. We found significant decrease in virus accumulation in cotton leaves co-infiltrated with multiplex cassette and virus compared to cotton leaves infiltrated with virus only. The results demonstrate future use of CRISPR-Cas9 system for engineering virus resistance in crops. Moreover, our results also advocate that resistance to mixed virus infections can be engineered using multiplex genome editing.
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Affiliation(s)
- Muhammad Salman Mubarik
- Centre of Agricultural Biochemistry and Biotechnology (CABB), University of Agriculture, Faisalabad, Pakistan
| | - Xiukang Wang
- College of Life Sciences, Yan'an University, Yan'an, Shaanxi, China
| | - Sultan Habibullah Khan
- Centre of Agricultural Biochemistry and Biotechnology (CABB), University of Agriculture, Faisalabad, Pakistan
| | - Aftab Ahmad
- Department of Biochemistry, University of Agriculture, Faisalabad, Pakistan
| | - Zulqurnain Khan
- Institute of Plant Breeding and Biotechnology (IPBB), MNS University of Agriculture, Multan, Pakistan
| | - Muhammad Waqas Amjid
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
| | - Muhammad Khuram Razzaq
- Soybean Research Institute, National Center for Soybean Improvement, Nanjing Agricultural University, Nanjing, China
| | - Zulfiqar Ali
- Institute of Plant Breeding and Biotechnology (IPBB), MNS University of Agriculture, Multan, Pakistan
| | - Muhammad Tehseen Azhar
- Institute of Molecular Biology and Biotechnology, Bahauddin Zakariya University, Multan, Pakistan.,School of Agriculture Sciences Zhengzhou University, Zhengzhou, China
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Kim YC, Kang Y, Yang EY, Cho MC, Schafleitner R, Lee JH, Jang S. Applications and Major Achievements of Genome Editing in Vegetable Crops: A Review. FRONTIERS IN PLANT SCIENCE 2021; 12:688980. [PMID: 34178006 PMCID: PMC8231707 DOI: 10.3389/fpls.2021.688980] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 05/18/2021] [Indexed: 05/04/2023]
Abstract
The emergence of genome-editing technology has allowed manipulation of DNA sequences in genomes to precisely remove or replace specific sequences in organisms resulting in targeted mutations. In plants, genome editing is an attractive method to alter gene functions to generate improved crop varieties. Genome editing is thought to be simple to use and has a lower risk of off-target effects compared to classical mutation breeding. Furthermore, genome-editing technology tools can also be applied directly to crops that contain complex genomes and/or are not easily bred using traditional methods. Currently, highly versatile genome-editing tools for precise and predictable editing of almost any locus in the plant genome make it possible to extend the range of application, including functional genomics research and molecular crop breeding. Vegetables are essential nutrient sources for humans and provide vitamins, minerals, and fiber to diets, thereby contributing to human health. In this review, we provide an overview of the brief history of genome-editing technologies and the components of genome-editing tool boxes, and illustrate basic modes of operation in representative systems. We describe the current and potential practical application of genome editing for the development of improved nutritious vegetables and present several case studies demonstrating the potential of the technology. Finally, we highlight future directions and challenges in applying genome-editing systems to vegetable crops for research and product development.
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Affiliation(s)
- Young-Cheon Kim
- Division of Life Sciences, Jeonbuk National University, Jeonju, South Korea
| | - Yeeun Kang
- World Vegetable Center Korea Office, Wanju-gun, South Korea
| | - Eun-Young Yang
- National Institute of Horticultural and Herbal Science (NIHHS), Rural Development Administration (RDA), Wanju-gun, South Korea
| | - Myeong-Cheoul Cho
- National Institute of Horticultural and Herbal Science (NIHHS), Rural Development Administration (RDA), Wanju-gun, South Korea
| | | | - Jeong Hwan Lee
- Division of Life Sciences, Jeonbuk National University, Jeonju, South Korea
| | - Seonghoe Jang
- World Vegetable Center Korea Office, Wanju-gun, South Korea
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Carrijo J, Illa-Berenguer E, LaFayette P, Torres N, Aragão FJL, Parrott W, Vianna GR. Two efficient CRISPR/Cas9 systems for gene editing in soybean. Transgenic Res 2021; 30:239-249. [PMID: 33797713 DOI: 10.1007/s11248-021-00246-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Accepted: 03/17/2021] [Indexed: 12/26/2022]
Abstract
Genome editing using CRISPR/Cas9 has been highlighted as a powerful tool for crop improvement. Nevertheless, its efficiency can be improved, especially for crops with a complex genome, such as soybean. In this work, using the CRISPR/Cas9 technology we evaluated two CRISPR systems, a one-component vs. a two-component strategy. In a simplified system, the single transcriptional unit (STU), SpCas9 and sgRNA are driven by only one promoter, and in the conventional system, the two-component transcriptional unit (TCTU), SpCas9, is under the control of a pol II promoter and the sgRNAs are under the control of a pol III promoter. A multiplex system with three targets was designed targeting two different genes, GmIPK1 and GmIPK2, coding for enzymes from the phytic acid synthesis pathway. Both systems were tested using the hairy root soybean methodology. Results showed gene-specific edition. For the GmIPK1 gene, edition was observed in both configurations, with a deletion of 1 to 749 base pairs; however, the TCTU showed higher indel frequencies. For GmIPK2 major exclusions were observed in both systems, but the editing efficiency was low for STU. Both systems (STU or TCTU) have been shown to be capable of promoting effective gene editing in soybean. The TCTU configuration proved to be preferable, since it was more efficient. The STU system was less efficient, but the size of the CRISPR/Cas cassette was smaller.
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Affiliation(s)
- Jéssica Carrijo
- Embrapa Recursos Genéticos e Biotecnologia, Parque Estação Biológica, PqEB, Av W5 Norte Final 716, Brasília, DF, 70770-917, Brazil
- Department of Molecular Biology, University of Brasilia, Brasília, DF, 70910-900, Brazil
| | - Eudald Illa-Berenguer
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA, 30602, USA
| | - Peter LaFayette
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA, 30602, USA
- Department of Crop and Soil Sciences, University of Georgia, Athens, GA, 30602, USA
| | - Nathalia Torres
- Department of Molecular Biology, University of Brasilia, Brasília, DF, 70910-900, Brazil
| | - Francisco J L Aragão
- Embrapa Recursos Genéticos e Biotecnologia, Parque Estação Biológica, PqEB, Av W5 Norte Final 716, Brasília, DF, 70770-917, Brazil
- Department of Molecular Biology, University of Brasilia, Brasília, DF, 70910-900, Brazil
| | - Wayne Parrott
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA, 30602, USA
- Department of Crop and Soil Sciences, University of Georgia, Athens, GA, 30602, USA
| | - Giovanni R Vianna
- Embrapa Recursos Genéticos e Biotecnologia, Parque Estação Biológica, PqEB, Av W5 Norte Final 716, Brasília, DF, 70770-917, Brazil.
- Department of Molecular Biology, University of Brasilia, Brasília, DF, 70910-900, Brazil.
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Fiaz S, Wang X, Khan SA, Ahmar S, Noor MA, Riaz A, Ali K, Abbas F, Mora-Poblete F, Figueroa CR, Alharthi B. Novel plant breeding techniques to advance nitrogen use efficiency in rice: A review. GM CROPS & FOOD 2021; 12:627-646. [PMID: 34034628 PMCID: PMC9208628 DOI: 10.1080/21645698.2021.1921545] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Recently, there has been a remarkable increase in rice production owing to genetic improvement and increase in application of synthetic fertilizers. For sustainable agriculture, there is dire need to maintain a balance between profitability and input cost. To meet the steady growing demands of the farming community, researchers are utilizing all available resources to identify nutrient use efficient germplasm, but with very little success. Therefore, it is essential to understand the underlying genetic mechanism controlling nutrients efficiency, with the nitrogen use efficiency (NUE) being the most important trait. Information regarding genetic factors controlling nitrogen (N) transporters, assimilators, and remobilizers can help to identify candidate germplasms via high-throughput technologies. Large-scale field trials have provided morphological, physiological, and biochemical trait data for the detection of genomic regions controlling NUE. The functional aspects of these attributes are time-consuming, costly, labor-intensive, and less accurate. Therefore, the application of novel plant breeding techniques (NPBTs) with context to genome engineering has opened new avenues of research for crop improvement programs. Most recently, genome editing technologies (GETs) have undergone enormous development with various versions from Cas9, Cpf1, base, and prime editing. These GETs have been vigorously adapted in plant sciences for novel trait development to insure food quantity and quality. Base editing has been successfully applied to improve NUE in rice, demonstrating the potential of GETs to develop germplasms with improved resource use efficiency. NPBTs continue to face regulatory setbacks in some countries due to genome editing being categorized in the same category as genetically modified (GM) crops. Therefore, it is essential to involve all stakeholders in a detailed discussion on NPBTs and to formulate uniform policies tackling biosafety, social, ethical, and environmental concerns. In the current review, we have discussed the genetic mechanism of NUE and NPBTs for crop improvement programs with proof of concepts, transgenic and GET application for the development of NUE germplasms, and regulatory aspects of genome edited crops with future directions considering NUE.
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Affiliation(s)
- Sajid Fiaz
- Department of Plant Breeding and Genetics, The University of Haripur 22620, Khyber, Pakhtunkhwa, Pakistan
| | - Xiukang Wang
- College of Life Sciences, Yan'an University, Yan'an, Shaanxi, China
| | - Sher Aslam Khan
- Department of Plant Breeding and Genetics, The University of Haripur 22620, Khyber, Pakhtunkhwa, Pakistan
| | - Sunny Ahmar
- Institute of Biological Sciences, Campus Talca, Universidad deTalca, Talca, Chile
| | - Mehmood Ali Noor
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Key Laboratory of Crop Physiology and Ecology, Ministry of Agriculture, Beijing, China
| | - Aamir Riaz
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, Zhejiang, China
| | - Kazim Ali
- National Institute for Genomics and Advanced Biotechnology, National Agricultural Research Centre, Islamabad, Pakistan
| | - Farhat Abbas
- Research Center for Ornamental Plants, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
| | - Freddy Mora-Poblete
- Institute of Biological Sciences, Campus Talca, Universidad deTalca, Talca, Chile
| | - Carlos R Figueroa
- Institute of Biological Sciences, Campus Talca, Universidad deTalca, Talca, Chile
| | - Badr Alharthi
- College of Khurma, Taif University, Taif, Saudi Arabia.,College of Science and Engineering, Flinders University, Adelaide, South Australia
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Fiaz S, Ahmar S, Saeed S, Riaz A, Mora-Poblete F, Jung KH. Evolution and Application of Genome Editing Techniques for Achieving Food and Nutritional Security. Int J Mol Sci 2021; 22:5585. [PMID: 34070430 PMCID: PMC8197453 DOI: 10.3390/ijms22115585] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 05/16/2021] [Accepted: 05/20/2021] [Indexed: 12/26/2022] Open
Abstract
A world with zero hunger is possible only through a sustainable increase in food production and distribution and the elimination of poverty. Scientific, logistical, and humanitarian approaches must be employed simultaneously to ensure food security, starting with farmers and breeders and extending to policy makers and governments. The current agricultural production system is facing the challenge of sustainably increasing grain quality and yield and enhancing resistance to biotic and abiotic stress under the intensifying pressure of climate change. Under present circumstances, conventional breeding techniques are not sufficient. Innovation in plant breeding is critical in managing agricultural challenges and achieving sustainable crop production. Novel plant breeding techniques, involving a series of developments from genome editing techniques to speed breeding and the integration of omics technology, offer relevant, versatile, cost-effective, and less time-consuming ways of achieving precision in plant breeding. Opportunities to edit agriculturally significant genes now exist as a result of new genome editing techniques. These range from random (physical and chemical mutagens) to non-random meganucleases (MegaN), zinc finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs), clustered regularly interspaced short palindromic repeats (CRISPR)/associated protein system 9 (CRISPR/Cas9), the CRISPR system from Prevotella and Francisella1 (Cpf1), base editing (BE), and prime editing (PE). Genome editing techniques that promote crop improvement through hybrid seed production, induced apomixis, and resistance to biotic and abiotic stress are prioritized when selecting for genetic gain in a restricted timeframe. The novel CRISPR-associated protein system 9 variants, namely BE and PE, can generate transgene-free plants with more frequency and are therefore being used for knocking out of genes of interest. We provide a comprehensive review of the evolution of genome editing technologies, especially the application of the third-generation genome editing technologies to achieve various plant breeding objectives within the regulatory regimes adopted by various countries. Future development and the optimization of forward and reverse genetics to achieve food security are evaluated.
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Affiliation(s)
- Sajid Fiaz
- Department of Plant Breeding and Genetics, The University of Haripur, Haripur 22620, Pakistan
| | - Sunny Ahmar
- Institute of Biological Sciences, University of Talca, 2 Norte 685, Talca 3460000, Chile
| | - Sajjad Saeed
- Department of Forestry and Wildlife Management, University of Haripur, Haripur 22620, Pakistan
| | - Aamir Riaz
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, China
| | - Freddy Mora-Poblete
- Institute of Biological Sciences, University of Talca, 2 Norte 685, Talca 3460000, Chile
| | - Ki-Hung Jung
- Graduate School of Biotechnology & Crop Biotech Institute, Kyung Hee University, Yongin 17104, Korea
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Adegoke TV, Wang Y, Chen L, Wang H, Liu W, Liu X, Cheng YC, Tong X, Ying J, Zhang J. Posttranslational Modification of Waxy to Genetically Improve Starch Quality in Rice Grain. Int J Mol Sci 2021; 22:4845. [PMID: 34063649 PMCID: PMC8124582 DOI: 10.3390/ijms22094845] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Revised: 04/26/2021] [Accepted: 04/29/2021] [Indexed: 01/07/2023] Open
Abstract
The waxy (Wx) gene, encoding the granule-bound starch synthase (GBSS), is responsible for amylose biosynthesis and plays a crucial role in defining eating and cooking quality. The waxy locus controls both the non-waxy and waxy rice phenotypes. Rice starch can be altered into various forms by either reducing or increasing the amylose content, depending on consumer preference and region. Low-amylose rice is preferred by consumers because of its softness and sticky appearance. A better way of improving crops other than downregulation and overexpression of a gene or genes may be achieved through the posttranslational modification of sites or regulatory enzymes that regulate them because of their significance. The impact of posttranslational GBSSI modifications on extra-long unit chains (ELCs) remains largely unknown. Numerous studies have been reported on different crops, such as wheat, maize, and barley, but the rice starch granule proteome remains largely unknown. There is a need to improve the yield of low-amylose rice by employing posttranslational modification of Wx, since the market demand is increasing every day in order to meet the market demand for low-amylose rice in the regional area that prefers low-amylose rice, particularly in China. In this review, we have conducted an in-depth review of waxy rice, starch properties, starch biosynthesis, and posttranslational modification of waxy protein to genetically improve starch quality in rice grains.
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Affiliation(s)
- Tosin Victor Adegoke
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou 311400, China; (T.V.A.); (Y.W.); (L.C.); (H.W.); (W.L.); (X.L.); (Y.-C.C.); (X.T.); (J.Y.)
- Graduate School of Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Yifeng Wang
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou 311400, China; (T.V.A.); (Y.W.); (L.C.); (H.W.); (W.L.); (X.L.); (Y.-C.C.); (X.T.); (J.Y.)
| | - Lijuan Chen
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou 311400, China; (T.V.A.); (Y.W.); (L.C.); (H.W.); (W.L.); (X.L.); (Y.-C.C.); (X.T.); (J.Y.)
| | - Huimei Wang
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou 311400, China; (T.V.A.); (Y.W.); (L.C.); (H.W.); (W.L.); (X.L.); (Y.-C.C.); (X.T.); (J.Y.)
| | - Wanning Liu
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou 311400, China; (T.V.A.); (Y.W.); (L.C.); (H.W.); (W.L.); (X.L.); (Y.-C.C.); (X.T.); (J.Y.)
| | - Xingyong Liu
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou 311400, China; (T.V.A.); (Y.W.); (L.C.); (H.W.); (W.L.); (X.L.); (Y.-C.C.); (X.T.); (J.Y.)
| | - Yi-Chen Cheng
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou 311400, China; (T.V.A.); (Y.W.); (L.C.); (H.W.); (W.L.); (X.L.); (Y.-C.C.); (X.T.); (J.Y.)
| | - Xiaohong Tong
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou 311400, China; (T.V.A.); (Y.W.); (L.C.); (H.W.); (W.L.); (X.L.); (Y.-C.C.); (X.T.); (J.Y.)
| | - Jiezheng Ying
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou 311400, China; (T.V.A.); (Y.W.); (L.C.); (H.W.); (W.L.); (X.L.); (Y.-C.C.); (X.T.); (J.Y.)
| | - Jian Zhang
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou 311400, China; (T.V.A.); (Y.W.); (L.C.); (H.W.); (W.L.); (X.L.); (Y.-C.C.); (X.T.); (J.Y.)
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Perspectives for epigenetic editing in crops. Transgenic Res 2021; 30:381-400. [PMID: 33891288 DOI: 10.1007/s11248-021-00252-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 03/29/2021] [Indexed: 01/10/2023]
Abstract
Site-specific nucleases (SSNs) have drawn much attention in plant biotechnology due to their ability to drive precision mutagenesis, gene targeting or allele replacement. However, when devoid of its nuclease activity, the underlying DNA-binding activity of SSNs can be used to bring other protein functional domains close to specific genomic sites, thus expanding further the range of applications of the technology. In particular, the addition of functional domains encoding epigenetic effectors and chromatin modifiers to the CRISPR/Cas ribonucleoprotein complex opens the possibility to introduce targeted epigenomic modifications in plants in an easily programmable manner. Here we examine some of the most important agronomic traits known to be controlled epigenetically and review the best studied epigenetic catalytic effectors in plants, such as DNA methylases/demethylases or histone acetylases/deacetylases and their associated marks. We also review the most efficient strategies developed to date to functionalize Cas proteins with both catalytic and non-catalytic epigenetic effectors, and the ability of these domains to influence the expression of endogenous genes in a regulatable manner. Based on these new technical developments, we discuss the possibilities offered by epigenetic editing tools in plant biotechnology and their implications in crop breeding.
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Mawia AM, Hui S, Zhou L, Li H, Tabassum J, Lai C, Wang J, Shao G, Wei X, Tang S, Luo J, Hu S, Hu P. Inorganic arsenic toxicity and alleviation strategies in rice. JOURNAL OF HAZARDOUS MATERIALS 2021; 408:124751. [PMID: 33418521 DOI: 10.1016/j.jhazmat.2020.124751] [Citation(s) in RCA: 75] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2020] [Revised: 11/29/2020] [Accepted: 11/30/2020] [Indexed: 05/28/2023]
Abstract
Direct or indirect exposure to inorganic arsenic (iAs) in the forms of AsIII (arsenite) and AsV (arsenate) through consumption of As-contaminated food materials and drinking water leads to arsenic poisoning. Rice (Oryza sativa L.) plant potentially accumulates a high amount of iAs from paddy fields than any other cereal crops. This makes it to be a major source of iAs especially among the population that uses it as their dominant source of diet. The accumulation of As in human bodies poses a serious global health risk to the human population. Various conventional methods have been applied to reduce the arsenic accumulation in rice plant. However, the success rate of these techniques is low. Therefore, the development of efficient and effective methods aimed at lowering iAs toxicity is a very crucial public concern. With the current advancement in technology, new strategies aimed at addressing this concern are being developed and utilized in various parts of the world. In this review, we discuss the recent advances in the management of iAs in rice plants emphasizing the use of nanotechnology and biotechnology approaches. Also, the prospects and challenges facing these approaches are described.
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Affiliation(s)
- Amos Musyoki Mawia
- State Key Laboratory of Rice Biology, China National Center for Rice Improvement, China National Rice Research Institute, Hangzhou 310006, China
| | - Suozhen Hui
- State Key Laboratory of Rice Biology, China National Center for Rice Improvement, China National Rice Research Institute, Hangzhou 310006, China
| | - Liang Zhou
- State Key Laboratory of Rice Biology, China National Center for Rice Improvement, China National Rice Research Institute, Hangzhou 310006, China
| | - Huijuan Li
- State Key Laboratory of Rice Biology, China National Center for Rice Improvement, China National Rice Research Institute, Hangzhou 310006, China
| | - Javaria Tabassum
- State Key Laboratory of Rice Biology, China National Center for Rice Improvement, China National Rice Research Institute, Hangzhou 310006, China
| | - Changkai Lai
- State Key Laboratory of Rice Biology, China National Center for Rice Improvement, China National Rice Research Institute, Hangzhou 310006, China
| | - Jingxin Wang
- State Key Laboratory of Rice Biology, China National Center for Rice Improvement, China National Rice Research Institute, Hangzhou 310006, China
| | - Gaoneng Shao
- State Key Laboratory of Rice Biology, China National Center for Rice Improvement, China National Rice Research Institute, Hangzhou 310006, China
| | - Xiangjin Wei
- State Key Laboratory of Rice Biology, China National Center for Rice Improvement, China National Rice Research Institute, Hangzhou 310006, China
| | - Shaoqing Tang
- State Key Laboratory of Rice Biology, China National Center for Rice Improvement, China National Rice Research Institute, Hangzhou 310006, China
| | - Ju Luo
- State Key Laboratory of Rice Biology, China National Center for Rice Improvement, China National Rice Research Institute, Hangzhou 310006, China.
| | - Shikai Hu
- State Key Laboratory of Rice Biology, China National Center for Rice Improvement, China National Rice Research Institute, Hangzhou 310006, China.
| | - Peisong Hu
- State Key Laboratory of Rice Biology, China National Center for Rice Improvement, China National Rice Research Institute, Hangzhou 310006, China.
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Tiozon RJN, Fernie AR, Sreenivasulu N. Meeting human dietary vitamin requirements in the staple rice via strategies of biofortification and post-harvest fortification. Trends Food Sci Technol 2021. [DOI: 10.1016/j.tifs.2021.01.023] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
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40
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Tyagi S, Kumar R, Kumar V, Won SY, Shukla P. Engineering disease resistant plants through CRISPR-Cas9 technology. GM CROPS & FOOD 2021; 12:125-144. [PMID: 33079628 PMCID: PMC7583490 DOI: 10.1080/21645698.2020.1831729] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Revised: 09/13/2020] [Accepted: 09/27/2020] [Indexed: 01/08/2023]
Abstract
Plants are susceptible to phytopathogens, including bacteria, fungi, and viruses, which cause colossal financial shortfalls (pre- and post-harvest) and threaten global food safety. To combat with these phytopathogens, plant possesses two-layer of defense in the form of PAMP-triggered immunity (PTI), or Effectors-triggered immunity (ETI). The understanding of plant-molecular interactions and revolution of high-throughput molecular techniques have opened the door for innovations in developing pathogen-resistant plants. In this context, Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-CRISPR-associated protein 9 (Cas9) has transformed genome editing (GE) technology and being harnessed for altering the traits. Here we have summarized the complexities of plant immune system and the use of CRISPR-Cas9 to edit the various components of plant immune system to acquire long-lasting resistance in plants against phytopathogens. This review also sheds the light on the limitations of CRISPR-Cas9 system, regulation of CRISPR-Cas9 edited crops and future prospective of this technology.
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Affiliation(s)
- Swati Tyagi
- Genomic Division, National Institute of Agriculture Science, Rural Development Administration, Jeonju, Republic of Korea
| | - Robin Kumar
- Department of Soil Science and Agricultural Chemistry, Acharya Narendra Dev University of Agriculture and Technology, Kumarganj, Ayodhya, India
- Department of Agriculture Engineering, Sardar Vallabhbhai Patel University of Agriculture and Technology, Meerut, India
| | - Vivak Kumar
- Department of Agriculture Engineering, Sardar Vallabhbhai Patel University of Agriculture and Technology, Meerut, India
| | - So Youn Won
- Genomic Division, National Institute of Agriculture Science, Rural Development Administration, Jeonju, Republic of Korea
| | - Pratyoosh Shukla
- Enzyme Technology and Protein Bioinformatics Laboratory, Department of Microbiology, Maharshi Dayanand University, Rohtak, India
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Ahmad S, Sheng Z, Jalal RS, Tabassum J, Ahmed FK, Hu S, Shao G, Wei X, Abd-Elsalam KA, Hu P, Tang S. CRISPR–Cas technology towards improvement of abiotic stress tolerance in plants. CRISPR AND RNAI SYSTEMS 2021:755-772. [DOI: 10.1016/b978-0-12-821910-2.00021-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
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Abd-Elsalam KA, Lim KT. Can CRISPRized crops save the global food supply? CRISPR AND RNAI SYSTEMS 2021:1-14. [DOI: 10.1016/b978-0-12-821910-2.00006-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
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Ding Y, Zhu J, Zhao D, Liu Q, Yang Q, Zhang T. Targeting Cis-Regulatory Elements for Rice Grain Quality Improvement. FRONTIERS IN PLANT SCIENCE 2021; 12:705834. [PMID: 34456947 PMCID: PMC8385297 DOI: 10.3389/fpls.2021.705834] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 07/08/2021] [Indexed: 05/05/2023]
Abstract
Rice is the most important source of food worldwide, providing energy, and nutrition for more than half of the population worldwide. Rice grain quality is a complex trait that is affected by several factors, such as the genotype and environment, and is a major target for rice breeders. Cis-regulatory elements (CREs) are the regions of non-coding DNA, which play a critical role in gene expression regulation. Compared with gene knockout, CRE modifications can fine-tune the expression levels of target genes. Genome editing has provided opportunities to modify the genomes of organisms in a precise and predictable way. Recently, the promoter modifications of coding genes using genome editing technologies in plant improvement have become popular. In this study, we reviewed the results of recent studies on the identification, characterization, and application of CREs involved in rice grain quality. We proposed CREs as preferred potential targets to create allelic diversity and to improve quality traits via genome editing strategies in rice. We also discussed potential challenges and experimental considerations for the improvement in grain quality in crop plants.
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Affiliation(s)
- Yu Ding
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Jiangsu Key Laboratory of Crop Genetics and Physiology, College of Agriculture, Yangzhou University, Yangzhou, China
| | - Jiannan Zhu
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Jiangsu Key Laboratory of Crop Genetics and Physiology, College of Agriculture, Yangzhou University, Yangzhou, China
| | - Dongsheng Zhao
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Jiangsu Key Laboratory of Crop Genetics and Physiology, College of Agriculture, Yangzhou University, Yangzhou, China
| | - Qiaoquan Liu
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Jiangsu Key Laboratory of Crop Genetics and Physiology, College of Agriculture, Yangzhou University, Yangzhou, China
| | - Qingqing Yang
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Jiangsu Key Laboratory of Crop Genetics and Physiology, College of Agriculture, Yangzhou University, Yangzhou, China
- Department of Biotechnology, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, China
- *Correspondence: Qingqing Yang
| | - Tao Zhang
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Jiangsu Key Laboratory of Crop Genetics and Physiology, College of Agriculture, Yangzhou University, Yangzhou, China
- Tao Zhang
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Fiaz S, Wang X, Younas A, Alharthi B, Riaz A, Ali H. Apomixis and strategies to induce apomixis to preserve hybrid vigor for multiple generations. GM CROPS & FOOD 2021; 12:57-70. [PMID: 32877304 PMCID: PMC7553744 DOI: 10.1080/21645698.2020.1808423] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Accepted: 08/06/2020] [Indexed: 11/16/2022]
Abstract
Hybrid seeds of several important crops with supreme qualities including yield, biotic and abiotic stress tolerance have been cultivated for decades. Thus far, a major challenge with hybrid seeds is that they do not have the ability to produce plants with the same qualities over subsequent generations. Apomixis, an asexual mode of reproduction by avoiding meiosis, exists naturally in flowering plants, and ultimately leads to seed production. Apomixis has the potential to preserve hybrid vigor for multiple generations in economically important plant genotypes. The evolution and genetics of asexual seed production are unclear, and much more effort will be required to determine the genetic architecture of this phenomenon. To fix hybrid vigor, synthetic apomixis has been suggested. The development of MiMe (mitosis instead of meiosis) genotypes has been utilized for clonal gamete production. However, the identification and parental origin of genes responsible for synthetic apomixis are little known and need further clarification. Genome modifications utilizing genome editing technologies (GETs), such as clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein (cas), a reverse genetics tool, have paved the way toward the utilization of emerging technologies in plant molecular biology. Over the last decade, several genes in important crops have been successfully edited. The vast availability of GETs has made functional genomics studies easy to conduct in crops important for food security. Disruption in the expression of genes specific to egg cell MATRILINEAL (MTL) through the CRISPR/Cas genome editing system promotes the induction of haploid seed, whereas triple knockout of the Baby Boom (BBM) genes BBM1, BBM2, and BBM3 cause embryo arrest and abortion, which can be fully rescued by male-transmitted BBM1. The establishment of synthetic apomixis by engineering the MiMe genotype by genome editing of BBM1 expression or disruption of MTL leads to clonal seed production and heritability for multiple generations. In the present review, we discuss current developments related to the use of CRISPR/Cas technology in plants and the possibility of promoting apomixis in crops to preserve hybrid vigor. In addition, genetics, evolution, epigenetic modifications, and strategies for MiMe genotype development are discussed in detail.
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Affiliation(s)
- Sajid Fiaz
- Department of Plant Breeding and Genetics, The University of Haripur 22620 , Khyber Pakhtunkhwa, Pakistan
| | - Xiukang Wang
- College of Life Sciences, Yan'an University , Yan'an, Shaanxi, China
| | - Afifa Younas
- Department of Botany, Lahore College for Women University , Lahore, Pakistan
| | - Badr Alharthi
- College of Science and Engineering, Flinders University , Adelaide, Australia
- University College of Khurma, Taif University , Taif, Saudi Arabia
| | - Adeel Riaz
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences , Beijing, China
| | - Habib Ali
- Department of Agricultural Engineering, Khawaja Fareed University of Engineering and Information Technology , Rahim Yar Khan, Pakistan
- Department of Entomology, Sub-Campus Depalpur, University of Agriculture Faisalabad , Faisalabad, Pakistan
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Chen G, Zhou Y, Kishchenko O, Stepanenko A, Jatayev S, Zhang D, Borisjuk N. Gene editing to facilitate hybrid crop production. Biotechnol Adv 2020; 46:107676. [PMID: 33285253 DOI: 10.1016/j.biotechadv.2020.107676] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2020] [Revised: 11/23/2020] [Accepted: 11/28/2020] [Indexed: 11/18/2022]
Abstract
Capturing heterosis (hybrid vigor) is a promising way to increase productivity in many crops; hybrid crops often have superior yields, disease resistance, and stress tolerance compared with their parental inbred lines. The full utilization of heterosis faces a number of technical problems related to the specifics of crop reproductive biology, such as difficulties with generating and maintaining male-sterile lines and the low efficiency of natural cross-pollination for some genetic combinations. Innovative technologies, such as development of artificial in vitro systems for hybrid production and apomixis-based systems for maintenance of the resulting heterotic progeny, may substantially facilitate the production of hybrids. Genome editing using specifically targeted nucleases, such as clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated nuclease 9 (CRISPR/Cas9) systems, which recognize targets by RNA:DNA complementarity, has recently become an integral part of research and development in life science. In this review, we summarize the progress of genome editing technologies for facilitating the generation of mutant male sterile lines, applications of haploids for hybrid production, and the use of apomixis for the clonal propagation of elite hybrid lines.
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Affiliation(s)
- Guimin Chen
- Jiangsu Key Laboratory for Eco-Agricultural Biotechnology around Hongze Lake, School of Life Sciences, Huaiyin Normal University, Huai'an, China; Jiangsu Collaborative Innovation Centre of Regional Modern Agriculture & Environmental Protection, Huaiyin Normal University, Huai'an, China
| | - Yuzhen Zhou
- Jiangsu Key Laboratory for Eco-Agricultural Biotechnology around Hongze Lake, School of Life Sciences, Huaiyin Normal University, Huai'an, China; Jiangsu Collaborative Innovation Centre of Regional Modern Agriculture & Environmental Protection, Huaiyin Normal University, Huai'an, China.
| | - Olena Kishchenko
- Jiangsu Key Laboratory for Eco-Agricultural Biotechnology around Hongze Lake, School of Life Sciences, Huaiyin Normal University, Huai'an, China; Jiangsu Collaborative Innovation Centre of Regional Modern Agriculture & Environmental Protection, Huaiyin Normal University, Huai'an, China; Institute of Cell Biology & Genetic Engineering, National Academy of Science of Ukraine, Kyiv, Ukraine.
| | - Anton Stepanenko
- Jiangsu Key Laboratory for Eco-Agricultural Biotechnology around Hongze Lake, School of Life Sciences, Huaiyin Normal University, Huai'an, China; Jiangsu Collaborative Innovation Centre of Regional Modern Agriculture & Environmental Protection, Huaiyin Normal University, Huai'an, China; Institute of Cell Biology & Genetic Engineering, National Academy of Science of Ukraine, Kyiv, Ukraine.
| | - Satyvaldy Jatayev
- Faculty of Agronomy, S. Seifullin Kazakh AgroTechnical University, Nur-Sultan, Kazakhstan
| | - Dabing Zhang
- Joint International Research Laboratory of Metabolic & Developmental Sciences, Shanghai Jiao Tong University-University of Adelaide Joint Centre for Agriculture and Health, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China; School of Agriculture, Food and Wine, University of Adelaide, Glen Osmond, SA, Australia.
| | - Nikolai Borisjuk
- Jiangsu Key Laboratory for Eco-Agricultural Biotechnology around Hongze Lake, School of Life Sciences, Huaiyin Normal University, Huai'an, China; Jiangsu Collaborative Innovation Centre of Regional Modern Agriculture & Environmental Protection, Huaiyin Normal University, Huai'an, China.
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Molecular Control and Application of Male Fertility for Two-Line Hybrid Rice Breeding. Int J Mol Sci 2020; 21:ijms21217868. [PMID: 33114094 PMCID: PMC7660317 DOI: 10.3390/ijms21217868] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Revised: 10/10/2020] [Accepted: 10/11/2020] [Indexed: 01/24/2023] Open
Abstract
The significance of the climate change may involve enhancement of plant growth as well as utilization of the environmental alterations in male fertility (MF) regulation via male sterility (MS) systems. We described that MS systems provide a fundamental platform for improvement in agriculture production and have been explicated for creating bulk germplasm of the two-line hybrids (EGMS) in rice as compared to the three-line, to gain production sustainability and exploit its immense potential. Environmental alterations such as photoperiod and/or temperature and humidity regulate MS in EGMS lines via genetic and epigenetic changes, regulation of the noncoding RNAs, and RNA-metabolism including the transcriptional factors (TFs) implication. Herein, this article enlightens a deep understanding of the molecular control of MF in EGMS lines and exploring the regulatory driving forces that function efficiently during plant adaption under a changing environment. We highlighted a possible solution in obtaining more stable hybrids through apomixis (single-line system) for seed production.
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Kishchenko O, Zhou Y, Jatayev S, Shavrukov Y, Borisjuk N. Gene editing applications to modulate crop flowering time and seed dormancy. ABIOTECH 2020; 1:233-245. [PMID: 36304127 PMCID: PMC9590486 DOI: 10.1007/s42994-020-00032-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Accepted: 10/10/2020] [Indexed: 02/07/2023]
Abstract
Gene editing technologies such as CRISPR/Cas9 have been used to improve many agricultural traits, from disease resistance to grain quality. Now, emerging research has used CRISPR/Cas9 and other gene editing technologies to target plant reproduction, including major areas such as flowering time and seed dormancy. Traits related to these areas have important implications for agriculture, as manipulation of flowering time has multiple applications, including tailoring crops for regional adaptation and improving yield. Moreover, understanding seed dormancy will enable approaches to improve germination upon planting and prevent pre-harvest sprouting. Here, we summarize trends and recent advances in using gene editing to gain a better understanding of plant reproduction and apply the resulting information for crop improvement.
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Affiliation(s)
- Olena Kishchenko
- Jiangsu Key Laboratory for Eco-Agricultural Biotechnology around Hongze Lake, School of Life Sciences, Huaiyin Normal University, Huai’an, China
- Jiangsu Collaborative Innovation Centre of Regional Modern Agriculture and Environmental Protection, Huaiyin Normal University, Huai’an, China
- Institute of Cell Biology and Genetic Engineering, NAS of Ukraine, Kiev, Ukraine
| | - Yuzhen Zhou
- Jiangsu Key Laboratory for Eco-Agricultural Biotechnology around Hongze Lake, School of Life Sciences, Huaiyin Normal University, Huai’an, China
- Jiangsu Collaborative Innovation Centre of Regional Modern Agriculture and Environmental Protection, Huaiyin Normal University, Huai’an, China
| | - Satyvaldy Jatayev
- Faculty of Agronomy, S. Seifullin Kazakh AgroTechnical University, Nur-Sultan, Kazakhstan
| | - Yuri Shavrukov
- College of Science and Engineering, Biological Sciences, Flinders University, Adelaide, Australia
| | - Nikolai Borisjuk
- Jiangsu Key Laboratory for Eco-Agricultural Biotechnology around Hongze Lake, School of Life Sciences, Huaiyin Normal University, Huai’an, China
- Jiangsu Collaborative Innovation Centre of Regional Modern Agriculture and Environmental Protection, Huaiyin Normal University, Huai’an, China
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CRISPR/Cas9: A Robust Genome-Editing Tool with Versatile Functions and Endless Application. Int J Mol Sci 2020; 21:ijms21145111. [PMID: 32698333 PMCID: PMC7404002 DOI: 10.3390/ijms21145111] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Accepted: 07/17/2020] [Indexed: 02/07/2023] Open
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Ansari WA, Chandanshive SU, Bhatt V, Nadaf AB, Vats S, Katara JL, Sonah H, Deshmukh R. Genome Editing in Cereals: Approaches, Applications and Challenges. Int J Mol Sci 2020; 21:E4040. [PMID: 32516948 PMCID: PMC7312557 DOI: 10.3390/ijms21114040] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Revised: 12/18/2019] [Accepted: 12/19/2019] [Indexed: 12/13/2022] Open
Abstract
Over the past decades, numerous efforts were made towards the improvement of cereal crops mostly employing traditional or molecular breeding approaches. The current scenario made it possible to efficiently explore molecular understanding by targeting different genes to achieve desirable plants. To provide guaranteed food security for the rising world population particularly under vulnerable climatic condition, development of high yielding stress tolerant crops is needed. In this regard, technologies upgradation in the field of genome editing looks promising. Clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 is a rapidly growing genome editing technique being effectively applied in different organisms, that includes both model and crop plants. In recent times CRISPR/Cas9 is being considered as a technology which revolutionized fundamental as well as applied research in plant breeding. Genome editing using CRISPR/Cas9 system has been successfully demonstrated in many cereal crops including rice, wheat, maize, and barley. Availability of whole genome sequence information for number of crops along with the advancement in genome-editing techniques provides several possibilities to achieve desirable traits. In this review, the options available for crop improvement by implementing CRISPR/Cas9 based genome-editing techniques with special emphasis on cereal crops have been summarized. Recent advances providing opportunities to simultaneously edit many target genes were also discussed. The review also addressed recent advancements enabling precise base editing and gene expression modifications. In addition, the article also highlighted limitations such as transformation efficiency, specific promoters and most importantly the ethical and regulatory issues related to commercial release of novel crop varieties developed through genome editing.
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Affiliation(s)
- Waquar A. Ansari
- Department of Botany, Savitribai Phule Pune University, Pune 411007, India; (W.A.A.); (S.U.C.); (V.B.)
| | - Sonali U. Chandanshive
- Department of Botany, Savitribai Phule Pune University, Pune 411007, India; (W.A.A.); (S.U.C.); (V.B.)
| | - Vacha Bhatt
- Department of Botany, Savitribai Phule Pune University, Pune 411007, India; (W.A.A.); (S.U.C.); (V.B.)
| | - Altafhusain B. Nadaf
- Department of Botany, Savitribai Phule Pune University, Pune 411007, India; (W.A.A.); (S.U.C.); (V.B.)
| | - Sanskriti Vats
- Agri-Biotechnology Division, National Agri-Food Biotechnology Institute (NABI), Mohali 140306, India; (S.V.); (H.S.)
| | | | - Humira Sonah
- Agri-Biotechnology Division, National Agri-Food Biotechnology Institute (NABI), Mohali 140306, India; (S.V.); (H.S.)
| | - Rupesh Deshmukh
- Agri-Biotechnology Division, National Agri-Food Biotechnology Institute (NABI), Mohali 140306, India; (S.V.); (H.S.)
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