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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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152
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Weckwerth W, Ghatak A, Bellaire A, Chaturvedi P, Varshney RK. PANOMICS meets germplasm. PLANT BIOTECHNOLOGY JOURNAL 2020; 18:1507-1525. [PMID: 32163658 PMCID: PMC7292548 DOI: 10.1111/pbi.13372] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2019] [Revised: 02/17/2020] [Accepted: 02/26/2020] [Indexed: 05/14/2023]
Abstract
Genotyping-by-sequencing has enabled approaches for genomic selection to improve yield, stress resistance and nutritional value. More and more resource studies are emerging providing 1000 and more genotypes and millions of SNPs for one species covering a hitherto inaccessible intraspecific genetic variation. The larger the databases are growing, the better statistical approaches for genomic selection will be available. However, there are clear limitations on the statistical but also on the biological part. Intraspecific genetic variation is able to explain a high proportion of the phenotypes, but a large part of phenotypic plasticity also stems from environmentally driven transcriptional, post-transcriptional, translational, post-translational, epigenetic and metabolic regulation. Moreover, regulation of the same gene can have different phenotypic outputs in different environments. Consequently, to explain and understand environment-dependent phenotypic plasticity based on the available genotype variation we have to integrate the analysis of further molecular levels reflecting the complete information flow from the gene to metabolism to phenotype. Interestingly, metabolomics platforms are already more cost-effective than NGS platforms and are decisive for the prediction of nutritional value or stress resistance. Here, we propose three fundamental pillars for future breeding strategies in the framework of Green Systems Biology: (i) combining genome selection with environment-dependent PANOMICS analysis and deep learning to improve prediction accuracy for marker-dependent trait performance; (ii) PANOMICS resolution at subtissue, cellular and subcellular level provides information about fundamental functions of selected markers; (iii) combining PANOMICS with genome editing and speed breeding tools to accelerate and enhance large-scale functional validation of trait-specific precision breeding.
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Affiliation(s)
- Wolfram Weckwerth
- Molecular Systems Biology (MOSYS)Department of Functional and Evolutionary EcologyFaculty of Life SciencesUniversity of ViennaViennaAustria
- Vienna Metabolomics Center (VIME)University of ViennaViennaAustria
| | - Arindam Ghatak
- Molecular Systems Biology (MOSYS)Department of Functional and Evolutionary EcologyFaculty of Life SciencesUniversity of ViennaViennaAustria
| | - Anke Bellaire
- Molecular Systems Biology (MOSYS)Department of Functional and Evolutionary EcologyFaculty of Life SciencesUniversity of ViennaViennaAustria
| | - Palak Chaturvedi
- Molecular Systems Biology (MOSYS)Department of Functional and Evolutionary EcologyFaculty of Life SciencesUniversity of ViennaViennaAustria
| | - Rajeev K. Varshney
- Center of Excellence in Genomics & Systems BiologyInternational Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)HyderabadTelanganaIndia
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153
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Weckwerth W, Ghatak A, Bellaire A, Chaturvedi P, Varshney RK. PANOMICS meets germplasm. PLANT BIOTECHNOLOGY JOURNAL 2020; 18. [PMID: 32163658 PMCID: PMC7292548 DOI: 10.1111/pbi.13372,10.13140/rg.2.1.1233.5760] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Genotyping-by-sequencing has enabled approaches for genomic selection to improve yield, stress resistance and nutritional value. More and more resource studies are emerging providing 1000 and more genotypes and millions of SNPs for one species covering a hitherto inaccessible intraspecific genetic variation. The larger the databases are growing, the better statistical approaches for genomic selection will be available. However, there are clear limitations on the statistical but also on the biological part. Intraspecific genetic variation is able to explain a high proportion of the phenotypes, but a large part of phenotypic plasticity also stems from environmentally driven transcriptional, post-transcriptional, translational, post-translational, epigenetic and metabolic regulation. Moreover, regulation of the same gene can have different phenotypic outputs in different environments. Consequently, to explain and understand environment-dependent phenotypic plasticity based on the available genotype variation we have to integrate the analysis of further molecular levels reflecting the complete information flow from the gene to metabolism to phenotype. Interestingly, metabolomics platforms are already more cost-effective than NGS platforms and are decisive for the prediction of nutritional value or stress resistance. Here, we propose three fundamental pillars for future breeding strategies in the framework of Green Systems Biology: (i) combining genome selection with environment-dependent PANOMICS analysis and deep learning to improve prediction accuracy for marker-dependent trait performance; (ii) PANOMICS resolution at subtissue, cellular and subcellular level provides information about fundamental functions of selected markers; (iii) combining PANOMICS with genome editing and speed breeding tools to accelerate and enhance large-scale functional validation of trait-specific precision breeding.
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Affiliation(s)
- Wolfram Weckwerth
- Molecular Systems Biology (MOSYS)Department of Functional and Evolutionary EcologyFaculty of Life SciencesUniversity of ViennaViennaAustria
- Vienna Metabolomics Center (VIME)University of ViennaViennaAustria
| | - Arindam Ghatak
- Molecular Systems Biology (MOSYS)Department of Functional and Evolutionary EcologyFaculty of Life SciencesUniversity of ViennaViennaAustria
| | - Anke Bellaire
- Molecular Systems Biology (MOSYS)Department of Functional and Evolutionary EcologyFaculty of Life SciencesUniversity of ViennaViennaAustria
| | - Palak Chaturvedi
- Molecular Systems Biology (MOSYS)Department of Functional and Evolutionary EcologyFaculty of Life SciencesUniversity of ViennaViennaAustria
| | - Rajeev K. Varshney
- Center of Excellence in Genomics & Systems BiologyInternational Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)HyderabadTelanganaIndia
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154
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Janni M, Gullì M, Maestri E, Marmiroli M, Valliyodan B, Nguyen HT, Marmiroli N. Molecular and genetic bases of heat stress responses in crop plants and breeding for increased resilience and productivity. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:3780-3802. [PMID: 31970395 PMCID: PMC7316970 DOI: 10.1093/jxb/eraa034] [Citation(s) in RCA: 94] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Accepted: 01/20/2020] [Indexed: 05/21/2023]
Abstract
To ensure the food security of future generations and to address the challenge of the 'no hunger zone' proposed by the FAO (Food and Agriculture Organization), crop production must be doubled by 2050, but environmental stresses are counteracting this goal. Heat stress in particular is affecting agricultural crops more frequently and more severely. Since the discovery of the physiological, molecular, and genetic bases of heat stress responses, cultivated plants have become the subject of intense research on how they may avoid or tolerate heat stress by either using natural genetic variation or creating new variation with DNA technologies, mutational breeding, or genome editing. This review reports current understanding of the genetic and molecular bases of heat stress in crops together with recent approaches to creating heat-tolerant varieties. Research is close to a breakthrough of global relevance, breeding plants fitter to face the biggest challenge of our time.
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Affiliation(s)
- Michela Janni
- Institute of Bioscience and Bioresources (IBBR), National Research Council (CNR), Via Amendola, Bari, Italy
- Institute of Materials for Electronics and Magnetism (IMEM), National Research Council (CNR), Parco Area delle Scienze, Parma, Italy
| | - Mariolina Gullì
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze, Parma, Italy
| | - Elena Maestri
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze, Parma, Italy
| | - Marta Marmiroli
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze, Parma, Italy
| | - Babu Valliyodan
- Division of Plant Sciences, University of Missouri, Columbia, MO, USA
- Lincoln University, Jefferson City, MO, USA
| | - Henry T Nguyen
- Division of Plant Sciences, University of Missouri, Columbia, MO, USA
| | - Nelson Marmiroli
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze, Parma, Italy
- CINSA Interuniversity Consortium for Environmental Sciences, Parma/Venice, Italy
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155
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Zhang J, Yang Y, Feng X, Xu H, Chen J, He Y. Identification of Bacterial Blight Resistant Rice Seeds Using Terahertz Imaging and Hyperspectral Imaging Combined With Convolutional Neural Network. FRONTIERS IN PLANT SCIENCE 2020; 11:821. [PMID: 32670316 PMCID: PMC7326944 DOI: 10.3389/fpls.2020.00821] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Accepted: 05/22/2020] [Indexed: 06/02/2023]
Abstract
Because bacterial blight (BB) disease seriously affects the yield and quality of rice, breeding BB resistant rice is an important priority for plant breeders but the process is time-consuming. The feasibility of using terahertz imaging technology and near-infrared hyperspectral imaging technology to identify BB resistant seeds has therefore been studied. The two-dimensional (2D) spectral images and one-dimensional (1D) spectra provided by both imaging methods were used to build discriminant models based on a deep learning method, the convolutional neural network (CNN), and traditional machine learning methods, support vector machine (SVM), random forest (RF), and partial least squares discriminant analysis (PLS-DA). The highest classification accuracy was achieved by the discriminate model based on CNN using the terahertz absorption spectra. Confusion matrixes were pictured to show the identification details. The t-distributed stochastic neighbor embedding (t-SNE) method was used to visualize the process of CNN data processing. Terahertz imaging technology combined with CNN has great potential to quickly identify BB resistant rice seeds and is more accurate than using near-infrared hyperspectral imaging.
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Affiliation(s)
- Jinnuo Zhang
- College of Biosystems Engineering and Food Science, Key Laboratory of Spectroscopy, Ministry of Agriculture and Rural Affairs, Zhejiang University, Hangzhou, China
| | - Yong Yang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Biotechnology for Plant Protection, Ministry of Agriculture and Rural Affairs, Zhejiang Provincial Key Laboratory of Biotechnology for Plant Protection, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Xuping Feng
- College of Biosystems Engineering and Food Science, Key Laboratory of Spectroscopy, Ministry of Agriculture and Rural Affairs, Zhejiang University, Hangzhou, China
| | - Hongxia Xu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Biotechnology for Plant Protection, Ministry of Agriculture and Rural Affairs, Zhejiang Provincial Key Laboratory of Biotechnology for Plant Protection, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Jianping Chen
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Biotechnology for Plant Protection, Ministry of Agriculture and Rural Affairs, Zhejiang Provincial Key Laboratory of Biotechnology for Plant Protection, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Biotechnology for Plant Protection, Ministry of Agriculture and Rural Affairs, Zhejiang Provincial Key Laboratory of Biotechnology for Plant Protection, Institute of Plant Virology, Ningbo University, Ningbo, China
| | - Yong He
- College of Biosystems Engineering and Food Science, Key Laboratory of Spectroscopy, Ministry of Agriculture and Rural Affairs, Zhejiang University, Hangzhou, China
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156
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Generation of High Yielding and Fragrant Rice ( Oryza sativa L.) Lines by CRISPR/Cas9 Targeted Mutagenesis of Three Homoeologs of Cytochrome P450 Gene Family and OsBADH2 and Transcriptome and Proteome Profiling of Revealed Changes Triggered by Mutations. PLANTS 2020; 9:plants9060788. [PMID: 32586052 PMCID: PMC7355857 DOI: 10.3390/plants9060788] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Revised: 06/19/2020] [Accepted: 06/19/2020] [Indexed: 12/12/2022]
Abstract
The significant increase in grain yield and quality are often antagonistic but a constant demand for breeders and consumers. Some genes related to cytochrome P450 family are known for rice organ growth but their role in controlling grain yield is still unknown. Here, we generated new rice mutants with high yield and improved aroma by simultaneously editing three cytochrome P450 homoeologs (Os03g0603100, Os03g0568400, and GL3.2) and OsBADH2 with the CRISPR/Cas9 system, and RNA-sequencing and proteomic analysis were performed to unveil the subsequent changes. High mutation efficiency was achieved in both target sites of each gene and the mutations were predominantly only deletions, while insertions were rare, and no mutations were detected in the five most likely off-target sites against each sgRNA. Mutants exhibited increased grain size, 2-acetyl-1-pyrroline (2AP) content, and grain cell numbers while there was no change in other agronomic traits. Transgene-DNA-free mutant lines appeared with a frequency of 44.44% and homozygous mutations were stably transmitted, and bi-allelic and heterozygous mutations followed Mendelian inheritance, while the inheritance of chimeric mutations was unpredictable. Deep RNA sequencing and proteomic results revealed the regulation of genes and proteins related to cytochrome P450 family, grain size and development, and cell cycle. The KEGG and hub-gene and protein network analysis showed that the gene and proteins related to ribosomal and photosynthesis pathways were mainly enriched, respectively. Our findings provide a broad and detailed basis to understand the role of CRISPR/Cas9 in rice yield and quality improvement.
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157
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Brandt KM, Gunn H, Moretti N, Zemetra RS. A Streamlined Protocol for Wheat ( Triticum aestivum) Protoplast Isolation and Transformation With CRISPR-Cas Ribonucleoprotein Complexes. FRONTIERS IN PLANT SCIENCE 2020; 11:769. [PMID: 32587597 PMCID: PMC7298111 DOI: 10.3389/fpls.2020.00769] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Accepted: 05/14/2020] [Indexed: 05/03/2023]
Abstract
The genetic engineering method CRISPR has been touted as an efficient, inexpensive, easily used, and targeted genetic modification technology that is widely suggested as having the potential to solve many of the problems facing agriculture now and in the future. Like all new technologies, however, it is not without challenges. One of the most difficult challenges to anticipate and detect is gene targets that are inaccessible due to the chromatin state at their specific location. There is currently no way to predict this during the process of designing a sgRNA target, and the only way to detect this issue before spending time and resources on full transformations is to test the cleavage ability of the sgRNA in vivo. In wheat, this is possible using protoplast isolation and PEG transformation with Cas9 ribonucleoprotein complexes. Therefore, we have developed a streamlined protocol for testing the accessibility of sgRNA targets in wheat. The first steps involve digesting wheat leaf tissue in an enzymatic solution and then isolating viable protoplasts using filters and a sucrose gradient. The protoplasts are then transformed using Cas9 ribonucleoprotein complexes via PEG-mediated transformation. DNA is isolated from the CRISPR-Cas-edited protoplasts and PCR is performed to amplify the gene target region. The PCR product is then used to assess the editing efficiency of the chosen sgRNA using Sanger sequencing. This simplified protocol for the isolation and transformation of wheat protoplast cells using Cas9 ribonucleoprotein complexes streamlines CRISPR transformation projects by allowing for a fast and easy test of sgRNA accessibility in vivo.
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Affiliation(s)
- Kali M. Brandt
- Wheat Breeding and Genetics, Crop and Soil Science, Oregon State University, Corvallis, OR, United States
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158
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Schreiber M, Mascher M, Wright J, Padmarasu S, Himmelbach A, Heavens D, Milne L, Clavijo BJ, Stein N, Waugh R. A Genome Assembly of the Barley 'Transformation Reference' Cultivar Golden Promise. G3 (BETHESDA, MD.) 2020; 10:1823-1827. [PMID: 32241919 DOI: 10.1101/2020.02.12.945550] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Barley (Hordeum vulgare) is one of the most important crops worldwide and is also considered a research model for the large-genome small grain temperate cereals. Despite genomic resources improving all the time, they are limited for the cv Golden Promise, the most efficient genotype for genetic transformation. We have developed a barley cv Golden Promise reference assembly integrating Illumina paired-end reads, long mate-pair reads, Dovetail Chicago in vitro proximity ligation libraries and chromosome conformation capture sequencing (Hi-C) libraries into a contiguous reference assembly. The assembled genome of 7 chromosomes and 4.13Gb in size, has a super-scaffold N50 after Chicago libraries of 4.14Mb and contains only 2.2% gaps. Using BUSCO (benchmarking universal single copy orthologous genes) as evaluation the genome assembly contains 95.2% of complete and single copy genes from the plant database. A high-quality Golden Promise reference assembly will be useful and utilized by the whole barley research community but will prove particularly useful for CRISPR-Cas9 experiments.
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Affiliation(s)
- Miriam Schreiber
- Cell and Molecular Sciences, The James Hutton Institute, Invergowrie, Dundee, Scotland DD2 5DA, UK
| | - Martin Mascher
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, 04103 Leipzig, Germany
| | - Jonathan Wright
- Earlham Institute, Norwich Research Park, Norwich NR4 7UH, UK
| | - Sudharasan Padmarasu
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
| | - Axel Himmelbach
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
| | - Darren Heavens
- Earlham Institute, Norwich Research Park, Norwich NR4 7UH, UK
| | - Linda Milne
- Information and Computational Sciences, The James Hutton Institute, Invergowrie, Dundee, Scotland DD2 5DA, UK
| | | | - Nils Stein
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
- CiBreed - Center for Integrated Breeding Research, Georg-August University Göttingen, Department of Crop Sciences, Von Siebold Straße 8, 37075 Göttingen, Germany
| | - Robbie Waugh
- Cell and Molecular Sciences, The James Hutton Institute, Invergowrie, Dundee, Scotland DD2 5DA, UK
- Division of Plant Sciences, University of Dundee at The James Hutton Institute, Invergowrie, Dundee, Scotland DD2 5DA, UK
- School of Agriculture and Wine, University of Adelaide, Plant Genome Building, Waite Campus, Urrbrae, Adelaide, South Australia
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159
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Huang S, Xin S, Xie G, Han J, Liu Z, Wang B, Zhang S, Wu Q, Cheng X. Mutagenesis reveals that the rice OsMPT3 gene is an important osmotic regulatory factor. ACTA ACUST UNITED AC 2020. [DOI: 10.1016/j.cj.2020.02.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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160
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Schreiber M, Mascher M, Wright J, Padmarasu S, Himmelbach A, Heavens D, Milne L, Clavijo BJ, Stein N, Waugh R. A Genome Assembly of the Barley 'Transformation Reference' Cultivar Golden Promise. G3 (BETHESDA, MD.) 2020; 10:1823-1827. [PMID: 32241919 PMCID: PMC7263683 DOI: 10.1534/g3.119.401010] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Accepted: 03/27/2020] [Indexed: 01/02/2023]
Abstract
Barley (Hordeum vulgare) is one of the most important crops worldwide and is also considered a research model for the large-genome small grain temperate cereals. Despite genomic resources improving all the time, they are limited for the cv Golden Promise, the most efficient genotype for genetic transformation. We have developed a barley cv Golden Promise reference assembly integrating Illumina paired-end reads, long mate-pair reads, Dovetail Chicago in vitro proximity ligation libraries and chromosome conformation capture sequencing (Hi-C) libraries into a contiguous reference assembly. The assembled genome of 7 chromosomes and 4.13Gb in size, has a super-scaffold N50 after Chicago libraries of 4.14Mb and contains only 2.2% gaps. Using BUSCO (benchmarking universal single copy orthologous genes) as evaluation the genome assembly contains 95.2% of complete and single copy genes from the plant database. A high-quality Golden Promise reference assembly will be useful and utilized by the whole barley research community but will prove particularly useful for CRISPR-Cas9 experiments.
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Affiliation(s)
- Miriam Schreiber
- Cell and Molecular Sciences, The James Hutton Institute, Invergowrie, Dundee, Scotland DD2 5DA, UK
| | - Martin Mascher
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, 04103 Leipzig, Germany
| | - Jonathan Wright
- Earlham Institute, Norwich Research Park, Norwich NR4 7UH, UK
| | - Sudharasan Padmarasu
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
| | - Axel Himmelbach
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
| | - Darren Heavens
- Earlham Institute, Norwich Research Park, Norwich NR4 7UH, UK
| | - Linda Milne
- Information and Computational Sciences, The James Hutton Institute, Invergowrie, Dundee, Scotland DD2 5DA, UK
| | | | - Nils Stein
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
- CiBreed - Center for Integrated Breeding Research, Georg-August University Göttingen, Department of Crop Sciences, Von Siebold Straße 8, 37075 Göttingen, Germany
| | - Robbie Waugh
- Cell and Molecular Sciences, The James Hutton Institute, Invergowrie, Dundee, Scotland DD2 5DA, UK
- Division of Plant Sciences, University of Dundee at The James Hutton Institute, Invergowrie, Dundee, Scotland DD2 5DA, UK
- School of Agriculture and Wine, University of Adelaide, Plant Genome Building, Waite Campus, Urrbrae, Adelaide, South Australia
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161
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Navet N, Tian M. Efficient targeted mutagenesis in allotetraploid sweet basil by CRISPR/Cas9. PLANT DIRECT 2020; 4:e00233. [PMID: 32537560 PMCID: PMC7287412 DOI: 10.1002/pld3.233] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Revised: 05/14/2020] [Accepted: 05/15/2020] [Indexed: 05/25/2023]
Abstract
Sweet basil (Ocimum basilicum) is an economically important herb and its global production is threatened by basil downy mildew caused by the obligate biotrophic oomycete Peronospora belbahrii. Effective tools are required for functional understanding of its genes involved in synthesis of valuable secondary metabolites in essential oil and disease resistance, and breeding for varieties with improved traits. Clustered regularly interspaced short palindromic repeat (CRISPR)/Cas9 gene editing technology has revolutionized crop breeding and functional genomics. The applicability and efficacy of this genomic tool in the allotetraploid sweet basil were tested by editing a potential susceptibility (S) gene ObDMR1, the basil homolog of Arabidopsis DMR1 (Downy Mildew Resistant 1) whose mutations conferred nearly complete resistance against Arabidopsis downy mildew pathogen, Hyaloperonospora arabidopsidis. Two single guide RNAs targeting two different sites of the ObDMR1 coding sequence were designed. A total of 56 transgenic lines were obtained via Agrobacterium-mediated stable transformation. Mutational analysis of 54 T0 transgenic lines identified 92.6% lines carrying mutations at target 1 site, while a very low mutation frequency was detected at target 2 site. Deep sequencing of six T0 lines revealed various mutations at target 1 site, with a complete knockout of all alleles in one line. ObDMR1 homozygous mutant plants with some being transgene free were identified from T1 segregating populations. T2 homozygous mutant plants with 1-bp frameshift mutations exhibited a dwarf phenotype at young seedling stage. In summary, this study established a highly efficient CRISPR/Cas9-mediated gene editing system for targeted mutagenesis in sweet basil. This system has the capacity to generate complete knockout mutants in this allotetraploid species at the first generation of transgenic plants and transgene-free homozygous mutants in the second generation. The establishment of this system is expected to accelerate basil functional genomics and breeding.
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Affiliation(s)
- Natasha Navet
- Department of Plant and Environmental Protection SciencesUniversity of Hawaii at ManoaHonoluluHIUSA
| | - Miaoying Tian
- Department of Plant and Environmental Protection SciencesUniversity of Hawaii at ManoaHonoluluHIUSA
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162
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Lu X, Zhou Y, Fan F, Peng J, Zhang J. Coordination of light, circadian clock with temperature: The potential mechanisms regulating chilling tolerance in rice. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2020; 62:737-760. [PMID: 31243851 DOI: 10.1111/jipb.12852] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Accepted: 06/19/2019] [Indexed: 06/09/2023]
Abstract
Rice (Oryza sativa L.) is a major staple food crop for over half of the world's population. As a crop species originated from the subtropics, rice production is hampered by chilling stress. The genetic mechanisms of rice responses to chilling stress have attracted much attention, focusing on chilling-related gene mining and functional analyses. Plants have evolved sophisticated regulatory systems to respond to chilling stress in coordination with light signaling pathway and internal circadian clock. However, in rice, information about light-signaling pathways and circadian clock regulation and their roles in chilling tolerance remains elusive. Further investigation into the regulatory network of chilling tolerance in rice is needed, as knowledge of the interaction between temperature, light, and circadian clock dynamics is limited. Here, based on phenotypic analysis of transgenic and mutant rice lines, we delineate the relevant genes with important regulatory roles in chilling tolerance. In addition, we discuss the potential coordination mechanism among temperature, light, and circadian clock in regulating chilling response and tolerance of rice, and provide perspectives for the ongoing chilling signaling network research in rice.
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Affiliation(s)
- Xuedan Lu
- Southern Regional Collaborative Innovation Center for Grain and Oil Crops in China, School of Agriculture, Hunan Agricultural University, Changsha, 410128, China
| | - Yan Zhou
- Southern Regional Collaborative Innovation Center for Grain and Oil Crops in China, School of Agriculture, Hunan Agricultural University, Changsha, 410128, China
| | - Fan Fan
- Southern Regional Collaborative Innovation Center for Grain and Oil Crops in China, School of Agriculture, Hunan Agricultural University, Changsha, 410128, China
| | - JunHua Peng
- Huazhi Rice Bio-tech Company Ltd., Changsha, 410128, China
| | - Jian Zhang
- Southern Regional Collaborative Innovation Center for Grain and Oil Crops in China, School of Agriculture, Hunan Agricultural University, Changsha, 410128, China
- Huazhi Rice Bio-tech Company Ltd., Changsha, 410128, China
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163
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Wada N, Ueta R, Osakabe Y, Osakabe K. Precision genome editing in plants: state-of-the-art in CRISPR/Cas9-based genome engineering. BMC PLANT BIOLOGY 2020; 20:234. [PMID: 32450802 PMCID: PMC7249668 DOI: 10.1186/s12870-020-02385-5] [Citation(s) in RCA: 83] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Accepted: 04/05/2020] [Indexed: 05/19/2023]
Abstract
Traditionally, generation of new plants with improved or desirable features has relied on laborious and time-consuming breeding techniques. Genome-editing technologies have led to a new era of genome engineering, enabling an effective, precise, and rapid engineering of the plant genomes. Clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (CRISPR/Cas9) has emerged as a new genome-editing tool, extensively applied in various organisms, including plants. The use of CRISPR/Cas9 allows generating transgene-free genome-edited plants ("null segregants") in a short period of time. In this review, we provide a critical overview of the recent advances in CRISPR/Cas9 derived technologies for inducing mutations at target sites in the genome and controlling the expression of target genes. We highlight the major breakthroughs in applying CRISPR/Cas9 to plant engineering, and challenges toward the production of null segregants. We also provide an update on the efforts of engineering Cas9 proteins, newly discovered Cas9 variants, and novel CRISPR/Cas systems for use in plants. The application of CRISPR/Cas9 and related technologies in plant engineering will not only facilitate molecular breeding of crop plants but also accelerate progress in basic research.
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Affiliation(s)
- Naoki Wada
- Graduate School of Technology, Industrial and Social Sciences, Tokushima University, Tokushima, Japan
| | - Risa Ueta
- Graduate School of Technology, Industrial and Social Sciences, Tokushima University, Tokushima, Japan
| | - Yuriko Osakabe
- Graduate School of Technology, Industrial and Social Sciences, Tokushima University, Tokushima, Japan
| | - Keishi Osakabe
- Graduate School of Technology, Industrial and Social Sciences, Tokushima University, Tokushima, Japan.
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164
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Tian Y, Chen K, Li X, Zheng Y, Chen F. Design of high-oleic tobacco (Nicotiana tabacum L.) seed oil by CRISPR-Cas9-mediated knockout of NtFAD2-2. BMC PLANT BIOLOGY 2020; 20:233. [PMID: 32450806 PMCID: PMC7249356 DOI: 10.1186/s12870-020-02441-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2019] [Accepted: 05/11/2020] [Indexed: 05/09/2023]
Abstract
BACKGROUND Tobacco seed oil could be used as an appropriate feedstock for biodiesel production. However, the high linoleic acid content of tobacco seed oil makes it susceptible to oxidation. Altering the fatty acid profile by increasing the content of oleic acid could improve the properties of biodiesel produced from tobacco seed oil. RESULTS Four FAD2 genes, NtFAD2-1a, NtFAD2-1b, NtFAD2-2a, and NtFAD2-2b, were identified in allotetraploid tobacco genome. Phylogenetic analysis of protein sequences showed that NtFAD2-1a and NtFAD2-2a originated from N. tomentosiformis, while NtFAD2-1b and NtFAD2-2b from N. sylvestris. Expression analysis revealed that NtFAD2-2a and NtFAD2-2b transcripts were more abundant in developing seeds than in other tissues, while NtFAD2-1a and NtFAD2-1b showed low transcript levels in developing seed. Phylogenic analysis showed that NtFAD2-2a and NtFAD2-2b were seed-type FAD2 genes. Heterologous expression in yeast cells demonstrated that both NtFAD2-2a and NtFAD2-2b protein could introduce a double bond at the Δ12 position of fatty acid chain. The fatty acid profile analysis of tobacco fad2-2 mutant seeds derived from CRISPR-Cas9 edited plants showed dramatic increase of oleic acid content from 11% to over 79%, whereas linoleic acid decreased from 72 to 7%. In addition, the fatty acid composition of leaf was not affected in fad2-2 mutant plants. CONCLUSION Our data showed that knockout of seed-type FAD2 genes in tobacco could significantly increase the oleic acid content in seed oil. This research suggests that CRISPR-Cas9 system offers a rapid and highly efficient method in the tobacco seed lipid engineering programs.
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Affiliation(s)
- Yinshuai Tian
- College of Landscape and Ecological Engineering, Hebei University of Engineering, No.19 Taiji Road, Economic and technological development area, Handan, 056038, Hebei, China
- Institute of New Energy and Low-carbon Technology, Sichuan University, Chuanda Road, Shuangliu district, Chengdu, 610207, Sichuan, China
| | - Kai Chen
- College of Landscape and Ecological Engineering, Hebei University of Engineering, No.19 Taiji Road, Economic and technological development area, Handan, 056038, Hebei, China
| | - Xiao Li
- Key Laboratory of Bio-resources and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, No.29 Wangjiang Road, Wuhou district, Chengdu, 610065, Sichuan, China
| | - Yunpu Zheng
- School of Water Conservancy and Hydroelectric Power, Hebei University of Engineering, No.19 Taiji Road, Economic and technological development area, Handan, 056038, Hebei, China
| | - Fang Chen
- Institute of New Energy and Low-carbon Technology, Sichuan University, Chuanda Road, Shuangliu district, Chengdu, 610207, Sichuan, China.
- Key Laboratory of Bio-resources and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, No.29 Wangjiang Road, Wuhou district, Chengdu, 610065, Sichuan, China.
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165
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Dheer P, Rautela I, Sharma V, Dhiman M, Sharma A, Sharma N, Sharma MD. Evolution in crop improvement approaches and future prospects of molecular markers to CRISPR/Cas9 system. Gene 2020; 753:144795. [PMID: 32450202 DOI: 10.1016/j.gene.2020.144795] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Revised: 05/07/2020] [Accepted: 05/19/2020] [Indexed: 01/03/2023]
Abstract
The advent of genetic selection and genome modification method assure about a real novel reformation in biotechnology and genetic engineering. With the extensive capabilities of molecular markers of them being stable, cost-effective and easy to use, they ultimately become a potent tool for variety of applications such a gene targeting, selection, editing, functional genomics; mainly for the improvisation of commercially important crops. Three main benefits of molecular marker in the field of agriculture and crop improvement programmes first, reduction of the duration of breeding programmes, second, they allow creation of new genetic variation and genetic diversity of plants and third most promising benefit is help in production of engineered plant for disease resistance, or resistance from pathogen and herbicides. This review is anticipated to present an outline how the techniques have been evolved from the simple conventional applications of DNA based molecular markers to highly throughput CRISPR technology and geared the crop yield. Techniques like using Zinc Finger Nucleases (ZFNs), Transcription Activator-Like Effector Nucleases (TALENs) and Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR/Cas9) systems have revolutionised in the field of genome editing. These have been promptly accepted in both the research and commercial industry. On the whole, the widespread use of molecular markers with their types, their appliance in plant breeding along with the advances in genetic selection and genome editing together being a novel strategy to boost crop yield has been reviewed.
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Affiliation(s)
- Pallavi Dheer
- Department of Life Sciences, Shri Guru Ram Rai Institute of Technology & Science, Patel Nagar, Dehradun, Uttarakhand, India
| | - Indra Rautela
- Department of Biotechnology, SALS, Uttaranchal University, Dehradun, Uttarakhand, India
| | - Vandana Sharma
- Department of Botany, K.L.DAV (PG) College, Roorkee,Uttarakhand, India
| | - Manjul Dhiman
- Department of Botany, K.L.DAV (PG) College, Roorkee,Uttarakhand, India
| | - Aditi Sharma
- Department of Biotechnology, Graphic Era University, Dehradun, Uttarakhand, India
| | - Nishesh Sharma
- Department of Biotechnology, SALS, Uttaranchal University, Dehradun, Uttarakhand, India
| | - Manish Dev Sharma
- Department of Biotechnology, School of Basic and Applied Sciences, Shri Guru Ram Rai University, Patel Nagar, Dehradun, Uttarakhand, India.
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Hrbáčková M, Dvořák P, Takáč T, Tichá M, Luptovčiak I, Šamajová O, Ovečka M, Šamaj J. Biotechnological Perspectives of Omics and Genetic Engineering Methods in Alfalfa. FRONTIERS IN PLANT SCIENCE 2020; 11:592. [PMID: 32508859 PMCID: PMC7253590 DOI: 10.3389/fpls.2020.00592] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Accepted: 04/20/2020] [Indexed: 05/07/2023]
Abstract
For several decades, researchers are working to develop improved major crops with better adaptability and tolerance to environmental stresses. Forage legumes have been widely spread in the world due to their great ecological and economic values. Abiotic and biotic stresses are main factors limiting legume production, however, alfalfa (Medicago sativa L.) shows relatively high level of tolerance to drought and salt stress. Efforts focused on alfalfa improvements have led to the release of cultivars with new traits of agronomic importance such as high yield, better stress tolerance or forage quality. Alfalfa has very high nutritional value due to its efficient symbiotic association with nitrogen-fixing bacteria, while deep root system can help to prevent soil water loss in dry lands. The use of modern biotechnology tools is challenging in alfalfa since full genome, unlike to its close relative barrel medic (Medicago truncatula Gaertn.), was not released yet. Identification, isolation, and improvement of genes involved in abiotic or biotic stress response significantly contributed to the progress of our understanding how crop plants cope with these environmental challenges. In this review, we provide an overview of the progress that has been made in high-throughput sequencing, characterization of genes for abiotic or biotic stress tolerance, gene editing, as well as proteomic and metabolomics techniques bearing biotechnological potential for alfalfa improvement.
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Affiliation(s)
| | | | | | | | | | | | | | - Jozef Šamaj
- Department of Cell Biology, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University Olomouc, Olomouc, Czechia
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167
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Jaganathan D, Bohra A, Thudi M, Varshney RK. Fine mapping and gene cloning in the post-NGS era: advances and prospects. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2020; 133:1791-1810. [PMID: 32040676 PMCID: PMC7214393 DOI: 10.1007/s00122-020-03560-w] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Accepted: 01/29/2020] [Indexed: 05/18/2023]
Abstract
Improvement in traits of agronomic importance is the top breeding priority of crop improvement programs. Majority of these agronomic traits show complex quantitative inheritance. Identification of quantitative trait loci (QTLs) followed by fine mapping QTLs and cloning of candidate genes/QTLs is central to trait analysis. Advances in genomic technologies revolutionized our understanding of genetics of complex traits, and genomic regions associated with traits were employed in marker-assisted breeding or cloning of QTLs/genes. Next-generation sequencing (NGS) technologies have enabled genome-wide methodologies for the development of ultra-high-density genetic linkage maps in different crops, thus allowing placement of candidate loci within few kbs in genomes. In this review, we compare the marker systems used for fine mapping and QTL cloning in the pre- and post-NGS era. We then discuss how different NGS platforms in combination with advanced experimental designs have improved trait analysis and fine mapping. We opine that efficient genotyping/sequencing assays may circumvent the need for cumbersome procedures that were earlier used for fine mapping. A deeper understanding of the trait architectures of agricultural significance will be crucial to accelerate crop improvement.
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Affiliation(s)
- Deepa Jaganathan
- Center of Excellence in Genomics and Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India
- Centre for Plant Molecular Biology and Biotechnology, Tamil Nadu Agricultural University (TNAU), Coimbatore, India
| | - Abhishek Bohra
- Crop Improvement Division, ICAR-Indian Institute of Pulses Research (IIPR), Kanpur, India
| | - Mahendar Thudi
- Center of Excellence in Genomics and Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India.
| | - Rajeev K Varshney
- Center of Excellence in Genomics and Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India.
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168
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Wei Z, Arazi T, Hod N, Zohar M, Isaacson T, Doron-Faigenboim A, Reznik N, Yedidia I. Transcriptome Profiling of Ornithogalum dubium Leaves and Flowers to Identify Key Carotenoid Genes for CRISPR Gene Editing. PLANTS 2020; 9:plants9040540. [PMID: 32326260 PMCID: PMC7238968 DOI: 10.3390/plants9040540] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Revised: 04/12/2020] [Accepted: 04/20/2020] [Indexed: 11/16/2022]
Abstract
Ornithogalum dubium is a popular ornamental monocot native to South Africa with flower colors ranging from pure white to deep orange. Gene editing based on the CRISPR/Cas9 system has recently been shown to hold potential for color improvement in ornamental flower crops. To apply this approach to Ornithogalum color manipulation, genomic or transcriptomic data must first be collected. Here, cDNA libraries of O. dubium leaves and flowers were constructed and sequenced using the Illumina HiSeq 2500. Over 155 million 100-bp paired-end reads were assembled into a transcriptome database of 360,689 contigs, of which 18,660 contigs were differentially expressed between leaves and flowers. Carotenoids are the main pigment imparting spectrum of orange hues to O. dubium flowers. By querying our database, we identified a total of 16 unique transcripts (unigenes) predicted to be involved in the carotenoid biosynthesis pathway of Ornithogalum. Combining carotenoid profiles, we further inferred several key unigenes responsible for floral coloration and accumulation in O. dubium, of which the gene LCYB/comp146645_c0 was found as a suitable target to generate potentially red flower varieties of O. dubium. Our research thus provides a framework for the application of CRISPR/Cas9 technology to improve this ornamental crop.
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Affiliation(s)
- Zunzheng Wei
- Institute of Plant Science, The Volcani Center, Agricultural Research Organization, Bet Dagan 50250, Israel; (Z.W.); (T.A.); (N.H.); (A.D.-F.); (N.R.)
| | - Tzahi Arazi
- Institute of Plant Science, The Volcani Center, Agricultural Research Organization, Bet Dagan 50250, Israel; (Z.W.); (T.A.); (N.H.); (A.D.-F.); (N.R.)
| | - Nofar Hod
- Institute of Plant Science, The Volcani Center, Agricultural Research Organization, Bet Dagan 50250, Israel; (Z.W.); (T.A.); (N.H.); (A.D.-F.); (N.R.)
| | - Matat Zohar
- Newe Yaar Research Center, Agricultural Research Organization, Ramat Yishay 30095, Israel; (M.Z.); (T.I.)
| | - Tal Isaacson
- Newe Yaar Research Center, Agricultural Research Organization, Ramat Yishay 30095, Israel; (M.Z.); (T.I.)
| | - Adi Doron-Faigenboim
- Institute of Plant Science, The Volcani Center, Agricultural Research Organization, Bet Dagan 50250, Israel; (Z.W.); (T.A.); (N.H.); (A.D.-F.); (N.R.)
| | - Noam Reznik
- Institute of Plant Science, The Volcani Center, Agricultural Research Organization, Bet Dagan 50250, Israel; (Z.W.); (T.A.); (N.H.); (A.D.-F.); (N.R.)
| | - Iris Yedidia
- Institute of Plant Science, The Volcani Center, Agricultural Research Organization, Bet Dagan 50250, Israel; (Z.W.); (T.A.); (N.H.); (A.D.-F.); (N.R.)
- Correspondence:
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169
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Whelan AI, Gutti P, Lema MA. Gene Editing Regulation and Innovation Economics. Front Bioeng Biotechnol 2020; 8:303. [PMID: 32363186 PMCID: PMC7181966 DOI: 10.3389/fbioe.2020.00303] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Accepted: 03/20/2020] [Indexed: 01/04/2023] Open
Abstract
Argentina was the first country that enacted regulatory criteria to assess if organisms resulting from new breeding techniques (NBTs) are to be regarded as genetically modified organisms (GMOs) or not. The country has now accumulated 4 year of experience applying such criteria, reaching a considerable number of cases, composed mostly of gene-edited plants, animals, and microorganisms of agricultural use. This article explores the effects on economic innovation of such regulatory experience. This is done by comparing the cases of products derived from gene editing and other NBTs that have been presented to the regulatory system, against the cases of GMOs that have been deregulated in the country. Albeit preliminary, this analysis suggests that products from gene editing will have different profiles and market release rates compared with the first wave of products from the so called “modern biotechnology.” Gene editing products seems to follow a much faster development rate from bench to market. Such development is driven by a more diverse group of developers, and led mostly by small and medium enterprises (SMEs) and public research institutions. In addition, product profiles are also more diversified in terms of traits and organisms. The inferences of these findings for the agricultural and biotechnology sectors, particularly in developing countries, are discussed.
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Affiliation(s)
- Agustina I Whelan
- Maestría en Política y Gestión de la Ciencia y la Tecnología, Universidad de Buenos Aires, Buenos Aires, Argentina.,Dirección de Biotecnología, Secretaría de Alimentos y Bioeconomía, Buenos Aires, Argentina
| | - Patricia Gutti
- Maestría en Política y Gestión de la Ciencia y la Tecnología, Universidad de Buenos Aires, Buenos Aires, Argentina.,Departamento de Ciencia y Tecnología & Maestría en Ciencia, Tecnología y Sociedad, Universidad Nacional de Quilmes, Bernal, Argentina
| | - Martin A Lema
- Dirección de Biotecnología, Secretaría de Alimentos y Bioeconomía, Buenos Aires, Argentina.,Departamento de Ciencia y Tecnología & Maestría en Ciencia, Tecnología y Sociedad, Universidad Nacional de Quilmes, Bernal, Argentina
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170
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Ramkumar TR, Lenka SK, Arya SS, Bansal KC. A Short History and Perspectives on Plant Genetic Transformation. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2020; 2124:39-68. [PMID: 32277448 DOI: 10.1007/978-1-0716-0356-7_3] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Plant genetic transformation is an important technological advancement in modern science, which has not only facilitated gaining fundamental insights into plant biology but also started a new era in crop improvement and commercial farming. However, for many crop plants, efficient transformation and regeneration still remain a challenge even after more than 30 years of technical developments in this field. Recently, FokI endonuclease-based genome editing applications in plants offered an exciting avenue for augmenting crop productivity but it is mainly dependent on efficient genetic transformation and regeneration, which is a major roadblock for implementing genome editing technology in plants. In this chapter, we have outlined the major historical developments in plant genetic transformation for developing biotech crops. Overall, this field needs innovations in plant tissue culture methods for simplification of operational steps for enhancing the transformation efficiency. Similarly, discovering genes controlling developmental reprogramming and homologous recombination need considerable attention, followed by understanding their role in enhancing genetic transformation efficiency in plants. Further, there is an urgent need for exploring new and low-cost universal delivery systems for DNA/RNA and protein into plants. The advancements in synthetic biology, novel vector systems for precision genome editing and gene integration could potentially bring revolution in crop-genetic potential enhancement for a sustainable future. Therefore, efficient plant transformation system standardization across species holds the key for translating advances in plant molecular biology to crop improvement.
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Affiliation(s)
- Thakku R Ramkumar
- Agronomy Department, IFAS, University of Florida, Gainesville, FL, USA
| | - Sangram K Lenka
- TERI-Deakin NanoBiotechnology Centre, The Energy and Resources Institute, New Delhi, India
| | - Sagar S Arya
- TERI-Deakin NanoBiotechnology Centre, The Energy and Resources Institute, New Delhi, India
| | - Kailash C Bansal
- TERI-Deakin NanoBiotechnology Centre, The Energy and Resources Institute, New Delhi, India.
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171
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Oropeza-Aburto A, Cervantes-Pérez SA, Albert VA, Herrera-Estrella L. Agrobacterium tumefaciens mediated transformation of the aquatic carnivorous plant Utricularia gibba. PLANT METHODS 2020; 16:50. [PMID: 32308728 PMCID: PMC7149871 DOI: 10.1186/s13007-020-00592-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2020] [Accepted: 03/31/2020] [Indexed: 05/02/2023]
Abstract
BACKGROUND The genus Utricularia belongs to Lentibulariaceae, the largest family of carnivorous plants, which includes terrestrial, epiphytic and aquatic species. The development of specialized structures that evolved for carnivory is a feature of this genus that has been of great interest to biologists since Darwin's early studies. Utricularia gibba is itself an aquatic plant with sophisticated bladder traps having one of the most complex suction mechanisms for trapping prey. However, the molecular characterization of the mechanisms that regulate trap development and the biophysical processes involved in prey trapping are still largely unknown due to the lack of a simple and reproducible gene transfer system. RESULTS Here, we report the establishment of a simple, fast and reproducible protocol for genetic transformation of U. gibba based on the T-DNA of Agrobacterium tumefaciens. An in vitro selection system using Phosphinotricin as a selective agent was established for U. gibba. Plant transformation was confirmed by histochemical GUS assays and PCR and qRT-PCR analyses. We report on the expression pattern of the 35S promoter and of the promoter of a trap-specific ribonuclease gene in transgenic U. gibba plants. CONCLUSIONS The genetic transformation protocol reported here is an effective method for studying developmental biology and functional genomics of this genus of carnivorous plants and advances the utility of U. gibba as a model system to study developmental processes involved in trap formation.
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Affiliation(s)
- A. Oropeza-Aburto
- Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, 36824 Irapuato, Guanajuato Mexico
| | - S. A. Cervantes-Pérez
- Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, 36824 Irapuato, Guanajuato Mexico
| | - V. A. Albert
- Department of Biological Sciences, University at Buffalo, Buffalo, NY 14260 USA
- School of Biological Sciences, Nanyang Technological University, Singapore, 637551 Singapore
| | - L. Herrera-Estrella
- Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, 36824 Irapuato, Guanajuato Mexico
- Institute of Genomics for Crop Abiotic Stress Tolerance, Plant and Soil Department, Texas Tech University, Lubbock, USA
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Hazzouri KM, Flowers JM, Nelson D, Lemansour A, Masmoudi K, Amiri KMA. Prospects for the Study and Improvement of Abiotic Stress Tolerance in Date Palms in the Post-genomics Era. FRONTIERS IN PLANT SCIENCE 2020; 11:293. [PMID: 32256513 PMCID: PMC7090123 DOI: 10.3389/fpls.2020.00293] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2019] [Accepted: 02/26/2020] [Indexed: 05/05/2023]
Abstract
Date palm (Phoenix dactylifera L.) is a socio-economically important crop in the Middle East and North Africa and a major contributor to food security in arid regions of the world. P. dactylifera is both drought and salt tolerant, but recent water shortages and increases in groundwater and soil salinity have threatened the continued productivity of the crop. Recent studies of date palm have begun to elucidate the physiological mechanisms of abiotic stress tolerance and the genes and biochemical pathways that control the response to these stresses. Here we review recent studies on tolerance of date palm to salinity and drought stress, the role of the soil and root microbiomes in abiotic stress tolerance, and highlight recent findings of omic-type studies. We present a perspective on future research of abiotic stress in date palm that includes improving existing genome resources, application of genetic mapping to determine the genetic basis of variation in tolerances among cultivars, and adoption of gene-editing technologies to the study of abiotic stress in date palms. Development of necessary resources and application of the proposed methods will provide a foundation for future breeders and genetic engineers aiming to develop more stress-tolerant cultivars of date palm.
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Affiliation(s)
- Khaled Michel Hazzouri
- Khalifa Center for Genetic Engineering and Biotechnology, United Arab Emirates University, Al Ain, United Arab Emirates
| | - Jonathan M. Flowers
- Center for Genomics and Systems Biology (CGSB), New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
- Center for Genomics and Systems Biology, New York University, New York, NY, United States
| | - David Nelson
- Center for Genomics and Systems Biology (CGSB), New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | | | - Khaled Masmoudi
- College of Food and Agriculture, Department of Integrative Agriculture, United Arab Emirates University, Al Ain, United Arab Emirates
| | - Khaled M. A. Amiri
- Khalifa Center for Genetic Engineering and Biotechnology, United Arab Emirates University, Al Ain, United Arab Emirates
- College of Science, Department of Biology, United Arab Emirates University, Al Ain, United Arab Emirates
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173
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Pompili V, Dalla Costa L, Piazza S, Pindo M, Malnoy M. Reduced fire blight susceptibility in apple cultivars using a high-efficiency CRISPR/Cas9-FLP/FRT-based gene editing system. PLANT BIOTECHNOLOGY JOURNAL 2020; 18:845-858. [PMID: 31495052 PMCID: PMC7004915 DOI: 10.1111/pbi.13253] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Revised: 08/27/2019] [Accepted: 08/28/2019] [Indexed: 05/20/2023]
Abstract
The bacterium Erwinia amylovora, the causal agent of fire blight disease in apple, triggers its infection through the DspA/E effector which interacts with the apple susceptibility protein MdDIPM4. In this work, MdDIPM4 knockout has been produced in two Malus × domestica susceptible cultivars using the CRISPR/Cas9 system delivered via Agrobacterium tumefaciens. Fifty-seven transgenic lines were screened to identify CRISPR/Cas9-induced mutations. An editing efficiency of 75% was obtained. Seven edited lines with a loss-of-function mutation were inoculated with the pathogen. Highly significant reduction in susceptibility was observed compared to control plants. Sequencing of five potential off-target sites revealed no mutation event. Moreover, our construct contained a heat-shock inducible FLP/FRT recombination system designed specifically to remove the T-DNA harbouring the expression cassettes for CRISPR/Cas9, the marker gene and the FLP itself. Six plant lines with reduced susceptibility to the pathogen were heat-treated and screened by real-time PCR to quantify the exogenous DNA elimination. The T-DNA removal was further validated by sequencing in one plant line. To our knowledge, this work demonstrates for the first time the development and application of a CRISPR/Cas9-FLP/FRT gene editing system for the production of edited apple plants carrying a minimal trace of exogenous DNA.
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Affiliation(s)
- Valerio Pompili
- Department of Genomics and Biology of Fruit CropsResearch and Innovation CentreFondazione Edmund MachSan Michele all'AdigeItaly
- Department of Agricultural, Food, Environmental and Animal SciencesUniversità degli Studi di UdineUdineItaly
| | - Lorenza Dalla Costa
- Department of Genomics and Biology of Fruit CropsResearch and Innovation CentreFondazione Edmund MachSan Michele all'AdigeItaly
| | - Stefano Piazza
- Department of Genomics and Biology of Fruit CropsResearch and Innovation CentreFondazione Edmund MachSan Michele all'AdigeItaly
| | - Massimo Pindo
- Department of Genomics and Biology of Fruit CropsResearch and Innovation CentreFondazione Edmund MachSan Michele all'AdigeItaly
| | - Mickael Malnoy
- Department of Genomics and Biology of Fruit CropsResearch and Innovation CentreFondazione Edmund MachSan Michele all'AdigeItaly
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Jardak R, Boubakri H, Zemni H, Gandoura S, Mejri S, Mliki A, Ghorbel A. Establishment of an in vitro regeneration system and genetic transformation of the Tunisian 'Maltese half-blood' ( Citrus sinensis): an agro-economically important variety. 3 Biotech 2020; 10:99. [PMID: 32099740 DOI: 10.1007/s13205-020-2097-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Accepted: 01/24/2020] [Indexed: 11/29/2022] Open
Abstract
An efficient in vitro regeneration system using epicotyl segments was developed and then used for optimizing genetic transformation of the Tunisian 'Maltese half-blood' (Citrus sinensis) variety using phosphinothricin (PPT) resistance as a selectable marker. The maximum regeneration efficiency was achieved after incubating epicotyl explants (excised in an oblique manner) in MT culture media containing BAP (4 mg/l) and IAA (0.3 mg/l) hormonal combination in the dark for 3 weeks before their transfer to light. Data from the genetic transformation assays indicated that the highest number of regenerated-transformants was reached when the selection phase was conducted in MT culture media containing PPT (0.25 mg/l) and Carbenicillin (500 mg/l) for 3 weeks in the dark followed by 8 weeks of light. After that, transformed buds were maintained for eight additional weeks in the same culture media but with reduced PPT concentration (0.125 mg/l) before decreasing Carbenicillin dose (250 mg/l) at the second half of this last incubation period which allowed both a good shoot proliferation and an optimal rooting efficiency. Based on molecular analyses, the transgenicity of 21.42% of the regenerated vitroplants was confirmed. The developed regeneration and transformation procedures of the elite 'Maltese half-blood' variety can be used for orchard renewal as well as for functional studies and genome editing purposes to develop new cultivars with the desired genetic traits.
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Affiliation(s)
- Rahma Jardak
- 1Laboratory of Plant Molecular Physiology, Centre of Biotechnology of Borj-Cedria, BP 901, 2050, Hammam-Lif, Tunisia
| | - Hatem Boubakri
- 2Laboratory of Leguminous, Centre of Biotechnology of Borj-Cedria, BP 901, 2050 Hammam-Lif, Tunisia
| | - Hassene Zemni
- 1Laboratory of Plant Molecular Physiology, Centre of Biotechnology of Borj-Cedria, BP 901, 2050, Hammam-Lif, Tunisia
| | - Samia Gandoura
- 1Laboratory of Plant Molecular Physiology, Centre of Biotechnology of Borj-Cedria, BP 901, 2050, Hammam-Lif, Tunisia
| | - Samiha Mejri
- 1Laboratory of Plant Molecular Physiology, Centre of Biotechnology of Borj-Cedria, BP 901, 2050, Hammam-Lif, Tunisia
| | - Ahmed Mliki
- 1Laboratory of Plant Molecular Physiology, Centre of Biotechnology of Borj-Cedria, BP 901, 2050, Hammam-Lif, Tunisia
| | - Abdelwahed Ghorbel
- 1Laboratory of Plant Molecular Physiology, Centre of Biotechnology of Borj-Cedria, BP 901, 2050, Hammam-Lif, Tunisia
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175
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Michno JM, Virdi K, Stec AO, Liu J, Wang X, Xiong Y, Stupar RM. Integration, abundance, and transmission of mutations and transgenes in a series of CRISPR/Cas9 soybean lines. BMC Biotechnol 2020; 20:10. [PMID: 32093670 PMCID: PMC7038615 DOI: 10.1186/s12896-020-00604-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Accepted: 02/13/2020] [Indexed: 01/29/2023] Open
Abstract
BACKGROUND As with many plant species, current genome editing strategies in soybean are initiated by stably transforming a gene that encodes an engineered nuclease into the genome. Expression of the transgene results in a double-stranded break and repair at the targeted locus, oftentimes resulting in mutation(s) at the intended site. As soybean is a self-pollinating species with 20 chromosome pairs, the transgene(s) in the T0 plant are generally expected to be unlinked to the targeted mutation(s), and the transgene(s)/mutation(s) should independently assort into the T1 generation, resulting in Mendellian combinations of transgene presence/absence and allelic states within the segregating family. This prediction, however, is not always consistent with observed results. RESULTS In this study, we investigated inheritance patterns among three different CRISPR/Cas9 transgenes and their respective induced mutations in segregating soybean families. Next-generation resequencing of four T0 plants and four T1 progeny plants, followed by broader assessments of the segregating families, revealed both expected and unexpected patterns of inheritance among the different lineages. These unexpected patterns included: (1) A family in which T0 transgenes and mutations were not transmitted to progeny; (2) A family with four unlinked transgene insertions, including two respectively located at paralogous CRISPR target break sites; (3) A family in which mutations were observed and transmitted, but without evidence of transgene integration nor transmission. CONCLUSIONS Genome resequencing provides high-resolution of transgene integration structures and gene editing events. Segregation patterns of these events can be complicated by several potential mechanisms. This includes, but is not limited to, plant chimeras, multiple unlinked transgene integrations, editing of intended and paralogous targets, linkage between the transgene integration and target site, and transient expression of the editing reagents without transgene integration into the host genome.
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Affiliation(s)
- Jean-Michel Michno
- Bioinformatics and Computational Biology Program, University of Minnesota, Minneapolis, MN USA
- Department of Agronomy and Plant Genetics, University of Minnesota, 1991 Upper Buford Circle, 411 Borlaug Hall, Saint Paul, MN 55108 USA
| | - Kamaldeep Virdi
- Department of Agronomy and Plant Genetics, University of Minnesota, 1991 Upper Buford Circle, 411 Borlaug Hall, Saint Paul, MN 55108 USA
| | - Adrian O. Stec
- Department of Agronomy and Plant Genetics, University of Minnesota, 1991 Upper Buford Circle, 411 Borlaug Hall, Saint Paul, MN 55108 USA
| | - Junqi Liu
- Department of Agronomy and Plant Genetics, University of Minnesota, 1991 Upper Buford Circle, 411 Borlaug Hall, Saint Paul, MN 55108 USA
| | - Xiaobo Wang
- Department of Agronomy and Plant Genetics, University of Minnesota, 1991 Upper Buford Circle, 411 Borlaug Hall, Saint Paul, MN 55108 USA
- School of Agronomy, Anhui Agricultural University, Hefei, China
| | - Yer Xiong
- Department of Agronomy and Plant Genetics, University of Minnesota, 1991 Upper Buford Circle, 411 Borlaug Hall, Saint Paul, MN 55108 USA
| | - Robert M. Stupar
- Bioinformatics and Computational Biology Program, University of Minnesota, Minneapolis, MN USA
- Department of Agronomy and Plant Genetics, University of Minnesota, 1991 Upper Buford Circle, 411 Borlaug Hall, Saint Paul, MN 55108 USA
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176
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Zhang N, Roberts HM, Van Eck J, Martin GB. Generation and Molecular Characterization of CRISPR/Cas9-Induced Mutations in 63 Immunity-Associated Genes in Tomato Reveals Specificity and a Range of Gene Modifications. FRONTIERS IN PLANT SCIENCE 2020; 11:10. [PMID: 32117361 PMCID: PMC7010635 DOI: 10.3389/fpls.2020.00010] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Accepted: 01/07/2020] [Indexed: 05/03/2023]
Abstract
The CRISPR/Cas9 system is a powerful tool for targeted gene editing in many organisms including plants. However, most of the reported uses of CRISPR/Cas9 in plants have focused on modifying one or a few genes, and thus the overall specificity, types of mutations, and heritability of gene alterations remain unclear. Here, we describe the molecular characterization of 361 T0 transgenic tomato plants that were generated using CRISPR/Cas9 to induce mutations in 63 immunity-associated genes. Among the T0 transformed plants, 245 carried mutations (68%), with 20% of those plants being homozygous for the mutation, 30% being heterozygous, 32% having two different mutations (biallelic), and 18% having multiple mutations (chimeric). The mutations were predominantly short insertions or deletions, with 87% of the affected sequences being smaller than 10 bp. The majority of 1 bp insertions were A (50%) or T (29%). The mutations from the T0 generation were stably transmitted to later generations, although new mutations were detected in some T1 plants. No mutations were detected in 18 potential off-target sites among 144 plants. Our study provides a broad and detailed view into the effectiveness of CRISPR/Cas9 for genome editing in an economically important plant species.
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Affiliation(s)
- Ning Zhang
- Boyce Thompson Institute for Plant Research, Ithaca, NY, United States
| | - Holly M. Roberts
- Boyce Thompson Institute for Plant Research, Ithaca, NY, United States
| | - Joyce Van Eck
- Boyce Thompson Institute for Plant Research, Ithaca, NY, United States
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, United States
| | - Gregory B. Martin
- Boyce Thompson Institute for Plant Research, Ithaca, NY, United States
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, United States
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177
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Young AE, Mansour TA, McNabb BR, Owen JR, Trott JF, Brown CT, Van Eenennaam AL. Genomic and phenotypic analyses of six offspring of a genome-edited hornless bull. Nat Biotechnol 2020; 38:225-232. [PMID: 31591551 PMCID: PMC7007412 DOI: 10.1038/s41587-019-0266-0] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Accepted: 08/28/2019] [Indexed: 12/20/2022]
Abstract
Genome editing followed by reproductive cloning was previously used to produce two hornless dairy bulls. We crossed one genome-edited dairy bull, homozygous for the dominant PC Celtic POLLED allele, with horned cows (pp) and obtained six heterozygous (PCp) polled calves. The calves had no horns and were otherwise healthy and phenotypically unremarkable. We conducted whole-genome sequencing of all animals using an Illumina HiSeq4000 to achieve ~20× coverage. Bioinformatics analyses revealed the bull was a compound heterozygote, carrying one naturally occurring PC Celtic POLLED allele and an allele containing an additional introgression of the homology-directed repair donor plasmid along with the PC Celtic allele. These alleles segregated in the offspring of this bull, and inheritance of either allele produced polled calves. No other unintended genomic alterations were observed. These data can be used to inform conversations in the scientific community, with regulatory authorities and with the public around 'intentional genomic alterations' and future regulatory actions regarding genome-edited animals.
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Affiliation(s)
- Amy E Young
- Department of Animal Science, University of California, Davis, CA, USA
| | - Tamer A Mansour
- Department of Clinical Pathology, School of Medicine, University of Mansoura, Mansoura, Egypt
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, CA, USA
| | - Bret R McNabb
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, CA, USA
| | - Joseph R Owen
- Department of Animal Science, University of California, Davis, CA, USA
| | - Josephine F Trott
- Department of Animal Science, University of California, Davis, CA, USA
| | - C Titus Brown
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, CA, USA
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178
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Lee JH, Mazarei M, Pfotenhauer AC, Dorrough AB, Poindexter MR, Hewezi T, Lenaghan SC, Graham DE, Stewart CN. Epigenetic Footprints of CRISPR/Cas9-Mediated Genome Editing in Plants. FRONTIERS IN PLANT SCIENCE 2020; 10:1720. [PMID: 32117329 PMCID: PMC7026911 DOI: 10.3389/fpls.2019.01720] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Accepted: 12/06/2019] [Indexed: 05/19/2023]
Abstract
CRISPR/Cas9 has been widely applied to various plant species accelerating the pace of plant genome editing and precision breeding in crops. Unintended effects beyond off-target nucleotide mutations are still somewhat unexplored. We investigated the degree and patterns of epigenetic changes after gene editing. We examined changes in DNA methylation in genome-edited promoters of naturally hypermethylated genes (AT1G72350 and AT1G09970) and hypomethylated genes (AT3G17320 and AT5G28770) from Arabidopsis. Transgenic plants were developed via Agrobacterium-mediated floral dip transformation. Homozygous edited lines were selected from segregated T2 plants by an in vitro digestion assay using ribonucleoprotein complex. Bisulfite sequencing comparisons were made between paired groups of edited and non-edited plants to identify changes in DNA methylation of the targeted loci. We found that directed mutagenesis via CRISPR/Cas9 resulted in no unintended morphological or epigenetic alterations. Phenotypes of wild-type, transgenic empty vector, and transgenic edited plants were similar. Epigenetic profiles revealed that methylation patterns of promoter regions flanking target sequences were identical among wild-type, transgenic empty vector, and transgenic edited plants. There was no effect of mutation type on epigenetic status. We also evaluated off-target mutagenesis effects in the edited plants. Potential off-target sites containing up to 4-bp mismatch of each target were sequenced. No off-target mutations were detected in candidate sites. Our results showed that CRISPR/Cas9 did not leave an epigenetic footprint on either the immediate gene-edited DNA and flanking DNA or introduce off-target mutations.
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Affiliation(s)
- Jun Hyung Lee
- Department of Plant Sciences, University of Tennessee, Knoxville, TN, United States
- Center for Agricultural Synthetic Biology, University of Tennessee Institute of Agriculture, Knoxville, TN, United States
| | - Mitra Mazarei
- Department of Plant Sciences, University of Tennessee, Knoxville, TN, United States
| | - Alexander C. Pfotenhauer
- Center for Agricultural Synthetic Biology, University of Tennessee Institute of Agriculture, Knoxville, TN, United States
- Department of Food Science, University of Tennessee, Knoxville, TN, United States
| | - Aubrey B. Dorrough
- Department of Plant Sciences, University of Tennessee, Knoxville, TN, United States
| | - Magen R. Poindexter
- Department of Plant Sciences, University of Tennessee, Knoxville, TN, United States
- Center for Agricultural Synthetic Biology, University of Tennessee Institute of Agriculture, Knoxville, TN, United States
| | - Tarek Hewezi
- Department of Plant Sciences, University of Tennessee, Knoxville, TN, United States
| | - Scott C. Lenaghan
- Center for Agricultural Synthetic Biology, University of Tennessee Institute of Agriculture, Knoxville, TN, United States
- Department of Food Science, University of Tennessee, Knoxville, TN, United States
| | - David E. Graham
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - C. Neal Stewart
- Department of Plant Sciences, University of Tennessee, Knoxville, TN, United States
- Center for Agricultural Synthetic Biology, University of Tennessee Institute of Agriculture, Knoxville, TN, United States
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179
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Jha AB, Warkentin TD. Biofortification of Pulse Crops: Status and Future Perspectives. PLANTS (BASEL, SWITZERLAND) 2020; 9:E73. [PMID: 31935879 PMCID: PMC7020478 DOI: 10.3390/plants9010073] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Revised: 01/02/2020] [Accepted: 01/02/2020] [Indexed: 01/08/2023]
Abstract
Biofortification through plant breeding is a sustainable approach to improve the nutritional profile of food crops. The majority of the world's population depends on staple food crops; however, most are low in key micronutrients. Biofortification to improve the nutritional profile of pulse crops has increased importance in many breeding programs in the past decade. The key micronutrients targeted have been iron, zinc, selenium, iodine, carotenoids, and folates. In recent years, several biofortified pulse crops including common beans and lentils have been released by HarvestPlus with global partners in developing countries, which has helped in overcoming micronutrient deficiency in the target population. This review will focus on recent research advances and future strategies for the biofortification of pulse crops.
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Affiliation(s)
| | - Thomas D. Warkentin
- Crop Development Centre/Department of Plant Sciences, University of Saskatchewan, 51 Campus Drive, Saskatoon, SK S7N 5A8, Canada;
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180
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Yoo BC, Yadav NS, Orozco EM, Sakai H. Cas9/gRNA-mediated genome editing of yeast mitochondria and Chlamydomonas chloroplasts. PeerJ 2020; 8:e8362. [PMID: 31934513 PMCID: PMC6951285 DOI: 10.7717/peerj.8362] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Accepted: 12/05/2019] [Indexed: 11/20/2022] Open
Abstract
We present a new approach to edit both mitochondrial and chloroplast genomes. Organelles have been considered off-limits to CRISPR due to their impermeability to most RNA and DNA. This has prevented applications of Cas9/gRNA-mediated genome editing in organelles while the tool has been widely used for engineering of nuclear DNA in a number of organisms in the last several years. To overcome the hurdle, we designed a new approach to enable organelle genome editing. The plasmids, designated "Edit Plasmids," were constructed with two expression cassettes, one for the expression of Cas9, codon-optimized for each organelle, under promoters specific to each organelle, and the other cassette for the expression of guide RNAs under another set of promoters specific to each organelle. In addition, Edit Plasmids were designed to carry the donor DNA for integration between two double-strand break sites induced by Cas9/gRNAs. Each donor DNA was flanked by the regions homologous to both ends of the integration site that were short enough to minimize spontaneous recombination events. Furthermore, the donor DNA was so modified that it did not carry functional gRNA target sites, allowing the stability of the integrated DNA without being excised by further Cas9/gRNAs activity. Edit Plasmids were introduced into organelles through microprojectile transformation. We confirmed donor DNA insertion at the target sites facilitated by homologous recombination only in the presence of Cas9/gRNA activity in yeast mitochondria and Chlamydomonas chloroplasts. We also showed that Edit Plasmids persist and replicate in mitochondria autonomously for several dozens of generations in the presence of the wild-type genomes. Finally, we did not find insertions and/or deletions at one of the Cas9 cleavage sites in Chloroplasts, which are otherwise hallmarks of Cas9/gRNA-mediated non-homologous end joining (NHEJ) repair events in nuclear DNA. This is consistent with previous reports of the lack of NHEJ repair system in most bacteria, which are believed to be ancestors of organelles. This is the first demonstration of CRISPR-mediated genome editing in both mitochondria and chloroplasts in two distantly related organisms. The Edit Plasmid approach is expected to open the door to engineer organelle genomes of a wide range of organisms in a precise fashion.
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181
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An overview of OECD activities related to modern techniques of biotechnology and genome editing : OECD conference on genome editing, June 2018. Transgenic Res 2020; 28:41-44. [PMID: 31321681 DOI: 10.1007/s11248-019-00131-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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182
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Abstract
Recent advances in genome engineering are revolutionizing crop research and plant breeding. The ability to make specific modifications to a plant's genetic material creates opportunities for rapid development of elite cultivars with desired traits. The plant genome can be altered in several ways, including targeted introduction of nucleotide changes, deleting DNA segments, introducing exogenous DNA fragments and epigenetic modifications. Targeted changes are mediated by sequence specific nucleases (SSNs), such as zinc-finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs), and CRISPR (clustered regularly interspersed short palindromic repeats)-Cas (CRISPR associated protein) systems. Recent advances in engineering chimeric Cas nucleases fused to base editing enzymes permit for even greater precision in base editing and control over gene expression. In addition to gene editing technologies, improvement in delivery systems of exogenous DNA into plant cells have increased the rate of successful gene editing events. Regeneration of fertile plants containing the desired edits remains challenging; however, manipulation of embryogenesis-related genes such as BABY BOOM (BBM) has been shown to facilitate regeneration through tissue culture, often a major hurdle in recalcitrant cultivars. Epigenome reprogramming for improved crop performance is another possibility for future breeders, with recent studies on MutS HOMOLOG 1 (MSH1) demonstrating epigenetic-dependent hybrid vigor in several crops. While these technologies offer plant breeders new tools in creating high yielding, better adapted crop varieties, constantly evolving government policy regarding the cultivation of plants containing transgenes may impede the widespread adoption of some of these techniques. This chapter summarizes advances in genome editing tools and discusses the future of these techniques for crop improvement.
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Affiliation(s)
- Andriy Bilichak
- Morden Research and Development Center, Agriculture and Agri-Food Canada, Morden, MB, Canada.
| | - Daniel Gaudet
- The University of Lethbridge, Lethbridge, AB, Canada
| | - John Laurie
- Agriculture and Agri-Food Canada, Lethbridge, AB, Canada
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183
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Knockout of the S-acyltransferase Gene, PbPAT14, Confers the Dwarf Yellowing Phenotype in First Generation Pear by ABA Accumulation. Int J Mol Sci 2019; 20:ijms20246347. [PMID: 31888281 PMCID: PMC6941133 DOI: 10.3390/ijms20246347] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2019] [Revised: 12/12/2019] [Accepted: 12/14/2019] [Indexed: 01/08/2023] Open
Abstract
The development of dwarf fruit trees with smaller and compact characteristics leads to significantly increased fruit production, which is a major objective of pear (Pyrus bretschneideri) breeding. We identified the S-acylation activity of PbPAT14, an S-acyltransferase gene related to plant development, using a yeast (Saccharomyces cerevisiae) complementation assay, and also PbPAT14 could rescue the growth defect of the Arabidopsis mutant atpat14. We further studied the function of PbPAT14 by designing three guide RNAs for PbPAT14 to use in the CRISPR/Cas9 system. We obtained 22 positive transgenic pear lines via Agrobacterium-mediated transformation using cotyledons from seeds of Pyrus betulifolia (‘Duli’). Six of these lines exhibited the dwarf yellowing phenotype and were homozygous mutations according to sequencing analysis. Ultrastructure analysis suggested that this dwarfism was manifested by shorter, thinner stems due to a reduction in cell number. A higher level of endogenous abscisic acid (ABA) and a higher transcript level of the ABA pathway genes in the mutant lines revealed that the PbPAT14 function was related to the ABA pathway. Overall, our experimental results increase the understanding of how PATs function in plants and help elucidate the mechanism of plant dwarfism.
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184
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Miroshnichenko DN, Shulga OA, Timerbaev VR, Dolgov SV. Achievements, Challenges, and Prospects in the Production of Nontransgenic, Genome-Edited Plants. APPL BIOCHEM MICRO+ 2019. [DOI: 10.1134/s0003683819090047] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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185
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Ritter C, Shriver A, McConnachie E, Robbins J, von Keyserlingk MAG, Weary DM. Public attitudes toward genetic modification in dairy cattle. PLoS One 2019; 14:e0225372. [PMID: 31790436 PMCID: PMC6886766 DOI: 10.1371/journal.pone.0225372] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2019] [Accepted: 11/04/2019] [Indexed: 12/22/2022] Open
Abstract
Genetic modification has been used to create dairy cattle without horns and with increased resistance to disease; applications that could be beneficial for animal welfare, farm profits, and worker safety. Our aim was to assess how different stated purposes were associated with public attitudes toward these two applications using a mixed methods approach. Using an online survey, U.S. participants were randomly assigned to one of ten treatments in a 2 (application: hornless or disease-resistant) x 5 (purposes: improved animal welfare, reduced costs, increased worker safety, all three purposes, or no purpose) factorial design. Each participant was asked to read a short description of the assigned treatment (e.g. hornlessness to improve calf welfare) and then respond to a series of questions designed to assess attitude toward the treatment using 7-point Likert scales (1 = most negative; 7 = most positive). Responses of 957 participants were averaged to creative an attitude construct score. Participants were also asked to explain their response to the treatment. Qualitative analysis of these text responses was used to identify themes associated with the participants’ reasoning. Participant attitudes were more favorable to disease resistance than to hornlessness (mean ± SE attitude score: 4.5 ± 0.15 vs. 3.7 ± 0.14). In the ‘disease-resistance’ group participants had more positive attitudes toward genetic modification when the described purpose was animal welfare versus reduction of costs (contrast = 1.00; 95% CI = 0.12–1.88). Attitudes were less favorable to the ‘hornless’ application if no purpose was provided versus when the stated purpose was either to improve animal welfare (contrast = 0.95; 95% CI = 0.26–1.64) or when all purposes were provided (contrast = 0.88; 95% CI = 0.19–1.58). Similarly, attitudes were less positive when the stated purpose was to reduce costs versus either improving animal welfare (contrast = 0.86; 95% CI = 0.09–1.64) or when all purposes were provided (contrast = 0.79; 95% CI = 0.02–1.56). Quantitative and qualitative analysis indicated that both the specific application and perceived purpose (particularly when related to animal welfare) can affect public attitudes toward genetic modification.
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Affiliation(s)
- Caroline Ritter
- Animal Welfare Program, Faculty of Land and Food Systems, University of British Columbia, Vancouver, British Columbia, Canada
| | - Adam Shriver
- Animal Welfare Program, Faculty of Land and Food Systems, University of British Columbia, Vancouver, British Columbia, Canada
| | - Emilie McConnachie
- Animal Welfare Program, Faculty of Land and Food Systems, University of British Columbia, Vancouver, British Columbia, Canada
| | - Jesse Robbins
- Animal Welfare Program, Faculty of Land and Food Systems, University of British Columbia, Vancouver, British Columbia, Canada
| | - Marina A. G. von Keyserlingk
- Animal Welfare Program, Faculty of Land and Food Systems, University of British Columbia, Vancouver, British Columbia, Canada
| | - Daniel M. Weary
- Animal Welfare Program, Faculty of Land and Food Systems, University of British Columbia, Vancouver, British Columbia, Canada
- * E-mail:
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186
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Filippova J, Matveeva A, Zhuravlev E, Stepanov G. Guide RNA modification as a way to improve CRISPR/Cas9-based genome-editing systems. Biochimie 2019; 167:49-60. [PMID: 31493470 DOI: 10.1016/j.biochi.2019.09.003] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Accepted: 09/02/2019] [Indexed: 02/07/2023]
Abstract
Genome-editing technologies, in particular, CRISPR systems, are widely used for targeted regulation of gene expression and obtaining modified human and animal cell lines, plants, fungi, and animals with preassigned features. Despite being well described and easy to perform, the most common methods for construction and delivery of CRISPR/Cas9-containing plasmid systems possess significant disadvantages, mostly associated with effects of the presence of exogenous DNA within the cell. Transfection with active ribonucleoprotein complexes of Cas9 with single-guide RNAs (sgRNAs) represents one of the most promising options because of faster production of sgRNAs, the ability of a researcher to control the amount of sgRNA delivered into the cell, and consequently, fewer off-target mutations. Artificial-RNA synthesis strategies allow for the introduction of various modified components, such as backbone alterations, native structural motifs, and labels for visualization. Modifications of RNA can increase its resistance to hydrolysis, alter the thermodynamic stability of RNA-protein and RNA-DNA complexes, and reduce the immunogenic and cytotoxic effects. This review describes various approaches to improving synthetic guide RNA function through nucleotide modification.
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Affiliation(s)
- Julia Filippova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch, Russian Academy of Sciences, Lavrentiev Avenue, 8, 630090, Novosibirsk, Russia.
| | - Anastasiya Matveeva
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch, Russian Academy of Sciences, Lavrentiev Avenue, 8, 630090, Novosibirsk, Russia; Novosibirsk State University, Pirogova Str, 1, 630090, Novosibirsk, Russia.
| | - Evgenii Zhuravlev
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch, Russian Academy of Sciences, Lavrentiev Avenue, 8, 630090, Novosibirsk, Russia.
| | - Grigory Stepanov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch, Russian Academy of Sciences, Lavrentiev Avenue, 8, 630090, Novosibirsk, Russia; Novosibirsk State University, Pirogova Str, 1, 630090, Novosibirsk, Russia.
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187
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Socioeconomic Impact of Genome Editing on Agricultural Value Chains: The Case of Fungal-Resistant and Coeliac-Safe Wheat. SUSTAINABILITY 2019. [DOI: 10.3390/su11226421] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Genome editing (GE) is gaining increasing importance in plant breeding, since it provides opportunities to develop improved crops with high precision and speed. However, little is known about the socioeconomic impact of genome editing on agricultural value chains. This qualitative study analyzes how genome-edited crops could affect agriculture value chains. Based on the hypothetical case of producing and processing fungal-resistant and coeliac-safe wheat in Germany, we conducted semi-structured, in-depth interviews with associations and companies operating in the value chains of wheat. A value chain analysis and qualitative content analysis were combined to assess the costs and benefits of the crops studied along the value chains of wheat. The results show that the use of fungal-resistant and coeliac-safe wheat can provide benefits at each step of the value chains. Fungal-resistant wheat benefits actors by reducing the problems and costs resulting from fungal-diseases and mycotoxins. Coeliac-safe wheat benefits actors by producing high value-added products, which can be safely consumed by patients suffering from coeliac disease. However, the results also show that low acceptance of GE by society and food retailers poses a significant barrier for the use of genome-edited crops in agricultural value chains.
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188
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Janjic A. Assisted Evolution in Astrobiology-Convergence of Ecology and Evolutionary Biology within the Context of Planetary Colonization. ASTROBIOLOGY 2019; 19:1410-1417. [PMID: 31657949 DOI: 10.1089/ast.2019.2061] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
In ecology and conservation biology, the concept of assisted evolution aims at the optimization of the resilience of organisms and populations to changing environmental conditions. What has hardly been considered so far is that this concept is also relevant for future astrobiological research, since in artificial extraterrestrial habitats (e.g., plants and insects in martian greenhouses) novel environmental conditions will also affect the survival and performance of organisms. The question therefore arises whether and how space-relevant organisms can be artificially adapted to the desired circumstances in advance. Based on several adaptation and acclimatization strategies in wild ecosystems of Earth, I discuss which methods can be considered for assisted evolution in the context of astrobiological research. This includes enhanced selective breeding, induction of epigenetic inheritance, and genetic engineering, as well as possible problems of these applications. This short overview article aims to stimulate an emerging discussion as to whether humans, which are already prominent drivers of Earth's evolution, should consider such interventions for future planetary colonization as well.
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Affiliation(s)
- Aleksandar Janjic
- Technical University of Munich, School of Life Sciences Weihenstephan, Freising, Germany
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189
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Merry R, Butenhoff K, Campbell BW, Michno JM, Wang D, Orf JH, Lorenz AJ, Stupar RM. Identification and Fine-Mapping of a Soybean Quantitative Trait Locus on Chromosome 5 Conferring Tolerance to Iron Deficiency Chlorosis. THE PLANT GENOME 2019; 12:1-13. [PMID: 33016589 DOI: 10.3835/plantgenome2019.01.0007] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Accepted: 07/12/2019] [Indexed: 06/11/2023]
Abstract
CORE IDEAS: 'Fiskeby III' harbors a combination of abiotic stress traits, including iron deficiency chlorosis (IDC) tolerance. An IDC quantitative trait locus on chromosome Gm05 was identified in genome-wide association studies and biparental populations. Fine-mapping resolved a 137-kb interval containing strong candidate genes. Iron deficiency chlorosis (IDC) is an important nutrient stress for soybean [Glycine max (L.) Merr.] grown in high-pH soils. Despite numerous agronomic attempts to alleviate IDC, genetic tolerance remains the most effective preventative measure against symptoms. In this study, two association mapping populations and a biparental mapping population were used for genetic mapping of IDC tolerance. Quantitative trait loci (QTLs) were identified on chromosomes Gm03, Gm05, and Gm06. Heterogenous inbred families were developed to fine-map the Gm05 QTL, which was uniquely supported in all three mapping populations. Fine-mapping resulted in a QTL with an interval size of 137 kb on the end of the short arm of Gm05, which produced up to a 1.5-point reduction in IDC severity on a 1 to 9 scale in near isogenic lines.
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Affiliation(s)
- Ryan Merry
- Dep. of Agronomy and Plant Genetics, Univ. of Minnesota, Saint Paul, MN, 55108
| | - Karl Butenhoff
- Dep. of Agronomy and Plant Genetics, Univ. of Minnesota, Saint Paul, MN, 55108
- Bayer Crop Science, 704 12th Street, Kalona, IA, 52247
| | - Benjamin W Campbell
- Dep. of Agronomy and Plant Genetics, Univ. of Minnesota, Saint Paul, MN, 55108
| | - Jean-Michel Michno
- Dep. of Agronomy and Plant Genetics, Univ. of Minnesota, Saint Paul, MN, 55108
| | - Dechun Wang
- Dep. of Plant, Soil and Microbial Sciences, Michigan State Univ., East Lansing, MI, 48824
| | - James H Orf
- Dep. of Agronomy and Plant Genetics, Univ. of Minnesota, Saint Paul, MN, 55108
| | - Aaron J Lorenz
- Dep. of Agronomy and Plant Genetics, Univ. of Minnesota, Saint Paul, MN, 55108
| | - Robert M Stupar
- Dep. of Agronomy and Plant Genetics, Univ. of Minnesota, Saint Paul, MN, 55108
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190
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Abstract
Genome editing followed by reproductive cloning was previously used to produce two hornless dairy bulls. We crossed one genome-edited dairy bull, homozygous for the dominant PC Celtic POLLED allele, with horned cows (pp) and obtained six heterozygous (PCp) polled calves. The calves had no horns and were otherwise healthy and phenotypically unremarkable. We conducted whole-genome sequencing of all animals using an Illumina HiSeq4000 to achieve ~20× coverage. Bioinformatics analyses revealed the bull was a compound heterozygote, carrying one naturally occurring PC Celtic POLLED allele and an allele containing an additional introgression of the homology-directed repair donor plasmid along with the PC Celtic allele. These alleles segregated in the offspring of this bull, and inheritance of either allele produced polled calves. No other unintended genomic alterations were observed. These data can be used to inform conversations in the scientific community, with regulatory authorities and with the public around 'intentional genomic alterations' and future regulatory actions regarding genome-edited animals.
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191
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Singh B, Salaria N, Thakur K, Kukreja S, Gautam S, Goutam U. Functional genomic approaches to improve crop plant heat stress tolerance. F1000Res 2019; 8:1721. [PMID: 31824669 PMCID: PMC6896246 DOI: 10.12688/f1000research.19840.1] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 09/02/2019] [Indexed: 12/21/2022] Open
Abstract
Heat stress as a yield limiting issue has become a major threat for food security as global warming progresses. Being sessile, plants cannot avoid heat stress. They respond to heat stress by activating complex molecular networks, such as signal transduction, metabolite production and expressions of heat stress-associated genes. Some plants have developed an intricate signalling network to respond and adapt it. Heat stress tolerance is a polygenic trait, which is regulated by various genes, transcriptional factors, proteins and hormones. Therefore, to improve heat stress tolerance, a sound knowledge of various mechanisms involved in the response to heat stress is required. The classical breeding methods employed to enhance heat stress tolerance has had limited success. In this era of genomics, next generation sequencing techniques, availability of genome sequences and advanced biotechnological tools open several windows of opportunities to improve heat stress tolerance in crop plants. This review discusses the potential of various functional genomic approaches, such as genome wide association studies, microarray, and suppression subtractive hybridization, in the process of discovering novel genes related to heat stress, and their functional validation using both reverse and forward genetic approaches. This review also discusses how these functionally validated genes can be used to improve heat stress tolerance through plant breeding, transgenics and genome editing approaches.
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Affiliation(s)
- Baljeet Singh
- Molecular Biology and Genetic Engineering, Lovely Professional University, Phagwara, Punjab, 144411, India
| | - Neha Salaria
- Molecular Biology and Genetic Engineering, Lovely Professional University, Phagwara, Punjab, 144411, India
| | - Kajal Thakur
- Molecular Biology and Genetic Engineering, Lovely Professional University, Phagwara, Punjab, 144411, India
| | - Sarvjeet Kukreja
- School of Agriculture, Lovely Professional University, Phagwara, Jalandhar, 144411, India
| | - Shristy Gautam
- Molecular Biology and Genetic Engineering, Lovely Professional University, Phagwara, Punjab, 144411, India
| | - Umesh Goutam
- Molecular Biology and Genetic Engineering, Lovely Professional University, Phagwara, Punjab, 144411, India
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192
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Han YJ, Kim JI. Application of CRISPR/Cas9-mediated gene editing for the development of herbicide-resistant plants. PLANT BIOTECHNOLOGY REPORTS 2019; 13:447-457. [PMID: 0 DOI: 10.1007/s11816-019-00575-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Accepted: 09/26/2019] [Indexed: 05/27/2023]
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193
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Wang H, Wu Y, Zhang Y, Yang J, Fan W, Zhang H, Zhao S, Yuan L, Zhang P. CRISPR/Cas9-Based Mutagenesis of Starch Biosynthetic Genes in Sweet Potato (Ipomoea Batatas) for the Improvement of Starch Quality. Int J Mol Sci 2019; 20:E4702. [PMID: 31547486 PMCID: PMC6801948 DOI: 10.3390/ijms20194702] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Revised: 09/12/2019] [Accepted: 09/18/2019] [Indexed: 12/13/2022] Open
Abstract
CRISPR/Cas9-mediated genome editing is a powerful technology that has been used for the genetic modification of a number of crop species. In order to evaluate the efficacy of CRISPR/Cas9 technology in the root crop, sweet potato (Ipomoea batatas), two starch biosynthetic pathway genes, IbGBSSI (encoding granule-bound starch synthase I), and IbSBEII (encoding starch branching enzyme II), were targeted in the starch-type cultivar Xushu22 and carotenoid-rich cultivar Taizhong6. I. batatas was transformed using a binary vector, in which the Cas9 gene is driven by the Arabidopsis AtUBQ promoter and the guide RNA is controlled by the Arabidopsis AtU6 promoter. A total of 72 Xushu22 and 35 Taizhong6 transgenic lines were generated and analyzed for mutations. The mutation efficiency was 62-92% with multi-allelic mutations in both cultivars. Most of the mutations were nucleotide substitutions that lead to amino acid changes and, less frequently, stop codons. In addition, short nucleotide insertions or deletions were also found in both IbGBSSI and IbSBEII. Furthermore, a 2658 bp deletion was found in one IbSBEII transgenic line. The total starch contents were not significantly changed in IbGBSSI- and IbSBEII-knockout transgenic lines compared to the wild-type control. However, in the allopolyploid sweet potato, the IbGBSSI-knockout reduced, while the IbSBEII-knockout increased, the amylose percentage. Our results demonstrate that CRISPR/Cas9 technology is an effective tool for the improvement of starch qualities in sweet potato and breeding of polyploid root crops.
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Affiliation(s)
- Hongxia Wang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Science, Shanghai 200032, China.
- Department of Plant and Soil Sciences and Kentucky Tobacco Research and Development Center, University of Kentucky, Lexington, KY 40546, USA.
| | - Yinliang Wu
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Science, Shanghai 200032, China.
- Shanghai Sanshu Biotechnology Co., LTD. Shanghai 201210, China.
| | - Yandi Zhang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Science, Shanghai 200032, China.
- University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Jun Yang
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Plant Science Research Center, Chinese Academy of Science, Shanghai Chenshan Botanical Garden, Shanghai 201602, China.
| | - Weijuan Fan
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Plant Science Research Center, Chinese Academy of Science, Shanghai Chenshan Botanical Garden, Shanghai 201602, China.
| | - Hui Zhang
- Shanghai Center for Plant Stress Biology, Chinese Academy of Sciences, Shanghai 201602, China.
| | - Shanshan Zhao
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Plant Science Research Center, Chinese Academy of Science, Shanghai Chenshan Botanical Garden, Shanghai 201602, China.
| | - Ling Yuan
- Department of Plant and Soil Sciences and Kentucky Tobacco Research and Development Center, University of Kentucky, Lexington, KY 40546, USA.
| | - Peng Zhang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Science, Shanghai 200032, China.
- University of Chinese Academy of Sciences, Beijing 100049, China.
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194
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Xu W, Fu W, Zhu P, Li Z, Wang C, Wang C, Zhang Y, Zhu S. Comprehensive Analysis of CRISPR/Cas9-Mediated Mutagenesis in Arabidopsis thaliana by Genome-wide Sequencing. Int J Mol Sci 2019; 20:E4125. [PMID: 31450868 PMCID: PMC6747142 DOI: 10.3390/ijms20174125] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Revised: 08/18/2019] [Accepted: 08/21/2019] [Indexed: 12/23/2022] Open
Abstract
The clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein (Cas) system has been widely applied in functional genomics research and plant breeding. In contrast to the off-target studies of mammalian cells, there is little evidence for the common occurrence of off-target sites in plants and a great need exists for accurate detection of editing sites. Here, we summarized the precision of CRISPR/Cas9-mediated mutations for 281 targets and found that there is a preference for single nucleotide deletions/insertions and longer deletions starting from 40 nt upstream or ending at 30 nt downstream of the cleavage site, which suggested the candidate sequences for editing sites detection by whole-genome sequencing (WGS). We analyzed the on-/off-target sites of 6 CRISPR/Cas9-mediated Arabidopsis plants by the optimized method. The results showed that the on-target editing frequency ranged from 38.1% to 100%, and one off target at a frequency of 9.8%-97.3% cannot be prevented by increasing the specificity or reducing the expression level of the Cas9 enzyme. These results indicated that designing guide RNA with high specificity may be the preferred factor to avoid the off-target events, and it is necessary to predict or detect off-target sites by WGS-based methods for preventing off targets caused by genome differences in different individuals.
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Affiliation(s)
- Wenjie Xu
- College of Plant Protection, China Agricultural University, Beijing 100193, China
- Institute of Plant Quarantine, Chinese Academy of Inspection and Quarantine, Beijing 100176, China
| | - Wei Fu
- Institute of Plant Quarantine, Chinese Academy of Inspection and Quarantine, Beijing 100176, China
| | - Pengyu Zhu
- Institute of Plant Quarantine, Chinese Academy of Inspection and Quarantine, Beijing 100176, China
| | - Zhihong Li
- College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Chenguang Wang
- Institute of Plant Quarantine, Chinese Academy of Inspection and Quarantine, Beijing 100176, China
| | - Chaonan Wang
- College of Plant Protection, China Agricultural University, Beijing 100193, China
- Institute of Plant Quarantine, Chinese Academy of Inspection and Quarantine, Beijing 100176, China
| | - Yongjiang Zhang
- Institute of Plant Quarantine, Chinese Academy of Inspection and Quarantine, Beijing 100176, China
| | - Shuifang Zhu
- College of Plant Protection, China Agricultural University, Beijing 100193, China.
- Institute of Plant Quarantine, Chinese Academy of Inspection and Quarantine, Beijing 100176, China.
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195
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Bari VK, Nassar JA, Kheredin SM, Gal-On A, Ron M, Britt A, Steele D, Yoder J, Aly R. CRISPR/Cas9-mediated mutagenesis of CAROTENOID CLEAVAGE DIOXYGENASE 8 in tomato provides resistance against the parasitic weed Phelipanche aegyptiaca. Sci Rep 2019; 9:11438. [PMID: 31391538 PMCID: PMC6685993 DOI: 10.1038/s41598-019-47893-z] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Accepted: 07/16/2019] [Indexed: 01/01/2023] Open
Abstract
Broomrapes (Phelipanche aegyptiaca and Orobanche spp.) are obligate plant parasites that cause extreme damage to crop plants. The parasite seeds have strict requirements for germination, involving preconditioning and exposure to specific chemicals strigolactones [SLs] exuded by the host roots. SLs are plant hormones derived from plant carotenoids via a pathway involving the Carotenoid Cleavage Dioxygenase 8 (CCD8). Having no effective means to control parasitic weeds in most crops, and with CRISPR/Cas9 being an effective gene-editing tool, here we demonstrate that CRISPR/Cas9-mediated mutagenesis of the CCD8 gene can be used to develop host resistance to the parasitic weed P. aegyptiaca. Cas9/single guide (sg) RNA constructs were targeted to the second exon of CCD8 in tomato (Solanum lycopersicum L.) plants. Several CCD8Cas9 mutated tomato lines with variable insertions or deletions in CCD8 were obtained with no identified off-targets. Genotype analysis of T1 plants showed that the introduced CCD8 mutations are inherited. Compared to control tomato plants, the CCD8Cas9 mutant had morphological changes that included dwarfing, excessive shoot branching and adventitious root formation. In addition, SL-deficient CCD8Cas9 mutants showed a significant reduction in parasite infestation compared to non-mutated tomato plants. In the CCD8Cas9 mutated lines, orobanchol (SL) content was significantly reduced but total carotenoids level and expression of genes related to carotenoid biosynthesis were increased, as compared to control plants. Taking into account, the impact of plant parasitic weeds on agriculture and difficulty to constitute efficient control methods, the current study offers insights into the development of a new, efficient method that could be combined with various collections of resistant tomato rootstocks.
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Affiliation(s)
- Vinay Kumar Bari
- Department of Plant Pathology and Weed Research, Newe Ya'ar Research Center, Agricultural Research Organization (ARO), Volcani Center, Ramat Yishay, Israel
| | - Jackline Abu Nassar
- Department of Plant Pathology and Weed Research, Newe Ya'ar Research Center, Agricultural Research Organization (ARO), Volcani Center, Ramat Yishay, Israel
| | - Sally Marzouk Kheredin
- Department of Plant Pathology and Weed Research, Newe Ya'ar Research Center, Agricultural Research Organization (ARO), Volcani Center, Ramat Yishay, Israel
| | - Amit Gal-On
- Department of Plant Pathology and Weed Research, Agricultural Research Organization (ARO), Volcani Center, Bet-Dagan, Israel
| | - Mily Ron
- Department of Plant Biology and Genome Center, University of California, Davis, USA
| | - Anne Britt
- Department of Plant Biology and Genome Center, University of California, Davis, USA
| | - Daniel Steele
- Department of Plant Sciences, University of California, Davis, USA
| | - John Yoder
- Department of Plant Sciences, University of California, Davis, USA
| | - Radi Aly
- Department of Plant Pathology and Weed Research, Newe Ya'ar Research Center, Agricultural Research Organization (ARO), Volcani Center, Ramat Yishay, Israel.
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196
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Jansing J, Schiermeyer A, Schillberg S, Fischer R, Bortesi L. Genome Editing in Agriculture: Technical and Practical Considerations. Int J Mol Sci 2019; 20:E2888. [PMID: 31200517 PMCID: PMC6627516 DOI: 10.3390/ijms20122888] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Revised: 05/29/2019] [Accepted: 06/06/2019] [Indexed: 01/31/2023] Open
Abstract
The advent of precise genome-editing tools has revolutionized the way we create new plant varieties. Three groups of tools are now available, classified according to their mechanism of action: Programmable sequence-specific nucleases, base-editing enzymes, and oligonucleotides. The corresponding techniques not only lead to different outcomes, but also have implications for the public acceptance and regulatory approval of genome-edited plants. Despite the high efficiency and precision of the tools, there are still major bottlenecks in the generation of new and improved varieties, including the efficient delivery of the genome-editing reagents, the selection of desired events, and the regeneration of intact plants. In this review, we evaluate current delivery and regeneration methods, discuss their suitability for important crop species, and consider the practical aspects of applying the different genome-editing techniques in agriculture.
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Affiliation(s)
- Julia Jansing
- Aachen-Maastricht Institute for Biobased Materials (AMIBM), Maastricht University, Brightlands Chemelot Campus, Urmonderbaan 22, 6167 RD Geleen, The Netherlands.
| | - Andreas Schiermeyer
- Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Forckenbeckstrasse 6, 52074 Aachen, Germany.
| | - Stefan Schillberg
- Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Forckenbeckstrasse 6, 52074 Aachen, Germany.
| | - Rainer Fischer
- Indiana Biosciences Research Institute (IBRI), 1345 W. 16th St. Suite 300, Indianapolis, IN 46202, USA.
| | - Luisa Bortesi
- Aachen-Maastricht Institute for Biobased Materials (AMIBM), Maastricht University, Brightlands Chemelot Campus, Urmonderbaan 22, 6167 RD Geleen, The Netherlands.
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197
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Zhou XR, Li J, Wan X, Hua W, Singh S. Harnessing Biotechnology for the Development of New Seed Lipid Traits in Brassica. PLANT & CELL PHYSIOLOGY 2019; 60:1197-1204. [PMID: 31076774 DOI: 10.1093/pcp/pcz070] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Accepted: 04/11/2019] [Indexed: 05/12/2023]
Abstract
The seed oil quality of Brassica oilseed species has been improved in the last few decades, using conventional breeding approaches. Modern biotechnology has enabled the significant development of new seed lipid traits in many oil crops. Alternation of seed lipid component with gene knockout by RNAi gene silencing, artificial microRNA or gene editing within the crop is relative straightforward. Introducing a new pathway from an exogenous source via biotechnology enables the creation of a new trait, where the biosynthetic pathway for such a new trait is not available in the host crop. This review updates the recent development of new seed lipid traits in six major Brassica species and highlights the capability of biotechnology to improve the composition of important fatty acids for both industrial and nutritional purposes.
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Affiliation(s)
| | - Jun Li
- Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Xia Wan
- Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Wei Hua
- Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, China
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198
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Lowry GV, Avellan A, Gilbertson LM. Opportunities and challenges for nanotechnology in the agri-tech revolution. NATURE NANOTECHNOLOGY 2019; 14:517-522. [PMID: 31168073 DOI: 10.1038/s41565-019-0461-7] [Citation(s) in RCA: 300] [Impact Index Per Article: 60.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Accepted: 04/18/2019] [Indexed: 05/21/2023]
Abstract
Current agricultural practices, developed during the green revolution, are becoming unsustainable, especially in the face of climate change and growing populations. Nanotechnology will be an important driver for the impending agri-tech revolution that promises a more sustainable, efficient and resilient agricultural system, while promoting food security. Here, we present the most promising new opportunities and approaches for the application of nanotechnology to improve the use efficiency of necessary inputs (light, water, soil) for crop agriculture, and for better managing biotic and abiotic stress. Potential development and implementation barriers are discussed, emphasizing the need for a systems approach to designing proposed nanotechnologies.
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Affiliation(s)
- Gregory V Lowry
- Civil and Environmental Engineering Department, Carnegie Mellon University, Pittsburgh, PA, USA.
- Center for Environmental Implications of Nanotechnology, Pittsburgh, PA, USA.
| | - Astrid Avellan
- Civil and Environmental Engineering Department, Carnegie Mellon University, Pittsburgh, PA, USA
- Center for Environmental Implications of Nanotechnology, Pittsburgh, PA, USA
| | - Leanne M Gilbertson
- Department of Civil and Environmental Engineering, University of Pittsburgh, Pittsburgh, PA, USA
- Department of Chemical and Petroleum Engineering, University of Pittsburgh, Pittsburgh, PA, USA
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199
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Kausch AP, Nelson-Vasilchik K, Hague J, Mookkan M, Quemada H, Dellaporta S, Fragoso C, Zhang ZJ. Edit at will: Genotype independent plant transformation in the era of advanced genomics and genome editing. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2019; 281:186-205. [PMID: 30824051 DOI: 10.1016/j.plantsci.2019.01.006] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Revised: 12/07/2018] [Accepted: 01/10/2019] [Indexed: 05/21/2023]
Abstract
The combination of advanced genomics, genome editing and plant transformation biology presents a powerful platform for basic plant research and crop improvement. Together these advances provide the tools to identify genes as targets for direct editing as single base pair changes, deletions, insertions and site specific homologous recombination. Recent breakthrough technologies using morphogenic regulators in plant transformation creates the ability to introduce reagents specific toward their identified targets and recover stably transformed and/or edited plants which are genotype independent. These technologies enable the possibility to alter a trait in any variety, without genetic disruption which would require subsequent extensive breeding, but rather to deliver the same variety with one trait changed. Regulatory issues regarding this technology will predicate how broadly these technologies will be implemented. In addition, education will play a crucial role for positive public acceptance. Taken together these technologies comprise a platform for advanced breeding which is an imperative for future world food security.
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Affiliation(s)
- Albert P Kausch
- Department of Cell and Molecular Biology, University of Rhode Island, RI 02892, USA.
| | | | - Joel Hague
- Department of Cell and Molecular Biology, University of Rhode Island, RI 02892, USA
| | - Muruganantham Mookkan
- Plant Transformation Core Facility, Division of Plant Sciences, University of Missouri, Columbia, MO 65211, USA
| | | | - Stephen Dellaporta
- Yale University, New Haven, CT 06520, USA; Verinomics Inc., New Haven, CT 06520, USA
| | | | - Zhanyuan J Zhang
- Plant Transformation Core Facility, Division of Plant Sciences, University of Missouri, Columbia, MO 65211, USA
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200
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Engqvist MKM, Rabe KS. Applications of Protein Engineering and Directed Evolution in Plant Research. PLANT PHYSIOLOGY 2019; 179:907-917. [PMID: 30626612 PMCID: PMC6393796 DOI: 10.1104/pp.18.01534] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Accepted: 12/25/2018] [Indexed: 05/06/2023]
Abstract
Engineered proteins can be used to optimize desired traits in plants; even though recent advances have resulted in new application areas, certain methodological challenges remain.
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Affiliation(s)
- Martin K M Engqvist
- Department of Biology and Biological Engineering, Chalmers University of Technology, Division of Systems and Synthetic Biology, Gothenburg, Sweden
| | - Kersten S Rabe
- Institute for Biological Interfaces (IBG 1), Karlsruhe Institute of Technology (KIT), Group for Molecular Evolution, Karlsruhe, Germany
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