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Kielich N, Mazur O, Musidlak O, Gracz-Bernaciak J, Nawrot R. Herbgenomics meets Papaveraceae: a promising -omics perspective on medicinal plant research. Brief Funct Genomics 2024; 23:579-594. [PMID: 37952099 DOI: 10.1093/bfgp/elad050] [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: 09/08/2023] [Revised: 10/09/2023] [Accepted: 10/20/2023] [Indexed: 11/14/2023] Open
Abstract
Herbal medicines were widely used in ancient and modern societies as remedies for human ailments. Notably, the Papaveraceae family includes well-known species, such as Papaver somniferum and Chelidonium majus, which possess medicinal properties due to their latex content. Latex-bearing plants are a rich source of diverse bioactive compounds, with applications ranging from narcotics to analgesics and relaxants. With the advent of high-throughput technologies and advancements in sequencing tools, an opportunity exists to bridge the knowledge gap between the genetic information of herbs and the regulatory networks underlying their medicinal activities. This emerging discipline, known as herbgenomics, combines genomic information with other -omics studies to unravel the genetic foundations, including essential gene functions and secondary metabolite biosynthesis pathways. Furthermore, exploring the genomes of various medicinal plants enables the utilization of modern genetic manipulation techniques, such as Clustered Regularly-Interspaced Short Palindromic Repeats (CRISPR/Cas9) or RNA interference. This technological revolution has facilitated systematic studies of model herbs, targeted breeding of medicinal plants, the establishment of gene banks and the adoption of synthetic biology approaches. In this article, we provide a comprehensive overview of the recent advances in genomic, transcriptomic, proteomic and metabolomic research on species within the Papaveraceae family. Additionally, it briefly explores the potential applications and key opportunities offered by the -omics perspective in the pharmaceutical industry and the agrobiotechnology field.
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Affiliation(s)
- Natalia Kielich
- Department of Molecular Virology, Institute of Experimental Biology, Adam Mickiewicz University, Poznań, Poland
| | - Oliwia Mazur
- Department of Molecular Virology, Institute of Experimental Biology, Adam Mickiewicz University, Poznań, Poland
| | - Oskar Musidlak
- Department of Molecular Virology, Institute of Experimental Biology, Adam Mickiewicz University, Poznań, Poland
| | - Joanna Gracz-Bernaciak
- Department of Molecular Virology, Institute of Experimental Biology, Adam Mickiewicz University, Poznań, Poland
| | - Robert Nawrot
- Department of Molecular Virology, Institute of Experimental Biology, Adam Mickiewicz University, Poznań, Poland
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Talarico E, Zambelli A, Araniti F, Greco E, Chiappetta A, Bruno L. Unravelling the Epigenetic Code: DNA Methylation in Plants and Its Role in Stress Response. EPIGENOMES 2024; 8:30. [PMID: 39189256 PMCID: PMC11348131 DOI: 10.3390/epigenomes8030030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2024] [Revised: 07/31/2024] [Accepted: 08/06/2024] [Indexed: 08/28/2024] Open
Abstract
Environmental stress significantly affects plant growth, development, and survival. Plants respond to stressors such as temperature fluctuations, water scarcity, nutrient deficiencies, and pathogen attacks through intricate molecular and physiological adaptations. Epigenetic mechanisms are crucial in regulating gene expression in response to environmental stress. This review explores the current understanding of epigenetic modifications, including DNA methylation, and their roles in modulating gene expression patterns under environmental stress conditions. The dynamic nature of epigenetic modifications, their crosstalk with stress-responsive pathways, and their potential implications for plant adaptation and crop improvement are highlighted in the face of changing environmental conditions.
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Affiliation(s)
- Emanuela Talarico
- Department of Biology, Ecology and Earth Sciences (DiBEST), University of Calabria, 87036 Rende, Italy; (E.T.); (E.G.); (A.C.)
| | - Alice Zambelli
- Department of Agricultural and Environmental Sciences—Production, Landscape, Agroenergy, University of Milan, 20133 Milan, Italy; (A.Z.); (F.A.)
| | - Fabrizio Araniti
- Department of Agricultural and Environmental Sciences—Production, Landscape, Agroenergy, University of Milan, 20133 Milan, Italy; (A.Z.); (F.A.)
| | - Eleonora Greco
- Department of Biology, Ecology and Earth Sciences (DiBEST), University of Calabria, 87036 Rende, Italy; (E.T.); (E.G.); (A.C.)
| | - Adriana Chiappetta
- Department of Biology, Ecology and Earth Sciences (DiBEST), University of Calabria, 87036 Rende, Italy; (E.T.); (E.G.); (A.C.)
| | - Leonardo Bruno
- Department of Biology, Ecology and Earth Sciences (DiBEST), University of Calabria, 87036 Rende, Italy; (E.T.); (E.G.); (A.C.)
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3
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Williams K, Subramani M, Lofton LW, Penney M, Todd A, Ozbay G. Tools and Techniques to Accelerate Crop Breeding. PLANTS (BASEL, SWITZERLAND) 2024; 13:1520. [PMID: 38891328 PMCID: PMC11174677 DOI: 10.3390/plants13111520] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2024] [Revised: 05/25/2024] [Accepted: 05/30/2024] [Indexed: 06/21/2024]
Abstract
As climate changes and a growing global population continue to escalate the need for greater production capabilities of food crops, technological advances in agricultural and crop research will remain a necessity. While great advances in crop improvement over the past century have contributed to massive increases in yield, classic breeding schemes lack the rate of genetic gain needed to meet future demands. In the past decade, new breeding techniques and tools have been developed to aid in crop improvement. One such advancement is the use of speed breeding. Speed breeding is known as the application of methods that significantly reduce the time between crop generations, thereby streamlining breeding and research efforts. These rapid-generation advancement tactics help to accelerate the pace of crop improvement efforts to sustain food security and meet the food, feed, and fiber demands of the world's growing population. Speed breeding may be achieved through a variety of techniques, including environmental optimization, genomic selection, CRISPR-Cas9 technology, and epigenomic tools. This review aims to discuss these prominent advances in crop breeding technologies and techniques that have the potential to greatly improve plant breeders' ability to rapidly produce vital cultivars.
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Affiliation(s)
- Krystal Williams
- Molecular Genetics and Epigenomics Laboratory, Department of Agriculture and Natural Resources, College of Agriculture, Science, and Technology, Delaware State University, Dover, DE 19901, USA;
| | - Mayavan Subramani
- Molecular Genetics and Epigenomics Laboratory, Department of Agriculture and Natural Resources, College of Agriculture, Science, and Technology, Delaware State University, Dover, DE 19901, USA;
| | - Lily W. Lofton
- Department of Plant Pathology, University of Georgia, Athens, GA 30602, USA;
- Toxicology & Mycotoxin Research Unit, US National Poultry Research Center, USDA-ARS, Athens, GA 30602, USA
| | - Miranda Penney
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA;
| | - Antonette Todd
- Molecular Genetics and Epigenomics Laboratory, Department of Agriculture and Natural Resources, College of Agriculture, Science, and Technology, Delaware State University, Dover, DE 19901, USA;
| | - Gulnihal Ozbay
- One Health Laboratory, Department of Agriculture and Natural Resources, College of Agriculture, Science, and Technology, Delaware State University, Dover, DE 19901, USA
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4
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Pilozo G, Villavicencio-Vásquez M, Chóez-Guaranda I, Murillo DV, Pasaguay CD, Reyes CT, Maldonado-Estupiñán M, Ruiz-Barzola O, León-Tamariz F, Manzano P. Chemical, antioxidant, and antifungal analysis of oregano and thyme essential oils from Ecuador: Effect of thyme against Lasiodiplodia theobromae and its application in banana rot. Heliyon 2024; 10:e31443. [PMID: 38831831 PMCID: PMC11145482 DOI: 10.1016/j.heliyon.2024.e31443] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Revised: 05/10/2024] [Accepted: 05/15/2024] [Indexed: 06/05/2024] Open
Abstract
The objective of this study was to evaluate the antioxidant capacity by spectrophotometric methods, the in vitro and in vivo antifungal effect against Lasiodiplodia theobromae and the constitution of the essential oils (EO) of oregano and thyme in comparison with their commercial counterparts. The results showed by the EOs of extracted thyme (T-EO), commercial thyme (CT-EO), extracted oregano (O-EO) and commercial oregano (CO-EO), demonstrated antioxidant profiles with a radical neutralizing potential (DPPH•) of IC50: 1.11 ± 0.019; 1.08 ± 0.05; 40.56 ± 0.227 and 0.69 ± 0.004 mg/mL, respectively. They also revealed a ferric ion reducing capacity (FRAP) of 93.05 ± 0.52; 97.72 ± 0.42; 21.85 ± 0.57 and 117.24 ± 0.64 mg Eq Trolox/g. A reduction in β-carotene degradation of 65.71 ± 0.04; 51.97 ± 0.66; 43.58 ± 1.56 and 57.46 ± 1.56 %. A total phenol content (Folin-Ciocalteu) of 132.97 ± 0.77; 141.89 ± 2.56; 152.04 ± 0.10 and 25.66 ± 0.40 mg EGA/g. Chemical characterization performed by gas chromatography mass spectrometry (GC-MS) showed that the respective major components of the samples were thymol (T-EO: 45.78 %), thymol (CT-EO: 43.57 %), alloaromadendrene (O-EO: 25.17 %) and carvacrol (CO-EO: 62.06 %). Regarding antifungal activity, it was evident that at the in vitro level, both commercial EOs had a MIC of 250 ppm while the extracted thyme EO had a MIC of 500 ppm; In vivo studies demonstrated that the application of thyme EO had a behavior similar to the synthetic fungicide, slowing down rot in bananas under storage conditions. Finally, partial least squares discriminant analysis (PLS-DA) and heat maps suggest p-cymene, carvacrol, linalool, eucalyptol, 4-terpineol, (z)-β-terpineol, alkanhol, caryophyllene, β-myrcene, d-limonene, α-terpinene, α-terpineol, d-α-pinene, camphene, caryophyllene oxide, δ-cadinene, terpinolene and thymol as relevant biomarkers associated with the assessed bioactive properties demonstrating the potential of extracted essential oils for the development of a botanical biofungicide.
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Affiliation(s)
- Glenda Pilozo
- Facultad de Ciencias de la Vida, ESPOL Polytechnic University, ESPOL, Campus Gustavo Galindo, Km. 30.5 Vía Perimetral, Guayaquil, 090902, Ecuador
- Centro de Investigaciones Biotecnológicas del Ecuador, ESPOL Polytechnic University, ESPOL, Campus Gustavo Galindo, Km. 30.5 Vía Perimetral, Guayaquil, 090902, Ecuador
| | - Mirian Villavicencio-Vásquez
- Centro de Investigaciones Biotecnológicas del Ecuador, ESPOL Polytechnic University, ESPOL, Campus Gustavo Galindo, Km. 30.5 Vía Perimetral, Guayaquil, 090902, Ecuador
| | - Ivan Chóez-Guaranda
- Centro de Investigaciones Biotecnológicas del Ecuador, ESPOL Polytechnic University, ESPOL, Campus Gustavo Galindo, Km. 30.5 Vía Perimetral, Guayaquil, 090902, Ecuador
| | - Damon Vera Murillo
- Facultad de Ciencias Naturales y Matemáticas, ESPOL Polytechnic University, ESPOL, Campus Gustavo Galindo, Km. 30.5 Vía Perimetral, Guayaquil, 090902, Ecuador
| | - Cynthia Duarte Pasaguay
- Facultad de Ciencias Naturales y Matemáticas, ESPOL Polytechnic University, ESPOL, Campus Gustavo Galindo, Km. 30.5 Vía Perimetral, Guayaquil, 090902, Ecuador
| | - Christofer Tomalá Reyes
- Facultad de Ciencias Naturales y Matemáticas, ESPOL Polytechnic University, ESPOL, Campus Gustavo Galindo, Km. 30.5 Vía Perimetral, Guayaquil, 090902, Ecuador
| | - Maria Maldonado-Estupiñán
- Facultad de Ciencias Naturales y Matemáticas, ESPOL Polytechnic University, ESPOL, Campus Gustavo Galindo, Km. 30.5 Vía Perimetral, Guayaquil, 090902, Ecuador
| | - Omar Ruiz-Barzola
- Facultad de Ciencias Naturales y Matemáticas, ESPOL Polytechnic University, ESPOL, Campus Gustavo Galindo, Km. 30.5 Vía Perimetral, Guayaquil, 090902, Ecuador
| | - Fabián León-Tamariz
- University of Cuenca, Universidad de Cuenca, Departamento de Biociencias, Facultad de Ciencias Químicas, Campus Central Av. 12 de Abril, Cuenca, Ecuador
| | - Patricia Manzano
- Facultad de Ciencias de la Vida, ESPOL Polytechnic University, ESPOL, Campus Gustavo Galindo, Km. 30.5 Vía Perimetral, Guayaquil, 090902, Ecuador
- Centro de Investigaciones Biotecnológicas del Ecuador, ESPOL Polytechnic University, ESPOL, Campus Gustavo Galindo, Km. 30.5 Vía Perimetral, Guayaquil, 090902, Ecuador
- Facultad de Ciencias Naturales y Matemáticas, ESPOL Polytechnic University, ESPOL, Campus Gustavo Galindo, Km. 30.5 Vía Perimetral, Guayaquil, 090902, Ecuador
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Azevedo V, Daddiego L, Cardone MF, Perrella G, Sousa L, Santos RB, Malhó R, Bergamini C, Marsico AD, Figueiredo A, Alagna F. Transcriptomic and methylation analysis of susceptible and tolerant grapevine genotypes following Plasmopara viticola infection. PHYSIOLOGIA PLANTARUM 2022; 174:e13771. [PMID: 36053855 PMCID: PMC9826190 DOI: 10.1111/ppl.13771] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 08/05/2022] [Accepted: 08/29/2022] [Indexed: 06/15/2023]
Abstract
Downy mildew, caused by the biotrophic oomycete Plasmopara viticola, is one of the most economically significant grapevine diseases worldwide. Current strategies to cope with this threat rely on the massive use of chemical compounds during each cultivation season. The economic costs and negative environmental impact associated with these applications increased the urge to search for sustainable strategies of disease control. Improved knowledge of plant mechanisms to counteract pathogen infection may allow the development of alternative strategies for plant protection. Epigenetic regulation, in particular DNA methylation, is emerging as a key factor in the context of plant-pathogen interactions associated with the expression modulation of defence genes. To improve our understanding of the genetic and epigenetic mechanisms underpinning grapevine response to P. viticola, we studied the modulation of both 5-mC methylation and gene expression at 6 and 24 h post-infection (hpi). Leaves of two table grape genotypes (Vitis vinifera), selected by breeding activities for their contrasting level of susceptibility to the pathogen, were analysed. Following pathogen infection, we found variations in the 5-mC methylation level and the gene expression profile. The results indicate a genotype-specific response to pathogen infection. The tolerant genotype (N23/018) at 6 hpi exhibits a lower methylation level compared to the susceptible one (N20/020), and it shows an early modulation (at 6 hpi) of defence and epigenetic-related genes during P. viticola infection. These data suggest that the timing of response is an important mechanism to efficiently counteract the pathogen attack.
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Affiliation(s)
- Vanessa Azevedo
- Faculdade de Ciências, Plant Biology Department, Biosystems & Integrative Sciences Institute (BioISI)Universidade de LisboaLisbonPortugal
| | - Loretta Daddiego
- Energy Technologies and Renewable Sources DepartmentNational Agency for New Technologies, Energy and Sustainable Economic Development (ENEA), Trisaia Research CentreRotondellaMateraItaly
| | - Maria Francesca Cardone
- Research Centre for Viticulture and EnologyCouncil for Agricultural Research and Economics (CREA)TuriBariItaly
| | | | - Lisete Sousa
- Department of Statistics and Operations Research, Faculdade de Ciências; Centre of Statistics and its Applications (CEAUL)Universidade de LisboaLisbonPortugal
| | - Rita B. Santos
- Faculdade de Ciências, Plant Biology Department, Biosystems & Integrative Sciences Institute (BioISI)Universidade de LisboaLisbonPortugal
| | - Rui Malhó
- Faculdade de Ciências, Plant Biology Department, Biosystems & Integrative Sciences Institute (BioISI)Universidade de LisboaLisbonPortugal
| | - Carlo Bergamini
- Research Centre for Viticulture and EnologyCouncil for Agricultural Research and Economics (CREA)TuriBariItaly
| | - Antonio Domenico Marsico
- Research Centre for Viticulture and EnologyCouncil for Agricultural Research and Economics (CREA)TuriBariItaly
| | - Andreia Figueiredo
- Faculdade de Ciências, Plant Biology Department, Biosystems & Integrative Sciences Institute (BioISI)Universidade de LisboaLisbonPortugal
| | - Fiammetta Alagna
- Energy Technologies and Renewable Sources DepartmentNational Agency for New Technologies, Energy and Sustainable Economic Development (ENEA), Trisaia Research CentreRotondellaMateraItaly
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6
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Auler PA, Nogueira do Amaral M, Bolacel Braga EJ, Maserti B. Drought stress memory in rice guard cells: Proteome changes and genomic stability of DNA. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2021; 169:49-62. [PMID: 34753074 DOI: 10.1016/j.plaphy.2021.10.028] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 10/19/2021] [Accepted: 10/20/2021] [Indexed: 06/13/2023]
Abstract
Drought is one of the major threats for crop plants among them rice, worldwide. The effects of drought vary depending on the plant growth phase and the occurrence of a previous stress, which can leave a memory of the stress. Stomata guard cells perform many essential functions and are highly responsive to hormonal and environmental stimuli. Therefore, information on how guard cells respond to drought might be useful for selecting drought tolerant plants. In this work, physiological analysis, comparative proteomics, gene expression and 5 - methylcytosine (%) analysis were used to elucidate the effects of drought in single stress event at vegetative or reproductive stage or recurrent at both stages in guard cells from rice plants. Photosynthesis and stomatal conductance decreased when drought was applied at reproductive stage in single and recurrent event. Twelve drought-responsive proteins were identified, belonging to photosynthesis pathway, response to oxidative stress, stress signalling and others. The expression of their encoding genes showed a positive relation with the protein abundance. Drought stress increased the total DNA methylation when applied at vegetative stage in single (35%) and recurrent event (18%) and decreased it in plants stressed at reproductive stage (9.8%), with respect to the levels measured in well-watered ones (13.84%). In conclusion, a first drought event seems to induce adaptation to water-deficit conditions through decreasing energy dissipation, increasing ATP energy provision, reducing oxidative damage in GC. Furthermore, the stress memory is associated with epigenetic markers.
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Affiliation(s)
- Priscila Ariane Auler
- Department of Botany, Biology Institute - Plant Physiology, Federal University of Pelotas, Pelotas, RS, Brazil; CNR- Istituto per la Protezione Sostenibile delle Piante (CNR-IPSP), UOS, Firenze, Area della Ricerca CNR di Firenze, via Madonna del Piano 10, 50019, Sesto Fiorentino, Firenze, Italy.
| | - Marcelo Nogueira do Amaral
- Department of Botany, Biology Institute - Plant Physiology, Federal University of Pelotas, Pelotas, RS, Brazil
| | | | - Biancaelena Maserti
- CNR- Istituto per la Protezione Sostenibile delle Piante (CNR-IPSP), UOS, Firenze, Area della Ricerca CNR di Firenze, via Madonna del Piano 10, 50019, Sesto Fiorentino, Firenze, Italy
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7
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Kordyum E, Dubyna D. The role of epigenetic regulation in adaptive phenotypic plasticity of plants. UKRAINIAN BOTANICAL JOURNAL 2021. [DOI: 10.15407/ukrbotj78.05.347] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
In recent decades, knowledge about the role of epigenetic regulation of gene expression in plant responses to external stimuli and in adaptation of plants to adverse environmental fluctuations have extended significantly. DNA methylation is considered as the main molecular mechanism that provides genomic information and contributes to the understanding of the molecular basis of phenotypic variations based on epigenetic modifications. Unfortunately, the vast majority of research in this area has been performed on the model species Arabidopsis thaliana. The development of the methylation-sensitive amplified polymorphism (MSAP) method has made it possible to implement the large-scale detection of DNA methylation alterations in wild non-model and agricultural plants with large and highly repetitive genomes in natural and manipulated habitats. The article presents current information on DNA methylation in species of natural communities and crops and its importance in plant development and adaptive phenotypic plasticity, along with brief reviews of current ideas about adaptive phenotypic plasticity and epigenetic regulation of gene expression. The great potential of further studies of the epigenetic role in phenotypic plasticity of a wide range of non-model species in natural populations and agrocenoses for understanding the molecular mechanisms of plant existence in the changing environment in onto- and phylogeny, directly related to the key tasks of forecasting the effects of global warming and crop selection, is emphasized. Specific taxa of the Ukrainian flora, which, in authors’ opinion, are promising and interesting for this type of research, are recommended.
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Zhang X, Man Y, Zhuang X, Shen J, Zhang Y, Cui Y, Yu M, Xing J, Wang G, Lian N, Hu Z, Ma L, Shen W, Yang S, Xu H, Bian J, Jing Y, Li X, Li R, Mao T, Jiao Y, Sodmergen, Ren H, Lin J. Plant multiscale networks: charting plant connectivity by multi-level analysis and imaging techniques. SCIENCE CHINA-LIFE SCIENCES 2021; 64:1392-1422. [PMID: 33974222 DOI: 10.1007/s11427-020-1910-1] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 03/04/2021] [Indexed: 12/21/2022]
Abstract
In multicellular and even single-celled organisms, individual components are interconnected at multiscale levels to produce enormously complex biological networks that help these systems maintain homeostasis for development and environmental adaptation. Systems biology studies initially adopted network analysis to explore how relationships between individual components give rise to complex biological processes. Network analysis has been applied to dissect the complex connectivity of mammalian brains across different scales in time and space in The Human Brain Project. In plant science, network analysis has similarly been applied to study the connectivity of plant components at the molecular, subcellular, cellular, organic, and organism levels. Analysis of these multiscale networks contributes to our understanding of how genotype determines phenotype. In this review, we summarized the theoretical framework of plant multiscale networks and introduced studies investigating plant networks by various experimental and computational modalities. We next discussed the currently available analytic methodologies and multi-level imaging techniques used to map multiscale networks in plants. Finally, we highlighted some of the technical challenges and key questions remaining to be addressed in this emerging field.
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Affiliation(s)
- Xi Zhang
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, 100083, China.,College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, China
| | - Yi Man
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, 100083, China.,College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, China
| | - Xiaohong Zhuang
- School of Life Sciences, Centre for Cell & Developmental Biology and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, 999077, China
| | - Jinbo Shen
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, 311300, China
| | - Yi Zhang
- Key Laboratory of Cell Proliferation and Regulation Biology, Ministry of Education, College of Life Science, Beijing Normal University, Beijing, 100875, China
| | - Yaning Cui
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, 100083, China.,College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, China
| | - Meng Yu
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, 100083, China.,College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, China
| | - Jingjing Xing
- Key Laboratory of Plant Stress Biology, School of Life Sciences, Henan University, Kaifeng, 457004, China
| | - Guangchao Wang
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, China
| | - Na Lian
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, 100083, China.,College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, China
| | - Zijian Hu
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, China
| | - Lingyu Ma
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, China
| | - Weiwei Shen
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, China
| | - Shunyao Yang
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, China
| | - Huimin Xu
- College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Jiahui Bian
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, China
| | - Yanping Jing
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, China
| | - Xiaojuan Li
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, 100083, China.,College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, China
| | - Ruili Li
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, 100083, China.,College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, China
| | - Tonglin Mao
- State Key Laboratory of Plant Physiology and Biochemistry, Department of Plant Sciences, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Yuling Jiao
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, and National Center for Plant Gene Research, Beijing, 100101, China
| | - Sodmergen
- Key Laboratory of Ministry of Education for Cell Proliferation and Differentiation, College of Life Sciences, Peking University, Beijing, 100871, China
| | - Haiyun Ren
- Key Laboratory of Cell Proliferation and Regulation Biology, Ministry of Education, College of Life Science, Beijing Normal University, Beijing, 100875, China
| | - Jinxing Lin
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, 100083, China. .,College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, China.
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Portera M, Mandrioli M. Who's afraid of epigenetics? Habits, instincts, and Charles Darwin's evolutionary theory. HISTORY AND PHILOSOPHY OF THE LIFE SCIENCES 2021; 43:20. [PMID: 33569656 PMCID: PMC7875938 DOI: 10.1007/s40656-021-00376-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Accepted: 01/27/2021] [Indexed: 06/12/2023]
Abstract
Our paper aims at bringing to the fore the crucial role that habits play in Charles Darwin's theory of evolution by means of natural selection. We have organized the paper in two steps: first, we analyse value and functions of the concept of habit in Darwin's early works, notably in his Notebooks, and compare these views to his mature understanding of the concept in the Origin of Species and later works; second, we discuss Darwin's ideas on habits in the light of today's theories of epigenetic inheritance, which describe the way in which the functioning and expression of genes is modified by the environment, and how these modifications are transmitted over generations. We argue that Darwin's lasting and multifaceted interest in the notion of habit, throughout his intellectual life, is both conceptually and methodologically relevant. From a conceptual point of view, intriguing similarities can be found between Darwin's (early) conception of habit and contemporary views on epigenetic inheritance. From a methodological point of view, we suggest that Darwin's plastic approach to habits, from his early writings up to the mature works, can provide today's evolutionary scientists with a viable methodological model to address the challenging task of extending and expanding evolutionary theory, with particular reference to the integration of epigenetic mechanisms into existing models of evolutionary change. Over his entire life Darwin has modified and reassessed his views on habits as many times as required by evidence: his work on this notion may represent the paradigm of a habit of good scientific research methodology.
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Affiliation(s)
- Mariagrazia Portera
- Dipartimento di Lettere e Filosofia, University of Florence, Firenze, Italy.
| | - Mauro Mandrioli
- Dipartimento di Scienze della Vita, University of Modena e Reggio Emilia, Modena, Italy
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Santos AP, Gaudin V, Mozgová I, Pontvianne F, Schubert D, Tek AL, Dvořáčková M, Liu C, Fransz P, Rosa S, Farrona S. Tidying-up the plant nuclear space: domains, functions, and dynamics. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:5160-5178. [PMID: 32556244 PMCID: PMC8604271 DOI: 10.1093/jxb/eraa282] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Accepted: 06/12/2020] [Indexed: 05/07/2023]
Abstract
Understanding how the packaging of chromatin in the nucleus is regulated and organized to guide complex cellular and developmental programmes, as well as responses to environmental cues is a major question in biology. Technological advances have allowed remarkable progress within this field over the last years. However, we still know very little about how the 3D genome organization within the cell nucleus contributes to the regulation of gene expression. The nuclear space is compartmentalized in several domains such as the nucleolus, chromocentres, telomeres, protein bodies, and the nuclear periphery without the presence of a membrane around these domains. The role of these domains and their possible impact on nuclear activities is currently under intense investigation. In this review, we discuss new data from research in plants that clarify functional links between the organization of different nuclear domains and plant genome function with an emphasis on the potential of this organization for gene regulation.
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Affiliation(s)
- Ana Paula Santos
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova
de Lisboa, Oeiras, Portugal
| | - Valérie Gaudin
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Université
Paris-Saclay, Versailles, France
| | - Iva Mozgová
- Biology Centre of the Czech Academy of Sciences, České
Budějovice, Czech Republic
- Faculty of Science, University of South Bohemia, České
Budějovice, Czech Republic
| | - Frédéric Pontvianne
- CNRS, Laboratoire Génome et Développement des Plantes (LGDP), Université de
Perpignan Via Domitia, Perpignan, France
| | - Daniel Schubert
- Institute for Biology, Freie Universität Berlin, Berlin, Germany
| | - Ahmet L Tek
- Agricultural Genetic Engineering Department, Niğde Ömer Halisdemir
University, Niğde, Turkey
| | | | - Chang Liu
- Center for Plant Molecular Biology (ZMBP), University of
Tübingen, Tübingen, Germany
- Institute of Biology, University of Hohenheim, Stuttgart,
Germany
| | - Paul Fransz
- University of Amsterdam, Amsterdam, The
Netherlands
| | - Stefanie Rosa
- Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Sara Farrona
- Plant and AgriBiosciences Centre, Ryan Institute, NUI Galway,
Galway, Ireland
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Recent Advances in MS-Based Plant Proteomics: Proteomics Data Validation Through Integration with Other Classic and -Omics Approaches. PROGRESS IN BOTANY 2019. [DOI: 10.1007/124_2019_32] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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Fritz MA, Rosa S, Sicard A. Mechanisms Underlying the Environmentally Induced Plasticity of Leaf Morphology. Front Genet 2018; 9:478. [PMID: 30405690 PMCID: PMC6207588 DOI: 10.3389/fgene.2018.00478] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Accepted: 09/26/2018] [Indexed: 01/23/2023] Open
Abstract
The primary function of leaves is to provide an interface between plants and their environment for gas exchange, light exposure and thermoregulation. Leaves have, therefore a central contribution to plant fitness by allowing an efficient absorption of sunlight energy through photosynthesis to ensure an optimal growth. Their final geometry will result from a balance between the need to maximize energy uptake while minimizing the damage caused by environmental stresses. This intimate relationship between leaf and its surroundings has led to an enormous diversification in leaf forms. Leaf shape varies between species, populations, individuals or even within identical genotypes when those are subjected to different environmental conditions. For instance, the extent of leaf margin dissection has, for long, been found to inversely correlate with the mean annual temperature, such that Paleobotanists have used models based on leaf shape to predict the paleoclimate from fossil flora. Leaf growth is not only dependent on temperature but is also regulated by many other environmental factors such as light quality and intensity or ambient humidity. This raises the question of how the different signals can be integrated at the molecular level and converted into clear developmental decisions. Several recent studies have started to shed the light on the molecular mechanisms that connect the environmental sensing with organ-growth and patterning. In this review, we discuss the current knowledge on the influence of different environmental signals on leaf size and shape, their integration as well as their importance for plant adaptation.
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Affiliation(s)
| | - Stefanie Rosa
- Department of Plant Biology, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala, Sweden
| | - Adrien Sicard
- Institut für Biochemie und Biologie, Universität Potsdam, Potsdam, Germany
- Department of Plant Biology, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala, Sweden
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