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Buell CR, Dardick C, Parrott W, Schmitz RJ, Shih PM, Tsai CJ, Urbanowicz B. Engineering custom morpho- and chemotypes of Populus for sustainable production of biofuels, bioproducts, and biomaterials. FRONTIERS IN PLANT SCIENCE 2023; 14:1288826. [PMID: 37965014 PMCID: PMC10642751 DOI: 10.3389/fpls.2023.1288826] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Accepted: 10/16/2023] [Indexed: 11/16/2023]
Abstract
Humans have been modifying plant traits for thousands of years, first through selection (i.e., domestication) then modern breeding, and in the last 30 years, through biotechnology. These modifications have resulted in increased yield, more efficient agronomic practices, and enhanced quality traits. Precision knowledge of gene regulation and function through high-resolution single-cell omics technologies, coupled with the ability to engineer plant genomes at the DNA sequence, chromatin accessibility, and gene expression levels, can enable engineering of complex and complementary traits at the biosystem level. Populus spp., the primary genetic model system for woody perennials, are among the fastest growing trees in temperate zones and are important for both carbon sequestration and global carbon cycling. Ample genomic and transcriptomic resources for poplar are available including emerging single-cell omics datasets. To expand use of poplar outside of valorization of woody biomass, chassis with novel morphotypes in which stem branching and tree height are modified can be fabricated thereby leading to trees with altered leaf to wood ratios. These morphotypes can then be engineered into customized chemotypes that produce high value biofuels, bioproducts, and biomaterials not only in specific organs but also in a cell-type-specific manner. For example, the recent discovery of triterpene production in poplar leaf trichomes can be exploited using cell-type specific regulatory sequences to synthesize high value terpenes such as the jet fuel precursor bisabolene specifically in the trichomes. By spatially and temporally controlling expression, not only can pools of abundant precursors be exploited but engineered molecules can be sequestered in discrete cell structures in the leaf. The structural diversity of the hemicellulose xylan is a barrier to fully utilizing lignocellulose in biomaterial production and by leveraging cell-type-specific omics data, cell wall composition can be modified in a tailored and targeted specific manner to generate poplar wood with novel chemical features that are amenable for processing or advanced manufacturing. Precision engineering poplar as a multi-purpose sustainable feedstock highlights how genome engineering can be used to re-imagine a crop species.
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Affiliation(s)
- C. Robin Buell
- Center for Applied Genetic Technologies, Institute of Plant Breeding, Genetics, and Genomics, Department of Crop and Soil Sciences, University of Georgia, Athens, GA, United States
| | - Christopher Dardick
- Agricultural Research Service, U.S. Department of Agriculture, Kearneysville, WV, United States
| | - Wayne Parrott
- Center for Applied Genetic Technologies, Institute of Plant Breeding, Genetics, and Genomics, Department of Crop and Soil Sciences, University of Georgia, Athens, GA, United States
| | - Robert J. Schmitz
- Department of Genetics, University of Georgia, Athens, GA, United States
| | - Patrick M. Shih
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, United States
| | - Chung-Jui Tsai
- Department of Genetics, University of Georgia, Athens, GA, United States
- Department of Plant Biology, University of Georgia, Athens, GA, United States
- Warnell School of Forestry and Natural Resources, University of Georgia, Athens, GA, United States
| | - Breeanna Urbanowicz
- Center for Complex Carbohydrate Research, Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, United States
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Thapliyal G, Bhandari MS, Vemanna RS, Pandey S, Meena RK, Barthwal S. Engineering traits through CRISPR/cas genome editing in woody species to improve forest diversity and yield. Crit Rev Biotechnol 2023; 43:884-903. [PMID: 35968912 DOI: 10.1080/07388551.2022.2092714] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 04/27/2022] [Accepted: 05/14/2022] [Indexed: 11/03/2022]
Abstract
Dangers confronting forest ecosystems are many and the strength of these biological systems is deteriorating, thus substantially affecting tree physiology, phenology, and growth. The establishment of genetically engineered trees into degraded woodlands, which would be adaptive to changing climate, could help in subsiding ecological threats and bring new prospects. This should not be resisted due to the apprehension of transgene dispersal in forests. Consequently, it is important to have a deep insight into the genetic structure and phenotypic limits of the reproductive capability of tree stands/population(s) to endure tolerance and survival. Importantly, for a better understanding of genes and their functional mechanisms, gene editing (GeEd) technology is an excellent molecular tool to unravel adaptation progressions. Therefore, GeEd could be harnessed for resolving the allelic interactions for the creation of gene diversity, and transgene dispersal may be alleviated among the population or species in different bioclimatic zones around the globe. This review highlights the potential of the CRISPR/Cas tools in genomic, transcriptomic, and epigenomic-based assorted and programmable alterations of genes in trees that might be able to fix the trait-specific gene function. Also, we have discussed the application of diverse forms of GeEd to genetically improve several traits, such as wood density, phytochemical constituents, biotic and abiotic stress tolerance, and photosynthetic efficiency in trees. We believe that the technology encourages fundamental research in the forestry sector besides addressing key aspects, which might fasten tree breeding and germplasm improvement programs worldwide.
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Affiliation(s)
- Garima Thapliyal
- Division of Genetics & Tree Improvement, Forest Research Institute, Dehradun, India
| | - Maneesh S Bhandari
- Division of Genetics & Tree Improvement, Forest Research Institute, Dehradun, India
| | - Ramu S Vemanna
- Regional Center for Biotechnology, NCR Biotech Science Cluster, Faridabad, India
| | - Shailesh Pandey
- Forest Pathology Discipline, Forest Protection Division, Forest Research Institute, Dehradun, India
| | - Rajendra K Meena
- Division of Genetics & Tree Improvement, Forest Research Institute, Dehradun, India
| | - Santan Barthwal
- Division of Genetics & Tree Improvement, Forest Research Institute, Dehradun, India
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Khan FS, Goher F, Zhang D, Shi P, Li Z, Htwe YM, Wang Y. Is CRISPR/Cas9 a way forward to fast-track genetic improvement in commercial palms? Prospects and limits. FRONTIERS IN PLANT SCIENCE 2022; 13:1042828. [PMID: 36578341 PMCID: PMC9791139 DOI: 10.3389/fpls.2022.1042828] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Accepted: 11/28/2022] [Indexed: 06/17/2023]
Abstract
Commercially important palms (oil palm, coconut, and date palm) are widely grown perennial trees with tremendous commercial significance due to food, edible oil, and industrial applications. The mounting pressure on the human population further reinforces palms' importance, as they are essential crops to meet vegetable oil needs around the globe. Various conventional breeding methods are used for the genetic improvement of palms. However, adopting new technologies is crucial to accelerate breeding and satisfy the expanding population's demands. CRISPR/Cas9 is an efficient genome editing tool that can incorporate desired traits into the existing DNA of the plant without losing common traits. Recent progress in genome editing in oil palm, coconut and date palm are preliminarily introduced to potential readers. Furthermore, detailed information on available CRISPR-based genome editing and genetic transformation methods are summarized for researchers. We shed light on the possibilities of genome editing in palm crops, especially on the modification of fatty acid biosynthesis in oil palm. Moreover, the limitations in genome editing, including inadequate target gene screening due to genome complexities and low efficiency of genetic transformation, are also highlighted. The prospects of CRISPR/Cas9-based gene editing in commercial palms to improve sustainable production are also addressed in this review paper.
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Affiliation(s)
- Faiza Shafique Khan
- Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions/Sanya Research Institute of Chinese Academy of Tropical Agricultural Sciences, Sanya, Hainan, China
- Hainan Yazhou Bay Seed Laboratory, Sanya, Hainan, China
- Hainan Key Laboratory of Tropical Oil Crops Biology, Coconut Research Institute of Chinese Academy of Tropical Agricultural Sciences, Wenchang, Hainan, China
| | - Farhan Goher
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, China
| | - Dapeng Zhang
- Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions/Sanya Research Institute of Chinese Academy of Tropical Agricultural Sciences, Sanya, Hainan, China
- Hainan Key Laboratory of Tropical Oil Crops Biology, Coconut Research Institute of Chinese Academy of Tropical Agricultural Sciences, Wenchang, Hainan, China
| | - Peng Shi
- Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions/Sanya Research Institute of Chinese Academy of Tropical Agricultural Sciences, Sanya, Hainan, China
- Hainan Key Laboratory of Tropical Oil Crops Biology, Coconut Research Institute of Chinese Academy of Tropical Agricultural Sciences, Wenchang, Hainan, China
| | - Zhiying Li
- Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions/Sanya Research Institute of Chinese Academy of Tropical Agricultural Sciences, Sanya, Hainan, China
- Hainan Key Laboratory of Tropical Oil Crops Biology, Coconut Research Institute of Chinese Academy of Tropical Agricultural Sciences, Wenchang, Hainan, China
| | - Yin Min Htwe
- Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions/Sanya Research Institute of Chinese Academy of Tropical Agricultural Sciences, Sanya, Hainan, China
- Hainan Yazhou Bay Seed Laboratory, Sanya, Hainan, China
- Hainan Key Laboratory of Tropical Oil Crops Biology, Coconut Research Institute of Chinese Academy of Tropical Agricultural Sciences, Wenchang, Hainan, China
| | - Yong Wang
- Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions/Sanya Research Institute of Chinese Academy of Tropical Agricultural Sciences, Sanya, Hainan, China
- Hainan Key Laboratory of Tropical Oil Crops Biology, Coconut Research Institute of Chinese Academy of Tropical Agricultural Sciences, Wenchang, Hainan, China
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New developments in the field of genomic technologies and their relevance to conservation management. CONSERV GENET 2021. [DOI: 10.1007/s10592-021-01415-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
AbstractRecent technological advances in the field of genomics offer conservation managers and practitioners new tools to explore for conservation applications. Many of these tools are well developed and used by other life science fields, while others are still in development. Considering these technological possibilities, choosing the right tool(s) from the toolbox is crucial and can pose a challenging task. With this in mind, we strive to inspire, inform and illuminate managers and practitioners on how conservation efforts can benefit from the current genomic and biotechnological revolution. With inspirational case studies we show how new technologies can help resolve some of the main conservation challenges, while also informing how implementable the different technologies are. We here focus specifically on small population management, highlight the potential for genetic rescue, and discuss the opportunities in the field of gene editing to help with adaptation to changing environments. In addition, we delineate potential applications of gene drives for controlling invasive species. We illuminate that the genomic toolbox offers added benefit to conservation efforts, but also comes with limitations for the use of these novel emerging techniques.
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Ahmar S, Ballesta P, Ali M, Mora-Poblete F. Achievements and Challenges of Genomics-Assisted Breeding in Forest Trees: From Marker-Assisted Selection to Genome Editing. Int J Mol Sci 2021; 22:10583. [PMID: 34638922 PMCID: PMC8508745 DOI: 10.3390/ijms221910583] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Revised: 09/26/2021] [Accepted: 09/27/2021] [Indexed: 12/23/2022] Open
Abstract
Forest tree breeding efforts have focused mainly on improving traits of economic importance, selecting trees suited to new environments or generating trees that are more resilient to biotic and abiotic stressors. This review describes various methods of forest tree selection assisted by genomics and the main technological challenges and achievements in research at the genomic level. Due to the long rotation time of a forest plantation and the resulting long generation times necessary to complete a breeding cycle, the use of advanced techniques with traditional breeding have been necessary, allowing the use of more precise methods for determining the genetic architecture of traits of interest, such as genome-wide association studies (GWASs) and genomic selection (GS). In this sense, main factors that determine the accuracy of genomic prediction models are also addressed. In turn, the introduction of genome editing opens the door to new possibilities in forest trees and especially clustered regularly interspaced short palindromic repeats and CRISPR-associated protein 9 (CRISPR/Cas9). It is a highly efficient and effective genome editing technique that has been used to effectively implement targetable changes at specific places in the genome of a forest tree. In this sense, forest trees still lack a transformation method and an inefficient number of genotypes for CRISPR/Cas9. This challenge could be addressed with the use of the newly developing technique GRF-GIF with speed breeding.
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Affiliation(s)
- Sunny Ahmar
- Institute of Biological Sciences, University of Talca, 1 Poniente 1141, Talca 3460000, Chile;
| | - Paulina Ballesta
- The National Fund for Scientific and Technological Development, Av. del Agua 3895, Talca 3460000, Chile
| | - Mohsin Ali
- Department of Forestry and Range Management, University of Agriculture Faisalabad, Faisalabad 38000, Pakistan;
| | - Freddy Mora-Poblete
- Institute of Biological Sciences, University of Talca, 1 Poniente 1141, Talca 3460000, Chile;
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Sattar MN, Iqbal Z, Al-Khayri JM, Jain SM. Induced Genetic Variations in Fruit Trees Using New Breeding Tools: Food Security and Climate Resilience. PLANTS (BASEL, SWITZERLAND) 2021; 10:1347. [PMID: 34371550 PMCID: PMC8309169 DOI: 10.3390/plants10071347] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/22/2021] [Revised: 06/23/2021] [Accepted: 06/28/2021] [Indexed: 12/22/2022]
Abstract
Fruit trees provide essential nutrients to humans by contributing to major agricultural outputs and economic growth globally. However, major constraints to sustainable agricultural productivity are the uncontrolled proliferation of the population, and biotic and abiotic stresses. Tree mutation breeding has been substantially improved using different physical and chemical mutagens. Nonetheless, tree plant breeding has certain crucial bottlenecks including a long life cycle, ploidy level, occurrence of sequence polymorphisms, nature of parthenocarpic fruit development and linkage. Genetic engineering of trees has focused on boosting quality traits such as productivity, wood quality, and resistance to biotic and abiotic stresses. Recent technological advances in genome editing provide a unique opportunity for the genetic improvement of woody plants. This review examines application of the CRISPR-Cas system to reduce disease susceptibility, alter plant architecture, enhance fruit quality, and improve yields. Examples are discussed of the contemporary CRISPR-Cas system to engineer easily scorable PDS genes, modify lignin, and to alter the flowering onset, fertility, tree architecture and certain biotic stresses.
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Affiliation(s)
- Muhammad Naeem Sattar
- Central Laboratories, King Faisal University, Al-Ahsa 31982, Saudi Arabia; (M.N.S.); (Z.I.)
| | - Zafar Iqbal
- Central Laboratories, King Faisal University, Al-Ahsa 31982, Saudi Arabia; (M.N.S.); (Z.I.)
| | - Jameel M. Al-Khayri
- Department of Agricultural Biotechnology, College of Agriculture and Food Sciences, King Faisal University, Al-Ahsa 31982, Saudi Arabia
| | - S. Mohan Jain
- Department of Agricultural Sciences, PL-27, University of Helsinki, 00014 Helsinki, Finland;
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Bing RG, Sulis DB, Wang JP, Adams MW, Kelly RM. Thermophilic microbial deconstruction and conversion of natural and transgenic lignocellulose. ENVIRONMENTAL MICROBIOLOGY REPORTS 2021; 13:272-293. [PMID: 33684253 PMCID: PMC10519370 DOI: 10.1111/1758-2229.12943] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 02/25/2021] [Accepted: 02/28/2021] [Indexed: 06/12/2023]
Abstract
The potential to convert renewable plant biomasses into fuels and chemicals by microbial processes presents an attractive, less environmentally intense alternative to conventional routes based on fossil fuels. This would best be done with microbes that natively deconstruct lignocellulose and concomitantly form industrially relevant products, but these two physiological and metabolic features are rarely and simultaneously observed in nature. Genetic modification of both plant feedstocks and microbes can be used to increase lignocellulose deconstruction capability and generate industrially relevant products. Separate efforts on plants and microbes are ongoing, but these studies lack a focus on optimal, complementary combinations of these disparate biological systems to obtain a convergent technology. Improving genetic tools for plants have given rise to the generation of low-lignin lines that are more readily solubilized by microorganisms. Most focus on the microbiological front has involved thermophilic bacteria from the genera Caldicellulosiruptor and Clostridium, given their capacity to degrade lignocellulose and to form bio-products through metabolic engineering strategies enabled by ever-improving molecular genetics tools. Bioengineering plant properties to better fit the deconstruction capabilities of candidate consolidated bioprocessing microorganisms has potential to achieve the efficient lignocellulose deconstruction needed for industrial relevance.
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Affiliation(s)
- Ryan G. Bing
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC 27695
| | - Daniel B. Sulis
- Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC 27695
| | - Jack P. Wang
- Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC 27695
| | - Michael W.W. Adams
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia 30602
| | - Robert M. Kelly
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC 27695
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8
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Omics and CRISPR-Cas9 Approaches for Molecular Insight, Functional Gene Analysis, and Stress Tolerance Development in Crops. Int J Mol Sci 2021; 22:ijms22031292. [PMID: 33525517 PMCID: PMC7866018 DOI: 10.3390/ijms22031292] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Revised: 01/19/2021] [Accepted: 01/26/2021] [Indexed: 12/28/2022] Open
Abstract
Plants are regularly exposed to biotic and abiotic stresses that adversely affect agricultural production. Omics has gained momentum in the last two decades, fueled by statistical methodologies, computational capabilities, mass spectrometry, nucleic-acid sequencing, and peptide-sequencing platforms. Functional genomics—especially metabolomics, transcriptomics, and proteomics—have contributed substantially to plant molecular responses to stress. Recent progress in reverse and forward genetics approaches have mediated high-throughput techniques for identifying stress-related genes. Furthermore, web-based genetic databases have mediated bioinformatics techniques for detecting families of stress-tolerant genes. Gene ontology (GO) databases provide information on the gene product’s functional features and help with the computational estimation of gene function. Functional omics data from multiple platforms are useful for positional cloning. Stress-tolerant plants have been engineered using stress response genes, regulatory networks, and pathways. The genome-editing tool, CRISPR-Cas9, reveals the functional features of several parts of the plant genome. Current developments in CRISPR, such as de novo meristem induction genome-engineering in dicots and temperature-tolerant LbCas12a/CRISPR, enable greater DNA insertion precision. This review discusses functional omics for molecular insight and CRISPR-Cas9-based validation of gene function in crop plants. Omics and CRISPR-Cas9 are expected to garner knowledge on molecular systems and gene function and stress-tolerant crop production.
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De Meester B, Madariaga Calderón B, de Vries L, Pollier J, Goeminne G, Van Doorsselaere J, Chen M, Ralph J, Vanholme R, Boerjan W. Tailoring poplar lignin without yield penalty by combining a null and haploinsufficient CINNAMOYL-CoA REDUCTASE2 allele. Nat Commun 2020; 11:5020. [PMID: 33024118 PMCID: PMC7538556 DOI: 10.1038/s41467-020-18822-w] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Accepted: 09/16/2020] [Indexed: 01/09/2023] Open
Abstract
Lignin causes lignocellulosic biomass recalcitrance to enzymatic hydrolysis. Engineered low-lignin plants have reduced recalcitrance but often exhibit yield penalties, offsetting their gains in fermentable sugar yield. Here, CRISPR/Cas9-generated CCR2(−/*) line 12 poplars have one knockout CCR2 allele while the other contains a 3-bp deletion, resulting in a 114I115A-to-114T conversion in the corresponding protein. Despite having 10% less lignin, CCR2(−/*) line 12 grows normally. On a plant basis, the saccharification efficiency of CCR2(−/*) line 12 is increased by 25–41%, depending on the pretreatment. Analysis of monoallelic CCR2 knockout lines shows that the reduced lignin amount in CCR2(−/*) line 12 is due to the combination of a null and the specific haploinsufficient CCR2 allele. Analysis of another CCR2(−/*) line shows that depending on the specific CCR2 amino-acid change, lignin amount and growth can be affected to different extents. Our findings open up new possibilities for stably fine-tuning residual gene function in planta. Plants with reduced amounts of lignin typically suffer from dwarfed growth, which offsets their gain in fermentable sugar yield. Here, the authors show that genome-edited poplar lines with a null and a haploinsufficient allele of CINNAMOYL-COA REDUCTASE2 (CCR2) can be obtained that have a reduced lignin level and normal growth.
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Affiliation(s)
- Barbara De Meester
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052, Ghent, Belgium.,VIB Center for Plant Systems Biology, Technologiepark 71, 9052, Ghent, Belgium
| | - Barbara Madariaga Calderón
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052, Ghent, Belgium.,VIB Center for Plant Systems Biology, Technologiepark 71, 9052, Ghent, Belgium
| | - Lisanne de Vries
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052, Ghent, Belgium.,VIB Center for Plant Systems Biology, Technologiepark 71, 9052, Ghent, Belgium
| | - Jacob Pollier
- VIB Metabolomics Core, Technologiepark 71, 9052, Ghent, Belgium
| | - Geert Goeminne
- VIB Metabolomics Core, Technologiepark 71, 9052, Ghent, Belgium
| | - Jan Van Doorsselaere
- Higher Institute for Nursing and Biotechnology, VIVES University College, Wilgenstraat 32, 8800, Roeselare, Belgium
| | - Mingjie Chen
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA.,US Department of Energy, Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, Madison, WI, 53726, USA
| | - John Ralph
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA.,US Department of Energy, Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, Madison, WI, 53726, USA
| | - Ruben Vanholme
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052, Ghent, Belgium.,VIB Center for Plant Systems Biology, Technologiepark 71, 9052, Ghent, Belgium
| | - Wout Boerjan
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052, Ghent, Belgium. .,VIB Center for Plant Systems Biology, Technologiepark 71, 9052, Ghent, Belgium.
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10
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Dort EN, Tanguay P, Hamelin RC. CRISPR/Cas9 Gene Editing: An Unexplored Frontier for Forest Pathology. FRONTIERS IN PLANT SCIENCE 2020; 11:1126. [PMID: 32793272 PMCID: PMC7387688 DOI: 10.3389/fpls.2020.01126] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Accepted: 07/08/2020] [Indexed: 05/07/2023]
Abstract
CRISPR/Cas9 gene editing technology has taken the scientific community by storm since its development in 2012. First discovered in 1987, CRISPR/Cas systems act as an adaptive immune response in archaea and bacteria that defends against invading bacteriophages and plasmids. CRISPR/Cas9 gene editing technology modifies this immune response to function in eukaryotic cells as a highly specific, RNA-guided complex that can edit almost any genetic target. This technology has applications in all biological fields, including plant pathology. However, examples of its use in forest pathology are essentially nonexistent. The aim of this review is to give researchers a deeper understanding of the native CRISPR/Cas systems and how they were adapted into the CRISPR/Cas9 technology used today in plant pathology-this information is crucial for researchers aiming to use this technology in the pathosystems they study. We review the current applications of CRISPR/Cas9 in plant pathology and propose future directions for research in forest pathosystems where this technology is currently underutilized.
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Affiliation(s)
- Erika N. Dort
- Department of Forest and Conservation Sciences, Faculty of Forestry, University of British Columbia, Vancouver, BC, Canada
| | - Philippe Tanguay
- Laurentian Forestry Centre, Canadian Forest Service, Natural Resources Canada, Québec, QC, Canada
| | - Richard C. Hamelin
- Department of Forest and Conservation Sciences, Faculty of Forestry, University of British Columbia, Vancouver, BC, Canada
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC, Canada
- Département des Sciences du bois et de la Forêt, Faculté de Foresterie et Géographie, Université Laval, Québec, QC, Canada
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Implementing the CRISPR/Cas9 Technology in Eucalyptus Hairy Roots Using Wood-Related Genes. Int J Mol Sci 2020; 21:ijms21103408. [PMID: 32408486 PMCID: PMC7279396 DOI: 10.3390/ijms21103408] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 05/06/2020] [Accepted: 05/08/2020] [Indexed: 01/25/2023] Open
Abstract
Eucalypts are the most planted hardwoods worldwide. The availability of the Eucalyptus grandis genome highlighted many genes awaiting functional characterization, lagging behind because of the lack of efficient genetic transformation protocols. In order to efficiently generate knock-out mutants to study the function of eucalypts genes, we implemented the powerful CRISPR/Cas9 gene editing technology with the hairy roots transformation system. As proofs-of-concept, we targeted two wood-related genes: Cinnamoyl-CoA Reductase1 (CCR1), a key lignin biosynthetic gene and IAA9A an auxin dependent transcription factor of Aux/IAA family. Almost all transgenic hairy roots were edited but the allele-editing rates and spectra varied greatly depending on the gene targeted. Most edition events generated truncated proteins, the prevalent edition types were small deletions but large deletions were also quite frequent. By using a combination of FT-IR spectroscopy and multivariate analysis (partial least square analysis (PLS-DA)), we showed that the CCR1-edited lines, which were clearly separated from the controls. The most discriminant wave-numbers were attributed to lignin. Histochemical analyses further confirmed the decreased lignification and the presence of collapsed vessels in CCR1-edited lines, which are characteristics of CCR1 deficiency. Although the efficiency of editing could be improved, the method described here is already a powerful tool to functionally characterize eucalypts genes for both basic research and industry purposes.
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12
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Taylor G, Donnison IS, Murphy-Bokern D, Morgante M, Bogeat-Triboulot MB, Bhalerao R, Hertzberg M, Polle A, Harfouche A, Alasia F, Petoussi V, Trebbi D, Schwarz K, Keurentjes JJB, Centritto M, Genty B, Flexas J, Grill E, Salvi S, Davies WJ. Sustainable bioenergy for climate mitigation: developing drought-tolerant trees and grasses. ANNALS OF BOTANY 2019; 124:513-520. [PMID: 31665761 PMCID: PMC6821384 DOI: 10.1093/aob/mcz146] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Accepted: 09/23/2019] [Indexed: 05/29/2023]
Abstract
BACKGROUND AND AIMS Bioenergy crops are central to climate mitigation strategies that utilize biogenic carbon, such as BECCS (bioenergy with carbon capture and storage), alongside the use of biomass for heat, power, liquid fuels and, in the future, biorefining to chemicals. Several promising lignocellulosic crops are emerging that have no food role - fast-growing trees and grasses - but are well suited as bioenergy feedstocks, including Populus, Salix, Arundo, Miscanthus, Panicum and Sorghum. SCOPE These promising crops remain largely undomesticated and, until recently, have had limited germplasm resources. In order to avoid competition with food crops for land and nature conservation, it is likely that future bioenergy crops will be grown on marginal land that is not needed for food production and is of poor quality and subject to drought stress. Thus, here we define an ideotype for drought tolerance that will enable biomass production to be maintained in the face of moderate drought stress. This includes traits that can readily be measured in wide populations of several hundred unique genotypes for genome-wide association studies, alongside traits that are informative but can only easily be assessed in limited numbers or training populations that may be more suitable for genomic selection. Phenotyping, not genotyping, is now the major bottleneck for progress, since in all lignocellulosic crops studied extensive use has been made of next-generation sequencing such that several thousand markers are now available and populations are emerging that will enable rapid progress for drought-tolerance breeding. The emergence of novel technologies for targeted genotyping by sequencing are particularly welcome. Genome editing has already been demonstrated for Populus and offers significant potential for rapid deployment of drought-tolerant crops through manipulation of ABA receptors, as demonstrated in Arabidopsis, with other gene targets yet to be tested. CONCLUSIONS Bioenergy is predicted to be the fastest-developing renewable energy over the coming decade and significant investment over the past decade has been made in developing genomic resources and in collecting wild germplasm from within the natural ranges of several tree and grass crops. Harnessing these resources for climate-resilient crops for the future remains a challenge but one that is likely to be successful.
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Affiliation(s)
- G Taylor
- School of Biological Sciences, University of Southampton, Southampton, UK
- Department of Plant Sciences, University of California at Davis, Davis, CA, USA
| | - I S Donnison
- Institute of Biological, Environmental & Rural Sciences (IBERS), Aberystwyth University, Plas Gogerddan, Aberystwyth, Ceredigion, UK
| | | | - M Morgante
- Department of Agricultural and Environmental Sciences, University of Udine, Via delle Scienze, Udine, Italy
| | | | - R Bhalerao
- Department of Forest Genetics and Plant Physiology, Umea Plant Sciences Centre, Swedish University of Agricultural Sciences, Umea, Sweden
| | - M Hertzberg
- SweTree Technologies AB, SE-904 03 Umeå, Sweden
| | - A Polle
- Büsgen‐Institute, Department of Forest Botany and Tree Physiology, Georg‐August University, Göttingen, Germany
| | - A Harfouche
- Department for Innovation in Biological, Agro-food and Forest Systems, University of Tuscia, Viterbo, Italy
| | - F Alasia
- Franco Alasia Vivai, Strada Solerette, Savigliano, Italy
| | - V Petoussi
- Department of Sociology, University of Crete, Rethymno, Greece
| | - D Trebbi
- Geneticlab, Via Roveredo, Pordenone, Italy
| | - K Schwarz
- Julius Kühn‐Institut (JKI) Bundesforschungsinstitut für Kulturpflanzen, Institute for Crop and Soil Science, Bundesallee 50, D‐38116 Braunschweig, Germany
| | - J J B Keurentjes
- Laboratory of Genetics, Wageningen University & Research, Droevendaalsesteeg, Wageningen, The Netherlands
| | - M Centritto
- Trees and Timber Institute, National Research Council of Italy, Sesto Fiorentino, Italy
| | - B Genty
- Aix-Marseille University, CEA, CNRS, BIAM, UMR 7265, Saint Paul lez Durance, France
| | - J Flexas
- Research Group on Plant Biology under Mediterranean Conditions, Departament de Biologia, Universitat de les Illes Balears, Carretera de Valldemossa, Palma de Mallorca, Illes Balears, Spain
| | - E Grill
- Lehrstuhl für Botanik, Technische Universität München, Freising, Germany
| | - S Salvi
- Department of Agricultural and Food Sciences, University of Bologna, Viale Fanin, Bologna, Italy
| | - W J Davies
- Lancaster Environment Centre, Lancaster University, Lancaster, UK
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Pazhany AS, Henry RJ. Genetic Modification of Biomass to Alter Lignin Content and Structure. Ind Eng Chem Res 2019. [DOI: 10.1021/acs.iecr.9b01163] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Adhini S. Pazhany
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, 4072 Queensland, Australia
- ICAR - Sugarcane Breeding Institute, Coimbatore, 641 007 Tamil Nadu, India
| | - Robert J. Henry
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, 4072 Queensland, Australia
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Busov VB. Manipulation of Growth and Architectural Characteristics in Trees for Increased Woody Biomass Production. FRONTIERS IN PLANT SCIENCE 2018; 9:1505. [PMID: 30459780 PMCID: PMC6232754 DOI: 10.3389/fpls.2018.01505] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Accepted: 09/26/2018] [Indexed: 06/09/2023]
Abstract
Growth and architectural traits in trees are economically and environmentally important and thus of considerable importance to the improvement of forest and fruit trees. These traits are complex and result from the operation of a number of molecular mechanisms. This review will focus on the regulation of crown architecture, secondary woody growth and adventitious rooting. These traits and processes have significant impact on deployment, management, and productivity of tree crops. The majority of the described work comes from experiments in model plants, poplar, apple, peach, and plum because these species allow functional analysis of the involved genes and have significant genomics resources. However, these studies convincingly show conserved mechanisms for elaboration of specific growth and architectural traits. The conservation of these mechanisms suggest that they can be used as a blueprint for the improvement of these traits and processes in phylogenetically diverse tree crops. We will specifically consider the involvement of flowering time, transcription factors and hormone-associated genes. The review will also discuss the impact of recent technological advances as well as the challenges to the dissection of these traits in trees.
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15
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De Meester B, de Vries L, Özparpucu M, Gierlinger N, Corneillie S, Pallidis A, Goeminne G, Morreel K, De Bruyne M, De Rycke R, Vanholme R, Boerjan W. Vessel-Specific Reintroduction of CINNAMOYL-COA REDUCTASE1 (CCR1) in Dwarfed ccr1 Mutants Restores Vessel and Xylary Fiber Integrity and Increases Biomass. PLANT PHYSIOLOGY 2018; 176:611-633. [PMID: 29158331 PMCID: PMC5761799 DOI: 10.1104/pp.17.01462] [Citation(s) in RCA: 65] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Accepted: 11/14/2017] [Indexed: 05/19/2023]
Abstract
Lignocellulosic biomass is recalcitrant toward deconstruction into simple sugars due to the presence of lignin. To render lignocellulosic biomass a suitable feedstock for the bio-based economy, plants can be engineered to have decreased amounts of lignin. However, engineered plants with the lowest amounts of lignin exhibit collapsed vessels and yield penalties. Previous efforts were not able to fully overcome this phenotype without settling in sugar yield upon saccharification. Here, we reintroduced CINNAMOYL-COENZYME A REDUCTASE1 (CCR1) expression specifically in the protoxylem and metaxylem vessel cells of Arabidopsis (Arabidopsis thaliana) ccr1 mutants. The resulting ccr1 ProSNBE:CCR1 lines had overcome the vascular collapse and had a total stem biomass yield that was increased up to 59% as compared with the wild type. Raman analysis showed that monolignols synthesized in the vessels also contribute to the lignification of neighboring xylary fibers. The cell wall composition and metabolome of ccr1 ProSNBE:CCR1 still exhibited many similarities to those of ccr1 mutants, regardless of their yield increase. In contrast to a recent report, the yield penalty of ccr1 mutants was not caused by ferulic acid accumulation but was (largely) the consequence of collapsed vessels. Finally, ccr1 ProSNBE:CCR1 plants had a 4-fold increase in total sugar yield when compared with wild-type plants.
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Affiliation(s)
- Barbara De Meester
- Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, B-9052 Ghent, Belgium
| | - Lisanne de Vries
- Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, B-9052 Ghent, Belgium
| | - Merve Özparpucu
- Institute for Building Materials, Swiss Federal Institute of Technology Zürich, 8093 Zuerich, Switzerland
- Applied Wood Materials, Swiss Federal Laboratories of Materials Science and Technology, 8600 Duebendorf, Switzerland
| | - Notburga Gierlinger
- Institute for Biophysics, University of Natural Resources and Life Sciences Vienna, 1190 Vienna, Austria
| | - Sander Corneillie
- Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, B-9052 Ghent, Belgium
| | - Andreas Pallidis
- Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, B-9052 Ghent, Belgium
| | - Geert Goeminne
- Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, B-9052 Ghent, Belgium
- VIB Metabolomics Core, B-9052 Ghent, Belgium
| | - Kris Morreel
- Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, B-9052 Ghent, Belgium
- VIB Metabolomics Core, B-9052 Ghent, Belgium
| | - Michiel De Bruyne
- Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, B-9052 Ghent, Belgium
| | - Riet De Rycke
- Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, B-9052 Ghent, Belgium
| | - Ruben Vanholme
- Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium
- VIB Metabolomics Core, B-9052 Ghent, Belgium
| | - Wout Boerjan
- Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, B-9052 Ghent, Belgium
- VIB Metabolomics Core, B-9052 Ghent, Belgium
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16
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Sattar MN, Iqbal Z, Tahir MN, Shahid MS, Khurshid M, Al-Khateeb AA, Al-Khateeb SA. CRISPR/Cas9: A Practical Approach in Date Palm Genome Editing. FRONTIERS IN PLANT SCIENCE 2017; 8:1469. [PMID: 28878801 PMCID: PMC5572371 DOI: 10.3389/fpls.2017.01469] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Accepted: 08/07/2017] [Indexed: 05/22/2023]
Abstract
The genetic modifications through breeding of crop plants have long been used to improve the yield and quality. However, precise genome editing (GE) could be a very useful supplementary tool for improvement of crop plants by targeted genome modifications. Various GE techniques including ZFNs (zinc finger nucleases), TALENs (transcription activator-like effector nucleases), and most recently clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 (CRISPR-associated protein 9)-based approaches have been successfully employed for various crop plants including fruit trees. CRISPR/Cas9-based approaches hold great potential in GE due to their simplicity, competency, and versatility over other GE techniques. However, to the best of our knowledge no such genetic improvement has ever been developed in date palm-an important fruit crop in Oasis agriculture. The applications of CRISPR/Cas9 can be a challenging task in date palm GE due to its large and complex genome, high rate of heterozygosity and outcrossing, in vitro regeneration and screening of mutants, high frequency of single-nucleotide polymorphism in the genome and ultimately genetic instability. In this review, we addressed the potential application of CRISPR/Cas9-based approaches in date palm GE to improve the sustainable date palm production. The availability of the date palm whole genome sequence has made it feasible to use CRISPR/Cas9 GE approach for genetic improvement in this species. Moreover, the future prospects of GE application in date palm are also addressed in this review.
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Affiliation(s)
- Muhammad N. Sattar
- Department of Environment and Natural Resources, Faculty of Agriculture and Food Sciences, King Faisal UniversityAl-Ahsa, Saudi Arabia
| | - Zafar Iqbal
- Akhuwat-Faisalabad Institute of Research, Science and TechnologyFaisalabad, Pakistan
| | - Muhammad N. Tahir
- National Institute for Biotechnology and Genetic EngineeringFaisalabad, Pakistan
| | - Muhammad S. Shahid
- Department of Crop Sciences, College of Agricultural and Marine Sciences, Sultan Qaboos UniversityAl-Khoud, Oman
| | - Muhammad Khurshid
- Institute of Biochemistry and Biotechnology, University of the PunjabLahore, Pakistan
| | - Abdullatif A. Al-Khateeb
- Plant Biotechnology Department, Faculty of Agricultural and Food Sciences, King Faisal UniversityAl-Ahsa, Saudi Arabia
| | - Suliman A. Al-Khateeb
- Department of Environment and Natural Resources, Faculty of Agriculture and Food Sciences, King Faisal UniversityAl-Ahsa, Saudi Arabia
- Ministry of Environment, Water and AgricultureRiyadh, Saudi Arabia
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17
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Özparpucu M, Rüggeberg M, Gierlinger N, Cesarino I, Vanholme R, Boerjan W, Burgert I. Unravelling the impact of lignin on cell wall mechanics: a comprehensive study on young poplar trees downregulated for CINNAMYL ALCOHOL DEHYDROGENASE (CAD). THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2017; 91:480-490. [PMID: 28440915 DOI: 10.1111/tpj.13584] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Accepted: 04/18/2017] [Indexed: 05/18/2023]
Abstract
Lignin engineering is a promising tool to reduce the energy input and the need of chemical pre-treatments for the efficient conversion of plant biomass into fermentable sugars for downstream applications. At the same time, lignin engineering can offer new insight into the structure-function relationships of plant cell walls by combined mechanical, structural and chemical analyses. Here, this comprehensive approach was applied to poplar trees (Populus tremula × Populus alba) downregulated for CINNAMYL ALCOHOL DEHYDROGENASE (CAD) in order to gain insight into the impact of lignin reduction on mechanical properties. The downregulation of CAD resulted in a significant decrease in both elastic modulus and yield stress. As wood density and cellulose microfibril angle (MFA) did not show any significant differences between the wild type and the transgenic lines, these structural features could be excluded as influencing factors. Fourier transform infrared spectroscopy (FTIR) and Raman imaging were performed to elucidate changes in the chemical composition directly on the mechanically tested tissue sections. Lignin content was identified as a mechanically relevant factor, as a correlation with a coefficient of determination (r²) of 0.65 between lignin absorbance (as an indicator of lignin content) and tensile stiffness was found. A comparison of the present results with those of previous investigations shows that the mechanical impact of lignin alteration under tensile stress depends on certain structural conditions, such as a high cellulose MFA, which emphasizes the complex relationship between the chemistry and mechanical properties in plant cell walls.
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Affiliation(s)
- Merve Özparpucu
- Institute for Building Materials (IfB), ETH Zurich, 8093, Zurich, Switzerland
- Laboratory of Applied Wood Materials, Empa, 8600, Dübendorf, Switzerland
| | - Markus Rüggeberg
- Institute for Building Materials (IfB), ETH Zurich, 8093, Zurich, Switzerland
- Laboratory of Applied Wood Materials, Empa, 8600, Dübendorf, Switzerland
| | - Notburga Gierlinger
- Department of Nanobiotechnology, Institute for Biophysics, University of Natural Resources and Life Sciences Vienna, 1190, Wien, Austria
| | - Igor Cesarino
- Department of Botany, Institute of Biosciences, University of São Paulo, São Paulo, SP, Brazil
| | - Ruben Vanholme
- Department of Plant Biotechnology and Bioinformatics, Technologiepark 927, Ghent University, 9052, Ghent, Belgium
- VIB Center for Plant Systems Biology, (Technologiepark 927), 9052, Ghent, Belgium
| | - Wout Boerjan
- Department of Plant Biotechnology and Bioinformatics, Technologiepark 927, Ghent University, 9052, Ghent, Belgium
- VIB Center for Plant Systems Biology, (Technologiepark 927), 9052, Ghent, Belgium
| | - Ingo Burgert
- Institute for Building Materials (IfB), ETH Zurich, 8093, Zurich, Switzerland
- Laboratory of Applied Wood Materials, Empa, 8600, Dübendorf, Switzerland
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18
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Zhang Y, Ma X, Xie X, Liu YG. CRISPR/Cas9-Based Genome Editing in Plants. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2017; 149:133-150. [PMID: 28712494 DOI: 10.1016/bs.pmbts.2017.03.008] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Recently, genome editing technologies have shown great potential in plants. The newly developed clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 system is a new generation of genome editing tool rapidly replacing the earlier zinc finger nucleases and transcription activator-like effector nucleases systems. Indeed, due to its advantages of simplicity and high efficiency, the CRISPR/Cas9-based genome editing system is becoming a powerful tool in plant science research. Here, we introduce the technical features of the plant CRISPR/Cas9-based genome editing system and its applications in plant functional genomics studies and genetic improvement.
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Affiliation(s)
- Yaling Zhang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangzhou, China; College of Life Sciences, South China Agricultural University, Guangzhou, China
| | - Xingliang Ma
- Global Institute for Food Security, University of Saskatchewan, Saskatoon, SK, Canada
| | - Xianrong Xie
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangzhou, China; College of Life Sciences, South China Agricultural University, Guangzhou, China
| | - Yao-Guang Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangzhou, China; College of Life Sciences, South China Agricultural University, Guangzhou, China.
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19
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Beckers B, Op De Beeck M, Weyens N, Boerjan W, Vangronsveld J. Structural variability and niche differentiation in the rhizosphere and endosphere bacterial microbiome of field-grown poplar trees. MICROBIOME 2017; 5:25. [PMID: 28231859 PMCID: PMC5324219 DOI: 10.1186/s40168-017-0241-2] [Citation(s) in RCA: 238] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2016] [Accepted: 02/03/2017] [Indexed: 05/18/2023]
Abstract
BACKGROUND The plant microbiome represents one of the key determinants of plant health and productivity by providing a plethora of functional capacities such as access to low-abundance nutrients, suppression of phytopathogens, and resistance to biotic and/or abiotic stressors. However, a robust understanding of the structural composition of the bacterial microbiome present in different plant microenvironments and especially the relationship between below-ground and above-ground communities has remained elusive. In this work, we addressed hypotheses regarding microbiome niche differentiation and structural stability of the bacterial communities within different ecological plant niches. METHODS We sampled the rhizosphere soil, root, stem, and leaf endosphere of field-grown poplar trees (Populus tremula × Populus alba) and applied 16S rRNA amplicon pyrosequencing to unravel the bacterial communities associated with the different plant habitats. RESULTS We found that the structural variability of rhizosphere microbiomes in field-grown poplar trees (P. tremula × P. alba) is much lower than that of the endosphere microbiomes. Furthermore, our data not only confirm microbiome niche differentiation reports at the rhizosphere soil-root interface but also clearly show additional fine-tuning and adaptation of the endosphere microbiome in the stem and leaf compartment. Each plant compartment represents an unique ecological niche for the bacterial communities. Finally, we identified the core bacterial microbiome associated with the different ecological niches of Populus. CONCLUSIONS Understanding the complex host-microbe interactions of Populus could provide the basis for the exploitation of the eukaryote-prokaryote associations in phytoremediation applications, sustainable crop production (bio-energy efficiency), and/or the production of secondary metabolites.
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Affiliation(s)
- Bram Beckers
- Centre for Environmental Sciences, Hasselt University, Agoralaan building D, B-3590, Diepenbeek, Belgium.
| | - Michiel Op De Beeck
- Centre for Environmental Sciences, Hasselt University, Agoralaan building D, B-3590, Diepenbeek, Belgium
- Current address: Department of Biology, Lund University, Ecology Building, SE-22 362, Lund, Sweden
| | - Nele Weyens
- Centre for Environmental Sciences, Hasselt University, Agoralaan building D, B-3590, Diepenbeek, Belgium
| | - Wout Boerjan
- Department of Plant Systems Biology, VIB, Technologiepark 927, B-9052, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, UGent, Technologiepark 927, B-9052, Ghent, Belgium
| | - Jaco Vangronsveld
- Centre for Environmental Sciences, Hasselt University, Agoralaan building D, B-3590, Diepenbeek, Belgium
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20
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Ingvarsson PK, Hvidsten TR, Street NR. Towards integration of population and comparative genomics in forest trees. THE NEW PHYTOLOGIST 2016; 212:338-44. [PMID: 27575589 DOI: 10.1111/nph.14153] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Accepted: 06/27/2016] [Indexed: 05/08/2023]
Abstract
Contents 338 I. 338 II. 339 III. 340 IV. 342 343 References 343 SUMMARY: The past decade saw the initiation of an ongoing revolution in sequencing technologies that is transforming all fields of biology. This has been driven by the advent and widespread availability of high-throughput, massively parallel short-read sequencing (MPS) platforms. These technologies have enabled previously unimaginable studies, including draft assemblies of the massive genomes of coniferous species and population-scale resequencing. Transcriptomics studies have likewise been transformed, with RNA-sequencing enabling studies in nonmodel organisms, the discovery of previously unannotated genes (novel transcripts), entirely new classes of RNAs and previously unknown regulatory mechanisms. Here we touch upon current developments in the areas of genome assembly, comparative regulomics and population genetics as they relate to studies of forest tree species.
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Affiliation(s)
- Pär K Ingvarsson
- Umeå Plant Science Centre, Department of Ecology and Environmental Science, Umeå University, 901 87, Umeå, Sweden
| | - Torgeir R Hvidsten
- Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, 1432, Ås, Norway
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, 901 87, Umeå, Sweden
| | - Nathaniel R Street
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, 901 87, Umeå, Sweden.
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Kumar V, Baweja M, Singh PK, Shukla P. Recent Developments in Systems Biology and Metabolic Engineering of Plant-Microbe Interactions. FRONTIERS IN PLANT SCIENCE 2016; 7:1421. [PMID: 27725824 PMCID: PMC5035732 DOI: 10.3389/fpls.2016.01421] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Accepted: 09/06/2016] [Indexed: 05/07/2023]
Abstract
Microorganisms play a crucial role in the sustainability of the various ecosystems. The characterization of various interactions between microorganisms and other biotic factors is a necessary footstep to understand the association and functions of microbial communities. Among the different microbial interactions in an ecosystem, plant-microbe interaction plays an important role to balance the ecosystem. The present review explores plant-microbe interactions using gene editing and system biology tools toward the comprehension in improvement of plant traits. Further, system biology tools like FBA (flux balance analysis), OptKnock, and constraint-based modeling helps in understanding such interactions as a whole. In addition, various gene editing tools have been summarized and a strategy has been hypothesized for the development of disease free plants. Furthermore, we have tried to summarize the predictions through data retrieved from various types of sources such as high throughput sequencing data (e.g., single nucleotide polymorphism detection, RNA-seq, proteomics) and metabolic models have been reconstructed from such sequences for species communities. It is well known fact that systems biology approaches and modeling of biological networks will enable us to learn the insight of such network and will also help further in understanding these interactions.
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Affiliation(s)
| | | | | | - Pratyoosh Shukla
- Enzyme Technology and Protein Bioinformatics Laboratory, Department of Microbiology, Maharshi Dayanand UniversityRohtak, India
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Pascual MB, El-Azaz J, de la Torre FN, Cañas RA, Avila C, Cánovas FM. Biosynthesis and Metabolic Fate of Phenylalanine in Conifers. FRONTIERS IN PLANT SCIENCE 2016; 7:1030. [PMID: 27468292 PMCID: PMC4942462 DOI: 10.3389/fpls.2016.01030] [Citation(s) in RCA: 70] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Accepted: 06/30/2016] [Indexed: 05/18/2023]
Abstract
The amino acid phenylalanine (Phe) is a critical metabolic node that plays an essential role in the interconnection between primary and secondary metabolism in plants. Phe is used as a protein building block but it is also as a precursor for numerous plant compounds that are crucial for plant reproduction, growth, development, and defense against different types of stresses. The metabolism of Phe plays a central role in the channeling of carbon from photosynthesis to the biosynthesis of phenylpropanoids. The study of this metabolic pathway is particularly relevant in trees, which divert large amounts of carbon into the biosynthesis of Phe-derived compounds, particularly lignin, an important constituent of wood. The trunks of trees are metabolic sinks that consume a considerable percentage of carbon and energy from photosynthesis, and carbon is finally immobilized in wood. This paper reviews recent advances in the biosynthesis and metabolic utilization of Phe in conifer trees. Two alternative routes have been identified: the ancient phenylpyruvate pathway that is present in microorganisms, and the arogenate pathway that possibly evolved later during plant evolution. Additionally, an efficient nitrogen recycling mechanism is required to maintain sustained growth during xylem formation. The relevance of phenylalanine metabolic pathways in wood formation, the biotic interactions, and ultraviolet protection is discussed. The genetic manipulation and transcriptional regulation of the pathways are also outlined.
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Affiliation(s)
| | | | | | | | | | - Francisco M. Cánovas
- Departamento de Biología Molecular y Bioquímica, Facultad de Ciencias, Universidad de MálagaMálaga, Spain
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Ma X, Zhu Q, Chen Y, Liu YG. CRISPR/Cas9 Platforms for Genome Editing in Plants: Developments and Applications. MOLECULAR PLANT 2016; 9:961-74. [PMID: 27108381 DOI: 10.1016/j.molp.2016.04.009] [Citation(s) in RCA: 244] [Impact Index Per Article: 30.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2016] [Revised: 04/14/2016] [Accepted: 04/15/2016] [Indexed: 05/19/2023]
Abstract
The clustered regularly interspaced short palindromic repeat (CRISPR)-associated protein9 (Cas9) genome editing system (CRISPR/Cas9) is adapted from the prokaryotic type II adaptive immunity system. The CRISPR/Cas9 tool surpasses other programmable nucleases, such as ZFNs and TALENs, for its simplicity and high efficiency. Various plant-specific CRISPR/Cas9 vector systems have been established for adaption of this technology to many plant species. In this review, we present an overview of current advances on applications of this technology in plants, emphasizing general considerations for establishment of CRISPR/Cas9 vector platforms, strategies for multiplex editing, methods for analyzing the induced mutations, factors affecting editing efficiency and specificity, and features of the induced mutations and applications of the CRISPR/Cas9 system in plants. In addition, we provide a perspective on the challenges of CRISPR/Cas9 technology and its significance for basic plant research and crop genetic improvement.
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Affiliation(s)
- Xingliang Ma
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangzhou 510642, China; Key Laboratory of Plant Functional Genomics and Biotechnology of Guangdong Provincial Higher Education Institutions, Guangzhou 510642, China; College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Qinlong Zhu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangzhou 510642, China; Key Laboratory of Plant Functional Genomics and Biotechnology of Guangdong Provincial Higher Education Institutions, Guangzhou 510642, China; College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Yuanling Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangzhou 510642, China; Key Laboratory of Plant Functional Genomics and Biotechnology of Guangdong Provincial Higher Education Institutions, Guangzhou 510642, China; College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Yao-Guang Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangzhou 510642, China; Key Laboratory of Plant Functional Genomics and Biotechnology of Guangdong Provincial Higher Education Institutions, Guangzhou 510642, China; College of Life Sciences, South China Agricultural University, Guangzhou 510642, China.
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