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Lorenzo CD, Blasco-Escámez D, Beauchet A, Wytynck P, Sanches M, Garcia Del Campo JR, Inzé D, Nelissen H. Maize mutant screens: from classical methods to new CRISPR-based approaches. THE NEW PHYTOLOGIST 2024. [PMID: 39212458 DOI: 10.1111/nph.20084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2024] [Accepted: 08/13/2024] [Indexed: 09/04/2024]
Abstract
Mutations play a pivotal role in shaping the trajectory and outcomes of a species evolution and domestication. Maize (Zea mays) has been a major staple crop and model for genetic research for more than 100 yr. With the arrival of site-directed mutagenesis and genome editing (GE) driven by the Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR), maize mutational research is once again in the spotlight. If we combine the powerful physiological and genetic characteristics of maize with the already available and ever increasing toolbox of CRISPR-Cas, prospects for its future trait engineering are very promising. This review aimed to give an overview of the progression and learnings of maize screening studies analyzing forward genetics, natural variation and reverse genetics to focus on recent GE approaches. We will highlight how each strategy and resource has contributed to our understanding of maize natural and induced trait variability and how this information could be used to design the next generation of mutational screenings.
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Affiliation(s)
- Christian Damian Lorenzo
- Center for Plant Systems Biology, VIB, B-9052, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052, Ghent, Belgium
| | - David Blasco-Escámez
- Center for Plant Systems Biology, VIB, B-9052, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052, Ghent, Belgium
| | - Arthur Beauchet
- Center for Plant Systems Biology, VIB, B-9052, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052, Ghent, Belgium
| | - Pieter Wytynck
- Center for Plant Systems Biology, VIB, B-9052, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052, Ghent, Belgium
| | - Matilde Sanches
- Center for Plant Systems Biology, VIB, B-9052, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052, Ghent, Belgium
| | - Jose Rodrigo Garcia Del Campo
- Center for Plant Systems Biology, VIB, B-9052, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052, Ghent, Belgium
| | - Dirk Inzé
- Center for Plant Systems Biology, VIB, B-9052, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052, Ghent, Belgium
| | - Hilde Nelissen
- Center for Plant Systems Biology, VIB, B-9052, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052, Ghent, Belgium
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Fang X, Li S, Kang W, Lin C, Wang J, Ke Q, Wang C, Wang Q, Chen Q. Enhanced algin oligosaccharide production through selective breeding and optimization of growth and degradation conditions in Cobetia sp. cqz5-12-M1. Sci Rep 2024; 14:19550. [PMID: 39174820 PMCID: PMC11341896 DOI: 10.1038/s41598-024-70472-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Accepted: 08/16/2024] [Indexed: 08/24/2024] Open
Abstract
Algin oligosaccharides have been applied in diverse industries and could be innovative synthesized by alginate-degrading bacteria. For enhance the alginate degradation efficiency to produce more algin oligosaccharides, a mutant strain (Cobetia sp. cqz5-12-M1) was obtained through the complex mutagenesis using UV and the alkylating agent 1-methyl-3-nitro-1-nitrosoguanidine. The enzyme activity of the fermentation supernatant of mutant exhibited a significant 38.09% (53.98 ± 0.69 U/mL) increase, and its optimal growth conditions were determined as: 5 g/L sodium alginate, 5 g/L yeast powder, 30 g/L NaCl, 2 g/L K2HPO4, 2 g/L KH2PO4, 1 g/L MgSO4•7H2O, 0.01 g/L FeSO4•7H2O, pH 6.5, and 34 ℃. Moreover, its optimal degradation conditions were identified as: 5 g/L sodium alginate, 5 g/L yeast powder, 30 g/L NaCl, 2 g/L K2HPO4, 2 g/L KH2PO4, 1 g/L MgSO4•7H2O, 0.01 g/L FeSO4•7H2O, pH 6.5, 31 ℃ and 72 h, yielding an enzyme activity of 120.98 ± 1.40 U/mL in the fermentation supernatant. Conclusive experiments on reagent tolerance revealed the growth of the mutant strain was significantly inhibited by 3% hydrogen peroxide, 5% carbolic acid, and 10 mg/mL gatifloxacin. Additionally, the alginate degradation capacity of mutant strain was highly significantly inhibited by 75% ethanol and all tested antibiotics.
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Affiliation(s)
- Xinru Fang
- College of Life and Environmental Science, Wenzhou University, Wenzhou, 325035, People's Republic of China
| | - Shuang Li
- College of Life and Environmental Science, Wenzhou University, Wenzhou, 325035, People's Republic of China
| | - Weixiao Kang
- College of Life and Environmental Science, Wenzhou University, Wenzhou, 325035, People's Republic of China
| | - Chaoyou Lin
- College of Life and Environmental Science, Wenzhou University, Wenzhou, 325035, People's Republic of China
| | - Jiangmei Wang
- College of Life and Environmental Science, Wenzhou University, Wenzhou, 325035, People's Republic of China
| | - Qiang Ke
- College of Life and Environmental Science, Wenzhou University, Wenzhou, 325035, People's Republic of China
| | - Chuanhua Wang
- College of Life and Environmental Science, Wenzhou University, Wenzhou, 325035, People's Republic of China
| | - Qi Wang
- College of Life and Environmental Science, Wenzhou University, Wenzhou, 325035, People's Republic of China
| | - Qiongzhen Chen
- College of Life and Environmental Science, Wenzhou University, Wenzhou, 325035, People's Republic of China.
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3
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Havlickova L, He Z, Berger M, Wang L, Sandmann G, Chew YP, Yoshikawa GV, Lu G, Hu Q, Banga SS, Beaudoin F, Bancroft I. Genomics of predictive radiation mutagenesis in oilseed rape: modifying seed oil composition. PLANT BIOTECHNOLOGY JOURNAL 2024; 22:738-750. [PMID: 37921406 PMCID: PMC10893948 DOI: 10.1111/pbi.14220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Revised: 10/12/2023] [Accepted: 10/20/2023] [Indexed: 11/04/2023]
Abstract
Rapeseed is a crop of global importance but there is a need to broaden the genetic diversity available to address breeding objectives. Radiation mutagenesis, supported by genomics, has the potential to supersede genome editing for both gene knockout and copy number increase, but detailed knowledge of the molecular outcomes of radiation treatment is lacking. To address this, we produced a genome re-sequenced panel of 1133 M2 generation rapeseed plants and analysed large-scale deletions, single nucleotide variants and small insertion-deletion variants affecting gene open reading frames. We show that high radiation doses (2000 Gy) are tolerated, gamma radiation and fast neutron radiation have similar impacts and that segments deleted from the genomes of some plants are inherited as additional copies by their siblings, enabling gene dosage decrease. Of relevance for species with larger genomes, we showed that these large-scale impacts can also be detected using transcriptome re-sequencing. To test the utility of the approach for predictive alteration of oil fatty acid composition, we produced lines with both decreased and increased copy numbers of Bna.FAE1 and confirmed the anticipated impacts on erucic acid content. We detected and tested a 21-base deletion expected to abolish function of Bna.FAD2.A5, for which we confirmed the predicted reduction in seed oil polyunsaturated fatty acid content. Our improved understanding of the molecular effects of radiation mutagenesis will underpin genomics-led approaches to more efficient introduction of novel genetic variation into the breeding of this crop and provides an exemplar for the predictive improvement of other crops.
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Affiliation(s)
| | - Zhesi He
- Department of BiologyUniversity of YorkYorkUK
| | | | - Lihong Wang
- Department of BiologyUniversity of YorkYorkUK
| | | | | | - Guilherme V. Yoshikawa
- Department of BiologyUniversity of YorkYorkUK
- Present address:
School of Agriculture, Food and Wine, Waite Research InstituteUniversity of AdelaideGlen OsmondSAAustralia
| | - Guangyuan Lu
- Department of Rapeseed Genetics and Breeding, Oil Crops Research InstituteCAASWuhanChina
- College of Biology and Food EngineeringGuangdong University of Petrochemical TechnologyMaomingChina
| | - Qiong Hu
- Department of Rapeseed Genetics and Breeding, Oil Crops Research InstituteCAASWuhanChina
| | - Surinder S. Banga
- Department of Plant Breeding and GeneticsPunjab Agricultural UniversityLudhianaIndia
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4
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Esquivel MM, Aboobucker SI, Suza WP. The impact of 'framing' in the adoption of GM crops. GM CROPS & FOOD 2023; 14:1-11. [PMID: 38100553 PMCID: PMC10730198 DOI: 10.1080/21645698.2023.2275723] [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: 07/27/2023] [Accepted: 10/23/2023] [Indexed: 12/17/2023]
Abstract
Genetically modified (GM) crops offer significant advantages in our crop improvement programs because they are created using a more targeted approach which is not possible in traditional breeding methods. Human benefit is one of the main objectives of crop improvement but the legal framework for the introduction of GM crops and the depiction and portrayal of GM crops in the media create barriers to these benefits. This article attempts to highlight the barriers to GM crop adoption particularly focusing on the idea of "framing" and the way GM technology is framed in the media. The resulting public health, economic, and ecological concerns about genetically modified plants, along with the reality of these misconceptions, are discussed with specific examples. Finally, we propose potential routes toward increased acceptance of GM crops.
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Affiliation(s)
| | | | - Walter P. Suza
- Department of Agronomy, Iowa State University, Ames, IA, USA
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Liu S, Jiang Y, Wang Y, Huo H, Cilkiz M, Chen P, Han Y, Li L, Wang K, Zhao M, Zhu L, Lei J, Wang Y, Zhang M. Genetic and molecular dissection of ginseng ( Panax ginseng Mey.) germplasm using high-density genic SNP markers, secondary metabolites, and gene expressions. FRONTIERS IN PLANT SCIENCE 2023; 14:1165349. [PMID: 37575919 PMCID: PMC10416250 DOI: 10.3389/fpls.2023.1165349] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Accepted: 06/27/2023] [Indexed: 08/15/2023]
Abstract
Genetic and molecular knowledge of a species is crucial to its gene discovery and enhanced breeding. Here, we report the genetic and molecular dissection of ginseng, an important herb for healthy food and medicine. A mini-core collection consisting of 344 cultivars and landraces was developed for ginseng that represents the genetic variation of ginseng existing in its origin and diversity center. We sequenced the transcriptomes of all 344 cultivars and landraces; identified over 1.5 million genic SNPs, thereby revealing the genic diversity of ginseng; and analyzed them with 26,600 high-quality genic SNPs or a selection of them. Ginseng had a wide molecular diversity and was clustered into three subpopulations. Analysis of 16 ginsenosides, the major bioactive components for healthy food and medicine, showed that ginseng had a wide variation in the contents of all 16 ginsenosides and an extensive correlation of their contents, suggesting that they are synthesized through a single or multiple correlated pathways. Furthermore, we pair-wisely examined the relationships between the cultivars and landraces, revealing their relationships in gene expression, gene variation, and ginsenoside biosynthesis. These results provide new knowledge and new genetic and genic resources for advanced research and breeding of ginseng and related species.
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Affiliation(s)
- Sizhang Liu
- College of Life Science, Jilin Agricultural University, Changchun, Jilin, China
| | - Yue Jiang
- College of Life Science, Jilin Agricultural University, Changchun, Jilin, China
| | - Yanfang Wang
- College of Chinese Medicinal Materials, Jilin Agricultural University, Changchun, Jilin, China
| | - Huimin Huo
- College of Life Science, Jilin Agricultural University, Changchun, Jilin, China
| | - Mustafa Cilkiz
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX, United States
| | - Ping Chen
- College of Life Science, Jilin Agricultural University, Changchun, Jilin, China
- Research Center for Ginseng Genetic Resources Development and Utilization, Jilin Province, Jilin Agricultural University, Changchun, Jilin, China
| | - Yilai Han
- College of Life Science, Jilin Agricultural University, Changchun, Jilin, China
| | - Li Li
- College of Life Science, Jilin Agricultural University, Changchun, Jilin, China
| | - Kangyu Wang
- College of Life Science, Jilin Agricultural University, Changchun, Jilin, China
- Research Center for Ginseng Genetic Resources Development and Utilization, Jilin Province, Jilin Agricultural University, Changchun, Jilin, China
| | - Mingzhu Zhao
- College of Life Science, Jilin Agricultural University, Changchun, Jilin, China
- Research Center for Ginseng Genetic Resources Development and Utilization, Jilin Province, Jilin Agricultural University, Changchun, Jilin, China
| | - Lei Zhu
- College of Life Science, Jilin Agricultural University, Changchun, Jilin, China
| | - Jun Lei
- College of Life Science, Jilin Agricultural University, Changchun, Jilin, China
- Research Center for Ginseng Genetic Resources Development and Utilization, Jilin Province, Jilin Agricultural University, Changchun, Jilin, China
| | - Yi Wang
- College of Life Science, Jilin Agricultural University, Changchun, Jilin, China
- Research Center for Ginseng Genetic Resources Development and Utilization, Jilin Province, Jilin Agricultural University, Changchun, Jilin, China
| | - Meiping Zhang
- College of Life Science, Jilin Agricultural University, Changchun, Jilin, China
- Research Center for Ginseng Genetic Resources Development and Utilization, Jilin Province, Jilin Agricultural University, Changchun, Jilin, China
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Shahwar D, Ahn N, Kim D, Ahn W, Park Y. Mutagenesis-based plant breeding approaches and genome engineering: A review focused on tomato. MUTATION RESEARCH. REVIEWS IN MUTATION RESEARCH 2023; 792:108473. [PMID: 37716439 DOI: 10.1016/j.mrrev.2023.108473] [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: 03/09/2023] [Revised: 09/08/2023] [Accepted: 09/08/2023] [Indexed: 09/18/2023]
Abstract
Breeding is the most important and efficient method for crop improvement involving repeated modification of the genetic makeup of a plant population over many generations. In this review, various accessible breeding approaches, such as conventional breeding and mutation breeding (physical and chemical mutagenesis and insertional mutagenesis), are discussed with respect to the actual impact of research on the economic improvement of tomato agriculture. Tomatoes are among the most economically important fruit crops consumed worldwide because of their high nutritional content and health-related benefits. Additionally, we summarize mutation-based mapping approaches, including Mutmap and MutChromeSeq, for the efficient mapping of several genes identified by random indel mutations that are beneficial for crop improvement. Difficulties and challenges in the adaptation of new genome editing techniques that provide opportunities to demonstrate precise mutations are also addressed. Lastly, this review focuses on various effective and convenient genome editing tools, such as RNA interference (RNAi), zinc finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs), and clustered regularly interspaced short palindromic repeats (CRISPR/Cas9), and their potential for the improvement of numerous desirable traits to allow the development of better varieties of tomato and other horticultural crops.
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Affiliation(s)
- Durre Shahwar
- Department of Horticultural Bioscience, Pusan National University, Miryang 50463, Republic of Korea
| | - Namju Ahn
- Daenong Seed Company, Hwasun-gun 58155, Republic of Korea
| | - Donghyun Kim
- Daenong Seed Company, Hwasun-gun 58155, Republic of Korea
| | - Wooseong Ahn
- Daenong Seed Company, Hwasun-gun 58155, Republic of Korea
| | - Younghoon Park
- Department of Horticultural Bioscience, Pusan National University, Miryang 50463, Republic of Korea.
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7
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Alfredo Zambrano J, Thyagarajan A, Sardari RR, Olsson O. Characterization of high Arabinoxylan oat lines identified from a mutagenized oat population. Food Chem 2023; 404:134687. [DOI: 10.1016/j.foodchem.2022.134687] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 10/11/2022] [Accepted: 10/16/2022] [Indexed: 11/07/2022]
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An Overview of Molecular Basis and Genetic Modification of Floral Organs Genes: Impact of Next-Generation Sequencing. Mol Biotechnol 2022; 65:833-848. [DOI: 10.1007/s12033-022-00633-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Accepted: 12/01/2022] [Indexed: 12/24/2022]
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9
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Sun K, Li D, Xia A, Zhao H, Wen Q, Jia S, Wang J, Yang G, Zhou D, Huang C, Wang H, Chen Z, Guo T. Targeted Identification of Rice Grain-Associated Gene Allelic Variation Through Mutation Induction, Targeted Sequencing, and Whole Genome Sequencing Combined with a Mixed-Samples Strategy. RICE (NEW YORK, N.Y.) 2022; 15:57. [PMID: 36326973 PMCID: PMC9633910 DOI: 10.1186/s12284-022-00603-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Accepted: 10/21/2022] [Indexed: 06/16/2023]
Abstract
BACKGROUND The mining of new allelic variation and the induction of new genetic variability are the basis for improving breeding efficiency. RESULTS In this study, in total, 3872 heavy ion-irradiated M2 generation rice seeds and individual leaves were collected. The grain length was between 8 and 10.22 mm. The grain width was between 1.54 and 2.87 mm. The results showed that there was extensive variation in granulotype. The allelic variation in GS3 and GW5 was detected in 484 mixed samples (8:1) using targeted sequencing technology, and 12 mixed samples containing potential mutations and 15 SNPs were obtained; combined with Sanger sequencing and phenotype data, 13 key mutants and their corresponding SNPs were obtained; protein structural and functional analysis of key mutants screened out 6 allelic variants leading to altered grain shape, as well as the corresponding mutants, including long-grain mutants GS3-2 and GS3-7, short-grain mutants GS3-3 and GS3-5, wide-grain mutant GW5-1 and narrow-grain mutant GW5-4; whole genome sequencing identified new grain length gene allelic variants GS3-G1, GS3-G2 and GS3-G3. CONCLUSION Based on the above studies, we found 6 granulotype mutants and 9 granulotype-related allelic variants, which provided new functional gene loci and a material basis for molecular breeding and genotype mutation and phenotype analysis. We propose a method for targeted identification of allelic variation in rice grain type genes by combining targeted sequencing of mixed samples and whole genome sequencing. The method has the characteristics of low detection cost, short detection period, and flexible detection of traits and genes.
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Affiliation(s)
- Kai Sun
- National Engineering Research Center of Plant Space Breeding, South China Agricultural University, 510642, Guangzhou, People's Republic of China
| | - Dandan Li
- National Engineering Research Center of Plant Space Breeding, South China Agricultural University, 510642, Guangzhou, People's Republic of China
| | - Aoyun Xia
- National Engineering Research Center of Plant Space Breeding, South China Agricultural University, 510642, Guangzhou, People's Republic of China
| | - Hua Zhao
- National Engineering Research Center of Plant Space Breeding, South China Agricultural University, 510642, Guangzhou, People's Republic of China
| | - Qin Wen
- National Engineering Research Center of Plant Space Breeding, South China Agricultural University, 510642, Guangzhou, People's Republic of China
| | - Sisi Jia
- National Engineering Research Center of Plant Space Breeding, South China Agricultural University, 510642, Guangzhou, People's Republic of China
| | - Jiafeng Wang
- National Engineering Research Center of Plant Space Breeding, South China Agricultural University, 510642, Guangzhou, People's Republic of China
| | - Guili Yang
- National Engineering Research Center of Plant Space Breeding, South China Agricultural University, 510642, Guangzhou, People's Republic of China
| | - Danhua Zhou
- National Engineering Research Center of Plant Space Breeding, South China Agricultural University, 510642, Guangzhou, People's Republic of China
| | - Cuihong Huang
- National Engineering Research Center of Plant Space Breeding, South China Agricultural University, 510642, Guangzhou, People's Republic of China
| | - Hui Wang
- National Engineering Research Center of Plant Space Breeding, South China Agricultural University, 510642, Guangzhou, People's Republic of China
| | - Zhiqiang Chen
- National Engineering Research Center of Plant Space Breeding, South China Agricultural University, 510642, Guangzhou, People's Republic of China
| | - Tao Guo
- National Engineering Research Center of Plant Space Breeding, South China Agricultural University, 510642, Guangzhou, People's Republic of China.
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Kalendar R, Hunter C, Orbovic V. Editorial: Innovative applications of sequencing technologies in plant science. FRONTIERS IN PLANT SCIENCE 2022; 13:1058347. [PMID: 36388574 PMCID: PMC9644194 DOI: 10.3389/fpls.2022.1058347] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 10/11/2022] [Indexed: 05/28/2023]
Affiliation(s)
- Ruslan Kalendar
- Helsinki Institute of Life Science HiLIFE, Biocenter 3, University of Helsinki, Helsinki, Finland
- National Laboratory Astana, Nazarbayev University, Astana, Kazakhstan
| | - Charles Hunter
- Chemistry Research Unit, United States Department of Agriculture (USDA) Agricultural Research Service, Gainesville, FL, United States
| | - Vladimir Orbovic
- Citrus Research and Education Center, University of Florida/Institute of Food and Agricultural Sciences (IFAS), Lake Alfred, FL, United States
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A Tomato EMS-Mutagenized Population Provides New Valuable Resources for Gene Discovery and Breeding of Developmental Traits. PLANTS 2022; 11:plants11192453. [PMID: 36235319 PMCID: PMC9571841 DOI: 10.3390/plants11192453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 09/12/2022] [Accepted: 09/13/2022] [Indexed: 11/23/2022]
Abstract
Tomato (Solanum lycopersicum L.) is a major horticultural crop and a model species among eudicots, especially for traits related to reproductive development. Although considerable progress has been made since the tomato genome sequence project was completed, most of the genes identified remain predictions with an unknown or hypothetical function. This lack of functional characterization hampers the use of the huge amount of genomic information available to improve the quality and productivity of this crop. Reverse genetics strategies such as artificial mutagenesis and next-generation sequencing approaches build the perfect tandem for increasing knowledge on functional annotation of tomato genes. This work reports the phenotypic characterization of a tomato mutant collection generated from an EMS chemical mutagenesis program aimed to identify interesting agronomic mutants and novel gene functions. Tomato mutants were grouped into fourteen phenotypic classes, including vegetative and reproductive development traits, and the inheritance pattern of the identified mutations was studied. In addition, causal mutation of a selected mutant line was isolated through a mapping-by-sequencing approach as a proof of concept of this strategy’s successful implementation. Results support tomato mutagenesis as an essential tool for functional genomics in this fleshy-fruited model species and a highly valuable resource for future breeding programs of this crop species aimed at the development of more productive and resilient new varieties under challenging climatic and production scenarios.
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Pandey PK, Bhowmik P, Kagale S. Optimized methods for random and targeted mutagenesis in field pea ( Pisum sativum L.). FRONTIERS IN PLANT SCIENCE 2022; 13:995542. [PMID: 36160971 PMCID: PMC9498975 DOI: 10.3389/fpls.2022.995542] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/16/2022] [Accepted: 08/19/2022] [Indexed: 06/16/2023]
Abstract
Field pea is an important pulse crop for its dense nutritional profile and contribution to sustainable agricultural practices. Recently, it has received extensive attention as a potential leading source of plant-based proteins. However, the adoption of peas as a mainstream source of proteins is affected by a relatively moderate protein content, anti-nutritional factors and high levels of off-flavor components that reduce protein quality. Availability of genetic variation for desirable seed quality traits is the foundation for the sustainable development of pea varieties with improved protein content and quality. Mutagenesis has been an important tool in gene functional characterization studies and creating genetic variability for crop breeding. Large-scale mutagenesis of a crop using physical and chemical agents requires diligent selection of the mutagen and optimization of its dose to increase the frequency of mutations. In this study, we present detailed optimized protocols for physical and chemical mutagenesis of pea using gamma irradiation and ethyl methanesulfonate (EMS), respectively. Gamma radiation and EMS titration kill curves were established to identify optimal doses of the two mutagenic agents. Based on germination, survival rate and growth phenotypes, a gamma radiation dose of 225 Gy and EMS concentration of 5 mm were selected as optimal dosages for mutagenesis in field pea. The presented protocol has been modified from previously established mutagenesis protocols in other crop plants. Our results indicate that the optimal mutagen dosage is genotype dependent. CRISPR/Cas-based gene editing provides a precise and rapid method for targeted genetic manipulation in plants. With the recent success of gene editing in pea using CRISPR/Cas, this innovative technology is expected to become an integral component of the gene discovery and crop improvement toolkit in pea. Here, we describe an optimized methods for targeted mutagenesis of pea protoplasts, including mesophyll protoplast extraction, PEG-mediated transformation and gene editing of a LOX gene using CRISPR/Cas system. The general strategies and methods of mutagenesis described here provide an essential resource for mutation breeding and functional genomics studies in pea. These methods also provide a foundation for similar studies in other crops.
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13
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Türkoğlu A, Tosun M, Haliloğlu K. Mutagenic effects of sodium azide on in vitro mutagenesis, polymorphism and genomic instability in wheat (Triticum aestivum L.). Mol Biol Rep 2022; 49:10165-10174. [PMID: 36029431 DOI: 10.1007/s11033-022-07896-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Accepted: 08/22/2022] [Indexed: 10/15/2022]
Abstract
INTRODUCTION Breeding studies are commonly conducted to develop new cultivars with high yield levels and improved quality traits. Chemically-induced mutations are used to create genetic variations in wheat genomes. Various physical and chemical mutagens are used to increase frequency of mutations and facilitate the selection processes. Sodium azide (SA) is largely employed to induce mutations of the genes regulating essential traits. Such mutations may also elucidate gene functions of the mutant phenotypes. Present experiments were conducted to investigate potential use of conventional chemical mutagenesis technique through SA for mature embryo culture in wheat. METHODS AND RESULTS Sodium azide mutagenesis was experimented with 4 treatment durations (1, 2, 3 and 4 h) and 5 treatment concentrations (0, 1, 2, 3 and 4 mM). Mature embryos were subjected to experimental treatments to detect optimum doses of mutagenesis and to estimate polymorphism and genomic instability. Primarily, 50% reduction in number of regenerated plants as compared to the control (LD50) was adopted as the optimum dose. Based on LD50 criterion, the optimum value was achieved at 1 h duration of 4 mM SA concentration. Afterwards, inter-primer binding site markers were applied to investigate polymorphism and genomic instability in the regenerated plants. CONCLUSIONS Present findings revealed that efficiency of chemical mutagenesis could be improved through the use of molecular technology and such mutations may assist plant breeders in developing high-yield cultivars.
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Affiliation(s)
- Aras Türkoğlu
- Department of Field Crops, Faculty of Agriculture, Necmettin Erbakan University, Konya, Türkiye.
| | - Metin Tosun
- Department of Field Crops, Faculty of Agriculture, Ataturk University, Erzurum, Türkiye
| | - Kamil Haliloğlu
- Department of Field Crops, Faculty of Agriculture, Ataturk University, Erzurum, Türkiye.,Department of Biology, Faculty of Science, Cankiri Karatekin University, Cankırı, Türkiye
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Mujib A, Fatima S, Malik MQ. Gamma ray-induced tissue responses and improved secondary metabolites accumulation in Catharanthus roseus. Appl Microbiol Biotechnol 2022; 106:6109-6123. [PMID: 35962802 DOI: 10.1007/s00253-022-12122-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 07/29/2022] [Accepted: 08/02/2022] [Indexed: 11/30/2022]
Abstract
The present study investigated the impact of gamma ray irradiation on callus biomass growth and the yield of vincristine and vinblastine of in vitro grown tissues of Catharanthus roseus. The biochemical alteration underlying the synthesis of secondary metabolites has also been studied and a comparison of yield was prepared. The embryogenic tissues were exposed to 20, 40, 60, 80, and 100 Gy gamma ray doses and the callus biomass fresh weight, the embryogenesis (the embryo numbers, germination, plant regeneration), the alteration of protein, proline, and sugar attributes at different morphogenetic stages were monitored. The callus biomass growth was maximum (1.65 g) in 20 Gy exposed tissues and was less in 100 Gy treatment (0.33 g). The gamma-irradiated embryogenic tissues differentiated into embryos but the embryogenesis % and somatic embryo number per culture reduced with increasing doses. It was least in 80 Gy where very low numbers of embryos were formed (3.45 and 3.30 mean torpedo and cotyledonary embryo numbers per callus mass, respectively) which later germinated into plantlets. Protein, proline, sugar, and different antioxidant enzymes, i.e., superoxide dismutase (SOD), ascorbate peroxidase (APX), and catalase (CAT) activities, were investigated as the tissues were exposed to gamma ray elicitation/signaling, evoking cellular stress. Increased 80 Gy gamma dose inhibited a 42.73% decrease in protein accumulation at initiation stages of embryogenic tissue. Soluble sugar level also declined gradually being least in 80 Gy treated tissues (14.51 mg gm-1 FW) compared to control (20.2 mg gm-1 FW). Proline content, however, increased with increasing gamma doses, maximum at 80 Gy (8.28 mg gm-1 FW). The SOD, APX, and CAT activity increased linearly with enhanced level of gamma doses and maximum, i.e., 3.91 EU min-1 mg-1, 1.71 EU min-1 mg-1, and 4.89 EU min-1 mg-1, protein activity was noted for SOD, APX, and CAT, respectively, at 80 Gy gamma rays treated tissues. The quantification of vinblastine and vincristine in gamma ray elicitated tissues was made by using high-pressure thin layer chromatography (HPTLC). Somatic embryo-regenerated plant's leaves had the maximum yield of vinblastine (15.13 µgm gm-1 DW) at 40 Gy irradiation dose compared to control (13.30 µgm gm-1 DW)-the increased yield % is 13.75. The stem is also rich source producing 11.98 µgm gm-1 DW of vinblastine. Among the various developmental stages of embryos, vinblastine content was highest in germinating stage of embryos (10.14 µgm gm-1 DW) compared to other three, i.e., initiation, proliferation, and maturation embryo stages. Similarly, highest accumulation of vincristine (6.32 µg gm-1 DW) was noted at low gamma irradiation dose (20 Gy) in leaf tissues. The present study indicates that the synthesis of vinblastine and vincristine was growth- and development-specific and the lower 20-40 Gy gamma levels were more effective in enriching alkaloids while higher doses declined yield. KEY POINTS: • Vinblastine and vincristine yield was quantified in in vitro grown tissues and leaves of embryo regenerated Catharanthus roseus after gamma ray treatment. • The accumulation of vinblastine and vincristine was maximum in regenerated leaves; low doses were more efficient in improving yield. • Gamma ray irradiation impacted biochemical profiles, caused cellular stress, and perhaps responsible for improved alkaloid yield.
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Affiliation(s)
- A Mujib
- Cellular Differentiation and Molecular Genetics Section, Department of Botany, Jamia Hamdard, New Delhi, India.
| | - Samar Fatima
- Cellular Differentiation and Molecular Genetics Section, Department of Botany, Jamia Hamdard, New Delhi, India
| | - Moien Qadir Malik
- Cellular Differentiation and Molecular Genetics Section, Department of Botany, Jamia Hamdard, New Delhi, India
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Opoku Gyamfi M, Eleblu JSY, Sarfoa LG, Asante IK, Opoku-Agyemang F, Danquah EY. Induced variations of ethyl methane sulfonate mutagenized cowpea ( Vigna unguiculata L. walp) plants. FRONTIERS IN PLANT SCIENCE 2022; 13:952247. [PMID: 36003816 PMCID: PMC9394701 DOI: 10.3389/fpls.2022.952247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Accepted: 07/18/2022] [Indexed: 06/15/2023]
Abstract
Unique variants are desired in the development of genetically improved crops to meet farmer and market needs hence ethyl methane sulfonate (EMS) was used to induce genetic variability in cowpea (Vigna unguiculata cv. Asontem). The main objective of this research was to characterize induced variations in EMS chemically mutagenized population of cowpea (Vigna unguiculata L. Walp Var. Asontem) in the M1 and M2 generations. The optimum concentration (LD50) of EMS for generating the mutagenized population was determined by treating seeds with different concentrations of EMS (0.0, 0.2, 0.4, 0.6, and 0.8% v/v) and observing the germination count after 5 days of planting the seeds in Petri dishes. Three thousand cowpea seeds were treated with the 0.4% EMS to generate the M1 and M2 populations that were evaluated for agronomic and morphological traits with untreated seeds serving as control. Data analysis involved distribution of qualitative and quantitative traits. Germination was significantly reduced in the mutagenized population (17.8%) and compared with that of the wild type (61.6%). Percentage survival was significantly higher in wild type (98.38%) as compared with the M1 population (78.46%). Percentage germination in the M2 population (74.03%) was lower than the wild type (80%). A wide spectrum of agro-morphological abnormalities was observed in the M2 population. Wide variations and uniquely different phenotypic classes were observed in leaf color, leaf shape, growth habit, plant pigmentation, twining tendency, pod curvature, seed shape, and seed coat color. M2 individuals were widely distributed for days to flowering, number of pods per plant, number of seeds per pod, number of locules per pods, percentage seed set, pod length and number of seeds per plant. In conclusion, the EMS mutagenesis was effective in inducing the unique variations that will be useful for breeding and development of new farmer preferred varieties.
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Affiliation(s)
- Muhammed Opoku Gyamfi
- West Africa Centre for Crop Improvement, College of Basic and Applied Sciences, University of Ghana, Accra, Ghana
- Department of Crop Science, School of Agriculture, University of Ghana, Accra, Ghana
| | - John Saviour Yaw Eleblu
- West Africa Centre for Crop Improvement, College of Basic and Applied Sciences, University of Ghana, Accra, Ghana
- Biotechnology Centre, College of Basic and Applied Sciences, University of Ghana, Accra, Ghana
| | - Lawrencia Gyamfi Sarfoa
- Department of Crop Science, School of Agriculture, University of Ghana, Accra, Ghana
- Biotechnology Centre, College of Basic and Applied Sciences, University of Ghana, Accra, Ghana
| | - Isaac Kojo Asante
- West Africa Centre for Crop Improvement, College of Basic and Applied Sciences, University of Ghana, Accra, Ghana
- Department of Plant and Environmental Biology, University of Ghana, Accra, Ghana
| | - Frank Opoku-Agyemang
- West Africa Centre for Crop Improvement, College of Basic and Applied Sciences, University of Ghana, Accra, Ghana
- Department of Crop Science, School of Agriculture, University of Ghana, Accra, Ghana
| | - Eric Yirenkyi Danquah
- West Africa Centre for Crop Improvement, College of Basic and Applied Sciences, University of Ghana, Accra, Ghana
- Department of Crop Science, School of Agriculture, University of Ghana, Accra, Ghana
- Biotechnology Centre, College of Basic and Applied Sciences, University of Ghana, Accra, Ghana
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Li Y, Gu J, Irshad A, Zhao L, Guo H, Xiong H, Xie Y, Zhao S, Ding Y, Zhou L, Kong F, Fang Z, Liu L. Physiological and Differential Proteomic Analysis at Seedling Stage by Induction of Heavy-Ion Beam Radiation in Wheat Seeds. Front Genet 2022; 13:942806. [PMID: 35928451 PMCID: PMC9343878 DOI: 10.3389/fgene.2022.942806] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Accepted: 06/20/2022] [Indexed: 11/13/2022] Open
Abstract
Novel genetic variations can be obtained by inducing mutations in the plant which help to achieve novel traits. The useful mutant can be obtained through radiation mutation in a short period which can be used as a new material to produce new varieties with high yield and good quality wheat. In this paper, the proteomic analysis of wheat treated with different doses of 12C and 7Li ion beam radiation at the seedling stage was carried out through a Tandem Mass Tag (TMT) tagging quantitative proteomic analysis platform based on high-resolution liquid chromatography-mass spectrometry, and the traditional 60Co-γ-ray radiation treatment for reference. A total of 4,764 up-regulated and 5,542 down-regulated differentially expressed proteins were identified. These proteins were mainly enriched in the KEGG pathway associated with amino acid metabolism, fatty acid metabolism, carbon metabolism, photosynthesis, signal transduction, protein synthesis, and DNA replication. Functional analysis of the differentially expressed proteins showed that the oxidative defense system in the plant defense system was fully involved in the defense response after 12C ion beam and 7Li ion beam radiation treatments. Photosynthesis and photorespiration were inhibited after 12C ion beam and 60Co-γ-ray irradiation treatments, while there was no effect on the plant with 7Li ion beam treatment. In addition, the synthesis of biomolecules such as proteins, as well as multiple signal transduction pathways also respond to radiations. Some selected differentially expressed proteins were verified by Parallel Reaction Monitoring (PRM) and qPCR, and the experimental results were consistent with the quantitative results of TMT. The present study shows that the physiological effect of 12C ion beam radiation treatment is different as compared to the 7Li ion beam, but its similar to the 60Co-γ ray depicting a significant effect on the plant by using the same dose. The results of this study will provide a theoretical basis for the application of 12C and 7Li ion beam radiation in the mutation breeding of wheat and other major crops and promote the development of heavy ion beam radiation mutation breeding technology.
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Affiliation(s)
- Yuqi Li
- College of Agriculture, Yangtze University, Jingzhou, China
- National Key Facility for Crop Gene Resources and Genetic Improvement, National Center of Space Mutagenesis for Crop Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jiayu Gu
- National Key Facility for Crop Gene Resources and Genetic Improvement, National Center of Space Mutagenesis for Crop Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Ahsan Irshad
- National Key Facility for Crop Gene Resources and Genetic Improvement, National Center of Space Mutagenesis for Crop Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Linshu Zhao
- National Key Facility for Crop Gene Resources and Genetic Improvement, National Center of Space Mutagenesis for Crop Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Huijun Guo
- National Key Facility for Crop Gene Resources and Genetic Improvement, National Center of Space Mutagenesis for Crop Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Hongchun Xiong
- National Key Facility for Crop Gene Resources and Genetic Improvement, National Center of Space Mutagenesis for Crop Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yongdun Xie
- National Key Facility for Crop Gene Resources and Genetic Improvement, National Center of Space Mutagenesis for Crop Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Shirong Zhao
- National Key Facility for Crop Gene Resources and Genetic Improvement, National Center of Space Mutagenesis for Crop Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yuping Ding
- National Key Facility for Crop Gene Resources and Genetic Improvement, National Center of Space Mutagenesis for Crop Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Libin Zhou
- Biophysics Group, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, China
| | - Fuquan Kong
- China Institute of Atomic Energy, Beijing, China
| | - Zhengwu Fang
- College of Agriculture, Yangtze University, Jingzhou, China
- *Correspondence: Luxiang Liu, ; Zhengwu Fang,
| | - Luxiang Liu
- National Key Facility for Crop Gene Resources and Genetic Improvement, National Center of Space Mutagenesis for Crop Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
- *Correspondence: Luxiang Liu, ; Zhengwu Fang,
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Pan-utai W, Iamtham S, Roytrakul S, Settachaimongkon S, Wattanasiritham LS, Boonbumrung S, Mookdasanit J, Sithtisarn S. Arthrospira platensis Mutagenesis for Protein and C-Phycocyanin Improvement and Proteomics Approaches. LIFE (BASEL, SWITZERLAND) 2022; 12:life12060911. [PMID: 35743942 PMCID: PMC9227609 DOI: 10.3390/life12060911] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 06/12/2022] [Accepted: 06/15/2022] [Indexed: 01/07/2023]
Abstract
Arthrospira (Spirulina) platensis is known for its use as a food supplement, with reported therapeutic properties including antiviral, anti-inflammatory and antioxidant activity. Arthrospira is also an excellent source of proteins and C-phycocyanin. The latter is a light-harvesting pigment-protein complex in cyanobacteria, located on the outer surface of the thylakoid membrane and comprising 40 to 60% of the total soluble protein in cells. Random mutagenesis is a useful tool as a non-genetically modified mutation method that has been widely used to generate mutants of different microorganisms. Exposure of microalgae or cyanobacteria to chemical stimuli affects their growth and many biological processes. Chemicals influence several proteins, including those involved in carbohydrate and energy metabolisms, photosynthesis and stress-related proteins (oxidative stress-reactive oxygen species (ROS) scavenging enzymes). Signal transduction pathways and ion transportation mechanisms are also impacted by chemical treatment, with changes causing the production of numerous biomolecules and stimulation of defence responses. This study compared the protein contents of A. platensis control and after mutagenesis using diethyl sulphate (DES) under various treatment concentrations for effective mutation of A. platensis. Results identified 1152 peptides using proteomics approaches. The proteins were classified into 23 functional categories. Random mutagenesis of A. platensis by DES was found to be highly effective for C-phycocyanin and protein production.
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Affiliation(s)
- Wanida Pan-utai
- Department of Applied Microbiology, Institute of Food Research and Product Development, Kasetsart University, Chatuchak, Bangkok 10900, Thailand;
- Correspondence:
| | - Siriluck Iamtham
- Department of Science, Faculty of Liberal Arts and Science, Kasetsart University, Kamphaeng Saen, Nakhon Pathom 73140, Thailand;
- Center for Agricultural Biotechnology, Kasetsart University, Kamphaeng Saen Campus, Nakhon Pathom 73140, Thailand
- Center of Excellence on Agricultural Biotechnology: (AG-BIO/PERDO-CHE), Bangkok 10900, Thailand
| | - Sittiruk Roytrakul
- Functional Ingredients and Food Innovation Research Group, National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Phahonyothin Rd., Pathum Thani 12120, Thailand;
| | - Sarn Settachaimongkon
- Department of Food Technology, Faculty of Science, Chulalongkorn University, Pathumwan, Bangkok 10330, Thailand;
| | - Ladda Sangduean Wattanasiritham
- Department of Food Chemistry and Physics, Institute of Food Research and Product Development, Kasetsart University, Chatuchak, Bangkok 10900, Thailand; (L.S.W.); (S.B.)
| | - Sumitra Boonbumrung
- Department of Food Chemistry and Physics, Institute of Food Research and Product Development, Kasetsart University, Chatuchak, Bangkok 10900, Thailand; (L.S.W.); (S.B.)
| | - Juta Mookdasanit
- Department of Fishery Products, Faculty of Fisheries, Kasetsart University, Chatuchak, Bangkok 10900, Thailand;
| | - Sayamon Sithtisarn
- Department of Applied Microbiology, Institute of Food Research and Product Development, Kasetsart University, Chatuchak, Bangkok 10900, Thailand;
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Uranga M, Daròs JA. Tools and targets: The dual role of plant viruses in CRISPR-Cas genome editing. THE PLANT GENOME 2022:e20220. [PMID: 35698891 DOI: 10.1002/tpg2.20220] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Accepted: 03/31/2022] [Indexed: 06/15/2023]
Abstract
The recent emergence of tools based on the clustered, regularly interspaced, short palindromic repeats (CRISPR) and CRISPR-associated (Cas) proteins have revolutionized targeted genome editing, thus holding great promise to both basic plant science and precision crop breeding. Conventional approaches for the delivery of editing components rely on transformation technologies or transient delivery to protoplasts, both of which are time-consuming, laborious, and can raise legal concerns. Alternatively, plant RNA viruses can be used as transient delivery vectors of CRISPR-Cas reaction components, following the so-called virus-induced genome editing (VIGE). During the last years, researchers have been able to engineer viral vectors for the delivery of CRISPR guide RNAs and Cas nucleases. Considering that each viral vector is limited to its molecular biology properties and a specific host range, here we review recent advances for improving the VIGE toolbox with a special focus on strategies to achieve tissue-culture-free editing in plants. We also explore the utility of CRISPR-Cas technology to enhance biotic resistance with a special focus on plant virus diseases. This can be achieved by either targeting the viral genome or modifying essential host susceptibility genes that mediate in the infection process. Finally, we discuss the challenges and potential that VIGE holds in future breeding technologies.
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Affiliation(s)
- Mireia Uranga
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas - University. Politècnica de València, Valencia, 46022, Spain
| | - José-Antonio Daròs
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas - University. Politècnica de València, Valencia, 46022, Spain
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19
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CRISPR/Cas technology for improving nutritional values in the agricultural sector: an update. Mol Biol Rep 2022; 49:7101-7110. [PMID: 35568789 DOI: 10.1007/s11033-022-07523-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Accepted: 04/26/2022] [Indexed: 02/06/2023]
Abstract
BACKGROUND The CRISPR/Cas9 (clustered regularly interspaced short palindromic repeats/CRISPR-associated protein 9) system was initially identified in bacteria and archaea as a defense mechanism to confer immunity against phages. Later on, it was developed as a gene editing tool for both prokaryotic and eukaryotic cells including plant cells. METHODS AND RESULTS CRISPR/Cas9 approach has wider applications in reverse genetics as well as in crop improvement. Various characters involved in enhancing economic value and crop sustainability against biotic/abiotic stresses can be targeted through this tool. Currently, CRISPR/Cas9 gene editing mechanism has been applied on around 20 crop species for improvement in several traits including yield enhancement and resistance against biotic and abiotic stresses. In the last five years, maximum genome editing research has been validated in rice, wheat, maize and soybean. Genes targeted in these plants has been involved in causing male sterility, conferring resistance against pathogens or having certain nutritional value. CONCLUSIONS Current review summarizes various applications of CRISPR/Cas system and its future prospects in plant biotechnology targeting crop improvement with higher yield, disease tolerance and enhanced nutritional value.
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Wang C, Liu B, Chen M, Ning J, Lu X, Wang C. Mutations in Growth-Related Genes Induced by EMS Treatment in Scallops. Front Genet 2022; 13:879844. [PMID: 35559043 PMCID: PMC9086186 DOI: 10.3389/fgene.2022.879844] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2022] [Accepted: 03/18/2022] [Indexed: 11/13/2022] Open
Abstract
Background: The goal of genetic breeding is to select variants with mutations that are related to expected traits, such as fast growth. Artificial induction has been widely used to obtain strains with more mutations for further selection. Ethylmethylsulfone (EMS) is one of the most commonly used chemical mutagens in plant and microorganism breeding. However, the application of EMS mutagenesis in shellfish has not been reported. The aim of this study is to evaluate the potential use of EMS as a mutagen in scallop breeding, especially in characterization of mutations in growth-related genes. Results: Our results indicated that hatching of about 50% of fertilized eggs was blocked by treatment with 20 mM EMS for 3 h and the resulted larvae developed normally into adult stages. We then evaluated the mutagenic effects of EMS by sequencing the genomes of 4 adult scallops from the control group and 12 from the treatment group at 8 months after fertilization. On average, after removing shared types of mutations, there were 1,151,380 ± 258,188 SNPs (Single Nucleotide Polymorphisms) and 229,256 ± 51,714 InDels (insertion-deletion) in each animal in the EMS treatment group, while there were only134841 ± 10,115 SNPs and 42,605 ± 5,136 InDels in the control group. The average mutation rate in the genome of the EMS treatment group (0.0137 ± 0.0013%) was about 9 times that of the control group (0.0015 ± 0.0002%). GO (Gene Ontology) annotation and KEGG (Kyoto Encyclopedia of Genes and Genomes) enrichment analyses revealed that mutations induced by EMS occurred evenly in most biological processes, cellular components and functions, as well in most pathways. However, significant lower percentage of mutations were found in the exonic region, in non-synonymous or Stopgain/Stoploss SNPs and in coding domains, suggesting apparent DNA repair or selection during grow-out stage. Analyses of the growth-related genes with mutations indicated that mutations in MFS (Major Facilitator Superfamily) and Tubulin were only found in the large-sized group (Five largest scallops: Treated-1, Treated-2, Treated-3, Treated-4, and Treated-5) and Homeobox and Socs (Suppressor of cytokine signaling) only in the small group (Two smallest scallops: Treated-11 and Treated-12). These results suggested that these genes may be involved in the regulation of growth in these animals, although further verification is certainly warranted. Conclusion: Treatment of fertilized eggs with 20 mM EMS for 3 h induced 9 times more mutations in scallop genomes. We found that mutations in MFS and Tubulin may be related to fast growth in the large-sized group and those mutations in Homeobox and SOCs may be involved in the slow growth in the small-sized scallops. EMS can be used to accelerate selection of economically important traits in molluscs.
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Affiliation(s)
- Caihui Wang
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, China
| | - Bo Liu
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, China
| | - Min Chen
- Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, China
| | - Junhao Ning
- Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, China
| | - Xia Lu
- Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, China
| | - Chunde Wang
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, China
- Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, China
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Placido DF, Lee CC. Potential of Industrial Hemp for Phytoremediation of Heavy Metals. PLANTS (BASEL, SWITZERLAND) 2022; 11:plants11050595. [PMID: 35270065 PMCID: PMC8912475 DOI: 10.3390/plants11050595] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Revised: 02/09/2022] [Accepted: 02/16/2022] [Indexed: 05/27/2023]
Abstract
The accumulation of anthropogenic heavy metals in soil is a major form of pollution. Such potentially toxic elements are nonbiodegradable and persist for many years as threats to human and environmental health. Traditional forms of remediation are costly and potentially damaging to the land. An alternative strategy is phytoremediation, where plants are used to capture metals from the environment. Industrial hemp (Cannabis sativa) is a promising candidate for phytoremediation. Hemp has deep roots and is tolerant to the accumulation of different metals. In addition, the crop biomass has many potential commercial uses after harvesting is completed. Furthermore, the recent availability of an annotated genome sequence provides a powerful tool for the bioengineering of C. sativa for better phytoremediation.
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22
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Chhabra B, Singh L, Wallace S, Schoen A, Dong Y, Tiwari V, Rawat N. Screening of an Ethyl Methane Sulfonate Mutagenized Population of a Wheat Cultivar Susceptible to Fusarium Head Blight Identifies Resistant Variants. PLANT DISEASE 2021; 105:3669-3676. [PMID: 34132597 DOI: 10.1094/pdis-03-21-0670-re] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Fusarium head blight (FHB) primarily caused by Fusarium graminearum is a key disease of small grains. Diseased spikes show symptoms of premature bleaching shortly after infection and have aborted or shriveled seeds, resulting in reduced yields. The fungus also deteriorates quality and safety of the grain because of production of mycotoxins, especially deoxynivalenol (DON), which can result in grain being docked or rejected at the point of sale. Genetic host resistance to FHB is quantitative, and no complete genetic resistance against this devastating disease is available. Alternative approaches to develop new sources of FHB resistance are needed. In this study, we performed extensive forward genetic screening of the M4 generation of an ethyl methane sulfonate-induced mutagenized population of cultivar Jagger to isolate variants with FHB resistance. In field testing, 74 mutant lines were found to have resistance against FHB spread, and 30 of these lines also had low DON content. Subsequent testing over 2 years in controlled greenhouse conditions revealed 10 M6 lines showing significantly lower FHB spread. Seven and 6 of those 10 lines also had reduced DON content and fewer Fusarium-damaged kernels, respectively. Future endeavors will include identification of the mutations that led to resistance in these variants.
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Affiliation(s)
- Bhavit Chhabra
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD 20742
| | - Lovepreet Singh
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD 20742
| | - Sydney Wallace
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD 20742
| | - Adam Schoen
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD 20742
| | - Yanhong Dong
- Department of Plant Pathology, University of Minnesota, St. Paul, MN 55108
| | - Vijay Tiwari
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD 20742
| | - Nidhi Rawat
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD 20742
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Della Coletta R, Lavell AA, Garvin DF. A Homolog of the Arabidopsis TIME FOR COFFEE Gene Is Involved in Nonhost Resistance to Wheat Stem Rust in Brachypodium distachyon. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2021; 34:1298-1306. [PMID: 34340534 DOI: 10.1094/mpmi-06-21-0137-r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Plants resist infection by pathogens using both preexisting barriers and inducible defense responses. Inducible responses are governed in a complex manner by various hormone signaling pathways. The relative contribution of hormone signaling pathways to nonhost resistance to pathogens is not well understood. In this study, we examined the molecular basis of disrupted nonhost resistance to the fungal species Puccinia graminis, which causes stem rust of wheat, in an induced mutant of the model grass Brachypodium distachyon. Through bioinformatic analysis, a 1-bp deletion in the mutant genotype was identified that introduces a premature stop codon in the gene Bradi1g24100, which is a homolog of the Arabidopsis thaliana gene TIME FOR COFFEE (TIC). In Arabidopsis, TIC is central to the regulation of the circadian clock and plays a crucial role in jasmonate signaling by attenuating levels of the transcription factor protein MYC2, and its mutational disruption results in enhanced susceptibility to the hemibiotroph Pseudomonas syringae. Our similar finding for an obligate biotroph suggests that the biochemical role of TIC in mediating disease resistance to biotrophs is conserved in grasses, and that the correct modulation of jasmonate signaling during infection by Puccinia graminis may be essential for nonhost resistance to wheat stem rust in B. distachyon.[Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY 4.0 International license.
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Affiliation(s)
- Rafael Della Coletta
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN 55108, U.S.A
- CAPES Foundation, Ministry of Education of Brazil, Brasilia, DF, Brazil
| | - Anastasiya A Lavell
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN 55108, U.S.A
| | - David F Garvin
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN 55108, U.S.A
- Plant Science Research Unit, United States Department of Agriculture-Agricultural Research Service, St. Paul, MN 55108, U.S.A
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Sattar MN, Iqbal Z, Al-Khayri JM, Jain SM. Induced Genetic Variations in Fruit Trees Using New Breeding Tools: Food Security and Climate Resilience. PLANTS (BASEL, SWITZERLAND) 2021; 10:1347. [PMID: 34371550 PMCID: PMC8309169 DOI: 10.3390/plants10071347] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/22/2021] [Revised: 06/23/2021] [Accepted: 06/28/2021] [Indexed: 12/22/2022]
Abstract
Fruit trees provide essential nutrients to humans by contributing to major agricultural outputs and economic growth globally. However, major constraints to sustainable agricultural productivity are the uncontrolled proliferation of the population, and biotic and abiotic stresses. Tree mutation breeding has been substantially improved using different physical and chemical mutagens. Nonetheless, tree plant breeding has certain crucial bottlenecks including a long life cycle, ploidy level, occurrence of sequence polymorphisms, nature of parthenocarpic fruit development and linkage. Genetic engineering of trees has focused on boosting quality traits such as productivity, wood quality, and resistance to biotic and abiotic stresses. Recent technological advances in genome editing provide a unique opportunity for the genetic improvement of woody plants. This review examines application of the CRISPR-Cas system to reduce disease susceptibility, alter plant architecture, enhance fruit quality, and improve yields. Examples are discussed of the contemporary CRISPR-Cas system to engineer easily scorable PDS genes, modify lignin, and to alter the flowering onset, fertility, tree architecture and certain biotic stresses.
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Affiliation(s)
- Muhammad Naeem Sattar
- Central Laboratories, King Faisal University, Al-Ahsa 31982, Saudi Arabia; (M.N.S.); (Z.I.)
| | - Zafar Iqbal
- Central Laboratories, King Faisal University, Al-Ahsa 31982, Saudi Arabia; (M.N.S.); (Z.I.)
| | - Jameel M. Al-Khayri
- Department of Agricultural Biotechnology, College of Agriculture and Food Sciences, King Faisal University, Al-Ahsa 31982, Saudi Arabia
| | - S. Mohan Jain
- Department of Agricultural Sciences, PL-27, University of Helsinki, 00014 Helsinki, Finland;
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Liu Y, Huang S, Han J, Hou C, Zheng D, Zhang Z, Wu J. Development and Molecular Cytogenetic Identification of a New Wheat- Psathyrostachys huashanica Keng Translocation Line Resistant to Powdery Mildew. FRONTIERS IN PLANT SCIENCE 2021; 12:689502. [PMID: 34163516 PMCID: PMC8215663 DOI: 10.3389/fpls.2021.689502] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Accepted: 05/18/2021] [Indexed: 06/13/2023]
Abstract
Psathyrostachys huashanica Keng, a wild relative of common wheat with many desirable traits, is an invaluable source of genetic material for wheat improvement. Few wheat-P. huashanica translocation lines resistant to powdery mildew have been reported. In this study, a wheat-P. huashanica line, E24-3-1-6-2-1, was generated via distant hybridization, ethyl methanesulfonate (EMS) mutagenesis, and backcross breeding. A chromosome karyotype of 2n = 44 was observed at the mitotic stage in E24-3-1-6-2-1. Genomic in situ hybridization (GISH) analysis revealed four translocated chromosomes in E24-3-1-6-2-1, and P. huashanica chromosome-specific marker analysis showed that the alien chromosome fragment was from the P. huashanica 4Ns chromosome. Moreover, fluorescence in situ hybridization (FISH) analysis demonstrated that reciprocal translocation had occurred between the P. huashanica 4Ns chromosome and the wheat 3D chromosome; thus, E24-3-1-6-2-1 carried two translocations: T3DS·3DL-4NsL and T3DL-4NsS. Translocation also occurred between wheat chromosomes 2A and 4A. At the adult stage, E24-3-1-6-2-1 was highly resistant to powdery mildew, caused by prevalent pathotypes in China. Further, the spike length, numbers of fertile spikelets, kernels per spike, thousand-kernel weight, and grain yield of E24-3-1-6-2-1 were significantly higher than those of its wheat parent 7182 and addition line 24-6-3-1. Thus, this translocation line that is highly resistant to powdery mildew and has excellent agronomic traits can be used as a novel promising germplasm for breeding resistant and high-yielding cultivars.
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Affiliation(s)
- Yuxiu Liu
- College of Agronomy, Northwest A&F University, Yangling, China
| | - Shuhua Huang
- College of Horticulture, Northwest A&F University, Yangling, China
| | - Jing Han
- College of Agronomy, Northwest A&F University, Yangling, China
| | - Chenchen Hou
- College of Agronomy, Northwest A&F University, Yangling, China
| | - Dasheng Zheng
- College of Agronomy, Northwest A&F University, Yangling, China
| | - Zhengmao Zhang
- College of Agronomy, Northwest A&F University, Yangling, China
| | - Jun Wu
- College of Agronomy, Northwest A&F University, Yangling, China
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Abstract
Crop improvement relies heavily on genetic variation that arises spontaneously through mutation. Modern breeding methods are very adept at combining this genetic variation in ways that achieve remarkable improvements in plant performance. Novel traits have also been created through mutation breeding and transgenesis. The advent of gene editing, however, marks a turning point: With gene editing, synthetic variation will increasingly supplement and, in some cases, supplant the genetic variation that occurs naturally. We are still in the very early stages of realizing the opportunity provided by plant gene editing. At present, typically only one or a few genes are targeted for mutation at a time, and most mutations result in loss of gene function. New technological developments, however, promise to make it possible to perform gene editing at scale. RNA virus vectors, for example, can deliver gene-editing reagents to the germ line through infection and create hundreds to thousands of diverse mutations in the progeny of infected plants. With developmental regulators, edited somatic cells can be induced to form meristems that yield seed-producing shoots, thereby increasing throughput and shrinking timescales for creating edited plants. As these approaches are refined and others developed, they will allow for accelerated breeding, the domestication of orphan crops and the reengineering of metabolism in a more directed manner than has ever previously been possible.
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Affiliation(s)
- Ryan A Nasti
- Department of Genetics, Cell Biology and Development, Center for Genome Engineering, Center for Precision Plant Genomics, University of Minnesota, St. Paul, MN 55108
| | - Daniel F Voytas
- Department of Genetics, Cell Biology and Development, Center for Genome Engineering, Center for Precision Plant Genomics, University of Minnesota, St. Paul, MN 55108
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Zenda T, Liu S, Dong A, Duan H. Advances in Cereal Crop Genomics for Resilience under Climate Change. Life (Basel) 2021; 11:502. [PMID: 34072447 PMCID: PMC8228855 DOI: 10.3390/life11060502] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Revised: 05/21/2021] [Accepted: 05/25/2021] [Indexed: 12/12/2022] Open
Abstract
Adapting to climate change, providing sufficient human food and nutritional needs, and securing sufficient energy supplies will call for a radical transformation from the current conventional adaptation approaches to more broad-based and transformative alternatives. This entails diversifying the agricultural system and boosting productivity of major cereal crops through development of climate-resilient cultivars that can sustainably maintain higher yields under climate change conditions, expanding our focus to crop wild relatives, and better exploitation of underutilized crop species. This is facilitated by the recent developments in plant genomics, such as advances in genome sequencing, assembly, and annotation, as well as gene editing technologies, which have increased the availability of high-quality reference genomes for various model and non-model plant species. This has necessitated genomics-assisted breeding of crops, including underutilized species, consequently broadening genetic variation of the available germplasm; improving the discovery of novel alleles controlling important agronomic traits; and enhancing creation of new crop cultivars with improved tolerance to biotic and abiotic stresses and superior nutritive quality. Here, therefore, we summarize these recent developments in plant genomics and their application, with particular reference to cereal crops (including underutilized species). Particularly, we discuss genome sequencing approaches, quantitative trait loci (QTL) mapping and genome-wide association (GWAS) studies, directed mutagenesis, plant non-coding RNAs, precise gene editing technologies such as CRISPR-Cas9, and complementation of crop genotyping by crop phenotyping. We then conclude by providing an outlook that, as we step into the future, high-throughput phenotyping, pan-genomics, transposable elements analysis, and machine learning hold much promise for crop improvements related to climate resilience and nutritional superiority.
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Affiliation(s)
- Tinashe Zenda
- State Key Laboratory of North China Crop Improvement and Regulation, Hebei Agricultural University, Baoding 071001, China; (S.L.); (A.D.)
- North China Key Laboratory for Crop Germplasm Resources of the Education Ministry, Hebei Agricultural University, Baoding 071001, China
- Department of Crop Genetics and Breeding, College of Agronomy, Hebei Agricultural University, Baoding 071001, China
- Department of Crop Science, Faculty of Agriculture and Environmental Science, Bindura University of Science Education, Bindura P. Bag 1020, Zimbabwe
| | - Songtao Liu
- State Key Laboratory of North China Crop Improvement and Regulation, Hebei Agricultural University, Baoding 071001, China; (S.L.); (A.D.)
- North China Key Laboratory for Crop Germplasm Resources of the Education Ministry, Hebei Agricultural University, Baoding 071001, China
- Department of Crop Genetics and Breeding, College of Agronomy, Hebei Agricultural University, Baoding 071001, China
| | - Anyi Dong
- State Key Laboratory of North China Crop Improvement and Regulation, Hebei Agricultural University, Baoding 071001, China; (S.L.); (A.D.)
- North China Key Laboratory for Crop Germplasm Resources of the Education Ministry, Hebei Agricultural University, Baoding 071001, China
- Department of Crop Genetics and Breeding, College of Agronomy, Hebei Agricultural University, Baoding 071001, China
| | - Huijun Duan
- State Key Laboratory of North China Crop Improvement and Regulation, Hebei Agricultural University, Baoding 071001, China; (S.L.); (A.D.)
- North China Key Laboratory for Crop Germplasm Resources of the Education Ministry, Hebei Agricultural University, Baoding 071001, China
- Department of Crop Genetics and Breeding, College of Agronomy, Hebei Agricultural University, Baoding 071001, China
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Um T, Park T, Shim JS, Kim YS, Lee GS, Choi IY, Kim JK, Seo JS, Park SC. Application of Upstream Open Reading Frames (uORFs) Editing for the Development of Stress-Tolerant Crops. Int J Mol Sci 2021; 22:ijms22073743. [PMID: 33916772 PMCID: PMC8038395 DOI: 10.3390/ijms22073743] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 03/27/2021] [Accepted: 03/31/2021] [Indexed: 12/20/2022] Open
Abstract
Global population growth and climate change are posing increasing challenges to the production of a stable crop supply using current agricultural practices. The generation of genetically modified (GM) crops has contributed to improving crop stress tolerance and productivity; however, many regulations are still in place that limit their commercialization. Recently, alternative biotechnology-based strategies, such as gene-edited (GE) crops, have been in the spotlight. Gene-editing technology, based on the clustered regularly interspaced short palindromic repeats (CRISPR) platform, has emerged as a revolutionary tool for targeted gene mutation, and has received attention as a game changer in the global biotechnology market. Here, we briefly introduce the concept of upstream open reading frames (uORFs) editing, which allows for control of the translation of downstream ORFs, and outline the potential for enhancing target gene expression by mutating uORFs. We discuss the current status of developing stress-tolerant crops, and discuss uORF targets associated with salt stress-responsive genes in rice that have already been verified by transgenic research. Finally, we overview the strategy for developing GE crops using uORF editing via the CRISPR-Cas9 system. A case is therefore made that the mutation of uORFs represents an efficient method for developing GE crops and an expansion of the scope of application of genome editing technology.
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Affiliation(s)
- Taeyoung Um
- Agriculture and Life Sciences Research Institute, Kangwon National University, Chuncheon 24341, Korea; (T.U.); (Y.S.K.)
| | - Taehyeon Park
- Crop Biotechnology Institute, GreenBio Science and Technology, Seoul National University, Pyeongchang 25354, Korea; (T.P.); (J.-K.K.)
| | - Jae Sung Shim
- School of Biological Sciences and Technology, Chonnam National University, Gwangju 61186, Korea;
| | - Youn Shic Kim
- Agriculture and Life Sciences Research Institute, Kangwon National University, Chuncheon 24341, Korea; (T.U.); (Y.S.K.)
| | - Gang-Seob Lee
- Department of Agricultural Biotechnology, National Academy of Agricultural Science, Rural Development Administration, Jeonju 54874, Korea;
| | - Ik-Young Choi
- Department of Agricultural and Life Industry, Kangwon National University, Chuncheon 24341, Korea;
| | - Ju-Kon Kim
- Crop Biotechnology Institute, GreenBio Science and Technology, Seoul National University, Pyeongchang 25354, Korea; (T.P.); (J.-K.K.)
| | - Jun Sung Seo
- Crop Biotechnology Institute, GreenBio Science and Technology, Seoul National University, Pyeongchang 25354, Korea; (T.P.); (J.-K.K.)
- Correspondence: (J.S.S.); (S.C.P.); Tel.: +82-33-339-5826 (J.S.S.); +82-63-238-4584 (S.C.P.)
| | - Soo Chul Park
- Department of Agricultural Biotechnology, National Academy of Agricultural Science, Rural Development Administration, Jeonju 54874, Korea;
- Correspondence: (J.S.S.); (S.C.P.); Tel.: +82-33-339-5826 (J.S.S.); +82-63-238-4584 (S.C.P.)
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Yan W, Deng XW, Yang C, Tang X. The Genome-Wide EMS Mutagenesis Bias Correlates With Sequence Context and Chromatin Structure in Rice. FRONTIERS IN PLANT SCIENCE 2021; 12:579675. [PMID: 33841451 PMCID: PMC8025102 DOI: 10.3389/fpls.2021.579675] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Accepted: 02/17/2021] [Indexed: 06/12/2023]
Abstract
Ethyl methanesulfonate (EMS) is a chemical mutagen believed to mainly induce G/C to A/T transitions randomly in plant genomes. However, mutant screening for phenotypes often gets multiple alleles for one gene but no mutant for other genes. We investigated the potential EMS mutagenesis bias and the possible correlations with sequence context and chromatin structure using the whole genome resequencing data collected from 52 rice EMS mutants. We defined the EMS-induced single nucleotide polymorphic sites (SNPs) and explored the genomic factors associated with EMS mutagenesis bias. Compared with natural SNPs presented in the Rice3K project, EMS showed a preference on G/C sites with flanking sequences also higher in GC contents. The composition of local dinucleotides and trinucleotides was also associated with the efficiency of EMS mutagenesis. The biased distribution of EMS-induced SNPs was positively correlated with CpG numbers, transposable element contents, and repressive epigenetic markers but negatively with gene expression, the euchromatin marker DNase I hypersensitive sites, and active epigenetic markers, suggesting that sequence context and chromatin structure might correlate with the efficiency of EMS mutagenesis. Exploring the genome-wide features of EMS mutagenesis and correlations with epigenetic modifications will help in the understanding of DNA repair mechanism.
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Affiliation(s)
- Wei Yan
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, China
- Shenzhen Institute of Molecular Crop Design, Shenzhen, China
| | - Xing Wang Deng
- Shenzhen Institute of Molecular Crop Design, Shenzhen, China
- School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Chengwei Yang
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, China
| | - Xiaoyan Tang
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, China
- Shenzhen Institute of Molecular Crop Design, Shenzhen, China
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30
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Li Y, Xiong H, Zhang J, Guo H, Zhou C, Xie Y, Zhao L, Gu J, Zhao S, Ding Y, Fang Z, Liu L. Genome-Wide and Exome-Capturing Sequencing of a Gamma-Ray-Induced Mutant Reveals Biased Variations in Common Wheat. FRONTIERS IN PLANT SCIENCE 2021; 12:793496. [PMID: 35095966 PMCID: PMC8790116 DOI: 10.3389/fpls.2021.793496] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Accepted: 12/09/2021] [Indexed: 05/13/2023]
Abstract
Induced mutagenesis is a powerful approach for the creation of novel germplasm and the improvement of agronomic traits. The evaluation of mutagenic effects and functional variations in crops is needed for breeding mutant strains. To investigate the mutagenic effects of gamma-ray irradiation in wheat, this study characterized genomic variations of wheat early heading mutant (eh1) as compared to wild-type (WT) Zhongyuan 9 (ZY9). Whole-genome resequencing of eh1 and ZY9 produced 737.7 Gb sequencing data and identified a total of 23,537,117 homozygous single nucleotide polymorphism (SNP) and 1,608,468 Indel. Analysis of SNP distribution across the chromosome suggests that mutation hotspots existed in certain chromosomal regions. Among the three subgenomes, the variation frequency in subgenome D was significantly lower than in subgenomes A and B. A total of 27.8 Gb data were obtained by exome-capturing sequencing, while 217,948 SNP and 13,554 Indel were identified. Variation annotation in the gene-coding sequences demonstrated that 5.0% of the SNP and 5.3% of the Indel were functionally important. Characterization of exomic variations in 12 additional gamma-ray-induced mutant lines further provided additional insights into the mutagenic effects of this approach. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genome (KEGG) analysis suggested that genes with functional variations were enriched in several metabolic pathways, including plant-pathogen interactions and ADP binding. Kompetitive allele-specific PCR (KASP) genotyping with selected SNP within functional genes indicated that 85.7% of the SNPs were polymorphic between the eh1 and wild type. This study provides a basic understanding of the mechanism behind gamma-ray irradiation in hexaploid wheat.
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Affiliation(s)
- Yuting Li
- Hubei Collaborative Innovation Center for Grain Industry, College of Agriculture, Yangtze University, Jingzhou, China
- National Engineering Laboratory of Crop Molecular Breeding/National Center of Space Mutagenesis for Crop Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Hongchun Xiong
- National Engineering Laboratory of Crop Molecular Breeding/National Center of Space Mutagenesis for Crop Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jiazi Zhang
- National Engineering Laboratory of Crop Molecular Breeding/National Center of Space Mutagenesis for Crop Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Huijun Guo
- National Engineering Laboratory of Crop Molecular Breeding/National Center of Space Mutagenesis for Crop Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Chunyun Zhou
- National Engineering Laboratory of Crop Molecular Breeding/National Center of Space Mutagenesis for Crop Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yongdun Xie
- National Engineering Laboratory of Crop Molecular Breeding/National Center of Space Mutagenesis for Crop Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Linshu Zhao
- National Engineering Laboratory of Crop Molecular Breeding/National Center of Space Mutagenesis for Crop Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jiayu Gu
- National Engineering Laboratory of Crop Molecular Breeding/National Center of Space Mutagenesis for Crop Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Shirong Zhao
- National Engineering Laboratory of Crop Molecular Breeding/National Center of Space Mutagenesis for Crop Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yuping Ding
- National Engineering Laboratory of Crop Molecular Breeding/National Center of Space Mutagenesis for Crop Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Zhengwu Fang
- Hubei Collaborative Innovation Center for Grain Industry, College of Agriculture, Yangtze University, Jingzhou, China
- Zhengwu Fang,
| | - Luxiang Liu
- National Engineering Laboratory of Crop Molecular Breeding/National Center of Space Mutagenesis for Crop Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
- *Correspondence: Luxiang Liu,
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31
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Atarashi H, Jayasinghe WH, Kwon J, Kim H, Taninaka Y, Igarashi M, Ito K, Yamada T, Masuta C, Nakahara KS. Artificially Edited Alleles of the Eukaryotic Translation Initiation Factor 4E1 Gene Differentially Reduce Susceptibility to Cucumber Mosaic Virus and Potato Virus Y in Tomato. Front Microbiol 2020; 11:564310. [PMID: 33362728 PMCID: PMC7758215 DOI: 10.3389/fmicb.2020.564310] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Accepted: 11/11/2020] [Indexed: 01/27/2023] Open
Abstract
Eukaryotic translation initiation factors, including eIF4E, are susceptibility factors for viral infection in host plants. Mutation and double-stranded RNA-mediated silencing of tomato eIF4E genes can confer resistance to viruses, particularly members of the Potyvirus genus. Here, we artificially mutated the eIF4E1 gene on chromosome 3 of a commercial cultivar of tomato (Solanum lycopersicum L.) by using CRISPR/Cas9. We obtained three alleles, comprising two deletions of three and nine nucleotides (3DEL and 9DEL) and a single nucleotide insertion (1INS), near regions that encode amino acid residues important for binding to the mRNA 5' cap structure and to eIF4G. Plants homozygous for these alleles were termed 3DEL, 9DEL, and 1INS plants, respectively. In accordance with previous studies, inoculation tests with potato virus Y (PVY; type member of the genus Potyvirus) yielded a significant reduction in susceptibility to the N strain (PVYN), but not to the ordinary strain (PVYO), in 1INS plants. 9DEL among three artificial alleles had a deleterious effect on infection by cucumber mosaic virus (CMV, type member of the genus Cucumovirus). When CMV was mechanically inoculated into tomato plants and viral coat accumulation was measured in the non-inoculated upper leaves, the level of viral coat protein was significantly lower in the 9DEL plants than in the parental cultivar. Tissue blotting of microperforated inoculated leaves of the 9DEL plants revealed significantly fewer infection foci compared with those of the parental cultivar, suggesting that 9DEL negatively affects the initial steps of infection with CMV in a mechanically inoculated leaf. In laboratory tests, viral aphid transmission from an infected susceptible plant to 9DEL plants was reduced compared with the parental control. Although many pathogen resistance genes have been discovered in tomato and its wild relatives, no CMV resistance genes have been used in practice. RNA silencing of eIF4E expression has previously been reported to not affect susceptibility to CMV in tomato. Our findings suggest that artificial gene editing can introduce additional resistance to that achieved with mutagenesis breeding, and that edited eIF4E alleles confer an alternative way to manage CMV in tomato fields.
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Affiliation(s)
- Hiroki Atarashi
- Research and Development Division, Kikkoman Corporation, Noda, Chiba, Japan
| | - Wikum Harshana Jayasinghe
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Japan.,Department of Agricultural Biology, Faculty of Agriculture, University of Peradeniya, Peradeniya, Sri Lanka
| | - Joon Kwon
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Japan
| | - Hangil Kim
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Japan
| | - Yosuke Taninaka
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Japan
| | - Manabu Igarashi
- Division of Global Epidemiology, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Japan.,Global Station for Zoonosis Control, Global Institution for Collaborative Research and Education, Hokkaido University, Sapporo, Japan
| | - Kotaro Ito
- Research and Development Division, Kikkoman Corporation, Noda, Chiba, Japan
| | - Tetsuya Yamada
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Japan
| | - Chikara Masuta
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Japan
| | - Kenji S Nakahara
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Japan
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Bru P, Nanda S, Malnoë A. A Genetic Screen to Identify New Molecular Players Involved in Photoprotection qH in Arabidopsis thaliana. PLANTS 2020; 9:plants9111565. [PMID: 33202829 PMCID: PMC7696684 DOI: 10.3390/plants9111565] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Revised: 10/30/2020] [Accepted: 11/11/2020] [Indexed: 12/23/2022]
Abstract
Photosynthesis is a biological process which converts light energy into chemical energy that is used in the Calvin-Benson cycle to produce organic compounds. An excess of light can induce damage to the photosynthetic machinery. Therefore, plants have evolved photoprotective mechanisms such as non-photochemical quenching (NPQ). To focus molecular insights on slowly relaxing NPQ processes in Arabidopsis thaliana, previously, a qE-deficient line-the PsbS mutant-was mutagenized and a mutant with high and slowly relaxing NPQ was isolated. The mutated gene was named suppressor of quenching 1, or SOQ1, to describe its function. Indeed, when present, SOQ1 negatively regulates or suppresses a form of antenna NPQ that is slow to relax and is photoprotective. We have now termed this component qH and identified the plastid lipocalin, LCNP, as the effector for this energy dissipation mode to occur. Recently, we found that the relaxation of qH1, ROQH1, protein is required to turn off qH. The aim of this study is to identify new molecular players involved in photoprotection qH by a whole genome sequencing approach of chemically mutagenized Arabidopsis thaliana. We conducted an EMS-mutagenesis on the soq1 npq4 double mutant and used chlorophyll fluorescence imaging to screen for suppressors and enhancers of qH. Out of 22,000 mutagenized plants screened, the molecular players cited above were found using a mapping-by-sequencing approach. Here, we describe the phenotypic characterization of the other mutants isolated from this genetic screen and an additional 8000 plants screened. We have classified them in several classes based on their fluorescence parameters, NPQ kinetics, and pigment content. A high-throughput whole genome sequencing approach on 65 mutants will identify the causal mutations thanks to allelic mutations from having reached saturation of the genetic screen. The candidate genes could be involved in the formation or maintenance of quenching sites for qH, in the regulation of qH at the transcriptional level, or be part of the quenching site itself.
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33
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Menz J, Modrzejewski D, Hartung F, Wilhelm R, Sprink T. Genome Edited Crops Touch the Market: A View on the Global Development and Regulatory Environment. FRONTIERS IN PLANT SCIENCE 2020; 11:586027. [PMID: 33163013 PMCID: PMC7581933 DOI: 10.3389/fpls.2020.586027] [Citation(s) in RCA: 83] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Accepted: 09/16/2020] [Indexed: 05/18/2023]
Abstract
Products of genome editing as the most promising "New Plant Breeding Technology" (NPBT) have made the transition from the lab to the market in a short time. Globally, research activities employing genome editing are constantly expanding and more and more plants with market-oriented traits are being developed, and companies have already released the first genome edited crops to the market. Few countries, most of which are located in the Americas, have adapted legislations to these technologies or released guidelines supporting the use of genome editing. Other countries are debating the path to come either because there is no clarity on the legal classification or due consensus is hampered by a renewed GMO debate. In recent years (2017-2020), eight countries have introduced guidelines clarifying the legal status of genome edited products and many of those are actively committed to international harmonization of their policies. In this publication we give an overview on the current and potentially future international regulatory environment and an update on plants derived by genome editing with market-oriented traits.
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Affiliation(s)
| | | | | | - Ralf Wilhelm
- Julius Kühn Institute (JKI) – Federal Research Centre for Cultivated Plants, Institute for Biosafety in Plant Biotechnology, Quedlinburg, Germany
| | - Thorben Sprink
- Julius Kühn Institute (JKI) – Federal Research Centre for Cultivated Plants, Institute for Biosafety in Plant Biotechnology, Quedlinburg, Germany
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34
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Fedorova M, Herman RA. Obligatory metabolomic profiling of gene-edited crops is risk disproportionate. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 103:1985-1988. [PMID: 32593232 PMCID: PMC7540486 DOI: 10.1111/tpj.14896] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Revised: 05/21/2020] [Accepted: 05/27/2020] [Indexed: 05/06/2023]
Abstract
It has been argued that the application of metabolomics to gene-edited crops would present value in three areas: (i) the detection of gene-edited crops; (ii) the characterization of unexpected changes that might affect safety; and (iii) building on the track record of rigorous government regulation in supporting consumer acceptance of genetically modified organisms (GMOs). Here, we offer a different perspective, relative to each of these areas: (i) metabolomics is unable to differentiate whether a mutation has resulted from gene editing or from traditional breeding techniques; (ii) it is risk-disproportionate to apply metabolomics for regulatory purposes to search for possible compositional differences within crops developed using the least likely technique to generate unexpected compositional changes; and (iii) onerous regulations for genetically engineered crops have only contributed to unwarranted public fears, and repeating this approach for gene-edited crops is unlikely to result in a different outcome. It is also suggested that article proposing the utility of specific analytical techniques to support risk assessment would benefit from the input of scientists with subject matter expertise in risk assessment.
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Affiliation(s)
- Maria Fedorova
- Corteva Agriscience7100 NW 62 AvePO Box 1000JohnstonIA50131USA
| | - Rod A. Herman
- Corteva Agriscience9330 Zionsville RoadIndianapolisIN46268USA
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Graham N, Patil GB, Bubeck DM, Dobert RC, Glenn KC, Gutsche AT, Kumar S, Lindbo JA, Maas L, May GD, Vega-Sanchez ME, Stupar RM, Morrell PL. Plant Genome Editing and the Relevance of Off-Target Changes. PLANT PHYSIOLOGY 2020; 183:1453-1471. [PMID: 32457089 PMCID: PMC7401131 DOI: 10.1104/pp.19.01194] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Accepted: 05/07/2020] [Indexed: 05/12/2023]
Abstract
Site-directed nucleases (SDNs) used for targeted genome editing are powerful new tools to introduce precise genetic changes into plants. Like traditional approaches, such as conventional crossing and induced mutagenesis, genome editing aims to improve crop yield and nutrition. Next-generation sequencing studies demonstrate that across their genomes, populations of crop species typically carry millions of single nucleotide polymorphisms and many copy number and structural variants. Spontaneous mutations occur at rates of ∼10-8 to 10-9 per site per generation, while variation induced by chemical treatment or ionizing radiation results in higher mutation rates. In the context of SDNs, an off-target change or edit is an unintended, nonspecific mutation occurring at a site with sequence similarity to the targeted edit region. SDN-mediated off-target changes can contribute to a small number of additional genetic variants compared to those that occur naturally in breeding populations or are introduced by induced-mutagenesis methods. Recent studies show that using computational algorithms to design genome editing reagents can mitigate off-target edits in plants. Finally, crops are subject to strong selection to eliminate off-type plants through well-established multigenerational breeding, selection, and commercial variety development practices. Within this context, off-target edits in crops present no new safety concerns compared to other breeding practices. The current generation of genome editing technologies is already proving useful to develop new plant varieties with consumer and farmer benefits. Genome editing will likely undergo improved editing specificity along with new developments in SDN delivery and increasing genomic characterization, further improving reagent design and application.
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Affiliation(s)
- Nathaniel Graham
- Department of Genetics, Cell Biology and Development, University of Minnesota, St. Paul, Minnesota 55108
- Pairwise, Durham, North Carolina 27709
| | - Gunvant B Patil
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota 55108
| | | | | | | | | | | | | | - Luis Maas
- Enza Zaden Research USA, San Juan Bautista, California 95045
| | | | | | - Robert M Stupar
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota 55108
| | - Peter L Morrell
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota 55108
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Shah D, Kamili AN, Wani AA, Majeed U, Wani ZA, Sajjad N, Ahmad P. Promoting the accumulation of scopolamine and hyoscyamine in Hyoscyamus niger L. through EMS based mutagenesis. PLoS One 2020; 15:e0231355. [PMID: 32437389 PMCID: PMC7241962 DOI: 10.1371/journal.pone.0231355] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Accepted: 03/21/2020] [Indexed: 11/18/2022] Open
Abstract
The overexploitation of medicinal plants is depleting gene pool at an alarming rate. In this scenario inducing the genetic variability through targeted mutations could be beneficial in generating varieties with increased content of active compounds. The present study aimed to develop a reproducible protocol for in vitro multiplication and mutagenesis of Hyoscyamus niger targeting putrescine N-methyltransferase (PMT) and 6β-hydroxy hyoscyamine (H6H) genes of alkaloid biosynthetic pathway. In vitro raised callus were treated with different concentrations (0.01% - 0.1%) of Ethyl Methane Sulfonate (EMS). Emerging multiple shoots and roots were obtained on the MS media supplemented with cytokinins and auxins. Significant effects on morphological characteristics were observed following exposure to different concentrations of EMS. EMS at a concentration of 0.03% was seen to be effective in enhancing the average shoot and root number from 14.5±0.30 to 22.2 ±0.77 and 7.2±0.12 to 8.8±0.72, respectively. The lethal dose (LD50) dose was calculated at 0.08% EMS. The results depicted that EMS has an intense effect on PMT and H6H gene expression and metabolite accumulation. The transcripts of PMT and H6H were significantly upregulated at 0.03-0.05% EMS compared to control. EMS treated explants showed increased accumulation of scopolamine (0.639 μg/g) and hyoscyamine (0.0344μg/g) compared to untreated.
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Affiliation(s)
- Durdana Shah
- Plant Tissue Culture Lab, Centre of Research for Development, University of Kashmir, Srinagar, J&K, India
- * E-mail: (DS); (PA)
| | - Azra N. Kamili
- Plant Tissue Culture Lab, Centre of Research for Development, University of Kashmir, Srinagar, J&K, India
| | - Aijaz A. Wani
- Cytogenetics and Reproductive Biology Lab, Department of Botany, University of Kashmir, Srinagar, J&K, India
| | - Umer Majeed
- Immunology Lab, Department of Biotechnology, University of Kashmir, Srinagar, J&K, India
| | - Zubair Ahmad Wani
- Immunology Lab, Department of Biotechnology, University of Kashmir, Srinagar, J&K, India
| | - Nasreena Sajjad
- Department of Biochemistry, University of Kashmir, Hazratbal, Jammu and Kashmir, India
| | - Parvaiz Ahmad
- King Saud University, Riyadh, Saudi Arabia
- Department of Botany and Microbiology, College of Science, Srinagar, Jammu and Kashmir, India
- * E-mail: (DS); (PA)
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Lethin J, Shakil SSM, Hassan S, Sirijovski N, Töpel M, Olsson O, Aronsson H. Development and characterization of an EMS-mutagenized wheat population and identification of salt-tolerant wheat lines. BMC PLANT BIOLOGY 2020; 20:18. [PMID: 31931695 PMCID: PMC6958588 DOI: 10.1186/s12870-019-2137-8] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2019] [Accepted: 11/13/2019] [Indexed: 05/24/2023]
Abstract
BACKGROUND Triticum aestivum (wheat) is one of the world's oldest crops and has been used for >8000 years as a food crop in North Africa, West Asia and Europe. Today, wheat is one of the most important sources of grain for humans, and is cultivated on greater areas of land than any other crop. As the human population increases and soil salinity becomes more prevalent, there is increased pressure on wheat breeders to develop salt-tolerant varieties in order to meet growing demands for yield and grain quality. Here we developed a mutant wheat population using the moderately salt-tolerant Bangladeshi variety BARI Gom-25, with the primary goal of further increasing salt tolerance. RESULTS After titrating the optimal ethyl methanesulfonate (EMS) concentration, ca 30,000 seeds were treated with 1% EMS, and 1676 lines, all originating from single seeds, survived through the first four generations. Most mutagenized lines showed a similar phenotype to BARI Gom-25, although visual differences such as dwarfing, giant plants, early and late flowering and altered leaf morphology were seen in some lines. By developing an assay for salt tolerance, and by screening the mutagenized population, we identified 70 lines exhibiting increased salt tolerance. The selected lines typically showed a 70% germination rate on filter paper soaked in 200 mM NaCl, compared to 0-30% for BARI Gom-25. From two of the salt-tolerant OlsAro lines (OA42 and OA70), genomic DNA was sequenced to 15x times coverage. A comparative analysis against the BARI Gom-25 genomic sequence identified a total of 683,201 (OA42), and 768,954 (OA70) SNPs distributed throughout the three sub-genomes (A, B and D). The mutation frequency was determined to be approximately one per 20,000 bp. All the 70 selected salt-tolerant lines were tested for root growth in the laboratory, and under saline field conditions in Bangladesh. The results showed that all the lines selected for tolerance showed a better salt tolerance phenotype than both BARI Gom-25 and other local wheat varieties tested. CONCLUSION The mutant wheat population developed here will be a valuable resource in the development of novel salt-tolerant varieties for the benefit of saline farming.
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Affiliation(s)
- Johanna Lethin
- Department of Biological and Environmental Sciences, University of Gothenburg, Box 461, SE-405 30 Gothenburg, Sweden
| | - Shahriar S. M. Shakil
- Department of Pure and Applied Biochemistry, University of Lund, Box 124, SE-221 00 Lund, Sweden
| | - Sameer Hassan
- Department of Biological and Environmental Sciences, University of Gothenburg, Box 461, SE-405 30 Gothenburg, Sweden
| | - Nick Sirijovski
- Department of Pure and Applied Biochemistry, University of Lund, Box 124, SE-221 00 Lund, Sweden
| | - Mats Töpel
- Department of Marine Sciences, University of Gothenburg, Box 461, SE-405 30 Gothenburg, Sweden
| | - Olof Olsson
- Department of Pure and Applied Biochemistry, University of Lund, Box 124, SE-221 00 Lund, Sweden
| | - Henrik Aronsson
- Department of Biological and Environmental Sciences, University of Gothenburg, Box 461, SE-405 30 Gothenburg, Sweden
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Erpen-Dalla Corte L, M. Mahmoud L, S. Moraes T, Mou Z, W. Grosser J, Dutt M. Development of Improved Fruit, Vegetable, and Ornamental Crops Using the CRISPR/Cas9 Genome Editing Technique. PLANTS (BASEL, SWITZERLAND) 2019; 8:E601. [PMID: 31847196 PMCID: PMC6963220 DOI: 10.3390/plants8120601] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/17/2019] [Revised: 12/06/2019] [Accepted: 12/11/2019] [Indexed: 02/06/2023]
Abstract
Horticultural crops, including fruit, vegetable, and ornamental plants are an important component of the agriculture production systems and play an important role in sustaining human life. With a steady growth in the world's population and the consequent need for more food, sustainable and increased fruit and vegetable crop production is a major challenge to guarantee future food security. Although conventional breeding techniques have significantly contributed to the development of important varieties, new approaches are required to further improve horticultural crop production. Clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9) has emerged as a valuable genome-editing tool able to change DNA sequences at precisely chosen loci. The CRISPR/Cas9 system was developed based on the bacterial adaptive immune system and comprises of an endonuclease guided by one or more single-guide RNAs to generate double-strand breaks. These breaks can then be repaired by the natural cellular repair mechanisms, during which genetic mutations are introduced. In a short time, the CRISPR/Cas9 system has become a popular genome-editing technique, with numerous examples of gene mutation and transcriptional regulation control in both model and crop plants. In this review, various aspects of the CRISPR/Cas9 system are explored, including a general presentation of the function of the CRISPR/Cas9 system in bacteria and its practical application as a biotechnological tool for editing plant genomes, particularly in horticultural crops.
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Affiliation(s)
| | - Lamiaa M. Mahmoud
- Pomology Department, Faculty of Agriculture, Mansoura University, 35516 Mansoura, Egypt;
- Citrus Research and Education Center, University of Florida, Lake Alfred, FL 33850, USA;
| | - Tatiana S. Moraes
- Centro de Energia Nuclear na Agricultura, Universidade de São Paulo, Piracicaba 13416-000, SP, Brazil;
| | - Zhonglin Mou
- Department of Microbiology and Cell Sciences, University of Florida, Gainesville, FL 32603, USA;
| | - Jude W. Grosser
- Citrus Research and Education Center, University of Florida, Lake Alfred, FL 33850, USA;
| | - Manjul Dutt
- Citrus Research and Education Center, University of Florida, Lake Alfred, FL 33850, USA;
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Chaudhary J, Deshmukh R, Sonah H. Mutagenesis Approaches and Their Role in Crop Improvement. PLANTS (BASEL, SWITZERLAND) 2019; 8:E467. [PMID: 31683624 PMCID: PMC6918138 DOI: 10.3390/plants8110467] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Accepted: 10/29/2019] [Indexed: 12/20/2022]
Abstract
Induced mutagenesis is one of the most efficient tools that has been utilized extensively to create genetic variation as well as for identification of key regulatory genes for economically important traits toward the crop improvement. Mutations can be induced by several techniques such as physical, chemical, and insertional mutagen treatments; however, these methods are not preferred because of cost and tedious process. Nonetheless, with the advancements in next-generation sequencing (NGS) techniques, millions of mutations can be detected in a very short period of time and, therefore, considered as convenient and cost efficient. Furthermore, induced mutagenesis coupled with whole-genome sequencing has provided a robust platform for forward and reverse genetic applications. Moreover, the availability of whole-genome sequence information for large number of crops has enabled target-specific genome editing techniques as a preferable method to engineer desired mutations. The available genome editing approaches such as ZFNs (Zinc Finger Nucleases), transcription activator like effector nucleases (TALENS), and clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated9 (Cas9) endonuclease have been utilized to perform site-specific mutations in several plant species. In particular, the CRISPR/Cas9 has transformed the genome editing because of its simplicity and robustness, therefore, have been utilized to enhance biotic and abiotic stress resistance. The Special Issue of Plants highlights the efforts by the scientific community utilizing mutagenesis techniques for the identification of novel genes toward crop improvement.
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Affiliation(s)
- Juhi Chaudhary
- Department of Biology, Oberlin College, Oberlin, OH 44074, USA.
| | - Rupesh Deshmukh
- National Agri-Food Biotechnology Institute (NABI), Sector 80, SAS Nagar, Mohali, Punjab 140306, India.
| | - Humira Sonah
- National Agri-Food Biotechnology Institute (NABI), Sector 80, SAS Nagar, Mohali, Punjab 140306, India.
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Bastet A, Zafirov D, Giovinazzo N, Guyon‐Debast A, Nogué F, Robaglia C, Gallois J. Mimicking natural polymorphism in eIF4E by CRISPR-Cas9 base editing is associated with resistance to potyviruses. PLANT BIOTECHNOLOGY JOURNAL 2019; 17:1736-1750. [PMID: 30784179 PMCID: PMC6686125 DOI: 10.1111/pbi.13096] [Citation(s) in RCA: 85] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Revised: 02/11/2019] [Accepted: 02/13/2019] [Indexed: 05/08/2023]
Abstract
In many crop species, natural variation in eIF4E proteins confers resistance to potyviruses. Gene editing offers new opportunities to transfer genetic resistance to crops that seem to lack natural eIF4E alleles. However, because eIF4E are physiologically important proteins, any introduced modification for virus resistance must not bring adverse phenotype effects. In this study, we assessed the role of amino acid substitutions encoded by a Pisum sativum eIF4E virus-resistance allele (W69L, T80D S81D, S84A, G114R and N176K) by introducing them independently into the Arabidopsis thaliana eIF4E1 gene, a susceptibility factor to the Clover yellow vein virus (ClYVV). Results show that most mutations were sufficient to prevent ClYVV accumulation in plants without affecting plant growth. In addition, two of these engineered resistance alleles can be combined with a loss-of-function eIFiso4E to expand the resistance spectrum to other potyviruses. Finally, we use CRISPR-nCas9-cytidine deaminase technology to convert the Arabidopsis eIF4E1 susceptibility allele into a resistance allele by introducing the N176K mutation with a single-point mutation through C-to-G base editing to generate resistant plants. This study shows how combining knowledge on pathogen susceptibility factors with precise genome-editing technologies offers a feasible solution for engineering transgene-free genetic resistance in plants, even across species barriers.
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Affiliation(s)
- Anna Bastet
- GAFLINRAMontfavetFrance
- Laboratoire de Génétique et Biophysique des PlantesCEACNRSBIAMAix Marseille UniversityMarseilleFrance
| | - Delyan Zafirov
- GAFLINRAMontfavetFrance
- Laboratoire de Génétique et Biophysique des PlantesCEACNRSBIAMAix Marseille UniversityMarseilleFrance
| | | | - Anouchka Guyon‐Debast
- Institut Jean‐Pierre BourginINRAAgroParisTechCNRSUniversité Paris‐SaclayVersaillesFrance
| | - Fabien Nogué
- Institut Jean‐Pierre BourginINRAAgroParisTechCNRSUniversité Paris‐SaclayVersaillesFrance
| | - Christophe Robaglia
- Laboratoire de Génétique et Biophysique des PlantesCEACNRSBIAMAix Marseille UniversityMarseilleFrance
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Insertional Mutagenesis Approaches and Their Use in Rice for Functional Genomics. PLANTS 2019; 8:plants8090310. [PMID: 31470516 PMCID: PMC6783850 DOI: 10.3390/plants8090310] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Revised: 08/07/2019] [Accepted: 08/07/2019] [Indexed: 01/01/2023]
Abstract
Insertional mutagenesis is an indispensable tool for engendering a mutant population using exogenous DNA as the mutagen. The advancement in the next-generation sequencing platform has allowed for faster screening and analysis of generated mutated populations. Rice is a major staple crop for more than half of the world's population; however, the functions of most of the genes in its genome are yet to be analyzed. Various mutant populations represent extremely valuable resources in order to achieve this goal. Here, we have reviewed different insertional mutagenesis approaches that have been used in rice, and have discussed their principles, strengths, and limitations. Comparisons between transfer DNA (T-DNA), transposons, and entrapment tagging approaches have highlighted their utilization in functional genomics studies in rice. We have also summarised different forward and reverse genetics approaches used for screening of insertional mutant populations. Furthermore, we have compiled information from several efforts made using insertional mutagenesis approaches in rice. The information presented here would serve as a database for rice insertional mutagenesis populations. We have also included various examples which illustrate how these populations have been useful for rice functional genomics studies. The information provided here will be very helpful for future functional genomics studies in rice aimed at its genetic improvement.
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Razzaq A, Saleem F, Kanwal M, Mustafa G, Yousaf S, Imran Arshad HM, Hameed MK, Khan MS, Joyia FA. Modern Trends in Plant Genome Editing: An Inclusive Review of the CRISPR/Cas9 Toolbox. Int J Mol Sci 2019; 20:E4045. [PMID: 31430902 PMCID: PMC6720679 DOI: 10.3390/ijms20164045] [Citation(s) in RCA: 72] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Revised: 08/14/2019] [Accepted: 08/15/2019] [Indexed: 12/17/2022] Open
Abstract
Increasing agricultural productivity via modern breeding strategies is of prime interest to attain global food security. An array of biotic and abiotic stressors affect productivity as well as the quality of crop plants, and it is a primary need to develop crops with improved adaptability, high productivity, and resilience against these biotic/abiotic stressors. Conventional approaches to genetic engineering involve tedious procedures. State-of-the-art OMICS approaches reinforced with next-generation sequencing and the latest developments in genome editing tools have paved the way for targeted mutagenesis, opening new horizons for precise genome engineering. Various genome editing tools such as transcription activator-like effector nucleases (TALENs), zinc-finger nucleases (ZFNs), and meganucleases (MNs) have enabled plant scientists to manipulate desired genes in crop plants. However, these approaches are expensive and laborious involving complex procedures for successful editing. Conversely, CRISPR/Cas9 is an entrancing, easy-to-design, cost-effective, and versatile tool for precise and efficient plant genome editing. In recent years, the CRISPR/Cas9 system has emerged as a powerful tool for targeted mutagenesis, including single base substitution, multiplex gene editing, gene knockouts, and regulation of gene transcription in plants. Thus, CRISPR/Cas9-based genome editing has demonstrated great potential for crop improvement but regulation of genome-edited crops is still in its infancy. Here, we extensively reviewed the availability of CRISPR/Cas9 genome editing tools for plant biotechnologists to target desired genes and its vast applications in crop breeding research.
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Affiliation(s)
- Ali Razzaq
- Centre of Agricultural Biochemistry and Biotechnology (CABB), University of Agriculture, Faisalabad 38040, Pakistan
| | - Fozia Saleem
- Centre of Agricultural Biochemistry and Biotechnology (CABB), University of Agriculture, Faisalabad 38040, Pakistan
| | - Mehak Kanwal
- Nuclear Institute for Agriculture and Biology (NIAB), P.O. Box 128, Faisalabad 38000, Pakistan
| | - Ghulam Mustafa
- Centre of Agricultural Biochemistry and Biotechnology (CABB), University of Agriculture, Faisalabad 38040, Pakistan
| | - Sumaira Yousaf
- Nuclear Institute for Agriculture and Biology (NIAB), P.O. Box 128, Faisalabad 38000, Pakistan
| | | | - Muhammad Khalid Hameed
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Muhammad Sarwar Khan
- Centre of Agricultural Biochemistry and Biotechnology (CABB), University of Agriculture, Faisalabad 38040, Pakistan
| | - Faiz Ahmad Joyia
- Centre of Agricultural Biochemistry and Biotechnology (CABB), University of Agriculture, Faisalabad 38040, Pakistan.
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Kumawat S, Rana N, Bansal R, Vishwakarma G, Mehetre ST, Das BK, Kumar M, Kumar Yadav S, Sonah H, Sharma TR, Deshmukh R. Expanding Avenue of Fast Neutron Mediated Mutagenesis for Crop Improvement. PLANTS (BASEL, SWITZERLAND) 2019; 8:E164. [PMID: 31185678 PMCID: PMC6631465 DOI: 10.3390/plants8060164] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Revised: 05/27/2019] [Accepted: 06/05/2019] [Indexed: 12/21/2022]
Abstract
: Fast neutron (FN) radiation mediated mutagenesis is a unique approach among the several induced mutagenesis methods being used in plant science in terms of impacted mutations. The FN mutagenesis usually creates deletions from few bases to several million bases (Mb). A library of random deletion generated using FN mutagenesis lines can provide indispensable resources for the reverse genetic approaches. In this review, information from several efforts made using FN mutagenesis has been compiled to understand the type of induced mutations, frequency, and genetic stability. Concerns regarding the utilization of FN mutagenesis technique for a plant with different level of ploidy and genome complexity are discussed. We have highlighted the utility of next-generation sequencing techniques that can be efficiently utilized for the characterization of mutant lines as well as for the mapping of causal mutations. Pros and cons of mapping by mutation (MutMap), mutant chromosome sequencing (MutChromSeq), exon capture, whole genome sequencing, MutRen-Seq, and different tilling approaches that can be used for the detection of FN-induced mutation has also been discussed. Genomic resources developed using the FN mutagenesis have been catalogued wooing to meaningful utilization of the available resources. The information provided here will be helpful for the efficient exploration for the crop improvement programs and for better understanding of genetic regulations.
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Affiliation(s)
- Surbhi Kumawat
- National Agri-food Biotechnology Institute (NABI), Mohali, Punjab 140308, India.
| | - Nitika Rana
- National Agri-food Biotechnology Institute (NABI), Mohali, Punjab 140308, India.
| | - Ruchi Bansal
- National Agri-food Biotechnology Institute (NABI), Mohali, Punjab 140308, India.
| | - Gautam Vishwakarma
- Nuclear Agriculture & Biotechnology Division, Bhabha Atomic Research Centre, Mumbai 400085, India.
| | - Sayaji T Mehetre
- Nuclear Agriculture & Biotechnology Division, Bhabha Atomic Research Centre, Mumbai 400085, India.
| | - Bikram Kishore Das
- Nuclear Agriculture & Biotechnology Division, Bhabha Atomic Research Centre, Mumbai 400085, India.
| | - Manish Kumar
- Department of Seed Science and Technology, College of Horticulture, Dr. Yashwant Singh Parmar University of Horticulture and Forestry, Nauni, Solan, Himachal Pradesh 173230, India.
| | | | - Humira Sonah
- National Agri-food Biotechnology Institute (NABI), Mohali, Punjab 140308, India.
| | - Tilak Raj Sharma
- National Agri-food Biotechnology Institute (NABI), Mohali, Punjab 140308, India.
| | - Rupesh Deshmukh
- National Agri-food Biotechnology Institute (NABI), Mohali, Punjab 140308, India.
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Liu W, Huang S, Liu Z, Lou T, Tan C, Wang Y, Feng H. A missense mutation of STERILE APETALA leads to female sterility in Chinese cabbage (Brassica campestris ssp. pekinensis). PLANT REPRODUCTION 2019; 32:217-228. [PMID: 30806770 DOI: 10.1007/s00497-019-00368-7] [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: 09/13/2018] [Accepted: 02/18/2019] [Indexed: 05/03/2023]
Abstract
Flower development is essential for the sexual reproduction and crop yield of plants. Thus, a better understanding of plant sterility from the perspective of morphological and molecular genetics is imperative. In our previous study, a recessive female-sterile Chinese cabbage mutant fsm was obtained from a doubled haploid line 'FT' via an isolated microspore culture combined with EMS mutagenesis. Pistil aniline blue staining and stigma scanning observation showed that the growth of the stigma papillar cells and pollen tubes of the mutant fsm were normal. Therefore, the female sterility was due to abnormal development of the ovules. To map the mutant fsm, 3108 F2 individuals were selected for linkage analysis. Two closely linked markers, Indel-I2 and Indel-I7, were localized on the flanking region of fsm at distances of 0.05 cM and 0.06 cM, respectively. The physical distance between Indel-I2 and Indel-I7 was ~ 1376 kb, with 107 genes remaining in the target region. This region was located on the chromosome A04 centromere, on which low recombination rates and a high frequency of repetitive sequences were present. Whole-genome re-sequencing detected a single-nucleotide (C-to-A) transition (TCG/TAG) on the exon of BraA04001030, resulting in a premature stop codon. Genotyping revealed that the female-sterile phenotype was fully cosegregated with this SNP. BraA04001030 encodes a homologue of STERILE APETALA (SAP) transcriptional regulator, which plays vital roles in floral development. The results of the present study suggest that BraA04001030 is a strong candidate gene for fsm and provide the basis for exploring the molecular mechanism underlying female sterility in Chinese cabbage.
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Affiliation(s)
- Wenjie Liu
- Department of Horticulture, Shenyang Agricultural University, 120 Dongling Road, Shenhe District, Shenyang, 110866, People's Republic of China
| | - Shengnan Huang
- Department of Horticulture, Shenyang Agricultural University, 120 Dongling Road, Shenhe District, Shenyang, 110866, People's Republic of China
| | - Zhiyong Liu
- Department of Horticulture, Shenyang Agricultural University, 120 Dongling Road, Shenhe District, Shenyang, 110866, People's Republic of China
| | - Tengxue Lou
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, People's Republic of China
| | - Chong Tan
- Department of Horticulture, Shenyang Agricultural University, 120 Dongling Road, Shenhe District, Shenyang, 110866, People's Republic of China
| | - Yiheng Wang
- Department of Horticulture, Shenyang Agricultural University, 120 Dongling Road, Shenhe District, Shenyang, 110866, People's Republic of China
| | - Hui Feng
- Department of Horticulture, Shenyang Agricultural University, 120 Dongling Road, Shenhe District, Shenyang, 110866, People's Republic of China.
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Krishnamurthy P, Fujisawa Y, Takahashi Y, Abe H, Yamane K, Mukaiyama K, Son HR, Hiraga S, Kaga A, Anai T, Tsukamoto C, Ishimoto M. High-Throughput Screening and Characterization of a High-Density Soybean Mutant Library Elucidate the Biosynthesis Pathway of Triterpenoid Saponins. PLANT & CELL PHYSIOLOGY 2019; 60:1082-1097. [PMID: 30753604 DOI: 10.1093/pcp/pcz025] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Accepted: 01/31/2019] [Indexed: 05/21/2023]
Abstract
Triterpenes (C30) constitute one of the diverse class of natural products with potential applications in food, cosmetic and pharmaceutical industries. Soyasaponins are oleanane-type triterpenoids widespread among legumes and particularly abundant in soybean seeds. They have associated with various pharmacological implications and undesirable taste properties of soybean-based food products. Uncovering the biosynthetic genes of soyasaponins will provide new opportunities to control the pathway for human benefits. However, the pathway of soyasaponin biosynthesis has not been fully elucidated in part because of a paucity of natural mutants. Here, we applied a structured high-density soybean mutant library for the forward genetic screening of triterpenoid biosynthesis. The seed soyasaponin polymorphism in the mutant library was evaluated using a high-throughput thin-layer chromatography and liquid chromatography tandem mass spectrometry analysis. This screening identified 35 mutants (3.85% of 909 mutant lines) with seven unusual soyasaponin phenotypes (Categories 1-7), which was greater than the number of natural mutants reported previously (22 mutants, 0.18% of ∼12,428 accessions). Nine unique intermediates of soyasaponin biosynthesis were identified and their chemical structures were estimated based on their MS/MS fragment patterns. Based on published information, 19 mutants could be associated with loss of function of four individual soyasaponin biosynthesis genes identified through expressed sequence tag mining or positional cloning, whereas the remaining 16 mutants were novel and may facilitate discovery of the unknown biosynthetic genes of soyasaponins. Our approach and library may help to identify new phenotype materials and causative genes associated with specialized metabolite production and other traits.
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Affiliation(s)
| | | | - Yuya Takahashi
- Faculty of Agriculture, Iwate University, Morioka, Iwate, Japan
| | - Hanako Abe
- Faculty of Agriculture, Iwate University, Morioka, Iwate, Japan
| | - Kentaro Yamane
- Faculty of Agriculture, Iwate University, Morioka, Iwate, Japan
| | | | - Hae-Reon Son
- Faculty of Agriculture, Iwate University, Morioka, Iwate, Japan
| | - Susumu Hiraga
- Institute of Crop Science, NARO, Tsukuba, Ibaraki, Japan
| | - Akito Kaga
- Institute of Crop Science, NARO, Tsukuba, Ibaraki, Japan
| | - Toyoaki Anai
- Faculty of Agriculture, Saga University, Saga, Japan
| | | | - Masao Ishimoto
- Institute of Crop Science, NARO, Tsukuba, Ibaraki, Japan
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Mutation Breeding of a N-methyl-N-nitrosourea (MNU)-Induced Rice (Oryza sativa L. ssp. Indica) Population for the Yield Attributing Traits. SUSTAINABILITY 2019. [DOI: 10.3390/su11041062] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Difficulties in breeding new rice cultivars that have a high yield, are acceptable quality, and are tolerant to environmental stresses have been the major constraint of rice production in many developing countries, as these traits are determined by multiple genes associated with complicated and uncontrollable gene segregations.Furthermore, the gene/QTL (quantitative trait locus) introduced to the cultivar is unstable due to the interaction among the active genes, which determine the phenotypic performance, not yet been well understood or controllable. In this study, the N-methyl-N-nitrosourea (MNU)-induced mutation was applied to the heterozygote of the F1 generation from the cross between TBR1 (female) and KD18 (male parent). The phenotype and genotype of the M2 and M3 generations were evaluated and showed that the mutant population phenotypes, including the plant height, semi-dwarfism, amylose content, protein content, gel consistency, grain yield, and spikelet fertility, varied. Interestingly, no segregation among the genotypes in the M2 and M3 generations was observed, while the genotypes of the control population were either paternally inherited or indeterminable when using 28 polymorphism simple sequence repeat (SSR) markers that were identified on parental lines from 200 markers. The MNU-induced mutation caused maternal inheritance in the segregating populations, as primarily important agronomic traits were maternally succeeded from the female line TBR1. The findings of this study indicated that, through the use of MNU, the breeding of rice cultivars with close genetic backgrounds (similarity coefficient = 0.52) could be shortened by the maternal control of important qualities, such as pest and disease resistance and high yield, thus contributing to sustainable rice production for rice farmers. Further examination of rice cultivars with a greater difference in the genetic background should be subsequently conducted.
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Anh TTT, Xuan TD, Huong CT, Dat TD. Phenotypic Performance of Rice ( Oryza sativa L .) Populations Induced by the MNU Mutant on the Adaptive Characteristics. ACTA ACUST UNITED AC 2019. [DOI: 10.18052/www.scipress.com/jhpr.5.13] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Mutation is an impressive method to induce potent characteristics in rice breeding. Evaluation on the phenotypic perfomance in mutant populations is important to examine the effectiveness of mutation. In this study, two rice populations of MNU ((N-methyl-N-Nitrosourea) -induced mutants were used to evaluate their phenotypes. The results showed that all of varieties and mutants expressed their ability to adapt with new environment condition via phenotypic expression. Grain yield of them ranged from 6.18 to 10.70 tons/ha. In general population S/TB performed their best characters. The distribution of related traits to grain yield and amylose content were also different from each population. It was observed that mutants expressed better characters than their parents. This study provided general information on phenotype of rice mutants and varieties in new environmental condition and revealed better adaptive characteristics of rice mutants. Findings of this study confirmed the the efficacy of MNU in rice breeding.
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Holme IB, Gregersen PL, Brinch-Pedersen H. Induced Genetic Variation in Crop Plants by Random or Targeted Mutagenesis: Convergence and Differences. FRONTIERS IN PLANT SCIENCE 2019; 10:1468. [PMID: 31803209 PMCID: PMC6868598 DOI: 10.3389/fpls.2019.01468] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Accepted: 10/22/2019] [Indexed: 05/18/2023]
Abstract
New Breeding Techniques (NBTs) include several new technologies for introduction of new variation into crop plants for plant breeding, in particular the methods that aim to make targeted mutagenesis at specific sites in the plant genome (NBT mutagenesis). However, following that the French highest legislative body for administrative justice, the Conseil d'État, has sought advice from The Court of Justice of the European Union (CJEU) in interpreting the scope of the genetically modified organisms (GMO) Directive, CJEU in a decision from 2018, stated that organisms modified by these new techniques are not exempted from the current EU GMO legislation. The decision was based in a context of conventional plant breeding using mutagenesis of crop plants by physical or chemical treatments. These plants are explicitly exempted from the EU GMO legislation, based on the long-termed use of mutagenesis. Following its decision, the EU Court considers that the NBTs operate "at a rate out of all proportion to those resulting from the application of conventional methods of mutagenesis." In this paper, we argue that in fact this is not the case anymore; instead, a convergence has taken place between conventional mutagenesis and NBTs, in particular due to the possibilities of TILLING methods that allow the fast detection of mutations in any gene of a genome. Thus, by both strategies mutations in any gene across the genome can be obtained at a rather high speed. However, the differences between the strategies are 1) the precision of the exact site of mutation in a target gene, and 2) the number of off-target mutations affecting other genes than the target gene. Both aspects favour the NBT methods, which provide more precision and fewer off-target mutations. This is in stark contrast to the different status of the two technologies with respect to EU GMO legislation. In the future, this situation is not sustainable for the European plant breeding industry, since it is expected that restrictions on the use of NBTs will be weaker outside Europe. This calls for reconsiderations of the EU legislation of plants generated via NBT mutagenesis.
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Jonas M, Navarro D. Induced mutations alter patterns of quantitative variation, phenotypic integration, and plasticity to elevated CO 2 in Arabidopsis thaliana. JOURNAL OF PLANT RESEARCH 2019; 132:33-47. [PMID: 30255212 DOI: 10.1007/s10265-018-1064-3] [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: 10/30/2017] [Accepted: 09/03/2018] [Indexed: 06/08/2023]
Abstract
A key step toward predicting responses to climate change is characterizing genetic variation in populations. While short-term responses will likely be shaped by currently available genetic variation, longer-term evolutionary responses will depend on the supply of novel variation by, ultimately, mutation. Studying mutational contributions to phenotypic variation can provide insights into the extent of potential variation on which selection may operate in future human-altered environments. Here we used the chemical mutagen ethyl methanesulfonate (EMS) to explore mutational contributions to phenotypic variation, integration, and plasticity to elevated carbon dioxide (eCO2) in three accessions of Arabidopsis thaliana. We found that (1) mutagenesis increased broad-sense heritabilities and variation in plasticity to eCO2 (genotype by environment interactions); (2) mutational effects varied among the three genetic backgrounds; (3) induced mutations had non-random (biased) effects on patterns of phenotypic integration. To our knowledge, this is the first study to address the effects of chemically induced mutations on phenotypic plasticity to eCO2 in a model plant. We discuss our results in light of emerging insights from theoretical and empirical quantitative genetics, suggest potential avenues of research, and identify approaches that may help advance our understanding of climate-driven evolution in plants.
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Affiliation(s)
- Mark Jonas
- Department of Biology, School of Natural and Social Sciences, State University of New York-Purchase College, 735 Anderson Hill Road, Purchase, NY, 10577, USA.
| | - Dania Navarro
- Department of Biology, School of Natural and Social Sciences, State University of New York-Purchase College, 735 Anderson Hill Road, Purchase, NY, 10577, USA
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Mousavi‐Derazmahalleh M, Bayer PE, Hane JK, Valliyodan B, Nguyen HT, Nelson MN, Erskine W, Varshney RK, Papa R, Edwards D. Adapting legume crops to climate change using genomic approaches. PLANT, CELL & ENVIRONMENT 2019; 42:6-19. [PMID: 29603775 PMCID: PMC6334278 DOI: 10.1111/pce.13203] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Accepted: 03/10/2018] [Indexed: 05/05/2023]
Abstract
Our agricultural system and hence food security is threatened by combination of events, such as increasing population, the impacts of climate change, and the need to a more sustainable development. Evolutionary adaptation may help some species to overcome environmental changes through new selection pressures driven by climate change. However, success of evolutionary adaptation is dependent on various factors, one of which is the extent of genetic variation available within species. Genomic approaches provide an exceptional opportunity to identify genetic variation that can be employed in crop improvement programs. In this review, we illustrate some of the routinely used genomics-based methods as well as recent breakthroughs, which facilitate assessment of genetic variation and discovery of adaptive genes in legumes. Although additional information is needed, the current utility of selection tools indicate a robust ability to utilize existing variation among legumes to address the challenges of climate uncertainty.
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Affiliation(s)
- Mahsa Mousavi‐Derazmahalleh
- UWA School of Agriculture and EnvironmentThe University of Western Australia35 Stirling HighwayCrawleyWestern Australia6009Australia
- School of Biological SciencesThe University of Western Australia35 Stirling HighwayCrawleyWestern Australia6009Australia
| | - Philipp E. Bayer
- School of Biological SciencesThe University of Western Australia35 Stirling HighwayCrawleyWestern Australia6009Australia
| | - James K. Hane
- CCDM BioinformaticsCentre for Crop Disease Management, Curtin UniversityBentleyWestern Australia6102Australia
| | - Babu Valliyodan
- Division of Plant Sciences and National Center for Soybean BiotechnologyUniversity of MissouriColumbiaMO65211USA
| | - Henry T. Nguyen
- Division of Plant Sciences and National Center for Soybean BiotechnologyUniversity of MissouriColumbiaMO65211USA
| | - Matthew N. Nelson
- UWA School of Agriculture and EnvironmentThe University of Western Australia35 Stirling HighwayCrawleyWestern Australia6009Australia
- Natural Capital and Plant HealthRoyal Botanic Gardens Kew, Wakehurst PlaceArdinglyWest SussexRH17 6TNUK
- The UWA Institute of AgricultureThe University of Western Australia35 Stirling HighwayPerthWestern Australia6009Australia
| | - William Erskine
- UWA School of Agriculture and EnvironmentThe University of Western Australia35 Stirling HighwayCrawleyWestern Australia6009Australia
- Centre for Plant Genetics and BreedingThe University of Western Australia35 Stirling HighwayCrawleyWestern Australia6009Australia
- The UWA Institute of AgricultureThe University of Western Australia35 Stirling HighwayPerthWestern Australia6009Australia
| | - Rajeev K. Varshney
- UWA School of Agriculture and EnvironmentThe University of Western Australia35 Stirling HighwayCrawleyWestern Australia6009Australia
- The UWA Institute of AgricultureThe University of Western Australia35 Stirling HighwayPerthWestern Australia6009Australia
- International Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)Patancheru502 324India
| | - Roberto Papa
- Department of Agricultural, Food, and Environmental SciencesUniversità Politecnica delle Marche60131AnconaItaly
| | - David Edwards
- School of Biological SciencesThe University of Western Australia35 Stirling HighwayCrawleyWestern Australia6009Australia
- The UWA Institute of AgricultureThe University of Western Australia35 Stirling HighwayPerthWestern Australia6009Australia
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