1
|
Bacelar E, Pinto T, Anjos R, Morais MC, Oliveira I, Vilela A, Cosme F. Impacts of Climate Change and Mitigation Strategies for Some Abiotic and Biotic Constraints Influencing Fruit Growth and Quality. PLANTS (BASEL, SWITZERLAND) 2024; 13:1942. [PMID: 39065469 PMCID: PMC11280748 DOI: 10.3390/plants13141942] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2024] [Revised: 07/07/2024] [Accepted: 07/11/2024] [Indexed: 07/28/2024]
Abstract
Factors such as extreme temperatures, light radiation, and nutritional condition influence the physiological, biochemical, and molecular processes associated with fruit development and its quality. Besides abiotic stresses, biotic constraints can also affect fruit growth and quality. Moreover, there can be interactions between stressful conditions. However, it is challenging to predict and generalize the risks of climate change scenarios on seasonal patterns of growth, development, yield, and quality of fruit species because their responses are often highly complex and involve changes at multiple levels. Advancements in genetic editing technologies hold great potential for the agricultural sector, particularly in enhancing fruit crop traits. These improvements can be tailored to meet consumer preferences, which is crucial for commercial success. Canopy management and innovative training systems are also key factors that contribute to maximizing yield efficiency and improving fruit quality, which are essential for the competitiveness of orchards. Moreover, the creation of habitats that support pollinators is a critical aspect of sustainable agriculture, as they play a significant role in the production of many crops, including fruits. Incorporating these strategies allows fruit growers to adapt to changing climate conditions, which is increasingly important for the stability of food production. By investing in these areas, fruit growers can stay ahead of challenges and opportunities in the industry, ultimately leading to increased success and profitability. In this review, we aim to provide an updated overview of the current knowledge on this important topic. We also provide recommendations for future research.
Collapse
Affiliation(s)
- Eunice Bacelar
- Centre for the Research and Technology of Agro-Environmental and Biological Sciences (CITAB), Institute for Innovation, Capacity Building and Sustainability of Agri-Food Production (Inov4Agro), University of Trás-of-Montes and Alto Douro, Quinta de Prados, P-5000-801 Vila Real, Portugal; (T.P.); (R.A.); (M.C.M.); (I.O.)
| | - Teresa Pinto
- Centre for the Research and Technology of Agro-Environmental and Biological Sciences (CITAB), Institute for Innovation, Capacity Building and Sustainability of Agri-Food Production (Inov4Agro), University of Trás-of-Montes and Alto Douro, Quinta de Prados, P-5000-801 Vila Real, Portugal; (T.P.); (R.A.); (M.C.M.); (I.O.)
| | - Rosário Anjos
- Centre for the Research and Technology of Agro-Environmental and Biological Sciences (CITAB), Institute for Innovation, Capacity Building and Sustainability of Agri-Food Production (Inov4Agro), University of Trás-of-Montes and Alto Douro, Quinta de Prados, P-5000-801 Vila Real, Portugal; (T.P.); (R.A.); (M.C.M.); (I.O.)
| | - Maria Cristina Morais
- Centre for the Research and Technology of Agro-Environmental and Biological Sciences (CITAB), Institute for Innovation, Capacity Building and Sustainability of Agri-Food Production (Inov4Agro), University of Trás-of-Montes and Alto Douro, Quinta de Prados, P-5000-801 Vila Real, Portugal; (T.P.); (R.A.); (M.C.M.); (I.O.)
| | - Ivo Oliveira
- Centre for the Research and Technology of Agro-Environmental and Biological Sciences (CITAB), Institute for Innovation, Capacity Building and Sustainability of Agri-Food Production (Inov4Agro), University of Trás-of-Montes and Alto Douro, Quinta de Prados, P-5000-801 Vila Real, Portugal; (T.P.); (R.A.); (M.C.M.); (I.O.)
| | - Alice Vilela
- Chemistry Research Centre–Vila Real (CQ-VR), Department of Agronomy, School of Agrarian and Veterinary Sciences (ECAV), University of Trás-os-Montes and Alto Douro, P-5000-801 Vila Real, Portugal;
| | - Fernanda Cosme
- Chemistry Research Centre–Vila Real (CQ-VR), Department of Biology and Environment, School of Life Sciences and Environment, University of Trás-os-Montes and Alto Douro, P-5000-801 Vila Real, Portugal;
| |
Collapse
|
2
|
Yang Y, Wheatley M, Meakem V, Galarneau E, Gutierrez B, Zhong G. Editing VvDXS1 for the creation of muscat flavour in Vitis vinifera cv. Scarlet Royal. PLANT BIOTECHNOLOGY JOURNAL 2024; 22:1610-1621. [PMID: 38243882 PMCID: PMC11123410 DOI: 10.1111/pbi.14290] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Revised: 12/01/2023] [Accepted: 01/04/2024] [Indexed: 01/22/2024]
Abstract
Muscat flavour represents a group of unique aromatic attributes in some grape varieties. Biochemically, grape berries with muscat flavour produce high levels of monoterpenes. Monoterpene biosynthesis is mainly through the DOXP/MEP pathway, and VvDXS1 encodes the first enzyme in this plastidial pathway of terpene biosynthesis in grapevine. A single-point mutation resulting in the substitution of a lysine with an asparagine at position 284 in the VvDXS1 protein has previously been identified as the major cause for producing muscat flavour in grapes. In this study, the same substitution in the VvDXS1 protein was successfully created through prime editing in the table grape Vitis vinifera cv. 'Scarlet Royal'. The targeted point mutation was detected in most of the transgenic vines, with varying editing efficiencies. No unintended mutations were detected in the edited alleles, either by PCR Sanger sequencing or by amplicon sequencing. More than a dozen edited vines were identified with an editing efficiency of more than 50%, indicating that these vines were likely derived from single cells in which one allele was edited. These vines had much higher levels of monoterpenes in their leaves than the control, similar to what was found in leaf samples between field-grown muscat and non-muscat grapes.
Collapse
Affiliation(s)
- Yingzhen Yang
- USDA‐Agricultural Research ServiceGrape Genetics Research UnitGenevaNew YorkUSA
| | - Matthew Wheatley
- USDA‐Agricultural Research ServiceGrape Genetics Research UnitGenevaNew YorkUSA
| | - Victoria Meakem
- USDA‐Agricultural Research ServicePlant Genetic Resources UnitGenevaNew YorkUSA
| | - Erin Galarneau
- USDA‐Agricultural Research ServicePlant Genetic Resources UnitGenevaNew YorkUSA
| | - Benjamin Gutierrez
- USDA‐Agricultural Research ServicePlant Genetic Resources UnitGenevaNew YorkUSA
| | - Gan‐Yuan Zhong
- USDA‐Agricultural Research ServiceGrape Genetics Research UnitGenevaNew YorkUSA
| |
Collapse
|
3
|
Djennane S, Gersch S, Le-Bohec F, Piron MC, Baltenweck R, Lemaire O, Merdinoglu D, Hugueney P, Nogué F, Mestre P. CRISPR/Cas9 editing of Downy mildew resistant 6 (DMR6-1) in grapevine leads to reduced susceptibility to Plasmopara viticola. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:2100-2112. [PMID: 38069501 DOI: 10.1093/jxb/erad487] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Accepted: 12/04/2023] [Indexed: 03/28/2024]
Abstract
Downy mildew of grapevine (Vitis vinifera), caused by the oomycete Plasmopara viticola, is an important disease that is present in cultivation areas worldwide, and using resistant varieties provides an environmentally friendly alternative to fungicides. DOWNY MILDEW RESISTANT 6 (DMR6) from Arabidopsis is a negative regulator of plant immunity and its loss of function confers resistance to downy mildew. In grapevine, DMR6 is present in two copies, named VvDMR6-1 and VvDMR6-2. Here, we describe the editing of VvDMR6-1 in embryogenic calli using CRISPR/Cas9 and the regeneration of the edited plants. All edited plants were found to be biallelic and chimeric, and whilst they all showed reduced growth compared with non-transformed control plants, they also had reduced susceptibility to P. viticola. Comparison between mock-inoculated genotypes showed that all edited lines presented higher levels of salicylic acid than controls, and lines subjected to transformation presented higher levels of cis-resveratrol than controls. Our results identify VvDMR6-1 as a promising target for breeding grapevine cultivars with improved resistance to downy mildew.
Collapse
Affiliation(s)
- Samia Djennane
- INRAE, Université de Strasbourg, UMR SVQV, 68000 Colmar, France
| | - Sophie Gersch
- INRAE, Université de Strasbourg, UMR SVQV, 68000 Colmar, France
| | | | | | | | - Olivier Lemaire
- INRAE, Université de Strasbourg, UMR SVQV, 68000 Colmar, France
| | | | | | - Fabien Nogué
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), 78000 Versailles, France
| | - Pere Mestre
- INRAE, Université de Strasbourg, UMR SVQV, 68000 Colmar, France
| |
Collapse
|
4
|
Villette J, Lecourieux F, Bastiancig E, Héloir MC, Poinssot B. New improvements in grapevine genome editing: high efficiency biallelic homozygous knock-out from regenerated plantlets by using an optimized zCas9i. PLANT METHODS 2024; 20:45. [PMID: 38500114 PMCID: PMC10949784 DOI: 10.1186/s13007-024-01173-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Accepted: 03/10/2024] [Indexed: 03/20/2024]
Abstract
BACKGROUND For ten years, CRISPR/cas9 system has become a very useful tool for obtaining site-specific mutations on targeted genes in many plant organisms. This technology opens up a wide range of possibilities for improved plant breeding in the future. In plants, the CRISPR/Cas9 system is mostly used through stable transformation with constructs that allow for the expression of the Cas9 gene and sgRNA. Numerous studies have shown that site-specific mutation efficiency can vary greatly between different plant species due to factors such as plant transformation efficiency, Cas9 expression, Cas9 nucleotide sequence, the addition of intronic sequences, and many other parameters. Since 2016, when the first edited grapevine was created, the number of studies using functional genomic approaches in grapevine has remained low due to difficulties with plant transformation and gene editing efficiency. In this study, we optimized the process to obtain site-specific mutations and generate knock-out mutants of grapevine (Vitis vinifera cv. 'Chardonnay'). Building on existing methods of grapevine transformation, we improved the method for selecting transformed plants at chosen steps of the developing process using fluorescence microscopy. RESULTS By comparison of two different Cas9 gene and two different promoters, we increased site-specific mutation efficiency using a maize-codon optimized Cas9 containing 13 introns (zCas9i), achieving up to 100% biallelic mutation in grapevine plantlets cv. 'Chardonnay'. These results are directly correlated with Cas9 expression level. CONCLUSIONS Taken together, our results highlight a complete methodology for obtaining a wide range of homozygous knock-out mutants for functional genomic studies and future breeding programs in grapevine.
Collapse
Affiliation(s)
- Jérémy Villette
- Agroécologie, INRAE, Institut Agro, Université de Bourgogne, Dijon, France
| | - Fatma Lecourieux
- UMR1287 EGFV, CNRS, Université de Bordeaux, INRAE, Bordeaux Sciences Agro, ISVV, Villenave d'Ornon, Dijon, France
| | - Eliot Bastiancig
- Agroécologie, INRAE, Institut Agro, Université de Bourgogne, Dijon, France
| | | | - Benoit Poinssot
- Agroécologie, INRAE, Institut Agro, Université de Bourgogne, Dijon, France.
| |
Collapse
|
5
|
Campa M, Miranda S, Licciardello C, Lashbrooke JG, Dalla Costa L, Guan Q, Spök A, Malnoy M. Application of new breeding techniques in fruit trees. PLANT PHYSIOLOGY 2024; 194:1304-1322. [PMID: 37394947 DOI: 10.1093/plphys/kiad374] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 06/05/2023] [Accepted: 06/05/2023] [Indexed: 07/04/2023]
Abstract
Climate change and rapid adaption of invasive pathogens pose a constant pressure on the fruit industry to develop improved varieties. Aiming to accelerate the development of better-adapted cultivars, new breeding techniques have emerged as a promising alternative to meet the demand of a growing global population. Accelerated breeding, cisgenesis, and CRISPR/Cas genome editing hold significant potential for crop trait improvement and have proven to be useful in several plant species. This review focuses on the successful application of these technologies in fruit trees to confer pathogen resistance and tolerance to abiotic stress and improve quality traits. In addition, we review the optimization and diversification of CRISPR/Cas genome editing tools applied to fruit trees, such as multiplexing, CRISPR/Cas-mediated base editing and site-specific recombination systems. Advances in protoplast regeneration and delivery techniques, including the use of nanoparticles and viral-derived replicons, are described for the obtention of exogenous DNA-free fruit tree species. The regulatory landscape and broader social acceptability for cisgenesis and CRISPR/Cas genome editing are also discussed. Altogether, this review provides an overview of the versatility of applications for fruit crop improvement, as well as current challenges that deserve attention for further optimization and potential implementation of new breeding techniques.
Collapse
Affiliation(s)
- Manuela Campa
- Research and Innovation Centre, Foundation Edmund Mach, 38098 San Michele all'Adige, Italy
- Department of Genetics, Stellenbosch University, Matieland, South Africa
| | - Simón Miranda
- Research and Innovation Centre, Foundation Edmund Mach, 38098 San Michele all'Adige, Italy
| | - Concetta Licciardello
- Research Center for Olive Fruit and Citrus Crops, Council for Agricultural Research and Economics, 95024 Acireale, Italy
| | | | - Lorenza Dalla Costa
- Research and Innovation Centre, Foundation Edmund Mach, 38098 San Michele all'Adige, Italy
| | - Qingmei Guan
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, No. 3 Taicheng Road, Yangling, Shaanxi 712100, China
| | - Armin Spök
- Science, Technology and Society Unit, Graz University of Technology, Graz, Austria
| | - Mickael Malnoy
- Research and Innovation Centre, Foundation Edmund Mach, 38098 San Michele all'Adige, Italy
| |
Collapse
|
6
|
Mishra A, Pandey VP. CRISPR/Cas system: A revolutionary tool for crop improvement. Biotechnol J 2024; 19:e2300298. [PMID: 38403466 DOI: 10.1002/biot.202300298] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Revised: 12/01/2023] [Accepted: 12/22/2023] [Indexed: 02/27/2024]
Abstract
World's population is elevating at an alarming rate thus, the rising demands of producing crops with better adaptability to biotic and abiotic stresses, superior nutritional as well as morphological qualities, and generation of high-yielding varieties have led to encourage the development of new plant breeding technologies. The availability and easy accessibility of genome sequences for a number of crop plants as well as the development of various genome editing technologies such as zinc finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs) has opened up possibilities to develop new varieties of crop plants with superior desirable traits. However, these approaches has limitation of being more expensive as well as having complex steps and time-consuming. The CRISPR/Cas genome editing system has been intensively studied for allowing versatile target-specific modifications of crop genome that fruitfully aid in the generation of novel varieties. It is an advanced and promising technology with the potential to meet hunger needs and contribute to food production for the ever-growing human population. This review summarizes the usage of novel CRISPR/Cas genome editing tool for targeted crop improvement in stress resistance, yield, quality and nutritional traits in the desired crop plants.
Collapse
Affiliation(s)
- Ayushi Mishra
- Department of Biochemistry, University of Lucknow, Lucknow, India
| | - Veda P Pandey
- Department of Biochemistry, University of Lucknow, Lucknow, India
| |
Collapse
|
7
|
Fang L, Wang Z, Su L, Gong L, Xin H. Vitis Myb14 confer cold and drought tolerance by activating lipid transfer protein genes expression and reactive oxygen species scavenge. Gene 2024; 890:147792. [PMID: 37714279 DOI: 10.1016/j.gene.2023.147792] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Revised: 09/04/2023] [Accepted: 09/08/2023] [Indexed: 09/17/2023]
Abstract
The R2R3 Myb transcription factor exhibits a wide range of functions and participates in various biological processes in plant development, secondary metabolism, and abiotic stress tolerance, among others. Vitis Myb14 initially identified for its involvement in resveratrol synthesis in grapevines. In this study, we investigate its role in abiotic stress tolerance. Significant differences in expression were observed between two grape varieties, Vitis amurensis (Cold-hardy) and V. vinifera (Cold-sentitive), under abiotic and hormone treatments. Both VvMyb14 and VaMyb14 demonstrated responsiveness to cold, drought and high salt treatment, but VaMyb14 exhibited a quicker and more pronounced response. To investigate further, we overexpressed VaMyb14 in A. thalina and found that VaMyb14 OE plants showed significantly enhanced cold and drought tolerance compared to wild-type plants. Additionally, the transgenic lines exhibited increased antioxidant enzyme activity, particularly POD activity, and reduced MDA content. Microarray analysis of VaMyb14 OE plants revealed up-regulation of several ABA metabolism and signal transduction genes, including several LTPs, PP2Cs, RD29B, COR78 and other structural genes, indicating that VaMyb14 has the capacity to reprogram a significant signaling pathway. Furthermore, comparative mRNA sequencing profiling of 35S:VaMyb14 grapevine callus indicated its involvement its function involved in ROS scavenging and ABA signaling. These findings collectively demonstrate that Vitis Myb14 serves as a critical regulator in grapevine stress responses, contributing to improved defense against necrotrophic pathogens, enhanced phytoalexin resveratrol production, and increased drought or cold tolerance.
Collapse
Affiliation(s)
| | - Zeming Wang
- Beijing Key Laboratory of Grape Sciences and Enology, Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, China; Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden/Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, China.
| | - Lingye Su
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden/Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, China.
| | - Linzhong Gong
- Institute of Fruit Trees and Tea, Hubei Academy of Agricultural Sciences, Wuhan, China.
| | - Haiping Xin
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden/Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, China.
| |
Collapse
|
8
|
Pathirana R, Carimi F. Studies on Improving the Efficiency of Somatic Embryogenesis in Grapevine ( Vitis vinifera L.) and Optimising Ethyl Methanesulfonate Treatment for Mutation Induction. PLANTS (BASEL, SWITZERLAND) 2023; 12:4126. [PMID: 38140453 PMCID: PMC10748286 DOI: 10.3390/plants12244126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Revised: 12/02/2023] [Accepted: 12/07/2023] [Indexed: 12/24/2023]
Abstract
Somatic embryogenesis (SE) has many applications in grapevine biotechnology including micropropagation, eradicating viral infections from infected cultivars, mass production of hypocotyl explants for micrografting, as a continuous source for haploid and doubled haploid plants, and for germplasm conservation. It is so far the only pathway for the genetic modification of grapevines through transformation. The single-cell origin of somatic embryos makes them an ideal explant for mutation breeding as the resulting mutants will be chimera-free. In the present research, two combinations of plant growth regulators and different explants from flower buds at two stages of maturity were tested in regard to the efficiency of callusing and embryo formation from the callus produced in three white grape cultivars. Also, the treatment of somatic embryos with the chemical mutagen ethyl methanesulfonate (EMS) was optimised. Medium 2339 supplemented with β-naphthoxyacetic acid (5 μM) and 6-benzylaminopurine (BAP-9.0 μM) produced significantly more calluses than medium 2337 supplemented with 2,4-dichlorophenoxyacetic acid (4.5 µM) and BAP (8.9 µM) in all explants. The calluses produced on medium 2337 were harder and more granular and produced more SEs. Although the stage of the maturity of floral bud did not have a significant effect on the callusing of the explants, calluses produced from immature floral bud explants in the premeiotic stage produced significantly more SEs than those from more mature floral buds. Overall, immature ovaries and cut floral buds exposing the cut ends of filaments, style, etc., tested for the first time in grapevine SE, produced the highest percentage of embryogenic calluses. It is much more efficient to cut the floral bud and culture than previously reported explants such as anthers, ovaries, stigmas and styles during the short flowering period when the immature flower buds are available. When the somatic embryos of the three cultivars were incubated for one hour with 0.1% EMS, their germination was reduced by 50%; an ideal treatment considered to obtain a high frequency of mutations for screening. Our research findings will facilitate more efficient SE induction in grapevines and inducing mutations for improving individual traits without altering the genetic background of the cultivar.
Collapse
Affiliation(s)
- Ranjith Pathirana
- The New Zealand Institute for Plant and Food Research Limited, Batchelar Road, Palmerston North 4472, New Zealand
| | - Francesco Carimi
- Istituto di Bioscienze e BioRisorse (IBBR), Consiglio Nazionale delle Ricerche, Via Ugo la Malfa, 153, 90146 Palermo, Italy;
| |
Collapse
|
9
|
Martín-Valmaseda M, Devin SR, Ortuño-Hernández G, Pérez-Caselles C, Mahdavi SME, Bujdoso G, Salazar JA, Martínez-Gómez P, Alburquerque N. CRISPR/Cas as a Genome-Editing Technique in Fruit Tree Breeding. Int J Mol Sci 2023; 24:16656. [PMID: 38068981 PMCID: PMC10705926 DOI: 10.3390/ijms242316656] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Revised: 11/20/2023] [Accepted: 11/21/2023] [Indexed: 12/18/2023] Open
Abstract
CRISPR (short for "Clustered Regularly Interspaced Short Palindromic Repeats") is a technology that research scientists use to selectively modify the DNA of living organisms. CRISPR was adapted for use in the laboratory from the naturally occurring genome-editing systems found in bacteria. In this work, we reviewed the methods used to introduce CRISPR/Cas-mediated genome editing into fruit species, as well as the impacts of the application of this technology to activate and knock out target genes in different fruit tree species, including on tree development, yield, fruit quality, and tolerance to biotic and abiotic stresses. The application of this gene-editing technology could allow the development of new generations of fruit crops with improved traits by targeting different genetic segments or even could facilitate the introduction of traits into elite cultivars without changing other traits. However, currently, the scarcity of efficient regeneration and transformation protocols in some species, the fact that many of those procedures are genotype-dependent, and the convenience of segregating the transgenic parts of the CRISPR system represent the main handicaps limiting the potential of genetic editing techniques for fruit trees. Finally, the latest news on the legislation and regulations about the use of plants modified using CRISPR/Cas systems has been also discussed.
Collapse
Affiliation(s)
- Marina Martín-Valmaseda
- Fruit Biotechnology Group, Department of Plant Breeding, CEBAS-CSIC (Centro de Edafología y Biología Aplicada del Segura-Consejo Superior de Investigaciones Científicas), Campus Universitario Espinardo, E-30100 Murcia, Spain (C.P.-C.); (N.A.)
| | - Sama Rahimi Devin
- Department of Horticultural Science, College of Agriculture, Shiraz University, Shiraz 7144165186, Iran; (S.R.D.); (S.M.E.M.)
| | - Germán Ortuño-Hernández
- Fruit Breeding Group, Department of Plant Breeding, CEBAS-CSIC (Centro de Edafología y Biología Aplicada del Segura-Consejo Superior de Investigaciones Científicas), Campus Universitario Espinardo, E-30100 Murcia, Spain; (G.O.-H.); (J.A.S.)
| | - Cristian Pérez-Caselles
- Fruit Biotechnology Group, Department of Plant Breeding, CEBAS-CSIC (Centro de Edafología y Biología Aplicada del Segura-Consejo Superior de Investigaciones Científicas), Campus Universitario Espinardo, E-30100 Murcia, Spain (C.P.-C.); (N.A.)
| | - Sayyed Mohammad Ehsan Mahdavi
- Department of Horticultural Science, College of Agriculture, Shiraz University, Shiraz 7144165186, Iran; (S.R.D.); (S.M.E.M.)
| | - Geza Bujdoso
- Research Centre for Fruit Growing, Hungarian University of Agriculture and Life Sciences, 1223 Budapest, Hungary;
| | - Juan Alfonso Salazar
- Fruit Breeding Group, Department of Plant Breeding, CEBAS-CSIC (Centro de Edafología y Biología Aplicada del Segura-Consejo Superior de Investigaciones Científicas), Campus Universitario Espinardo, E-30100 Murcia, Spain; (G.O.-H.); (J.A.S.)
| | - Pedro Martínez-Gómez
- Fruit Breeding Group, Department of Plant Breeding, CEBAS-CSIC (Centro de Edafología y Biología Aplicada del Segura-Consejo Superior de Investigaciones Científicas), Campus Universitario Espinardo, E-30100 Murcia, Spain; (G.O.-H.); (J.A.S.)
| | - Nuria Alburquerque
- Fruit Biotechnology Group, Department of Plant Breeding, CEBAS-CSIC (Centro de Edafología y Biología Aplicada del Segura-Consejo Superior de Investigaciones Científicas), Campus Universitario Espinardo, E-30100 Murcia, Spain (C.P.-C.); (N.A.)
| |
Collapse
|
10
|
Jacobson S, Bondarchuk N, Nguyen TA, Canada A, McCord L, Artlip TS, Welser P, Klocko AL. Apple CRISPR-Cas9-A Recipe for Successful Targeting of AGAMOUS-like Genes in Domestic Apple. PLANTS (BASEL, SWITZERLAND) 2023; 12:3693. [PMID: 37960050 PMCID: PMC10649517 DOI: 10.3390/plants12213693] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 10/19/2023] [Accepted: 10/24/2023] [Indexed: 11/15/2023]
Abstract
Fruit trees and other fruiting hardwood perennials are economically valuable, and there is interest in developing improved varieties. Both conventional breeding and biotechnology approaches are being utilized towards the goal of developing advanced cultivars. Increased knowledge of the effectiveness and efficiency of biotechnology approaches can help guide use of the CRISPR gene-editing technology. Here, we examined CRISPR-Cas9-directed genome editing in the valuable commodity fruit tree Malus x domestica (domestic apple). We transformed two cultivars with dual CRISPR-Cas9 constructs designed to target two AGAMOUS-like genes simultaneously. The main goal was to determine the effectiveness of this approach for achieving target gene changes. We obtained 6 Cas9 control and 38 independent CRISPR-Cas9 events. Of the 38 CRISPR-Cas9 events, 34 (89%) had gene edits and 14 (37%) showed changes to all alleles of both target genes. The most common change was large deletions, which were present in 59% of all changed alleles, followed by small deletions (21%), small insertions (12%), and a combination of small insertions and deletions (8%). Overall, a high rate of successful gene alterations was found. Many of these changes are predicted to cause frameshifts and alterations to the predicted peptides. Future work will include monitoring the floral development and floral form.
Collapse
Affiliation(s)
- Seth Jacobson
- Department of Biology, University of Colorado Colorado Springs, Colorado Springs, CO 80918, USA
| | - Natalie Bondarchuk
- Department of Biology, University of Colorado Colorado Springs, Colorado Springs, CO 80918, USA
| | - Thy Anh Nguyen
- Department of Biology, University of Colorado Colorado Springs, Colorado Springs, CO 80918, USA
| | - Allison Canada
- Department of Biology, University of Colorado Colorado Springs, Colorado Springs, CO 80918, USA
| | - Logan McCord
- Department of Biology, University of Colorado Colorado Springs, Colorado Springs, CO 80918, USA
| | - Timothy S. Artlip
- U.S. Department of Agriculture, Agricultural Research Service (USDA-ARS), The Appalachian Fruit Research Station, 2217 Wiltshire Road, Kearneysville, WV 25430, USA;
| | - Philipp Welser
- U.S. Department of Agriculture, Agricultural Research Service (USDA-ARS), The Appalachian Fruit Research Station, 2217 Wiltshire Road, Kearneysville, WV 25430, USA;
| | - Amy L. Klocko
- Department of Biology, University of Colorado Colorado Springs, Colorado Springs, CO 80918, USA
| |
Collapse
|
11
|
Ren C, Gathunga EK, Li X, Li H, Kong J, Dai Z, Liang Z. Efficient genome editing in grapevine using CRISPR/LbCas12a system. MOLECULAR HORTICULTURE 2023; 3:21. [PMID: 37853418 PMCID: PMC10583370 DOI: 10.1186/s43897-023-00069-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Accepted: 10/06/2023] [Indexed: 10/20/2023]
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR) /Cas12a system, also known as CRISPR/Cpf1, has been successfully harnessed for genome engineering in many plants, but not in grapevine yet. Here we developed and demonstrated the efficacy of CRISPR/Cas12a from Lachnospiraceae bacterium ND2006 (LbCas12a) in inducing targeted mutagenesis by targeting the tonoplastic monosaccharide transporter1 (TMT1) and dihydroflavonol-4-reductase 1 (DFR1) genes in 41B cells. Knockout of DFR1 gene altered flavonoid accumulation in dfr1 mutant cells. Heat treatment (34℃) improved the editing efficiencies of CRISPR/LbCas12a system, and the editing efficiencies of TMT1-crRNA1 and TMT1-crRNA2 increased from 35.3% to 44.6% and 29.9% to 37.3% after heat treatment, respectively. Moreover, the sequences of crRNAs were found to be predominant factor affecting editing efficiencies irrespective of the positions within the crRNA array designed for multiplex genome editing. In addition, genome editing with truncated crRNAs (trucrRNAs) showed that trucrRNAs with 20 nt guide sequences were as effective as original crRNAs with 24 nt guides in generating targeted mutagenesis, whereas trucrRNAs with shorter regions of target complementarity ≤ 18 nt in length may not induce detectable mutations in 41B cells. All these results provide evidence for further applications of CRISPR/LbCas12a system in grapevine as a powerful tool for genome engineering.
Collapse
Affiliation(s)
- Chong Ren
- Beijing Key Laboratory of Grape Sciences and Enology, Beijing, 100093, PR China
- State Key Laboratory of Plant Diversity and Specialty Crops, Beijing, 100093, PR China
- China National Botanical Garden, Beijing, 100093, PR China
| | - Elias Kirabi Gathunga
- Beijing Key Laboratory of Grape Sciences and Enology, Beijing, 100093, PR China
- State Key Laboratory of Plant Diversity and Specialty Crops, Beijing, 100093, PR China
- University of Chinese Academy of Sciences, Beijing, 100049, PR China
| | - Xue Li
- Beijing Key Laboratory of Grape Sciences and Enology, Beijing, 100093, PR China
- State Key Laboratory of Plant Diversity and Specialty Crops, Beijing, 100093, PR China
- University of Chinese Academy of Sciences, Beijing, 100049, PR China
| | - Huayang Li
- Beijing Key Laboratory of Grape Sciences and Enology, Beijing, 100093, PR China
- State Key Laboratory of Plant Diversity and Specialty Crops, Beijing, 100093, PR China
- University of Chinese Academy of Sciences, Beijing, 100049, PR China
| | - Junhua Kong
- Beijing Key Laboratory of Grape Sciences and Enology, Beijing, 100093, PR China
- State Key Laboratory of Plant Diversity and Specialty Crops, Beijing, 100093, PR China
- China National Botanical Garden, Beijing, 100093, PR China
| | - Zhanwu Dai
- Beijing Key Laboratory of Grape Sciences and Enology, Beijing, 100093, PR China
- State Key Laboratory of Plant Diversity and Specialty Crops, Beijing, 100093, PR China
- China National Botanical Garden, Beijing, 100093, PR China
| | - Zhenchang Liang
- Beijing Key Laboratory of Grape Sciences and Enology, Beijing, 100093, PR China.
- State Key Laboratory of Plant Diversity and Specialty Crops, Beijing, 100093, PR China.
- China National Botanical Garden, Beijing, 100093, PR China.
- Institute of Botany, the Chinese Academy of Sciences, Haidian District, Nanxin Village 20, XiangshanBeijing, 100093, China.
| |
Collapse
|
12
|
Cardi T, Murovec J, Bakhsh A, Boniecka J, Bruegmann T, Bull SE, Eeckhaut T, Fladung M, Galovic V, Linkiewicz A, Lukan T, Mafra I, Michalski K, Kavas M, Nicolia A, Nowakowska J, Sági L, Sarmiento C, Yıldırım K, Zlatković M, Hensel G, Van Laere K. CRISPR/Cas-mediated plant genome editing: outstanding challenges a decade after implementation. TRENDS IN PLANT SCIENCE 2023; 28:1144-1165. [PMID: 37331842 DOI: 10.1016/j.tplants.2023.05.012] [Citation(s) in RCA: 31] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 05/09/2023] [Accepted: 05/15/2023] [Indexed: 06/20/2023]
Abstract
The discovery of the CRISPR/Cas genome-editing system has revolutionized our understanding of the plant genome. CRISPR/Cas has been used for over a decade to modify plant genomes for the study of specific genes and biosynthetic pathways as well as to speed up breeding in many plant species, including both model and non-model crops. Although the CRISPR/Cas system is very efficient for genome editing, many bottlenecks and challenges slow down further improvement and applications. In this review we discuss the challenges that can occur during tissue culture, transformation, regeneration, and mutant detection. We also review the opportunities provided by new CRISPR platforms and specific applications related to gene regulation, abiotic and biotic stress response improvement, and de novo domestication of plants.
Collapse
Affiliation(s)
- Teodoro Cardi
- Consiglio Nazionale delle Ricerche (CNR), Institute of Biosciences and Bioresources (IBBR), Portici, Italy; CREA Research Centre for Vegetable and Ornamental Crops, Pontecagnano, Italy
| | - Jana Murovec
- University of Ljubljana, Biotechnical Faculty, Ljubljana, Slovenia
| | - Allah Bakhsh
- Department of Agricultural Genetic Engineering, Faculty of Agricultural Sciences and Technologies, Nigde Omer Halisdemir University, Nigde, Turkey; Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Justyna Boniecka
- Department of Genetics, Faculty of Biological and Veterinary Sciences, Nicolaus Copernicus University, Toruń, Poland; Centre for Modern Interdisciplinary Technologies, Nicolaus Copernicus University, Toruń, Poland
| | | | - Simon E Bull
- Molecular Plant Breeding, Institute of Agricultural Sciences, Eidgenössische Technische Hochschule (ETH) Zurich, Switzerland; Plant Biochemistry, Institute of Molecular Plant Biology, ETH, Zurich, Switzerland
| | - Tom Eeckhaut
- Flanders Research Institute for Agricultural, Fisheries and Food, Melle, Belgium
| | | | - Vladislava Galovic
- University of Novi Sad, Institute of Lowland Forestry and Environment (ILFE), Novi Sad, Serbia
| | - Anna Linkiewicz
- Molecular Biology and Genetics Department, Institute of Biological Sciences, Faculty of Biology and Environmental Sciences, Cardinal Stefan Wyszyński University, Warsaw, Poland
| | - Tjaša Lukan
- National Institute of Biology, Department of Biotechnology and Systems Biology, Ljubljana, Slovenia
| | - Isabel Mafra
- Rede de Química e Tecnologia (REQUIMTE) Laboratório Associado para a Química Verde (LAQV), Faculdade de Farmácia, Universidade do Porto, Porto, Portugal
| | - Krzysztof Michalski
- Plant Breeding and Acclimatization Institute, National Research Institute, Błonie, Poland
| | - Musa Kavas
- Department of Molecular Biology and Genetics, Faculty of Science, Ondokuz Mayis University, Samsun, Turkey
| | - Alessandro Nicolia
- CREA Research Centre for Vegetable and Ornamental Crops, Pontecagnano, Italy
| | - Justyna Nowakowska
- Molecular Biology and Genetics Department, Institute of Biological Sciences, Faculty of Biology and Environmental Sciences, Cardinal Stefan Wyszyński University, Warsaw, Poland
| | - Laszlo Sági
- Centre for Agricultural Research, Loránd Eötvös Research Network, Martonvásár, Hungary
| | - Cecilia Sarmiento
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Tallinn, Estonia
| | - Kubilay Yıldırım
- Department of Molecular Biology and Genetics, Faculty of Science, Ondokuz Mayis University, Samsun, Turkey
| | - Milica Zlatković
- University of Novi Sad, Institute of Lowland Forestry and Environment (ILFE), Novi Sad, Serbia
| | - Goetz Hensel
- Heinrich-Heine-University, Institute of Plant Biochemistry, Centre for Plant Genome Engineering, Düsseldorf, Germany; Division of Molecular Biology, Centre of the Region Hana for Biotechnological and Agriculture Research, Faculty of Science, Palacký University, Olomouc, Czech Republic
| | - Katrijn Van Laere
- Flanders Research Institute for Agricultural, Fisheries and Food, Melle, Belgium.
| |
Collapse
|
13
|
Shelake RM, Jadhav AM, Bhosale PB, Kim JY. Unlocking secrets of nature's chemists: Potential of CRISPR/Cas-based tools in plant metabolic engineering for customized nutraceutical and medicinal profiles. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 203:108070. [PMID: 37816270 DOI: 10.1016/j.plaphy.2023.108070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 09/26/2023] [Accepted: 09/28/2023] [Indexed: 10/12/2023]
Abstract
Plant species have evolved diverse metabolic pathways to effectively respond to internal and external signals throughout their life cycle, allowing adaptation to their sessile and phototropic nature. These pathways selectively activate specific metabolic processes, producing plant secondary metabolites (PSMs) governed by genetic and environmental factors. Humans have utilized PSM-enriched plant sources for millennia in medicine and nutraceuticals. Recent technological advances have significantly contributed to discovering metabolic pathways and related genes involved in the biosynthesis of specific PSM in different food crops and medicinal plants. Consequently, there is a growing demand for plant materials rich in nutrients and bioactive compounds, marketed as "superfoods". To meet the industrial demand for superfoods and therapeutic PSMs, modern methods such as system biology, omics, synthetic biology, and genome editing (GE) play a crucial role in identifying the molecular players, limiting steps, and regulatory circuitry involved in PSM production. Among these methods, clustered regularly interspaced short palindromic repeats-CRISPR associated protein (CRISPR/Cas) is the most widely used system for plant GE due to its simple design, flexibility, precision, and multiplexing capabilities. Utilizing the CRISPR-based toolbox for metabolic engineering (ME) offers an ideal solution for developing plants with tailored preventive (nutraceuticals) and curative (therapeutic) metabolic profiles in an ecofriendly way. This review discusses recent advances in understanding the multifactorial regulation of metabolic pathways, the application of CRISPR-based tools for plant ME, and the potential research areas for enhancing plant metabolic profiles.
Collapse
Affiliation(s)
- Rahul Mahadev Shelake
- Division of Applied Life Science (BK21 Four Program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, 52828, Republic of Korea.
| | - Amol Maruti Jadhav
- Research Institute of Green Energy Convergence Technology (RIGET), Gyeongsang National University, 501 Jinju-daero, Jinju, 52828, Republic of Korea
| | - Pritam Bhagwan Bhosale
- Department of Veterinary Medicine, Research Institute of Life Science, Gyeongsang National University, 501 Jinju-daero, Jinju, 52828, Republic of Korea
| | - Jae-Yean Kim
- Division of Applied Life Science (BK21 Four Program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, 52828, Republic of Korea; Division of Life Science, Gyeongsang National University, 501 Jinju-daero, Jinju, 52828, Republic of Korea; Nulla Bio Inc, 501 Jinju-daero, Jinju, 52828, Republic of Korea.
| |
Collapse
|
14
|
Liu W, Mu H, Yuan L, Li Y, Li Y, Li S, Ren C, Duan W, Fan P, Dai Z, Zhou Y, Liang Z, Li S, Wang L. VvBBX44 and VvMYBA1 form a regulatory feedback loop to balance anthocyanin biosynthesis in grape. HORTICULTURE RESEARCH 2023; 10:uhad176. [PMID: 37868620 PMCID: PMC10585713 DOI: 10.1093/hr/uhad176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Accepted: 08/25/2023] [Indexed: 10/24/2023]
Abstract
Anthocyanins are essential for the quality of perennial horticultural crops, such as grapes. In grapes, ELONGATED HYPOCOTYL 5 (HY5) and MYBA1 are two critical transcription factors that regulate anthocyanin biosynthesis. Our previous work has shown that Vitis vinifera B-box protein 44 (VvBBX44) inhibits anthocyanin synthesis and represses VvHY5 expression in grape calli. However, the regulatory mechanism underlying this regulation was unclear. In this study, we found that loss of VvBBX44 function resulted in increased anthocyanin accumulation in grapevine callus. VvBBX44 directly represses VvMYBA1, which activates VvBBX44. VvMYBA1, but not VvBBX44, directly modulates the expression of grape UDP flavonoid 3-O-glucosyltransferase (VvUFGT). We demonstrated that VvBBX44 represses the transcriptional activation of VvUFGT and VvBBX44 induced by VvMYBA1. However, VvBBX44 and VvMYBA1 did not physically interact in yeast. The application of exogenous anthocyanin stimulated VvBBX44 expression in grapevine suspension cells and tobacco leaves. These findings suggest that VvBBX44 and VvMYBA1 form a transcriptional feedback loop to prevent overaccumulation of anthocyanin and reduce metabolic costs. Our work sheds light on the complex regulatory network that controls anthocyanin biosynthesis in grapevine.
Collapse
Affiliation(s)
- Wenwen Liu
- Beijing Key Laboratory of Grape Science and Enology and State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, Chinese Academy of Science, Beijing 100093, China
- China National Botanical Garden, Beijing 100093, China
- University of Chinese Academy of Sciences, Beijing 10049, China
- National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518000, China
| | - Huayuan Mu
- Beijing Key Laboratory of Grape Science and Enology and State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, Chinese Academy of Science, Beijing 100093, China
- China National Botanical Garden, Beijing 100093, China
- University of Chinese Academy of Sciences, Beijing 10049, China
| | - Ling Yuan
- Department of Plant and Soil Sciences, Kentucky Tobacco Research and Development Center, University of Kentucky, Lexington, Kentucky 40546, USA
| | - Yang Li
- Beijing Key Laboratory of Grape Science and Enology and State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, Chinese Academy of Science, Beijing 100093, China
- China National Botanical Garden, Beijing 100093, China
| | - Yuting Li
- Beijing Key Laboratory of Grape Science and Enology and State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, Chinese Academy of Science, Beijing 100093, China
- China National Botanical Garden, Beijing 100093, China
- University of Chinese Academy of Sciences, Beijing 10049, China
| | - Shenchang Li
- Beijing Key Laboratory of Grape Science and Enology and State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, Chinese Academy of Science, Beijing 100093, China
- China National Botanical Garden, Beijing 100093, China
- University of Chinese Academy of Sciences, Beijing 10049, China
| | - Chong Ren
- Beijing Key Laboratory of Grape Science and Enology and State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, Chinese Academy of Science, Beijing 100093, China
- China National Botanical Garden, Beijing 100093, China
| | - Wei Duan
- Beijing Key Laboratory of Grape Science and Enology and State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, Chinese Academy of Science, Beijing 100093, China
- China National Botanical Garden, Beijing 100093, China
| | - Peige Fan
- Beijing Key Laboratory of Grape Science and Enology and State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, Chinese Academy of Science, Beijing 100093, China
- China National Botanical Garden, Beijing 100093, China
| | - Zhanwu Dai
- Beijing Key Laboratory of Grape Science and Enology and State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, Chinese Academy of Science, Beijing 100093, China
- China National Botanical Garden, Beijing 100093, China
| | - Yongfeng Zhou
- National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518000, China
| | - Zhenchang Liang
- Beijing Key Laboratory of Grape Science and Enology and State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, Chinese Academy of Science, Beijing 100093, China
- China National Botanical Garden, Beijing 100093, China
| | - Shaohua Li
- Beijing Key Laboratory of Grape Science and Enology and State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, Chinese Academy of Science, Beijing 100093, China
- China National Botanical Garden, Beijing 100093, China
| | - Lijun Wang
- Beijing Key Laboratory of Grape Science and Enology and State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, Chinese Academy of Science, Beijing 100093, China
- China National Botanical Garden, Beijing 100093, China
| |
Collapse
|
15
|
Bashir T, Ul Haq SA, Masoom S, Ibdah M, Husaini AM. Quality trait improvement in horticultural crops: OMICS and modern biotechnological approaches. Mol Biol Rep 2023; 50:8729-8742. [PMID: 37642759 DOI: 10.1007/s11033-023-08728-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Accepted: 07/31/2023] [Indexed: 08/31/2023]
Abstract
Horticultural crops are an essential part of food and nutritional security. Moreover, these form an integral part of the agricultural economy and have enormous economic potential. They are a rich source of nutrients that are beneficial to human health. Plant breeding of horticultural crops has focussed primarily on increasing the productivity and related traits of these crops. However, fruit and vegetable quality is paramount to their perishability, marketability, and consumer acceptance. The improved nutritional value is beneficial to underprivileged and undernourished communities. Due to a declining genetic base, conventional plant breeding does not contribute much to quality improvement as the existing natural allelic variations and crossing barriers between cultivated and wild species limit it. Over the past two decades, 'omics' and modern biotechnological approaches have made it possible to decode the complex genomes of crop plants, assign functions to the otherwise many unknown genes, and develop genome-wide DNA markers. Genetic engineering has enabled the validation of these genes and the introduction of crucial agronomic traits influencing various quality parameters directly or indirectly. This review discusses the significant advances in the quality improvement of horticultural crops, including shelf life, aroma, browning, nutritional value, colour, and many other related traits.
Collapse
Affiliation(s)
- Tanzeel Bashir
- Genome Engineering and Societal Biotechnology Lab, Division of Plant Biotechnology, SKUAST-K, Shalimar, Srinagar, Jammu and Kashmir, India
| | - Syed Anam Ul Haq
- Genome Engineering and Societal Biotechnology Lab, Division of Plant Biotechnology, SKUAST-K, Shalimar, Srinagar, Jammu and Kashmir, India
| | - Salsabeel Masoom
- Genome Engineering and Societal Biotechnology Lab, Division of Plant Biotechnology, SKUAST-K, Shalimar, Srinagar, Jammu and Kashmir, India
| | - Mwafaq Ibdah
- Newe Yaar Research Center, Agricultural Research Organization, Ramat Yishay, 30095, Israel
| | - Amjad M Husaini
- Genome Engineering and Societal Biotechnology Lab, Division of Plant Biotechnology, SKUAST-K, Shalimar, Srinagar, Jammu and Kashmir, India.
| |
Collapse
|
16
|
Sabnam N, Hussain A, Saha P. The secret password: Cell death-inducing proteins in filamentous phytopathogens - As versatile tools to develop disease-resistant crops. Microb Pathog 2023; 183:106276. [PMID: 37541554 DOI: 10.1016/j.micpath.2023.106276] [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: 05/05/2023] [Revised: 07/25/2023] [Accepted: 07/27/2023] [Indexed: 08/06/2023]
Abstract
Cell death-inducing proteins (CDIPs) are some of the secreted effector proteins manifested by filamentous oomycetes and fungal pathogens to invade the plant tissue and facilitate infection. Along with their involvement in different developmental processes and virulence, CDIPs play a crucial role in plant-pathogen interactions. As the name implies, CDIPs cause necrosis and trigger localised cell death in the infected host tissues by the accumulation of higher concentrations of hydrogen peroxide (H2O2), oxidative burst, accumulation of nitric oxide (NO), and electrolyte leakage. They also stimulate the biosynthesis of defense-related phytohormones such as salicylic acid (SA), jasmonic acid (JA), abscisic acid (ABA), and ethylene (ET), as well as the expression of pathogenesis-related (PR) genes that are important in disease resistance. Altogether, the interactions result in the hypersensitive response (HR) in the host plant, which might confer systemic acquired resistance (SAR) in some cases against a vast array of related and unrelated pathogens. The CDIPs, due to their capability of inducing host resistance, are thus unique among the array of proteins secreted by filamentous plant pathogens. More interestingly, a few transgenic plant lines have also been developed expressing the CDIPs with added resistance. Thus, CDIPs have opened an interesting hot area of research. The present study critically reviews the current knowledge of major types of CDIPs identified across filamentous phytopathogens and their modes of action in the last couple of years. This review also highlights the recent breakthrough technologies in studying plant-pathogen interactions as well as crop improvement by enhancing disease resistance through CDIPs.
Collapse
Affiliation(s)
- Nazmiara Sabnam
- Department of Life Sciences, Presidency University, Kolkata, India.
| | - Afzal Hussain
- Department of Bioinformatics, Maulana Azad National Institute of Technology, Bhopal, India
| | - Pallabi Saha
- Biotechnology Institute, University of Minnesota, Saint Paul, Minnesota, 55108, United States; Department of Biotechnology, National Institute of Technology, Durgapur, India
| |
Collapse
|
17
|
Huang W, Zheng A, Huang H, Chen Z, Ma J, Li X, Liang Q, Li L, Liu R, Huang Z, Qin Y, Tang Y, Li H, Zhang F, Wang Q, Sun B. Effects of sgRNAs, Promoters, and Explants on the Gene Editing Efficiency of the CRISPR/Cas9 System in Chinese Kale. Int J Mol Sci 2023; 24:13241. [PMID: 37686051 PMCID: PMC10487834 DOI: 10.3390/ijms241713241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Revised: 08/21/2023] [Accepted: 08/24/2023] [Indexed: 09/10/2023] Open
Abstract
The CRISPR/Cas9 system is extensively used for plant gene editing. This study developed an efficient CRISPR/Cas9 system for Chinese kale using multiple sgRNAs and two promoters to create various CRISPR/Cas9 vectors. These vectors targeted BoaZDS and BoaCRTISO in Chinese kale protoplasts and cotyledons. Transient transformation of Chinese kale protoplasts was assessed for editing efficiency at three BoaZDS sites. Notably, sgRNA: Z2 achieved the highest efficiency (90%). Efficiency reached 100% when two sgRNAs targeted BoaZDS with a deletion of a large fragment (576 bp) between them. However, simultaneous targeting of BoaZDS and BoaCRTISO yielded lower efficiency. Transformation of cotyledons led to Chinese kale mutants with albino phenotypes for boazds mutants and orange-mottled phenotypes for boacrtiso mutants. The mutation efficiency of 35S-CRISPR/Cas9 (92.59%) exceeded YAO-CRISPR/Cas9 (70.97%) in protoplasts, and YAO-CRISPR/Cas9 (96.49%) surpassed 35S-CRISPR/Cas9 (58%) in cotyledons. These findings introduce a strategy for enhancing CRISPR/Cas9 editing efficiency in Chinese kale.
Collapse
Affiliation(s)
- Wenli Huang
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China; (W.H.); (A.Z.); (H.H.); (X.L.); (Q.L.); (L.L.); (R.L.); (Z.H.); (Y.Q.); (Y.T.); (H.L.); (F.Z.)
| | - Aihong Zheng
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China; (W.H.); (A.Z.); (H.H.); (X.L.); (Q.L.); (L.L.); (R.L.); (Z.H.); (Y.Q.); (Y.T.); (H.L.); (F.Z.)
| | - Huanhuan Huang
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China; (W.H.); (A.Z.); (H.H.); (X.L.); (Q.L.); (L.L.); (R.L.); (Z.H.); (Y.Q.); (Y.T.); (H.L.); (F.Z.)
| | - Zhifeng Chen
- College of Biology and Agricultural Technology, Zunyi Normal University, Zunyi 563006, China;
| | - Jie Ma
- Bijie lnstitute of Agricultural Science, Bijie 551700, China;
| | - Xiangxiang Li
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China; (W.H.); (A.Z.); (H.H.); (X.L.); (Q.L.); (L.L.); (R.L.); (Z.H.); (Y.Q.); (Y.T.); (H.L.); (F.Z.)
| | - Qiannan Liang
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China; (W.H.); (A.Z.); (H.H.); (X.L.); (Q.L.); (L.L.); (R.L.); (Z.H.); (Y.Q.); (Y.T.); (H.L.); (F.Z.)
| | - Ling Li
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China; (W.H.); (A.Z.); (H.H.); (X.L.); (Q.L.); (L.L.); (R.L.); (Z.H.); (Y.Q.); (Y.T.); (H.L.); (F.Z.)
| | - Ruobin Liu
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China; (W.H.); (A.Z.); (H.H.); (X.L.); (Q.L.); (L.L.); (R.L.); (Z.H.); (Y.Q.); (Y.T.); (H.L.); (F.Z.)
| | - Zhi Huang
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China; (W.H.); (A.Z.); (H.H.); (X.L.); (Q.L.); (L.L.); (R.L.); (Z.H.); (Y.Q.); (Y.T.); (H.L.); (F.Z.)
| | - Yaoguo Qin
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China; (W.H.); (A.Z.); (H.H.); (X.L.); (Q.L.); (L.L.); (R.L.); (Z.H.); (Y.Q.); (Y.T.); (H.L.); (F.Z.)
| | - Yi Tang
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China; (W.H.); (A.Z.); (H.H.); (X.L.); (Q.L.); (L.L.); (R.L.); (Z.H.); (Y.Q.); (Y.T.); (H.L.); (F.Z.)
| | - Huanxiu Li
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China; (W.H.); (A.Z.); (H.H.); (X.L.); (Q.L.); (L.L.); (R.L.); (Z.H.); (Y.Q.); (Y.T.); (H.L.); (F.Z.)
| | - Fen Zhang
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China; (W.H.); (A.Z.); (H.H.); (X.L.); (Q.L.); (L.L.); (R.L.); (Z.H.); (Y.Q.); (Y.T.); (H.L.); (F.Z.)
| | - Qiaomei Wang
- Department of Horticulture, Zhejiang University, Hangzhou 310058, China
| | - Bo Sun
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China; (W.H.); (A.Z.); (H.H.); (X.L.); (Q.L.); (L.L.); (R.L.); (Z.H.); (Y.Q.); (Y.T.); (H.L.); (F.Z.)
| |
Collapse
|
18
|
Nishiguchi M, Futamura N, Endo M, Mikami M, Toki S, Katahata SI, Ohmiya Y, Konagaya KI, Nanasato Y, Taniguchi T, Maruyama TE. CRISPR/Cas9-mediated disruption of CjACOS5 confers no-pollen formation on sugi trees (Cryptomeria japonica D. Don). Sci Rep 2023; 13:11779. [PMID: 37479866 PMCID: PMC10361980 DOI: 10.1038/s41598-023-38339-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Accepted: 07/06/2023] [Indexed: 07/23/2023] Open
Abstract
Sugi (Cryptomeria japonica D. Don) is an economically important coniferous tree in Japan. However, abundant sugi pollen grains are dispersed and transported by the wind each spring and cause a severe pollen allergy syndrome (Japanese cedar pollinosis). The use of pollen-free sugi that cannot produce pollen has been thought as a countermeasure to Japanese cedar pollinosis. The sugi CjACOS5 gene is an ortholog of Arabidopsis ACOS5 and rice OsACOS12, which encode an acyl-CoA synthetase that is involved in the synthesis of sporopollenin in pollen walls. To generate pollen-free sugi, we mutated CjACOS5 using the CRISPR/Cas9 system. As a result of sugi transformation mediated by Agrobacterium tumefaciens harboring the CjACOS5-targeted CRISPR/Cas9 vector, 1 bp-deleted homo biallelic mutant lines were obtained. Chimeric mutant lines harboring both mutant and wild-type CjACOS5 genes were also generated. The homo biallelic mutant lines had no-pollen in male strobili, whereas chimeric mutant lines had male strobili with or without pollen grains. Our results suggest that CjACOS5 is essential for the production of pollen in sugi and that its disruption is useful for the generation of pollen-free sugi. In addition to conventional transgenic technology, genome editing technology, including CRISPR/Cas9, can confer new traits on sugi.
Collapse
Affiliation(s)
- Mitsuru Nishiguchi
- Department of Forest Molecular Genetics and Biotechnology, Forestry and Forest Products Research Institute (FFPRI), 1 Matsunosato, Tsukuba, Ibaraki, 305-8687, Japan.
| | - Norihiro Futamura
- Department of Forest Molecular Genetics and Biotechnology, Forestry and Forest Products Research Institute (FFPRI), 1 Matsunosato, Tsukuba, Ibaraki, 305-8687, Japan
| | - Masaki Endo
- Institute of Agrobiological Sciences, National Agriculture and Food Research Organization (NARO), 1-2 Owashi, Tsukuba, Ibaraki, 305-8634, Japan
- Graduate School of Nanobioscience, Yokohama City University, 22-2 Seto, Kanazawa-ku, Yokohama, Kanagawa, 236-0027, Japan
| | - Masafumi Mikami
- Institute of Agrobiological Sciences, National Agriculture and Food Research Organization (NARO), 1-2 Owashi, Tsukuba, Ibaraki, 305-8634, Japan
| | - Seiichi Toki
- Institute of Agrobiological Sciences, National Agriculture and Food Research Organization (NARO), 1-2 Owashi, Tsukuba, Ibaraki, 305-8634, Japan
- Graduate School of Nanobioscience, Yokohama City University, 22-2 Seto, Kanazawa-ku, Yokohama, Kanagawa, 236-0027, Japan
- Department of Plant Life Science, Faculty of Agriculture, Ryukoku University, 1-5 Yokotani, Seta Oe-cho, Otsu, Shiga, 520-2194, Japan
- Kihara Institute for Biological Research, Yokohama City University, 641-12 Maioka-cho, Totsuka-ku, Yokohama, Kanagawa, 244-0813, Japan
| | - Shin-Ichiro Katahata
- Faculty of Applied Biological Sciences, Gifu University, Yanagido 1-1, Gifu, 501-1193, Japan
| | - Yasunori Ohmiya
- Extension and International Cooperation Department, Forest Tree Breeding Center, Forestry and Forest Products Research Institute (FFPRI), 3809-1 Ishi, Juo, Hitachi, Ibaraki, 319-1301, Japan
| | - Ken-Ichi Konagaya
- Forest Bio-Research Center, Forestry and Forest Products Research Institute (FFPRI), 3809-1 Ishi, Juo, Hitachi, Ibaraki, 319-1301, Japan
| | - Yoshihiko Nanasato
- Forest Bio-Research Center, Forestry and Forest Products Research Institute (FFPRI), 3809-1 Ishi, Juo, Hitachi, Ibaraki, 319-1301, Japan
| | - Toru Taniguchi
- Forest Bio-Research Center, Forestry and Forest Products Research Institute (FFPRI), 3809-1 Ishi, Juo, Hitachi, Ibaraki, 319-1301, Japan
| | - Tsuyoshi Emilio Maruyama
- Department of Forest Molecular Genetics and Biotechnology, Forestry and Forest Products Research Institute (FFPRI), 1 Matsunosato, Tsukuba, Ibaraki, 305-8687, Japan
| |
Collapse
|
19
|
Nakajima I, Kawahigashi H, Nishitani C, Azuma A, Haji T, Toki S, Endo M. Targeted deletion of grape retrotransposon associated with fruit skin color via CRISPR/Cas9 in Vitis labrascana 'Shine Muscat'. PLoS One 2023; 18:e0286698. [PMID: 37289779 PMCID: PMC10249860 DOI: 10.1371/journal.pone.0286698] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Accepted: 05/19/2023] [Indexed: 06/10/2023] Open
Abstract
Transposition of transposable elements affect expression levels, splicing and epigenetic status, and function of genes located in, or near, the inserted/excised locus. For example, in grape, presence of the Gret1 retrotransposon in the promoter region of the VvMYBA1a allele at the VvMYBA1 locus suppress the expression of the VvMYBA1 transcription factor gene for the anthocyanin biosynthesis and this transposon insertion is responsible for the green berry skin color of Vitis labrascana, 'Shine Muscat', a major grape cultivar in Japan. To prove that transposons in grape genome can be removed by genome editing, we focused on Gret1 in the VvMYBA1a allele as a target of CRISPR/Cas9 mediated transposon removal. PCR amplification and sequencing detected Gret1 eliminated cells in 19 of 45 transgenic plants. Although we have not yet confirmed any effects on grape berry skin color, we were successful in demonstrating that cleaving the long terminal repeat (LTR) present at both ends of Gret1 can efficiently eliminate the transposon.
Collapse
Affiliation(s)
- Ikuko Nakajima
- Institute of Fruit Tree and Tea Science, National Agriculture and Food Research Organization, Tsukuba, Japan
| | - Hiroyuki Kawahigashi
- Institute of Fruit Tree and Tea Science, National Agriculture and Food Research Organization, Tsukuba, Japan
| | - Chikako Nishitani
- Institute of Fruit Tree and Tea Science, National Agriculture and Food Research Organization, Tsukuba, Japan
| | - Akifumi Azuma
- Institute of Fruit Tree and Tea Science, National Agriculture and Food Research Organization, Tsukuba, Japan
| | - Takashi Haji
- Institute of Fruit Tree and Tea Science, National Agriculture and Food Research Organization, Tsukuba, Japan
| | - Seiichi Toki
- Institute of Agrobiological Sciences, National Agriculture and Food Research Organization, Tsukuba, Ibaraki, Japan
- Faculty of Agriculture, Ryukoku University, Otsu, Shiga, Japan
- Graduate School of Nanobioscience, Yokohama City University, Yokohama, Kanagawa, Japan
| | - Masaki Endo
- Institute of Agrobiological Sciences, National Agriculture and Food Research Organization, Tsukuba, Ibaraki, Japan
| |
Collapse
|
20
|
Chen H, Liu X, Li S, Yuan L, Mu H, Wang Y, Li Y, Duan W, Fan P, Liang Z, Wang L. The class B heat shock factor HSFB1 regulates heat tolerance in grapevine. HORTICULTURE RESEARCH 2023; 10:uhad001. [PMID: 36938570 PMCID: PMC10018785 DOI: 10.1093/hr/uhad001] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Accepted: 12/28/2022] [Indexed: 06/01/2023]
Abstract
Grape is a widely cultivated crop with high economic value. Most cultivars derived from mild or cooler climates may not withstand increasing heat stress. Therefore, dissecting the mechanisms of heat tolerance in grapes is of particular significance. Here, we performed comparative transcriptome analysis of Vitis davidii 'Tangwei' (heat tolerant) and Vitis vinifera 'Jingxiu' (heat sensitive) grapevines after exposure to 25°C, 40°C, or 45°C for 2 h. More differentially expressed genes (DEGs) were detected in 'Tangwei' than in 'Jingxiu' in response to heat stress, and the number of DEGs increased with increasing treatment temperatures. We identified a class B Heat Shock Factor, HSFB1, which was significantly upregulated in 'Tangwei', but not in 'Jingxiu', at high temperature. VdHSFB1 from 'Tangwei' and VvHSFB1 from 'Jingxiu' differ in only one amino acid, and both showed similar transcriptional repression activities. Overexpression and RNA interference of HSFB1 in grape indicated that HSFB1 positively regulates the heat tolerance. Moreover, the heat tolerance of HSFB1-overexpressing plants was positively correlated to HSFB1 expression level. The activity of the VdHSFB1 promoter is higher than that of VvHSFB1 under both normal and high temperatures. Promoter analysis showed that more TATA-box and AT~TATA-box cis-elements are present in the VdHSFB1 promoter than the VvHSFB1 promoter. The promoter sequence variations between VdHSFB1 and VvHSFB1 likely determine the HSFB1 expression levels that influence heat tolerance of the two grape germplasms with contrasting thermotolerance. Collectively, we validated the role of HSFB1 in heat tolerance, and the knowledge gained will advance our ability to breed heat-tolerant grape cultivars.
Collapse
Affiliation(s)
- Haiyang Chen
- Beijing Key Laboratory of Grape Science and Enology and Key Laboratory of Plant Resources, Institute of Botany, The Chinese Academy of Sciences, Beijing 100093, China
- China National Botanical Garden, Beijing 100093, China
- University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Xinna Liu
- Beijing Key Laboratory of Grape Science and Enology and Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- China National Botanical Garden, Beijing 100093, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shenchang Li
- Beijing Key Laboratory of Grape Science and Enology and Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- China National Botanical Garden, Beijing 100093, China
- University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Ling Yuan
- Department of Plant and Soil Sciences, University of Kentucky, Lexington, Kentucky 40546, USA
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement and Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Huayuan Mu
- Beijing Key Laboratory of Grape Science and Enology and Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- China National Botanical Garden, Beijing 100093, China
- University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Yi Wang
- Beijing Key Laboratory of Grape Science and Enology and Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- China National Botanical Garden, Beijing 100093, China
| | - Yang Li
- Beijing Key Laboratory of Grape Science and Enology and Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- China National Botanical Garden, Beijing 100093, China
| | - Wei Duan
- Beijing Key Laboratory of Grape Science and Enology and Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- China National Botanical Garden, Beijing 100093, China
| | - Peige Fan
- Beijing Key Laboratory of Grape Science and Enology and Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- China National Botanical Garden, Beijing 100093, China
| | - Zhenchang Liang
- Beijing Key Laboratory of Grape Science and Enology and Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- China National Botanical Garden, Beijing 100093, China
| | | |
Collapse
|
21
|
Ma Z, Ma L, Zhou J. Applications of CRISPR/Cas genome editing in economically important fruit crops: recent advances and future directions. MOLECULAR HORTICULTURE 2023; 3:1. [PMID: 37789479 PMCID: PMC10515014 DOI: 10.1186/s43897-023-00049-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Accepted: 01/10/2023] [Indexed: 10/05/2023]
Abstract
Fruit crops, consist of climacteric and non-climacteric fruits, are the major sources of nutrients and fiber for human diet. Since 2013, CRISPR/Cas (Clustered Regularly Interspersed Short Palindromic Repeats and CRISPR-Associated Protein) genome editing system has been widely employed in different plants, leading to unprecedented progress in the genetic improvement of many agronomically important fruit crops. Here, we summarize latest advancements in CRISPR/Cas genome editing of fruit crops, including efforts to decipher the mechanisms behind plant development and plant immunity, We also highlight the potential challenges and improvements in the application of genome editing tools to fruit crops, including optimizing the expression of CRISPR/Cas cassette, improving the delivery efficiency of CRISPR/Cas reagents, increasing the specificity of genome editing, and optimizing the transformation and regeneration system. In addition, we propose the perspectives on the application of genome editing in crop breeding especially in fruit crops and highlight the potential challenges. It is worth noting that efforts to manipulate fruit crops with genome editing systems are urgently needed for fruit crops breeding and demonstration.
Collapse
Affiliation(s)
- Zhimin Ma
- Peking University Institute of Advanced Agricultural Sciences, Weifang, 261000, Shandong, China
| | - Lijing Ma
- Peking University Institute of Advanced Agricultural Sciences, Weifang, 261000, Shandong, China
| | - Junhui Zhou
- Peking University Institute of Advanced Agricultural Sciences, Weifang, 261000, Shandong, China.
| |
Collapse
|
22
|
Evaluation of CRISPR/Cas9 Constructs in Wheat Cell Suspension Cultures. Int J Mol Sci 2023; 24:ijms24032162. [PMID: 36768486 PMCID: PMC9916915 DOI: 10.3390/ijms24032162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 01/13/2023] [Accepted: 01/18/2023] [Indexed: 01/25/2023] Open
Abstract
Despite intensive optimization efforts, developing an efficient sequence-specific CRISPR/Cas-mediated genome editing method remains a challenge, especially in polyploid cereal species such as wheat. Validating the efficacy of nuclease constructs prior to using them in planta is, thus, a major step of every editing experiment. Several construct evaluation strategies were proposed, with PEG-mediated plasmid transfection of seedling-derived protoplasts becoming the most popular. However, the usefulness of this approach is affected by associated construct copy number bias and chromatin relaxation, both influencing the outcome. Therefore, to achieve a reliable evaluation of CRISPR/Cas9 constructs, we proposed a system based on an Agrobacterium-mediated transformation of established wheat cell suspension cultures. This system was used for the evaluation of a CRISPR/Cas9 construct designed to target the ABA 8'-hydroxylase 1 gene. The efficiency of editing was verified by cost-effective means of Sanger sequencing and bioinformatic analysis. We discuss advantages and potential future developments of this method in contrast to other in vitro approaches.
Collapse
|
23
|
Nascimento FDS, Rocha ADJ, Soares JMDS, Mascarenhas MS, Ferreira MDS, Morais Lino LS, Ramos APDS, Diniz LEC, Mendes TADO, Ferreira CF, dos Santos-Serejo JA, Amorim EP. Gene Editing for Plant Resistance to Abiotic Factors: A Systematic Review. PLANTS (BASEL, SWITZERLAND) 2023; 12:305. [PMID: 36679018 PMCID: PMC9860801 DOI: 10.3390/plants12020305] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2022] [Revised: 01/02/2023] [Accepted: 01/05/2023] [Indexed: 05/22/2023]
Abstract
Agricultural crops are exposed to various abiotic stresses, such as salinity, water deficits, temperature extremes, floods, radiation, and metal toxicity. To overcome these challenges, breeding programs seek to improve methods and techniques. Gene editing by Clustered Regularly Interspaced Short Palindromic Repeats-CRISPR/Cas-is a versatile tool for editing in all layers of the central dogma with focus on the development of cultivars of plants resistant or tolerant to multiple biotic or abiotic stresses. This systematic review (SR) brings new contributions to the study of the use of CRISPR/Cas in gene editing for tolerance to abiotic stress in plants. Articles deposited in different electronic databases, using a search string and predefined inclusion and exclusion criteria, were evaluated. This SR demonstrates that the CRISPR/Cas system has been applied to several plant species to promote tolerance to the main abiotic stresses. Among the most studied crops are rice and Arabidopsis thaliana, an important staple food for the population, and a model plant in genetics/biotechnology, respectively, and more recently tomato, whose number of studies has increased since 2021. Most studies were conducted in Asia, specifically in China. The Cas9 enzyme is used in most articles, and only Cas12a is used as an additional gene editing tool in plants. Ribonucleoproteins (RNPs) have emerged as a DNA-free strategy for genome editing without exogenous DNA. This SR also identifies several genes edited by CRISPR/Cas, and it also shows that plant responses to stress factors are mediated by many complex-signaling pathways. In addition, the quality of the articles included in this SR was validated by a risk of bias analysis. The information gathered in this SR helps to understand the current state of CRISPR/Cas in the editing of genes and noncoding sequences, which plays a key role in the regulation of various biological processes and the tolerance to multiple abiotic stresses, with potential for use in plant genetic improvement programs.
Collapse
Affiliation(s)
| | - Anelita de Jesus Rocha
- Department of Biological Sciences, Feira de Santana State University, Feira de Santana 44036-900, BA, Brazil
| | | | | | - Mileide dos Santos Ferreira
- Department of Biological Sciences, Feira de Santana State University, Feira de Santana 44036-900, BA, Brazil
| | | | | | | | | | | | | | | |
Collapse
|
24
|
Najafi S, Bertini E, D’Incà E, Fasoli M, Zenoni S. DNA-free genome editing in grapevine using CRISPR/Cas9 ribonucleoprotein complexes followed by protoplast regeneration. HORTICULTURE RESEARCH 2023; 10:uhac240. [PMID: 37077374 PMCID: PMC10108004 DOI: 10.1093/hr/uhac240] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Accepted: 10/17/2022] [Indexed: 05/03/2023]
Abstract
CRISPR/Cas9 genome editing technology can overcome many limitations of traditional breeding, offering enormous potential for crop improvement and food production. Although the direct delivery of Cas9-single guide RNA (sgRNA) ribonucleoprotein (RNP) complexes to grapevine (Vitis vinifera) protoplasts has been shown before, the regeneration of edited protoplasts into whole plants has not been reported. Here, we describe an efficient approach to obtain transgene-free edited grapevine plants by the transfection and subsequent regeneration of protoplasts isolated from embryogenic callus. As proof of concept, a single-copy green fluorescent protein reporter gene (GFP) in the grapevine cultivar Thompson Seedless was targeted and knocked out by the direct delivery of RNPs to protoplasts. CRISPR/Cas9 activity, guided by two independent sgRNAs, was confirmed by the loss of GFP fluorescence. The regeneration of GFP- protoplasts into whole plants was monitored throughout development, confirming that the edited grapevine plants were comparable in morphology and growth habit to wild-type controls. We report the first highly efficient protocol for DNA-free genome editing in grapevine by the direct delivery of preassembled Cas9-sgRNA RNP complexes into protoplasts, helping to address the regulatory concerns related to genetically modified plants. This technology could encourage the application of genome editing for the genetic improvement of grapevine and other woody crop plants.
Collapse
Affiliation(s)
- Samaneh Najafi
- Department of Biotechnology, University of Verona, 37134 Verona, Italy
| | - Edoardo Bertini
- Department of Biotechnology, University of Verona, 37134 Verona, Italy
| | - Erica D’Incà
- Department of Biotechnology, University of Verona, 37134 Verona, Italy
| | - Marianna Fasoli
- Department of Biotechnology, University of Verona, 37134 Verona, Italy
| | | |
Collapse
|
25
|
Sharma P, Pandey A, Malviya R, Dey S, Karmakar S, Gayen D. Genome editing for improving nutritional quality, post-harvest shelf life and stress tolerance of fruits, vegetables, and ornamentals. Front Genome Ed 2023; 5:1094965. [PMID: 36911238 PMCID: PMC9998953 DOI: 10.3389/fgeed.2023.1094965] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Accepted: 02/03/2023] [Indexed: 03/14/2023] Open
Abstract
Agricultural production relies on horticultural crops, including vegetables, fruits, and ornamental plants, which sustain human life. With an alarming increase in human population and the consequential need for more food, it has become necessary for increased production to maintain food security. Conventional breeding has subsidized the development of improved verities but to enhance crop production, new breeding techniques need to be acquired. CRISPR-Cas9 system is a unique and powerful genome manipulation tool that can change the DNA in a precise way. Based on the bacterial adaptive immune system, this technique uses an endonuclease that creates double-stranded breaks (DSBs) at the target loci under the guidance of a single guide RNA. These DSBs can be repaired by a cellular repair mechanism that installs small insertion and deletion (indels) at the cut sites. When equated to alternate editing tools like ZFN, TALENs, and meganucleases, CRISPR- The cas-based editing tool has quickly gained fast-forward for its simplicity, ease to use, and low off-target effect. In numerous horticultural and industrial crops, the CRISPR technology has been successfully used to enhance stress tolerance, self-life, nutritional improvements, flavor, and metabolites. The CRISPR-based tool is the most appropriate one with the prospective goal of generating non-transgenic yields and avoiding the regulatory hurdles to release the modified crops into the market. Although several challenges for editing horticultural, industrial, and ornamental crops remain, this new novel nuclease, with its crop-specific application, makes it a dynamic tool for crop improvement.
Collapse
Affiliation(s)
- Punam Sharma
- Department of Biochemistry, School of Life Sciences, Central University of Rajasthan, Ajmer, India
| | - Anuradha Pandey
- Department of Biochemistry, School of Life Sciences, Central University of Rajasthan, Ajmer, India
| | - Rinku Malviya
- Department of Biochemistry, School of Life Sciences, Central University of Rajasthan, Ajmer, India
| | - Sharmistha Dey
- Department of Biochemistry, School of Life Sciences, Central University of Rajasthan, Ajmer, India
| | | | - Dipak Gayen
- Department of Biochemistry, School of Life Sciences, Central University of Rajasthan, Ajmer, India
| |
Collapse
|
26
|
Scintilla S, Salvagnin U, Giacomelli L, Zeilmaker T, Malnoy MA, Rouppe van der Voort J, Moser C. Regeneration of non-chimeric plants from DNA-free edited grapevine protoplasts. FRONTIERS IN PLANT SCIENCE 2022; 13:1078931. [PMID: 36531381 PMCID: PMC9752144 DOI: 10.3389/fpls.2022.1078931] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Accepted: 11/16/2022] [Indexed: 05/19/2023]
Abstract
The application of New Breeding Techniques (NBTs) in Vitis vinifera is highly desirable to introduce valuable traits while preserving the genotype of the elite cultivars. However, a broad application of NBTs through standard DNA-based transformation is poorly accepted by public opinion and law regulations in Europe and other countries due to the stable integration of exogenous DNA, which leads to transgenic plants possibly affected by chimerism. A single-cell based approach, coupled with a DNA-free transfection of the CRISPR/Cas editing machinery, constitutes a powerful tool to overcome these problems and maintain the original genetic make-up in the whole organism. We here describe a successful single-cell based, DNA-free methodology to obtain edited grapevine plants, regenerated from protoplasts isolated from embryogenic callus of two table grapevine varieties (V. vinifera cv. Crimson seedless and Sugraone). The regenerated, non-chimeric plants were edited on the downy- and powdery-mildew susceptibility genes, VviDMR6 and VviMlo6 respectively, either as single or double mutants.
Collapse
Affiliation(s)
- Simone Scintilla
- Centro Ricerca ed Innovazione, Fondazione E. Mach. Via E. Mach 1, San Michele all’Adige, Trento, Italy
| | - Umberto Salvagnin
- Centro Ricerca ed Innovazione, Fondazione E. Mach. Via E. Mach 1, San Michele all’Adige, Trento, Italy
- Consorzio Innovazione Vite (CIVIT), Trento, TN, Italy
| | - Lisa Giacomelli
- Centro Ricerca ed Innovazione, Fondazione E. Mach. Via E. Mach 1, San Michele all’Adige, Trento, Italy
- Scienza Biotechnologies BV., Enkhuizen, Netherlands
| | | | - Mickael A. Malnoy
- Centro Ricerca ed Innovazione, Fondazione E. Mach. Via E. Mach 1, San Michele all’Adige, Trento, Italy
| | | | - Claudio Moser
- Centro Ricerca ed Innovazione, Fondazione E. Mach. Via E. Mach 1, San Michele all’Adige, Trento, Italy
| |
Collapse
|
27
|
Töpfer R, Trapp O. A cool climate perspective on grapevine breeding: climate change and sustainability are driving forces for changing varieties in a traditional market. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:3947-3960. [PMID: 35389053 PMCID: PMC9729149 DOI: 10.1007/s00122-022-04077-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 03/07/2022] [Indexed: 05/04/2023]
Abstract
A multitude of diverse breeding goals need to be combined in a new cultivar, which always forces to compromise. The biggest challenge grapevine breeders face is the extraordinarily complex trait of wine quality, which is the all-pervasive and most debated characteristic. Since the 1920s, Germany runs continuous grapevine breeding programmes. This continuity was the key to success and lead to various new cultivars on the market, so called PIWIs. Initially, introduced pests and diseases such as phylloxera, powdery and downy mildew were the driving forces for breeding. However, preconceptions about the wine quality of new resistant selections impeded the market introduction. These preconceptions are still echoing today and may be the reason in large parts of the viticultural community for: (1) ignoring substantial breeding progress, and (2) sticking to successful markets of well-known varietal wines or blends (e.g. Chardonnay, Cabernet Sauvignon, Riesling). New is the need to improve viticulture´s sustainability and to adapt to changing environmental conditions. Climate change with its extreme weather will impose the need for a change in cultivars in many wine growing regions. Therefore, a paradigm shift is knocking on the door: new varieties (PIWIs) versus traditional varieties for climate adapted and sustainable viticulture. However, it will be slow process and viticulture is politically well advised to pave the way to variety innovation. In contrast to the widely available PIWIs, competitive cultivars created by means of new breeding technologies (NBT, e.g. through CRISPR/Cas) are still decades from introduction to the market.
Collapse
Affiliation(s)
- Reinhard Töpfer
- Julius Kühn-Institut, Federal Research Centre for Cultivated Plants, Institute for Grapevine Breeding Geilweilerhof, Siebeldingen, Germany.
| | - Oliver Trapp
- Julius Kühn-Institut, Federal Research Centre for Cultivated Plants, Institute for Grapevine Breeding Geilweilerhof, Siebeldingen, Germany
| |
Collapse
|
28
|
Yang Y, Ke J, Han X, Wuddineh WA, Song GQ, Zhong GY. Removal of a 10-kb Gret1 transposon from VvMybA1 of Vitis vinifera cv. Chardonnay. HORTICULTURE RESEARCH 2022; 9:uhac201. [PMID: 36406285 PMCID: PMC9669667 DOI: 10.1093/hr/uhac201] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Accepted: 08/31/2022] [Indexed: 06/10/2023]
Abstract
Many white grape cultivars have a nonfunctional VvMybA1 gene due to the presence of a 10-kb Gret1 transposon in its promoter. In this study, we successfully demonstrated removal of the 10-kb Gret1 transposon and functional restoration of a VvMybA1 allele in Vitis vinifera cv. Chardonnay through transgenic expression of Cas9 and two gRNAs simultaneously targeting two junction sequences between Gret1 LTRs and VvMybA1. We generated 67 and 24 Cas9-positive vines via Agrobacterium-mediated and biolistic bombardment transformation, respectively. While the editing efficiencies were as high as 17% for the 5' target site and 65% for the 3' target site, simultaneous editing of both 5' and 3' target sites resulting in the removal of Gret1 transposon from the VvMybA1 promoter was 0.5% or less in most transgenic calli, suggesting that these calli had very limited numbers of cells with the Gret1 removed. Nevertheless, two bombardment-transformed vines, which shared the same unique editing features and were likely derived from a singly edited event, were found to have the Gret1 successfully edited out from one of their two VvMybA1 alleles. The edited allele was functionally restored based on the detection of its expression and a positive coloring assay result in leaves. Precise removal of more than a 10-kb DNA fragment from a gene locus in grape broadens the possibilities of using gene editing technologies to modify various trait genes in grapes and other plants.
Collapse
Affiliation(s)
- Yingzhen Yang
- USDA-Agricultural Research Service Grape Genetics Research Unit, Geneva, NY 14456, USA
| | - John Ke
- USDA-Agricultural Research Service Grape Genetics Research Unit, Geneva, NY 14456, USA
| | - Xiaoyan Han
- Department of Horticulture, Michigan State University, East Lansing, MI 48823, USA
| | - Wegi A Wuddineh
- USDA-Agricultural Research Service Grape Genetics Research Unit, Geneva, NY 14456, USA
| | - Guo-qing Song
- Department of Horticulture, Michigan State University, East Lansing, MI 48823, USA
| | - Gan-Yuan Zhong
- USDA-Agricultural Research Service Grape Genetics Research Unit, Geneva, NY 14456, USA
| |
Collapse
|
29
|
CRISPR-Based Genome Editing and Its Applications in Woody Plants. Int J Mol Sci 2022; 23:ijms231710175. [PMID: 36077571 PMCID: PMC9456532 DOI: 10.3390/ijms231710175] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 08/18/2022] [Accepted: 08/31/2022] [Indexed: 12/21/2022] Open
Abstract
CRISPR/Cas-based genome editing technology provides straightforward, proficient, and multifunctional ways for the site-directed modification of organism genomes and genes. The application of CRISPR-based technology in plants has a vast potential value in gene function research, germplasm innovation, and genetic improvement. The complexity of woody plants genome may pose significant challenges in the application and expansion of various new editing techniques, such as Cas9, 12, 13, and 14 effectors, base editing, particularly for timberland species with a long life span, huge genome, and ploidy. Therefore, many novel optimisms have been drawn to molecular breeding research based on woody plants. This review summarizes the recent development of CRISPR/Cas applications for essential traits, including wood properties, flowering, biological stress, abiotic stress, growth, and development in woody plants. We outlined the current problems and future development trends of this technology in germplasm and the improvement of products in woody plants.
Collapse
|
30
|
Yao L, Zhang H, Liu Y, Ji Q, Xie J, Zhang R, Huang L, Mei K, Wang J, Gao W. Engineering of triterpene metabolism and overexpression of the lignin biosynthesis gene PAL promotes ginsenoside Rg 3 accumulation in ginseng plant chassis. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2022; 64:1739-1754. [PMID: 35731022 DOI: 10.1111/jipb.13315] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Accepted: 06/20/2022] [Indexed: 05/28/2023]
Abstract
The ginsenoside Rg3 found in Panax species has extensive pharmacological properties, in particular anti-cancer effects. However, its natural yield in Panax plants is limited. Here, we report a multi-modular strategy to improve yields of Rg3 in a Panax ginseng chassis, combining engineering of triterpene metabolism and overexpression of a lignin biosynthesis gene, phenylalanine ammonia lyase (PAL). We first performed semi-rational design and site mutagenesis to improve the enzymatic efficiency of Pq3-O-UGT2, a glycosyltransferase that directly catalyzes the biosynthesis of Rg3 from Rh2 . Next, we used clustered regularly interspaced palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9) gene editing to knock down the branch pathway of protopanaxatriol-type ginsenoside biosynthesis to enhance the metabolic flux of the protopanaxadiol-type ginsenoside Rg3 . Overexpression of PAL accelerated the formation of the xylem structure, significantly improving ginsenoside Rg3 accumulation (to 6.19-fold higher than in the control). We combined overexpression of the ginsenoside aglycon synthetic genes squalene epoxidase, Pq3-O-UGT2, and PAL with CRISPR/Cas9-based knockdown of CYP716A53v2 to improve ginsenoside Rg3 accumulation. Finally, we produced ginsenoside Rg3 at a yield of 83.6 mg/L in a shake flask (7.0 mg/g dry weight, 21.12-fold higher than with wild-type cultures). The high-production system established in this study could be a potential platform to produce the ginsenoside Rg3 commercially for pharmaceutical use.
Collapse
Affiliation(s)
- Lu Yao
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, 300072, China
- Wenzhou Safety (Emergency) Institute of Tianjin University, Wenzhou, 325000, China
- Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin University, Tianjin, 300072, China
| | - Huanyu Zhang
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, 300072, China
- Wenzhou Safety (Emergency) Institute of Tianjin University, Wenzhou, 325000, China
- Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin University, Tianjin, 300072, China
| | - Yirong Liu
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, 300072, China
| | - Qiushuang Ji
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, 300072, China
| | - Jing Xie
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, 300072, China
| | - Ru Zhang
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, 300072, China
| | - Luqi Huang
- National Resource Center for Chinese Meteria Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Kunrong Mei
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, 300072, China
| | - Juan Wang
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, 300072, China
- Wenzhou Safety (Emergency) Institute of Tianjin University, Wenzhou, 325000, China
- Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin University, Tianjin, 300072, China
| | - Wenyuan Gao
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, 300072, China
- Wenzhou Safety (Emergency) Institute of Tianjin University, Wenzhou, 325000, China
- Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin University, Tianjin, 300072, China
| |
Collapse
|
31
|
Kumar D, Yadav A, Ahmad R, Dwivedi UN, Yadav K. CRISPR-Based Genome Editing for Nutrient Enrichment in Crops: A Promising Approach Toward Global Food Security. Front Genet 2022; 13:932859. [PMID: 35910203 PMCID: PMC9329789 DOI: 10.3389/fgene.2022.932859] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Accepted: 06/08/2022] [Indexed: 12/21/2022] Open
Abstract
The global malnutrition burden imparts long-term developmental, economic, social, and medical consequences to individuals, communities, and countries. The current developments in biotechnology have infused biofortification in several food crops to fight malnutrition. However, these methods are not sustainable and suffer from several limitations, which are being solved by the CRISPR-Cas-based system of genome editing. The pin-pointed approach of CRISPR-based genome editing has made it a top-notch method due to targeted gene editing, thus making it free from ethical issues faced by transgenic crops. The CRISPR-Cas genome-editing tool has been extensively used in crop improvement programs due to its more straightforward design, low methodology cost, high efficiency, good reproducibility, and quick cycle. The system is now being utilized in the biofortification of cereal crops such as rice, wheat, barley, and maize, including vegetable crops such as potato and tomato. The CRISPR-Cas-based crop genome editing has been utilized in imparting/producing qualitative enhancement in aroma, shelf life, sweetness, and quantitative improvement in starch, protein, gamma-aminobutyric acid (GABA), oleic acid, anthocyanin, phytic acid, gluten, and steroidal glycoalkaloid contents. Some varieties have even been modified to become disease and stress-resistant. Thus, the present review critically discusses CRISPR-Cas genome editing-based biofortification of crops for imparting nutraceutical properties.
Collapse
Affiliation(s)
- Dileep Kumar
- Department of Biochemistry, University of Lucknow, Lucknow, India
| | - Anurag Yadav
- Department of Microbiology, College of Basic Science and Humanities, Sardarkrushinagar Dantiwada Agriculture University, Banaskantha, India
| | - Rumana Ahmad
- Department of Biochemistry, Era Medical University and Hospital, Lucknow, India
| | | | - Kusum Yadav
- Department of Biochemistry, University of Lucknow, Lucknow, India
| |
Collapse
|
32
|
Ren C, Kuang Y, Lin Y, Guo Y, Li H, Fan P, Li S, Liang Z. Overexpression of grape ABA receptor gene VaPYL4 enhances tolerance to multiple abiotic stresses in Arabidopsis. BMC PLANT BIOLOGY 2022; 22:271. [PMID: 35655129 PMCID: PMC9161562 DOI: 10.1186/s12870-022-03663-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Accepted: 05/27/2022] [Indexed: 05/30/2023]
Abstract
BACKGROUND Abscisic acid (ABA) plays a crucial role in abiotic stress responses. The pyrabactin resistance (PYR)/PYR-like (PYL)/regulatory component of ABA receptor (RCAR) proteins that have been characterized as ABA receptors function as the core components in ABA signaling pathway. However, the functions of grape PYL genes in response to different abiotic stresses, particularly cold stress, remain less studied. RESULTS In this study, we investigated the expression profiles of grape PYL genes upon cold treatment and isolated the VaPYL4 gene from Vitis amurensis, a cold-hardy grape species. Overexpression of VaPYL4 gene in grape calli and Arabidopsis resulted in enhanced cold tolerance. Moreover, plant resistance to drought and salt stress was also improved by overexpressing VaPYL4 in Arabidopsis. More importantly, we evaluated the contribution of VaPYL4 to plant growth and development after the treatment with cold, salt and drought stress simultaneously. The transgenic plants showed higher survival rates, earlier flowering phenotype, and heavier fresh weight of seedlings and siliques when compared with wild-type plants. Physiological analyses showed that transgenic plants had much lower content of malondialdehyde (MDA) and higher peroxidase (POD) activity. Stress-responsive genes such as RD29A (Responsive to desiccation 29A), COR15A (Cold responsive 15A) and KIN2 (Kinase 2) were also significantly up-regulated in VaPYL4-overexpressing Arabidopsis plants. CONCLUSIONS Our results show that overexpression of VaPYL4 could improve plant performance upon different abiotic stresses, which therefore provides a useful strategy for engineering future crops to deal with adverse environments.
Collapse
Affiliation(s)
- Chong Ren
- Beijing Key Laboratory of Grape Sciences and Enology, Key Laboratory of Plant Resource, Institute of Botany, Chinese Academy of Sciences, Nanxin Village 20, Xiangshan, Haidian District, Beijing, 100093 People’s Republic of China
| | - Yangfu Kuang
- Beijing Key Laboratory of Grape Sciences and Enology, Key Laboratory of Plant Resource, Institute of Botany, Chinese Academy of Sciences, Nanxin Village 20, Xiangshan, Haidian District, Beijing, 100093 People’s Republic of China
- University of Chinese Academy of Sciences, Beijing, 100049 People’s Republic of China
| | - Yanping Lin
- Beijing Key Laboratory of Grape Sciences and Enology, Key Laboratory of Plant Resource, Institute of Botany, Chinese Academy of Sciences, Nanxin Village 20, Xiangshan, Haidian District, Beijing, 100093 People’s Republic of China
- University of Chinese Academy of Sciences, Beijing, 100049 People’s Republic of China
| | - Yuchen Guo
- Beijing Key Laboratory of Grape Sciences and Enology, Key Laboratory of Plant Resource, Institute of Botany, Chinese Academy of Sciences, Nanxin Village 20, Xiangshan, Haidian District, Beijing, 100093 People’s Republic of China
- University of Chinese Academy of Sciences, Beijing, 100049 People’s Republic of China
| | - Huayang Li
- Beijing Key Laboratory of Grape Sciences and Enology, Key Laboratory of Plant Resource, Institute of Botany, Chinese Academy of Sciences, Nanxin Village 20, Xiangshan, Haidian District, Beijing, 100093 People’s Republic of China
- University of Chinese Academy of Sciences, Beijing, 100049 People’s Republic of China
| | - Peige Fan
- Beijing Key Laboratory of Grape Sciences and Enology, Key Laboratory of Plant Resource, Institute of Botany, Chinese Academy of Sciences, Nanxin Village 20, Xiangshan, Haidian District, Beijing, 100093 People’s Republic of China
| | - Shaohua Li
- Beijing Key Laboratory of Grape Sciences and Enology, Key Laboratory of Plant Resource, Institute of Botany, Chinese Academy of Sciences, Nanxin Village 20, Xiangshan, Haidian District, Beijing, 100093 People’s Republic of China
| | - Zhenchang Liang
- Beijing Key Laboratory of Grape Sciences and Enology, Key Laboratory of Plant Resource, Institute of Botany, Chinese Academy of Sciences, Nanxin Village 20, Xiangshan, Haidian District, Beijing, 100093 People’s Republic of China
| |
Collapse
|
33
|
Mir TUG, Wani AK, Akhtar N, Shukla S. CRISPR/Cas9: Regulations and challenges for law enforcement to combat its dual-use. Forensic Sci Int 2022; 334:111274. [DOI: 10.1016/j.forsciint.2022.111274] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 02/19/2022] [Accepted: 03/13/2022] [Indexed: 12/15/2022]
|
34
|
Kumari C, Sharma M, Kumar V, Sharma R, Kumar V, Sharma P, Kumar P, Irfan M. Genome Editing Technology for Genetic Amelioration of Fruits and Vegetables for Alleviating Post-Harvest Loss. Bioengineering (Basel) 2022; 9:bioengineering9040176. [PMID: 35447736 PMCID: PMC9028506 DOI: 10.3390/bioengineering9040176] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Revised: 02/02/2022] [Accepted: 04/15/2022] [Indexed: 01/13/2023] Open
Abstract
Food security and crop production are challenged worldwide due to overpopulation, changing environmental conditions, crop establishment failure, and various kinds of post-harvest losses. The demand for high-quality foods with improved nutritional quality is also growing day by day. Therefore, production of high-quality produce and reducing post-harvest losses of produce, particularly of perishable fruits and vegetables, are vital. For many decades, attempts have been made to improve the post-harvest quality traits of horticultural crops. Recently, modern genetic tools such as genome editing emerged as a new approach to manage and overcome post-harvest effectively and efficiently. The different genome editing tools including ZFNs, TALENs, and CRISPR/Cas9 system effectively introduce mutations (In Dels) in many horticultural crops to address and resolve the issues associated with post-harvest storage quality. Henceforth, we provide a broad review of genome editing applications in horticulture crops to improve post-harvest stability traits such as shelf life, texture, and resistance to pathogens without compromising nutritional value. Moreover, major roadblocks, challenges, and their possible solutions for employing genome editing tools are also discussed.
Collapse
Affiliation(s)
- Chanchal Kumari
- Department of Biotechnology, Dr. Yashwant Singh Parmar University of Horticulture and Forestry, Solan, Himachal Pradesh 173230, India; (C.K.); (M.S.); (V.K.); (R.S.); (P.K.)
| | - Megha Sharma
- Department of Biotechnology, Dr. Yashwant Singh Parmar University of Horticulture and Forestry, Solan, Himachal Pradesh 173230, India; (C.K.); (M.S.); (V.K.); (R.S.); (P.K.)
| | - Vinay Kumar
- Department of Biotechnology, Dr. Yashwant Singh Parmar University of Horticulture and Forestry, Solan, Himachal Pradesh 173230, India; (C.K.); (M.S.); (V.K.); (R.S.); (P.K.)
| | - Rajnish Sharma
- Department of Biotechnology, Dr. Yashwant Singh Parmar University of Horticulture and Forestry, Solan, Himachal Pradesh 173230, India; (C.K.); (M.S.); (V.K.); (R.S.); (P.K.)
| | - Vinay Kumar
- Department of Physiology and Cell Biology, Department of Internal Medicine, The Ohio State University Wexner Medical Center, Columbus, OH 43210, USA;
| | - Parul Sharma
- Department of Biotechnology, Dr. Yashwant Singh Parmar University of Horticulture and Forestry, Solan, Himachal Pradesh 173230, India; (C.K.); (M.S.); (V.K.); (R.S.); (P.K.)
- Correspondence: (P.S.); (M.I.)
| | - Pankaj Kumar
- Department of Biotechnology, Dr. Yashwant Singh Parmar University of Horticulture and Forestry, Solan, Himachal Pradesh 173230, India; (C.K.); (M.S.); (V.K.); (R.S.); (P.K.)
| | - Mohammad Irfan
- Plant Biology Section, School of Integrative Plant Sciences, Cornell University, Ithaca, NY 14853, USA
- Correspondence: (P.S.); (M.I.)
| |
Collapse
|
35
|
Naik BJ, Shimoga G, Kim SC, Manjulatha M, Subramanyam Reddy C, Palem RR, Kumar M, Kim SY, Lee SH. CRISPR/Cas9 and Nanotechnology Pertinence in Agricultural Crop Refinement. FRONTIERS IN PLANT SCIENCE 2022; 13:843575. [PMID: 35463432 PMCID: PMC9024397 DOI: 10.3389/fpls.2022.843575] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/26/2021] [Accepted: 02/07/2022] [Indexed: 05/08/2023]
Abstract
The CRISPR/Cas9 (Clustered Regularly Interspaced Short Palindromic Repeats/CRISPR-associated protein 9) method is a versatile technique that can be applied in crop refinement. Currently, the main reasons for declining agricultural yield are global warming, low rainfall, biotic and abiotic stresses, in addition to soil fertility issues caused by the use of harmful chemicals as fertilizers/additives. The declining yields can lead to inadequate supply of nutritional food as per global demand. Grains and horticultural crops including fruits, vegetables, and ornamental plants are crucial in sustaining human life. Genomic editing using CRISPR/Cas9 and nanotechnology has numerous advantages in crop development. Improving crop production using transgenic-free CRISPR/Cas9 technology and produced fertilizers, pesticides, and boosters for plants by adopting nanotechnology-based protocols can essentially overcome the universal food scarcity. This review briefly gives an overview on the potential applications of CRISPR/Cas9 and nanotechnology-based methods in developing the cultivation of major agricultural crops. In addition, the limitations and major challenges of genome editing in grains, vegetables, and fruits have been discussed in detail by emphasizing its applications in crop refinement strategy.
Collapse
Affiliation(s)
- Banavath Jayanna Naik
- Research Institute of Climate Change and Agriculture, National Institute of Horticultural and Herbal Science, Rural Development Administration (RDA), Jeju, South Korea
| | - Ganesh Shimoga
- Interaction Laboratory, Future Convergence Engineering, Advanced Technology Research Center, Korea University of Technology and Education, Cheonan-si, South Korea
| | - Seong-Cheol Kim
- Research Institute of Climate Change and Agriculture, National Institute of Horticultural and Herbal Science, Rural Development Administration (RDA), Jeju, South Korea
| | | | | | | | - Manu Kumar
- Department of Life Science, College of Life Science and Biotechnology, Dongguk University, Seoul, South Korea
| | - Sang-Youn Kim
- Interaction Laboratory, Future Convergence Engineering, Advanced Technology Research Center, Korea University of Technology and Education, Cheonan-si, South Korea
| | - Soo-Hong Lee
- Department of Medical Biotechnology, Dongguk University, Seoul, South Korea
| |
Collapse
|
36
|
Computational tools and resources for CRISPR/Cas genome editing. GENOMICS, PROTEOMICS & BIOINFORMATICS 2022:S1672-0229(22)00027-4. [PMID: 35341983 PMCID: PMC10372911 DOI: 10.1016/j.gpb.2022.02.006] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 02/22/2022] [Accepted: 02/28/2022] [Indexed: 12/21/2022]
Abstract
The past decade has witnessed a rapid evolution in identifying more versatile clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein (Cas) nucleases and their functional variants as well as in developing precise CRISPR/Cas-derived genome editors. The programmable and robust features of the genomic editors provide an effective RNA-guided platform for fundamental life science research and subsequent applications in diverse scenarios, including biomedical innovation and targeted crop improvement. One of the most essential principles is to guide alterations in genomic sequences or genes in the intended manner without undesired off-target impacts, which strongly depends on the efficiency and specificity of single guide RNA (sgRNA)-directed recognition of targeted DNA sequences. Recent advances in empirical scoring algorithms and machine learning models have facilitated sgRNA design and off-target prediction. In this review, we first briefly introduced the different features of CRISPR/Cas tools that should be taken into consideration to achieve specific purposes. Secondly, we focused on the computer-assisted tools and resources that are widely used in designing sgRNAs and analyzing CRISPR/Cas-induced on- and off-target mutations. Thirdly, we provide insights on the limitations of available computational tools that surely help researchers of this field for further optimization. Lastly, we suggested a simple but effective workflow for choosing and applying web-based resources and tools for CRISPR/Cas genome editing.
Collapse
|
37
|
Nagamine A, Ezura H. Genome Editing for Improving Crop Nutrition. Front Genome Ed 2022; 4:850104. [PMID: 35224538 PMCID: PMC8864126 DOI: 10.3389/fgeed.2022.850104] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Accepted: 01/24/2022] [Indexed: 11/22/2022] Open
Abstract
Genome editing technologies, including CRISPR/Cas9 and TALEN, are excellent genetic modification techniques and are being proven to be powerful tools not only in the field of basic science but also in the field of crop breeding. Recently, two genome-edited crops targeted for nutritional improvement, high GABA tomatoes and high oleic acid soybeans, have been released to the market. Nutritional improvement in cultivated crops has been a major target of conventional genetic modification technologies as well as classical breeding methods. Mutations created by genome editing are considered to be almost identical to spontaneous genetic mutations because the mutation inducer, the transformed foreign gene, can be completely eliminated from the final genome-edited hosts after causing the mutation. Therefore, genome-edited crops are expected to be relatively easy to supply to the market, unlike GMO crops. On the other hand, due to their technical feature, the main goal of current genome-edited crop creation is often the total or partial disruption of genes rather than gene delivery. Therefore, to obtain the desired trait using genome editing technology, in some cases, a different approach from that of genetic recombination technology may be required. In this mini-review, we will review several nutritional traits in crops that have been considered suitable targets for genome editing, including the two examples mentioned above, and discuss how genome editing technology can be an effective breeding technology for improving nutritional traits in crops.
Collapse
Affiliation(s)
- Ai Nagamine
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan
| | - Hiroshi Ezura
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan
- Tsukuba Plant Innovation Research Center, University of Tsukuba, Tsukuba, Japan
- *Correspondence: Hiroshi Ezura,
| |
Collapse
|
38
|
Nguyen TM, Lu CA, Huang LF. Applications of CRISPR/Cas9 in a rice protein expression system via an intron-targeted insertion approach. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2022; 315:111132. [PMID: 35067302 DOI: 10.1016/j.plantsci.2021.111132] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 10/28/2021] [Accepted: 11/23/2021] [Indexed: 06/14/2023]
Abstract
The sugar starvation-inducible rice αAmy3 promoter and signal peptide are widely used to produce valuable recombinant proteins in rice suspension culture cells. Conventionally, the recombinant gene expression cassette is inserted into the genome at random locations by Agrobacterium- or particle bombardment-mediated transformation. CRISPR/Cas9 gene editing enables gene insertion at a precise target site in the genome. In this study the CRISPR/Cas9 approach was modified for intron-targeted insertion by adding an artificial 3' splicing site upstream of the recombinant gene. Knock-in transgenic rice cell lines containing the recombinant GFP gene inserted in intron 1 of αAmy3 were generated. The endogenous αAmy3 promoter regulated recombinant gene expression and the αAmy3 signal peptide directed secretion of the recombinant GFP protein into the culture medium. In addition, the recombinant GFP protein was localized in amyloplasts, identical to the subcellular localization of endogenous αAmy3 reported previously. This modified CRISPR/Cas9 knock-in approach is simple and highly efficient, and the recombinant gene insertion frequency attained 12.5%. The approach can be applied in the production of pharmaceutical proteins in rice suspension cell cultures. The high efficiency of the GFP reporter gene knock-in method and the maintenance of target gene behavior also make the strategy applicable to endogenous gene functional studies in rice.
Collapse
Affiliation(s)
- Thi Mai Nguyen
- Graduate School of Biotechnology and Bioengineering, Yuan Ze University, Taoyuan City 320, Taiwan, ROC; Department of Life Sciences, National Central University, Taoyuan City 320, Taiwan, ROC
| | - Chung-An Lu
- Department of Life Sciences, National Central University, Taoyuan City 320, Taiwan, ROC.
| | - Li-Fen Huang
- Graduate School of Biotechnology and Bioengineering, Yuan Ze University, Taoyuan City 320, Taiwan, ROC.
| |
Collapse
|
39
|
Yan Y, Zhu X, Yu Y, Li C, Zhang Z, Wang F. Nanotechnology Strategies for Plant Genetic Engineering. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2022; 34:e2106945. [PMID: 34699644 DOI: 10.1002/adma.202106945] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Revised: 10/21/2021] [Indexed: 06/13/2023]
Abstract
Plant genetic engineering is essential for improving crop yield, quality, and resistance to abiotic/biotic stresses for sustainable agriculture. Agrobacterium-, biolistic bombardment-, electroporation-, and poly(ethylene glycol) (PEG)-mediated genetic-transformation systems are extensively used in plant genetic engineering. However, these systems have limitations, including species dependency, destruction of plant tissues, low transformation efficiency, and high cost. Recently, nanotechnology-based gene-delivery methods have been developed for plant genetic transformation. This nanostrategy shows excellent transformation efficiency, good biocompatibility, adequate protection of exogenous nucleic acids, and the potential for plant regeneration. However, the nanomaterial-mediated gene-delivery system in plants is still in its infancy, and there are many challenges for its broad applications. Herein, the conventional genetic transformation techniques used in plants are briefly discussed. After that, the progress in the development of nanomaterial-based gene-delivery systems is considered. CRISPR-Cas-mediated genome editing and its combined applications with plant nanotechnology are also discussed. The conceptual innovations, methods, and practical applications of nanomaterial-mediated genetic transformation summarized herein will be beneficial for promoting plant genetic engineering in modern agriculture.
Collapse
Affiliation(s)
- Yong Yan
- School of Food and Biological Engineering, Hefei University of Technology, Hefei, Anhui, 230009, P. R. China
| | - Xiaojun Zhu
- School of Food and Biological Engineering, Hefei University of Technology, Hefei, Anhui, 230009, P. R. China
| | - Yue Yu
- School of Food and Biological Engineering, Hefei University of Technology, Hefei, Anhui, 230009, P. R. China
| | - Chao Li
- School of Food and Biological Engineering, Hefei University of Technology, Hefei, Anhui, 230009, P. R. China
| | - Zhaoliang Zhang
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, 130 Changjiang West Road, Hefei, Anhui, 230036, P. R. China
| | - Feng Wang
- School of Food and Biological Engineering, Hefei University of Technology, Hefei, Anhui, 230009, P. R. China
| |
Collapse
|
40
|
Dal Santo S, De Paoli E, Pagliarani C, Amato A, Celii M, Boccacci P, Zenoni S, Gambino G, Perrone I. Stress responses and epigenomic instability mark the loss of somatic embryogenesis competence in grapevine. PLANT PHYSIOLOGY 2022; 188:490-508. [PMID: 34726761 PMCID: PMC8774814 DOI: 10.1093/plphys/kiab477] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Accepted: 09/17/2021] [Indexed: 06/13/2023]
Abstract
Somatic embryogenesis (SE) represents the most appropriate tool for next-generation breeding methods in woody plants such as grapevine (Vitis vinifera L.). However, in this species, the SE competence is strongly genotype-dependent and the molecular basis of this phenomenon is poorly understood. We explored the genetic and epigenetic basis of SE in grapevine by profiling the transcriptome, epigenome, and small RNAome of undifferentiated, embryogenic, and non-embryogenic callus tissues derived from two genotypes differing in competence for SE, Sangiovese and Cabernet Sauvignon. During the successful formation of embryonic callus, we observed the upregulation of epigenetic-related transcripts and short interfering RNAs in association with DNA hypermethylation at transposable elements in both varieties. Nevertheless, the switch to nonembryonic development matched the incomplete reinforcement of transposon silencing, and the evidence of such effect was more apparent in the recalcitrant Cabernet Sauvignon. Transcriptomic differences between the two genotypes were maximized already at early stage of culture where the recalcitrant variety expressed a broad panel of genes related to stress responses and secondary metabolism. Our data provide a different angle on the SE molecular dynamics that can be exploited to leverage SE as a biotechnological tool for fruit crop breeding.
Collapse
Affiliation(s)
- Silvia Dal Santo
- Department of Biotechnology, University of Verona, Verona 37134, Italy
| | - Emanuele De Paoli
- Department of Agri-Food, Environmental and Animal Sciences, University of Udine, Udine 33100, Italy
| | - Chiara Pagliarani
- Institute for Sustainable Plant Protection, National Research Council (IPSP-CNR), Torino 10135, Italy
| | - Alessandra Amato
- Department of Biotechnology, University of Verona, Verona 37134, Italy
| | - Mirko Celii
- Department of Agri-Food, Environmental and Animal Sciences, University of Udine, Udine 33100, Italy
| | - Paolo Boccacci
- Institute for Sustainable Plant Protection, National Research Council (IPSP-CNR), Torino 10135, Italy
| | - Sara Zenoni
- Department of Biotechnology, University of Verona, Verona 37134, Italy
| | - Giorgio Gambino
- Institute for Sustainable Plant Protection, National Research Council (IPSP-CNR), Torino 10135, Italy
| | - Irene Perrone
- Institute for Sustainable Plant Protection, National Research Council (IPSP-CNR), Torino 10135, Italy
| |
Collapse
|
41
|
Ren C, Li H, Liu Y, Li S, Liang Z. Highly efficient activation of endogenous gene in grape using CRISPR/dCas9-based transcriptional activators. HORTICULTURE RESEARCH 2022; 9:uhab037. [PMID: 35039855 PMCID: PMC8807946 DOI: 10.1093/hr/uhab037] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Revised: 01/18/2022] [Accepted: 10/15/2021] [Indexed: 06/14/2023]
Abstract
Overexpression and knockout (or knockdown) of gene of interest are two commonly used strategies for gene functional study. Clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 system-mediated gene knockout had been applied in most plant species, including grapevine. However, CRISPR/dCas9 (deactivated Cas9)-based transcriptional activation is still unreported in fruit crops, although a few studies had been documented in Arabidopsis and rice. Here, we tested two transcriptional activators VP64 and TV for transcriptional activation of endogenous genes in grape. Both the dCas9-VP64 and dCas9-TV systems are efficient enough for transcriptional activation of the UDP-glucose flavonoid glycosyltransferases (UFGT) gene in grape cells. The effectiveness of the dCas9-VP64 system in UFGT activation was about 1.6- to 5.6-fold, while the efficiency of the dCas9-TV system was around 5.7- to 7.2-fold. Moreover, in grapevine plants, highly efficient activation of the cold-responsive transcription factor gene CBF4 was achieved by using the dCas9-TV system. The expression of CBF4 was increased 3.7- to 42.3-fold in transgenic plants. Compared with the wild-type plants, the CBF4-activated plants exhibited lower electrolyte leakage after cold treatment. Our results demonstrate the effectiveness of the dCas9-VP64 and dCas9-TV system in gene activation in grape, which will facilitate application of transcriptional activation in this economically important species.
Collapse
Affiliation(s)
- Chong Ren
- Beijing Key Laboratory of Grape Sciences and Enology, Key Laboratory of Plant Resource, Institute of Botany, Chinese Academy of Sciences, 20 Nanxincun, Xiangshan, Beijing 100093, China
| | - Huayang Li
- Beijing Key Laboratory of Grape Sciences and Enology, Key Laboratory of Plant Resource, Institute of Botany, Chinese Academy of Sciences, 20 Nanxincun, Xiangshan, Beijing 100093, China
- University of Chinese Academy of Sciences,
19 Yuquan Rd, Beijing 100049, China
| | - Yanfei Liu
- Beijing Key Laboratory of Grape Sciences and Enology, Key Laboratory of Plant Resource, Institute of Botany, Chinese Academy of Sciences, 20 Nanxincun, Xiangshan, Beijing 100093, China
- University of Chinese Academy of Sciences,
19 Yuquan Rd, Beijing 100049, China
| | - Shaohua Li
- Beijing Key Laboratory of Grape Sciences and Enology, Key Laboratory of Plant Resource, Institute of Botany, Chinese Academy of Sciences, 20 Nanxincun, Xiangshan, Beijing 100093, China
| | - Zhenchang Liang
- Beijing Key Laboratory of Grape Sciences and Enology, Key Laboratory of Plant Resource, Institute of Botany, Chinese Academy of Sciences, 20 Nanxincun, Xiangshan, Beijing 100093, China
| |
Collapse
|
42
|
Zhang S, Wu S, Hu C, Yang Q, Dong T, Sheng O, Deng G, He W, Dou T, Li C, Sun C, Yi G, Bi F. Increased mutation efficiency of CRISPR/Cas9 genome editing in banana by optimized construct. PeerJ 2022; 10:e12664. [PMID: 35036088 PMCID: PMC8742547 DOI: 10.7717/peerj.12664] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 11/30/2021] [Indexed: 01/07/2023] Open
Abstract
The CRISPR/Cas9-mediated genome editing system has been used extensively to engineer targeted mutations in a wide variety of species. Its application in banana, however, has been hindered because of the species' triploid nature and low genome editing efficiency. This has delayed the development of a DNA-free genome editing approach. In this study, we reported that the endogenous U6 promoter and banana codon-optimized Cas9 apparently increased mutation frequency in banana, and we generated a method to validate the mutation efficiency of the CRISPR/Cas9-mediated genome editing system based on transient expression in protoplasts. The activity of the MaU6c promoter was approximately four times higher than that of the OsU6a promoter in banana protoplasts. The application of this promoter and banana codon-optimized Cas9 in CRISPR/Cas9 cassette resulted in a fourfold increase in mutation efficiency compared with the previous CRISPR/Cas9 cassette for banana. Our results indicated that the optimized CRISPR/Cas9 system was effective for mutating targeted genes in banana and thus will improve the applications for basic functional genomics. These findings are relevant to future germplasm improvement and provide a foundation for developing DNA-free genome editing technology in banana.
Collapse
Affiliation(s)
- Sen Zhang
- Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization (Ministry of Agriculture and Rural Affairs), Guangdong Key Laboratory of Tropical and Subtropical Fruit Tree Research, Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong, China,College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Shaoping Wu
- Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization (Ministry of Agriculture and Rural Affairs), Guangdong Key Laboratory of Tropical and Subtropical Fruit Tree Research, Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong, China,College of Life Sciences, Zhaoqing University, Zhaoqing, Guangdong, China
| | - Chunhua Hu
- Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization (Ministry of Agriculture and Rural Affairs), Guangdong Key Laboratory of Tropical and Subtropical Fruit Tree Research, Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong, China
| | - Qiaosong Yang
- Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization (Ministry of Agriculture and Rural Affairs), Guangdong Key Laboratory of Tropical and Subtropical Fruit Tree Research, Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong, China
| | - Tao Dong
- Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization (Ministry of Agriculture and Rural Affairs), Guangdong Key Laboratory of Tropical and Subtropical Fruit Tree Research, Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong, China
| | - Ou Sheng
- Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization (Ministry of Agriculture and Rural Affairs), Guangdong Key Laboratory of Tropical and Subtropical Fruit Tree Research, Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong, China
| | - Guiming Deng
- Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization (Ministry of Agriculture and Rural Affairs), Guangdong Key Laboratory of Tropical and Subtropical Fruit Tree Research, Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong, China
| | - Weidi He
- Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization (Ministry of Agriculture and Rural Affairs), Guangdong Key Laboratory of Tropical and Subtropical Fruit Tree Research, Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong, China
| | - Tongxin Dou
- Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization (Ministry of Agriculture and Rural Affairs), Guangdong Key Laboratory of Tropical and Subtropical Fruit Tree Research, Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong, China
| | - Chunyu Li
- Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization (Ministry of Agriculture and Rural Affairs), Guangdong Key Laboratory of Tropical and Subtropical Fruit Tree Research, Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong, China
| | - Chenkang Sun
- Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization (Ministry of Agriculture and Rural Affairs), Guangdong Key Laboratory of Tropical and Subtropical Fruit Tree Research, Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong, China,College of Life Sciences, South China Agricultural University, Guangzhou, Guangdong
| | - Ganjun Yi
- Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization (Ministry of Agriculture and Rural Affairs), Guangdong Key Laboratory of Tropical and Subtropical Fruit Tree Research, Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong, China
| | - Fangcheng Bi
- Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization (Ministry of Agriculture and Rural Affairs), Guangdong Key Laboratory of Tropical and Subtropical Fruit Tree Research, Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong, China
| |
Collapse
|
43
|
Sharma SK, Gupta OP, Pathaw N, Sharma D, Maibam A, Sharma P, Sanasam J, Karkute SG, Kumar S, Bhattacharjee B. CRISPR-Cas-Led Revolution in Diagnosis and Management of Emerging Plant Viruses: New Avenues Toward Food and Nutritional Security. Front Nutr 2022; 8:751512. [PMID: 34977113 PMCID: PMC8716883 DOI: 10.3389/fnut.2021.751512] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2021] [Accepted: 10/31/2021] [Indexed: 12/14/2022] Open
Abstract
Plant viruses pose a serious threat to agricultural production systems worldwide. The world's population is expected to reach the 10-billion mark by 2057. Under the scenario of declining cultivable land and challenges posed by rapidly emerging and re-emerging plant pathogens, conventional strategies could not accomplish the target of keeping pace with increasing global food demand. Gene-editing techniques have recently come up as promising options to enable precise changes in genomes with greater efficiency to achieve the target of higher crop productivity. Of genome engineering tools, clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated (Cas) proteins have gained much popularity, owing to their simplicity, reproducibility, and applicability in a wide range of species. Also, the application of different Cas proteins, such as Cas12a, Cas13a, and Cas9 nucleases, has enabled the development of more robust strategies for the engineering of antiviral mechanisms in many plant species. Recent studies have revealed the use of various CRISPR-Cas systems to either directly target a viral gene or modify a host genome to develop viral resistance in plants. This review provides a comprehensive record of the use of the CRISPR-Cas system in the development of antiviral resistance in plants and discusses its applications in the overall enhancement of productivity and nutritional landscape of cultivated plant species. Furthermore, the utility of this technique for the detection of various plant viruses could enable affordable and precise in-field or on-site detection. The futuristic potential of CRISPR-Cas technologies and possible challenges with their use and application are highlighted. Finally, the future of CRISPR-Cas in sustainable management of viral diseases, and its practical utility and regulatory guidelines in different parts of the globe are discussed systematically.
Collapse
Affiliation(s)
| | - Om Prakash Gupta
- Division of Quality & Basic Science, ICAR-Indian Institute of Wheat and Barley Research, Karnal, India
| | - Neeta Pathaw
- ICAR Research Complex for NEH Region, Manipur Centre, Imphal, India
| | - Devender Sharma
- Crop Improvement Division, ICAR-Vivekananda Parvatiya Krishi Anusandhan Sansthan, Almora, India
| | - Albert Maibam
- ICAR Research Complex for NEH Region, Manipur Centre, Imphal, India
| | - Parul Sharma
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, India
| | - Jyotsana Sanasam
- ICAR Research Complex for NEH Region, Manipur Centre, Imphal, India
| | - Suhas Gorakh Karkute
- Division of Crop Improvement, ICAR-Indian Institute of Vegetable Research, Varanasi, India
| | - Sandeep Kumar
- Department of Plant Pathology, Odisha University of Agriculture & Technology, Bhubaneswar, India
| | | |
Collapse
|
44
|
Scintilla S, Salvagnin U, Giacomelli L, Zeilmaker T, Malnoy MA, Rouppe van der Voort J, Moser C. Regeneration of non-chimeric plants from DNA-free edited grapevine protoplasts. FRONTIERS IN PLANT SCIENCE 2022; 13:1078931. [PMID: 36531381 DOI: 10.1101/2021.07.16.452503] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Accepted: 11/16/2022] [Indexed: 05/20/2023]
Abstract
The application of New Breeding Techniques (NBTs) in Vitis vinifera is highly desirable to introduce valuable traits while preserving the genotype of the elite cultivars. However, a broad application of NBTs through standard DNA-based transformation is poorly accepted by public opinion and law regulations in Europe and other countries due to the stable integration of exogenous DNA, which leads to transgenic plants possibly affected by chimerism. A single-cell based approach, coupled with a DNA-free transfection of the CRISPR/Cas editing machinery, constitutes a powerful tool to overcome these problems and maintain the original genetic make-up in the whole organism. We here describe a successful single-cell based, DNA-free methodology to obtain edited grapevine plants, regenerated from protoplasts isolated from embryogenic callus of two table grapevine varieties (V. vinifera cv. Crimson seedless and Sugraone). The regenerated, non-chimeric plants were edited on the downy- and powdery-mildew susceptibility genes, VviDMR6 and VviMlo6 respectively, either as single or double mutants.
Collapse
Affiliation(s)
- Simone Scintilla
- Centro Ricerca ed Innovazione, Fondazione E. Mach. Via E. Mach 1, San Michele all'Adige, Trento, Italy
| | - Umberto Salvagnin
- Centro Ricerca ed Innovazione, Fondazione E. Mach. Via E. Mach 1, San Michele all'Adige, Trento, Italy
- Consorzio Innovazione Vite (CIVIT), Trento, TN, Italy
| | - Lisa Giacomelli
- Centro Ricerca ed Innovazione, Fondazione E. Mach. Via E. Mach 1, San Michele all'Adige, Trento, Italy
- Scienza Biotechnologies BV., Enkhuizen, Netherlands
| | | | - Mickael A Malnoy
- Centro Ricerca ed Innovazione, Fondazione E. Mach. Via E. Mach 1, San Michele all'Adige, Trento, Italy
| | | | - Claudio Moser
- Centro Ricerca ed Innovazione, Fondazione E. Mach. Via E. Mach 1, San Michele all'Adige, Trento, Italy
| |
Collapse
|
45
|
Zlenko V, Kosyuk M, Pavlova I, Luschay E, Abdurashitova A. Features of somatic embryogenesis in the culture in vitro in hybrid grape form E-342. BIO WEB OF CONFERENCES 2022. [DOI: 10.1051/bioconf/20225302004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Correlation analysis of the influence of media variants with introducing various biologically active substances on the development of somatic embryoids and germinating seedlings in the hybrid form E-342 was carried out during two repeated subculturings on the same variant of media, and during the third subculturing - on different variants of media. The repeated subculturing in media with the same growth regulator BAP or IAA caused the development of abnormal large somatic embryoids without the expressed hypocotyls and cotyledons. Only the use of medium variant with DLPA in two subculturings (the third subculturing into the medium with BAP or IAA) and the third repeated subculturing with DLPA, but to a smaller extent, have led to the development of torpedo-shaped embryoids, to be growing into germinating seedlings. Strong positive correlation dependence of influence was established for: BAP on the development of heart-shaped embryoids; IAA on the increase in the size of globular embryoids and transformation of heart-shaped embryoids into torpedo-shaped ones; DLPA on the development of a great number of normal torpedo-shaped embryoids. After longstanding culturing of suspensions of cells and embryoids, it was not possible to get rid of chlorophyll deficiency in the resulting germinating seedlings due to somaclonal variability.
Collapse
|
46
|
Movahedi A, Hajiahmadi Z, Wei H, Yang L, Ruan H, Zhuge Q. A Method to Reduce off-Targets in CRISPR/Cas9 System in Plants. Methods Mol Biol 2022; 2408:317-324. [PMID: 35325432 DOI: 10.1007/978-1-0716-1875-2_21] [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] [Indexed: 06/14/2023]
Abstract
One of the strategies to reduce the off-target mutations in CRISPR/Cas9 system is to use the temperature-independent gene transformation method. Mesoporous silica nanoparticles (MSNs)-gene delivery system is temperature-independent; thus, it can transfer the interesting plasmid (pDNA) to the target plant at different temperatures, including 37 °C. Due to the high activity of SpCas9 at 37 °C compared to lower temperatures, on-target mutagenesis increases at 37 °C. Therefore, we describe the synthesis of the functionalized MSNs with the particle size of less than 40 nm, binding pDNA to the MSNs, and transferring of the pDNA-MSNs into the target plants.
Collapse
Affiliation(s)
- Ali Movahedi
- Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of Forest Genetics & Biotechnology, Ministry of Education, Nanjing Forestry University, Nanjing, China.
| | - Zahra Hajiahmadi
- Department of Biotechnology, Faculty of Agricultural Sciences, University of Guilan, Rasht, Iran
| | - Hui Wei
- Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of Forest Genetics & Biotechnology, Ministry of Education, Nanjing Forestry University, Nanjing, China
| | - Liming Yang
- Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of Forest Genetics & Biotechnology, Ministry of Education, Nanjing Forestry University, Nanjing, China
| | - Honghua Ruan
- Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of Forest Genetics & Biotechnology, Ministry of Education, Nanjing Forestry University, Nanjing, China
| | - Qiang Zhuge
- Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of Forest Genetics & Biotechnology, Ministry of Education, Nanjing Forestry University, Nanjing, China
| |
Collapse
|
47
|
Olivares F, Loyola R, Olmedo B, Miccono MDLÁ, Aguirre C, Vergara R, Riquelme D, Madrid G, Plantat P, Mora R, Espinoza D, Prieto H. CRISPR/Cas9 Targeted Editing of Genes Associated With Fungal Susceptibility in Vitis vinifera L. cv. Thompson Seedless Using Geminivirus-Derived Replicons. FRONTIERS IN PLANT SCIENCE 2021; 12:791030. [PMID: 35003180 PMCID: PMC8733719 DOI: 10.3389/fpls.2021.791030] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Accepted: 11/29/2021] [Indexed: 05/14/2023]
Abstract
The woody nature of grapevine (Vitis vinifera L.) has hindered the development of efficient gene editing strategies to improve this species. The lack of highly efficient gene transfer techniques, which, furthermore, are applied in multicellular explants such as somatic embryos, are additional technical handicaps to gene editing in the vine. The inclusion of geminivirus-based replicons in regular T-DNA vectors can enhance the expression of clustered regularly interspaced short palindromic repeats/CRISPR-associated protein 9 (CRISPR/Cas9) elements, thus enabling the use of these multicellular explants as starting materials. In this study, we used Bean yellow dwarf virus (BeYDV)-derived replicon vectors to express the key components of CRISPR/Cas9 system in vivo and evaluate their editing capability in individuals derived from Agrobacterium-mediated gene transfer experiments of 'Thompson Seedless' somatic embryos. Preliminary assays using a BeYDV-derived vector for green fluorescent protein reporter gene expression demonstrated marker visualization in embryos for up to 33 days post-infiltration. A universal BeYDV-based vector (pGMV-U) was assembled to produce all CRISPR/Cas9 components with up to four independent guide RNA (gRNA) expression cassettes. With a focus on fungal tolerance, we used gRNA pairs to address considerably large deletions of putative grape susceptibility genes, including AUXIN INDUCED IN ROOT CULTURE 12 (VviAIR12), SUGARS WILL EVENTUALLY BE EXPORTED TRANSPORTER 4 (VviSWEET4), LESION INITIATION 2 (VviLIN2), and DIMERIZATION PARTNER-E2F-LIKE 1 (VviDEL1). The editing functionality of gRNA pairs in pGMV-U was evaluated by grapevine leaf agroinfiltration assays, thus enabling longer-term embryo transformations. These experiments allowed for the establishment of greenhouse individuals exhibiting a double-cut edited status for all targeted genes under different allele-editing conditions. After approximately 18 months, the edited grapevine plants were preliminary evaluated regarding its resistance to Erysiphe necator and Botrytis cinerea. Assays have shown that a transgene-free VviDEL1 double-cut edited line exhibits over 90% reduction in symptoms triggered by powdery mildew infection. These results point to the use of geminivirus-based replicons for gene editing in grapevine and other relevant fruit species.
Collapse
Affiliation(s)
- Felipe Olivares
- Biotechnology Laboratory, La Platina Research Station, National Institute of Agriculture Research, Santiago, Chile
| | - Rodrigo Loyola
- Biotechnology Laboratory, La Platina Research Station, National Institute of Agriculture Research, Santiago, Chile
| | - Blanca Olmedo
- Biotechnology Laboratory, La Platina Research Station, National Institute of Agriculture Research, Santiago, Chile
| | - María de los Ángeles Miccono
- Biotechnology Laboratory, La Platina Research Station, National Institute of Agriculture Research, Santiago, Chile
| | - Carlos Aguirre
- Biotechnology Laboratory, La Platina Research Station, National Institute of Agriculture Research, Santiago, Chile
| | - Ricardo Vergara
- Biotechnology Laboratory, La Platina Research Station, National Institute of Agriculture Research, Santiago, Chile
| | - Danae Riquelme
- Phytopathology Laboratory, La Platina Research Station, National Institute of Agriculture Research, Santiago, Chile
| | - Gabriela Madrid
- Biotechnology Laboratory, La Platina Research Station, National Institute of Agriculture Research, Santiago, Chile
| | - Philippe Plantat
- Biotechnology Laboratory, La Platina Research Station, National Institute of Agriculture Research, Santiago, Chile
| | - Roxana Mora
- Biotechnology Laboratory, La Platina Research Station, National Institute of Agriculture Research, Santiago, Chile
| | - Daniel Espinoza
- Biotechnology Laboratory, La Platina Research Station, National Institute of Agriculture Research, Santiago, Chile
| | - Humberto Prieto
- Biotechnology Laboratory, La Platina Research Station, National Institute of Agriculture Research, Santiago, Chile
| |
Collapse
|
48
|
Wang T, Zhang C, Zhang H, Zhu H. CRISPR/Cas9-Mediated Gene Editing Revolutionizes the Improvement of Horticulture Food Crops. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:13260-13269. [PMID: 33734711 DOI: 10.1021/acs.jafc.1c00104] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Horticultural food crops are important sources of nutrients for humans. With the increase of the global population, enhanced horticulture food crop production has become a new challenge, and enriching their nutritional content has also been required. Gene editing systems, such as zinc finger nucleases, transcription activator-like effector nucleases, and clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated 9 (Cas9), have accelerated crop improvement through the modification of targeted genomes precisely. Here, we review the development of various gene editors and compare their advantages and shortcomings, especially the newly emerging CRISPR/Cas systems, such as base editing and prime editing. We also summarize their practical applications in crop trait improvement, including yield, nutritional quality, and other consumer traits.
Collapse
Affiliation(s)
- Tian Wang
- College of Life Science, Shandong Normal University, Jinan, Shandong 250014, People's Republic of China
| | - Chunjiao Zhang
- Supervision, Inspection & Testing Center of Agricultural Products Quality, Ministry of Agriculture and Rural Affairs, Beijing 100083, People's Republic of China
| | - Hongyan Zhang
- College of Life Science, Shandong Normal University, Jinan, Shandong 250014, People's Republic of China
| | - Hongliang Zhu
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, People's Republic of China
| |
Collapse
|
49
|
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: 11] [Impact Index Per Article: 3.7] [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.
Collapse
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;
| |
Collapse
|
50
|
Savadi S, Mangalassery S, Sandesh MS. Advances in genomics and genome editing for breeding next generation of fruit and nut crops. Genomics 2021; 113:3718-3734. [PMID: 34517092 DOI: 10.1016/j.ygeno.2021.09.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Revised: 08/21/2021] [Accepted: 09/02/2021] [Indexed: 12/18/2022]
Abstract
Fruit tree crops are an essential part of the food production systems and are key to achieve food and nutrition security. Genetic improvement of fruit trees by conventional breeding has been slow due to the long juvenile phase. Advancements in genomics and molecular biology have paved the way for devising novel genetic improvement tools like genome editing, which can accelerate the breeding of these perennial crops to a great extent. In this article, advancements in genomics of fruit trees covering genome sequencing, transcriptome sequencing, genome editing technologies (GET), CRISPR-Cas system based genome editing, potential applications of CRISPR-Cas9 in fruit tree crops improvement, the factors influencing the CRISPR-Cas editing efficiency and the challenges for CRISPR-Cas9 applications in fruit tree crops improvement are reviewed. Besides, base editing, a recently emerging more precise editing system, and the future perspectives of genome editing in the improvement of fruit and nut crops are covered.
Collapse
Affiliation(s)
- Siddanna Savadi
- ICAR- Directorate of Cashew Research (DCR), Puttur 574 202, Dakshina Kannada, Karnataka, India.
| | | | - M S Sandesh
- ICAR- Directorate of Cashew Research (DCR), Puttur 574 202, Dakshina Kannada, Karnataka, India
| |
Collapse
|