1
|
Manchanda P, Sharma D, Kaur G, Kaur H, Vanshika. Exploring the Significance of Somaclonal Variations in Horticultural Crops. Mol Biotechnol 2024:10.1007/s12033-024-01214-6. [PMID: 38896180 DOI: 10.1007/s12033-024-01214-6] [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: 04/17/2024] [Accepted: 06/02/2024] [Indexed: 06/21/2024]
Abstract
Genetic and epigenetic variations produced via cell and tissue culture open up new sources of variability intra-species which can be used to improve crops. The use of in vitro generated somaclonal variations for selecting novel variants aids in the development of novel genotypes having desirable agronomic traits that can be released as varieties or utilized for breeding purposes. Horticultural crops give higher yield and productivity per unit area than other crops, as well as provide good economic returns which have led to an increase in their potential benefits throughout time. The last three to four decades have seen the selection and release of a number of valuable somaclonal variants, many of which possess remarkable features including disease resistance, high yield, improved nutritional quality and abiotic stress tolerance. Generating somaclonal variations has given breeders a novel alternative option for obtaining genetic diversity in horticultural crops and without advanced technologies. The variations introduced through tissue culture process, methods to determine and validate genetic changes in vitro regenerated plantlets, along with prospective application of such variations in horticultural crops' improvement are reviewed in the present work.
Collapse
Affiliation(s)
- Pooja Manchanda
- School of Agricultural Biotechnology, College of Agriculture, Punjab Agricultural University, Ludhiana, 141004, India.
| | - Deepansh Sharma
- Department of Plant Pathology, College of Agriculture, Punjab Agricultural University, Ludhiana, 141004, India
| | - Gurpreet Kaur
- School of Agricultural Biotechnology, College of Agriculture, Punjab Agricultural University, Ludhiana, 141004, India
| | - Harleen Kaur
- School of Agricultural Biotechnology, College of Agriculture, Punjab Agricultural University, Ludhiana, 141004, India
| | - Vanshika
- School of Agricultural Biotechnology, College of Agriculture, Punjab Agricultural University, Ludhiana, 141004, India
| |
Collapse
|
2
|
Yan X, Zheng K, Li P, Zhong X, Zhu Z, Zhou H, Zhu M. An efficient in vitro organogenesis protocol for the endangered relic tree species Bretschneidera sinensis and genetic fidelity assessment using DNA markers. FRONTIERS IN PLANT SCIENCE 2024; 15:1259925. [PMID: 38660444 PMCID: PMC11039884 DOI: 10.3389/fpls.2024.1259925] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Accepted: 03/14/2024] [Indexed: 04/26/2024]
Abstract
Bretschneidera sinensis is a monotypic species of rare and tertiary relic trees mainly distributed in China. B. sinensis is a potentially valuable horticultural plant, which has significant ornamental and research value, and is a crucial tool for the study of phylogeography. The artificial cultivation of B. sinensis is of great scientific value and practical significance. In this study, we developed a direct organogenesis process of B. sinensis using mature zygotic embryos as initial materials. The highest sterile germination induction (54.5%) from the mature zygotic embryo was obtained in a Murashige and Skoog (MS) medium with 2.0 mg·L-1 6-benzylaminopurine (6-BA) and 0.2 mg·L-1 α-naphthaleneacetic acid (NAA). The highest percentage of shoot regeneration (90.37%) was attained using 1.0 mg·L-1 6-BA and 0.01 mg·L-1 NAA in the MS medium. The Woody Plant Medium (WPM) had the greatest adventitious shoot elongation rate of 93.33%. The most optimized rooting rate was 88.89% in a half-strength MS medium containing 2.0 mg·L-1 indole-3-butyric acid (IBA) and 1.0 mg·L-1 NAA. The genetic fidelity of in vitro regenerated plantlets was assessed using inter-simple sequence repeats and random amplified polymorphic DNA molecular markers, confirming the genetic uniformity and stability of regenerated B. sinensis plantlets. Our research presents an effective in vitro propagation system for B. sinensis, laying the groundwork for its germplasm conservation and large-scale production while maintaining high genetic integrity.
Collapse
Affiliation(s)
- Xuetong Yan
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Shanghai, China
- National Key Laboratory of Plant Molecular Genetics (NKLPMG), Chinese Academy of Sciences (CAS) Center for Excellence in Molecular Plant Sciences, Shanghai, China
| | - Keyuan Zheng
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Shanghai, China
- National Key Laboratory of Plant Molecular Genetics (NKLPMG), Chinese Academy of Sciences (CAS) Center for Excellence in Molecular Plant Sciences, Shanghai, China
| | - Peng Li
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Shanghai, China
| | - Xin Zhong
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Shanghai, China
| | - Zongwei Zhu
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Shanghai, China
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Huijing Zhou
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Shanghai, China
| | - Mulan Zhu
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Shanghai, China
- National Key Laboratory of Plant Molecular Genetics (NKLPMG), Chinese Academy of Sciences (CAS) Center for Excellence in Molecular Plant Sciences, Shanghai, China
| |
Collapse
|
3
|
Iiyama CM, Vilcherrez-Atoche JA, Germanà MA, Vendrame WA, Cardoso JC. Breeding of ornamental orchids with focus on Phalaenopsis: current approaches, tools, and challenges for this century. Heredity (Edinb) 2024; 132:163-178. [PMID: 38302667 PMCID: PMC10997592 DOI: 10.1038/s41437-024-00671-8] [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: 07/12/2022] [Revised: 01/09/2024] [Accepted: 01/11/2024] [Indexed: 02/03/2024] Open
Abstract
Ornamental orchid breeding programs have been conducted to develop commercially valuable cultivars with improved characteristics of commercial interest, such as size, flower color, pattern, shape, and resistance to pathogens. Conventional breeding, including sexual hybridization followed by selection of desirable characteristics in plants, has so far been the main method for ornamental breeding, but other techniques, including mutation induction by polyploidization and gamma irradiation, and biotechnological techniques, such as genetic transformation, have also been studied and used in ornamental breeding programs. Orchids are one of the most commercially important families in floriculture industry, having very particular reproductive biology characteristics and being a well-studied group of ornamentals in terms of genetic improvement. The present review focuses on the conventional and biotechnological techniques and approaches specially employed in breeding Phalaenopsis orchids, the genus with highest worldwide importance as an ornamental orchid, highlighting the main limitations and strengths of the approaches. Furthermore, new opportunities and future prospects for ornamental breeding in the CRISPR/Cas9 genome editing era are also discussed. We conclude that conventional hybridization remains the most used method to obtain new cultivars in orchids. However, the emergence of the first biotechnology-derived cultivars, as well as the new biotechnological tools available, such as CRISPR-Cas9, rekindled the full potential of biotechnology approaches and their importance for improve ornamental orchid breeding programs.
Collapse
Affiliation(s)
- Carla Midori Iiyama
- Laboratory of Plant Physiology and Tissue Culture, Department of Biotechnology, Plant and Animal Production, Centro de Ciências Agrárias, Universidade Federal de São Carlos (CCA/UFSCar), Rodovia Anhanguera, km 174, CEP13600-970, Araras, SP, Brazil.
- Graduate Program in Plant Production and Associated Bioprocesses, CCA/UFSCar, Araras, Brazil.
| | - Joe Abdul Vilcherrez-Atoche
- Laboratory of Plant Physiology and Tissue Culture, Department of Biotechnology, Plant and Animal Production, Centro de Ciências Agrárias, Universidade Federal de São Carlos (CCA/UFSCar), Rodovia Anhanguera, km 174, CEP13600-970, Araras, SP, Brazil
- Graduate Program in Plant Production and Associated Bioprocesses, CCA/UFSCar, Araras, Brazil
| | - Maria Antonietta Germanà
- Dipartimento Scienze Agrarie, Alimentari e Forestali (SAAF), Università degli Studi di Palermo, Palermo, Italy
| | - Wagner Aparecido Vendrame
- Environmental Horticulture Department, University of Florida, 2550 Hull Rd., Gainesville, FL, 32611, USA
| | - Jean Carlos Cardoso
- Laboratory of Plant Physiology and Tissue Culture, Department of Biotechnology, Plant and Animal Production, Centro de Ciências Agrárias, Universidade Federal de São Carlos (CCA/UFSCar), Rodovia Anhanguera, km 174, CEP13600-970, Araras, SP, Brazil.
- Graduate Program in Plant Production and Associated Bioprocesses, CCA/UFSCar, Araras, Brazil.
| |
Collapse
|
4
|
Orłowska R, Zimny J, Zebrowski J, Androsiuk P, Bednarek PT. An insight into tissue culture-induced variation origin shared between anther culture-derived triticale regenerants. BMC PLANT BIOLOGY 2024; 24:43. [PMID: 38200422 PMCID: PMC10782687 DOI: 10.1186/s12870-023-04679-w] [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: 06/19/2023] [Accepted: 12/11/2023] [Indexed: 01/12/2024]
Abstract
BACKGROUND The development of the plant in vitro techniques has brought about the variation identified in regenerants known as somaclonal or tissue culture-induced variation (TCIV). S-adenosyl-L-methionine (SAM), glutathione (GSH), low methylated pectins (LMP), and Cu(II) ions may be implicated in green plant regeneration efficiency (GPRE) and TCIV, according to studies in barley (Hordeum vulgare L.) and partially in triticale (× Triticosecale spp. Wittmack ex A. Camus 1927). Using structural equation models (SEM), these metabolites have been connected to the metabolic pathways (Krebs and Yang cycles, glycolysis, transsulfuration), but not for triticale. Using metabolomic and (epi)genetic data, the study sought to develop a triticale regeneration efficiency statistical model. The culture's induction medium was supplemented with various quantities of Cu(II) and Ag(I) ions for regeneration. The period of plant regeneration has also changed. The donor plant, anther-derived regenerants, and metAFLP were utilized to analyze TCIV concerning DNA in symmetric (CG, CHG) and asymmetric (CHH) sequence contexts. Attenuated Total Reflectance-Fourier Transfer Infrared (ATR-FTIR) spectroscopy was used to gather the metabolomic information on LMP, SAM, and GSH. To frame the data, a structural equation model was employed. RESULTS According to metAFLP analysis, the average sequence change in the CHH context was 8.65%, and 0.58% was de novo methylation. Absorbances of FTIR spectra in regions specific for LMP, SAM, and GSH were used as variables values introduced to the SEM model. The average number of green regenerants per 100 plated anthers was 2.55. CONCLUSIONS The amounts of pectin demethylation, SAM, de novo methylation, and GSH are connected in the model to explain GPRE. By altering the concentration of Cu(II) ions in the medium, which influences the amount of pectin, triticale's GPRE can be increased.
Collapse
Affiliation(s)
- Renata Orłowska
- Plant Breeding and Acclimatization Institute, National Research Institute, Radzików, Błonie, 05-870, Poland
| | - Janusz Zimny
- Plant Breeding and Acclimatization Institute, National Research Institute, Radzików, Błonie, 05-870, Poland
| | - Jacek Zebrowski
- Institute of Biotechnology, College of Natural Science, University of Rzeszow, Al. Rejtana 16c, Rzeszow, 35-959, Poland
| | - Piotr Androsiuk
- Department of Plant Physiology, Genetics and Biotechnology, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, Olsztyn, 10-719, Poland
| | - Piotr T Bednarek
- Plant Breeding and Acclimatization Institute, National Research Institute, Radzików, Błonie, 05-870, Poland.
| |
Collapse
|
5
|
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: 24] [Impact Index Per Article: 24.0] [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
|
6
|
Pachota KA, Orłowska R. Effect of copper and silver ions on sequence and DNA methylation changes in triticale regenerants gained via somatic embryogenesis. J Appl Genet 2022; 63:663-675. [PMID: 35984629 PMCID: PMC9637072 DOI: 10.1007/s13353-022-00717-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 08/01/2022] [Accepted: 08/05/2022] [Indexed: 11/19/2022]
Abstract
Somatic embryogenesis is a plant regeneration method that can be exploited in tissue culture systems for a variety of tasks, such as genetic modification or the selection of somaclones with advantageous characteristics. Therefore, it is crucial to create efficient regeneration procedures and comprehend how medium components affect regeneration effectiveness or the degree of variation created in plant tissue cultures. The level of tissue culture-induced variation in triticale regenerants was examined in the current study in relation to the concentration of copper and silver ions in the induction media as well as the length of time immature zygotic embryo explants were incubated on these media. The high degree of variation (45%) revealed by the methylation-sensitive amplified fragment length polymorphism approach for estimating variation included 38% DNA sequence alterations, 6% DNA demethylation, and 1% de novo DNA methylation. Different levels of variance were found in relation to various DNA sequence settings. The CHG context had the most alterations, whereas CG experienced the fewest; sequence variation predominated in each sequence context. Lower copper ion concentrations showed the most variance. However, it could not be connected to the duration of in vitro culture or the effect of silver ions. Accordingly, we think that altering the concentration of copper ions in the induction medium may throw off the equilibrium of the metabolic processes in which copper is involved, resulting in tissue culture-induced variation.
Collapse
Affiliation(s)
- Katarzyna Anna Pachota
- Plant Breeding and Acclimatization Institute - National Research Institute, Radzików, 05-870, Błonie, Poland
| | - Renata Orłowska
- Plant Breeding and Acclimatization Institute - National Research Institute, Radzików, 05-870, Błonie, Poland.
| |
Collapse
|
7
|
Reed KM, Bargmann BOR. Protoplast Regeneration and Its Use in New Plant Breeding Technologies. Front Genome Ed 2021; 3:734951. [PMID: 34713266 PMCID: PMC8525371 DOI: 10.3389/fgeed.2021.734951] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Accepted: 08/11/2021] [Indexed: 11/13/2022] Open
Abstract
The development of gene-editing technology holds tremendous potential for accelerating crop trait improvement to help us address the need to feed a growing global population. However, the delivery and access of gene-editing tools to the host genome and subsequent recovery of successfully edited plants form significant bottlenecks in the application of new plant breeding technologies. Moreover, the methods most suited to achieve a desired outcome vary substantially, depending on species' genotype and the targeted genetic changes. Hence, it is of importance to develop and improve multiple strategies for delivery and regeneration in order to be able to approach each application from various angles. The use of transient transformation and regeneration of plant protoplasts is one such strategy that carries unique advantages and challenges. Here, we will discuss the use of protoplast regeneration in the application of new plant breeding technologies and review pertinent literature on successful protoplast regeneration.
Collapse
Affiliation(s)
| | - Bastiaan O. R. Bargmann
- School of Plant and Environmental Sciences, College of Agriculture and Life Sciences, Virginia Tech, Blacksburg, VA, United States
| |
Collapse
|