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Labella-Ortega M, Martín C, Valledor L, Castiglione S, Castillejo MÁ, Jorrín-Novo JV, Rey MD. Unravelling DNA methylation dynamics during developmental stages in Quercus ilex subsp. ballota [Desf.] Samp. BMC PLANT BIOLOGY 2024; 24:823. [PMID: 39223458 PMCID: PMC11370289 DOI: 10.1186/s12870-024-05553-z] [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: 05/23/2024] [Accepted: 08/29/2024] [Indexed: 09/04/2024]
Abstract
BACKGROUND DNA methylation is a critical factor influencing plant growth, adaptability, and phenotypic plasticity. While extensively studied in model and crop species, it remains relatively unexplored in holm oak and other non-domesticated forest trees. This study conducts a comprehensive in-silico mining of DNA methyltransferase and demethylase genes within the holm oak genome to enhance our understanding of this essential process in these understudied species. The expression levels of these genes in adult and seedling leaves, as well as embryos, were analysed using quantitative real-time PCR (qRT-PCR). Global DNA methylation patterns were assessed through methylation-sensitive amplified polymorphism (MSAP) techniques. Furthermore, specific methylated genomic sequences were identified via MSAP sequencing (MSAP-Seq). RESULT A total of 13 DNA methyltransferase and three demethylase genes were revealed in the holm oak genome. Expression levels of these genes varied significantly between organs and developmental stages. MSAP analyses revealed a predominance of epigenetic over genetic variation among organs and developmental stages, with significantly higher global DNA methylation levels observed in adult leaves. Embryos exhibited frequent demethylation events, while de novo methylation was prevalent in seedling leaves. Approximately 35% of the genomic sequences identified by MSAP-Seq were methylated, predominantly affecting nuclear genes and intergenic regions, as opposed to repetitive sequences and chloroplast genes. Methylation was found to be more pronounced in the exonic regions of nuclear genes compared to their promoter and intronic regions. The methylated genes were predominantly associated with crucial biological processes such as photosynthesis, ATP synthesis-coupled electron transport, and defence response. CONCLUSION This study opens a new research direction in analysing variability in holm oak by evaluating the epigenetic events and mechanisms based on DNA methylation. It sheds light on the enzymatic machinery governing DNA (de)methylation, and the changes in the expression levels of methylases and demethylases in different organs along the developmental stages. The expression level was correlated with the DNA methylation pattern observed, showing the prevalence of de novo methylation and demethylation events in seedlings and embryos, respectively. Several methylated genes involved in the regulation of transposable element silencing, lipid biosynthesis, growth and development, and response to biotic and abiotic stresses are highlighted. MSAP-seq integrated with whole genome bisulphite sequencing and advanced sequencing technologies, such as PacBio or Nanopore, will bring light on epigenetic mechanisms regulating the expression of specific genes and its correlation with the phenotypic variability and the differences in the response to environmental cues, especially those related to climate change.
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Affiliation(s)
- Mónica Labella-Ortega
- Agroforestry and Plant Biochemistry, Proteomics and Systems Biology, Department of Biochemistry and Molecular Biology, University of Cordoba, UCO-CeiA3, Cordoba, 14014, Spain.
| | - Carmen Martín
- Department of Biotechnology-Plant Biology, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid (UPM), Ciudad Universitaria s/n, Madrid, 28040, Spain
| | - Luis Valledor
- Plant Physiology Lab, Department of Organisms and Systems Biology and University Institute of Biotechnology (IUBA), University of Oviedo, Cat. Rodrigo Uría s/n, Oviedo, 33006, Spain
| | - Stefano Castiglione
- Department of Chemistry and Biology "A. Zambelli", University of Salerno, via Giovanni Paolo II 132, Fisciano, Salerno, 84084, Italy
| | - María-Ángeles Castillejo
- Agroforestry and Plant Biochemistry, Proteomics and Systems Biology, Department of Biochemistry and Molecular Biology, University of Cordoba, UCO-CeiA3, Cordoba, 14014, Spain
| | - Jesús V Jorrín-Novo
- Agroforestry and Plant Biochemistry, Proteomics and Systems Biology, Department of Biochemistry and Molecular Biology, University of Cordoba, UCO-CeiA3, Cordoba, 14014, Spain
| | - María-Dolores Rey
- Agroforestry and Plant Biochemistry, Proteomics and Systems Biology, Department of Biochemistry and Molecular Biology, University of Cordoba, UCO-CeiA3, Cordoba, 14014, Spain.
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Ye T, Ma T, Chen Y, Liu C, Jiao Z, Wang X, Xue H. The role of redox-active small molecules and oxidative protein post-translational modifications in seed aging. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 213:108810. [PMID: 38857563 DOI: 10.1016/j.plaphy.2024.108810] [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: 02/21/2024] [Revised: 05/25/2024] [Accepted: 06/07/2024] [Indexed: 06/12/2024]
Abstract
Seed vigor is a crucial indicator of seed quality. Variations in seed vigor are closely associated with seed properties and storage conditions. The vigor of mature seeds progressively declines during storage, which is called seed deterioration or aging. Seed aging induces a cascade of cellular damage, including impaired subcellular structures and macromolecules, such as lipids, proteins, and DNA. Reactive oxygen species (ROS) act as signaling molecules during seed aging causing oxidative damage and triggering programmed cell death (PCD). Mitochondria are the main site of ROS production and change morphology and function before other organelles during aging. The roles of other small redox-active molecules in regulating cell and seed vigor, such as nitric oxide (NO) and hydrogen sulfide (H2S), were identified later. ROS, NO, and H2S typically regulate protein function through post-translational modifications (PTMs), including carbonylation, S-glutathionylation, S-nitrosylation, and S-sulfhydration. These signaling molecules as well as the PTMs they induce interact to regulate cell fate and seed vigor. This review was conducted to describe the physiological changes and underlying molecular mechanisms that in seed aging and provides a comprehensive view of how ROS, NO, and H2S affect cell death and seed vigor.
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Affiliation(s)
- Tiantian Ye
- State Key Laboratory of Tree Genetics and Breeding, National Engineering Research Center of Tree Breeding and Ecological Remediation, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, China.
| | - Tianxiao Ma
- State Key Laboratory of Tree Genetics and Breeding, National Engineering Research Center of Tree Breeding and Ecological Remediation, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, China.
| | - Yang Chen
- State Key Laboratory of Tree Genetics and Breeding, National Engineering Research Center of Tree Breeding and Ecological Remediation, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, China.
| | - Chang Liu
- State Key Laboratory of Tree Genetics and Breeding, National Engineering Research Center of Tree Breeding and Ecological Remediation, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, China.
| | - Zhiyuan Jiao
- State Key Laboratory of Tree Genetics and Breeding, National Engineering Research Center of Tree Breeding and Ecological Remediation, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, China.
| | - Xiaofeng Wang
- State Key Laboratory of Tree Genetics and Breeding, National Engineering Research Center of Tree Breeding and Ecological Remediation, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, China.
| | - Hua Xue
- State Key Laboratory of Tree Genetics and Breeding, National Engineering Research Center of Tree Breeding and Ecological Remediation, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, China.
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3
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Li J, Han F, Yuan T, Li W, Li Y, Wu HX, Wei H, Niu S. The methylation landscape of giga-genome and the epigenetic timer of age in Chinese pine. Nat Commun 2023; 14:1947. [PMID: 37029142 PMCID: PMC10082083 DOI: 10.1038/s41467-023-37684-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Accepted: 03/27/2023] [Indexed: 04/09/2023] Open
Abstract
Epigenetics has been revealed to play a crucial role in the long-term memory in plants. However, little is known about whether the epigenetic modifications occur with age progressively in conifers. Here, we present the single-base resolution DNA methylation landscapes of the 25-gigabase Chinese pine (Pinus tabuliformis) genome at different ages. The result shows that DNA methylation is closely coupled with the regulation of gene transcription. The age-dependent methylation profile with a linearly increasing trend is the most significant pattern of DMRs between ages. Two segments at the five-prime end of the first ultra-long intron in DAL1, a conservative age biomarker in conifers, shows a gradual decline of CHG methylation as the age increased, which is highly correlated with its expression profile. Similar high correlation is also observed in nine other age marker genes. Our results suggest that DNA methylation serves as an important epigenetic signature of developmental age in conifers.
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Affiliation(s)
- Jiang Li
- National Engineering Research Center of Tree Breeding and Ecological Restoration, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, PR China
| | - Fangxu Han
- National Engineering Research Center of Tree Breeding and Ecological Restoration, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, PR China
| | - Tongqi Yuan
- College of Material Science and Technology, Beijing Forestry University, Beijing, 100083, P. R. China
| | - Wei Li
- National Engineering Research Center of Tree Breeding and Ecological Restoration, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, PR China
| | - Yue Li
- National Engineering Research Center of Tree Breeding and Ecological Restoration, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, PR China
| | - Harry X Wu
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Linnaeus väg 6, SE-901 83, Umeå, Sweden
- CSIRO National Research Collection Australia, Black Mountain Laboratory, Canberra, ACT, 2601, Australia
| | - Hairong Wei
- College of Forest Resources and Environmental Science, Michigan Technological University, Houghton, MI, 49931, USA
| | - Shihui Niu
- National Engineering Research Center of Tree Breeding and Ecological Restoration, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, PR China.
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Bhushan S, Singh AK, Thakur Y, Baskar R. Persistence of parental age effect on somatic mutation rates across generations in Arabidopsis. BMC PLANT BIOLOGY 2023; 23:152. [PMID: 36944916 PMCID: PMC10031922 DOI: 10.1186/s12870-023-04150-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Accepted: 03/02/2023] [Indexed: 06/18/2023]
Abstract
In the model plant Arabidopsis thaliana, parental age is known to affect somatic mutation rates in their immediate progeny and here we show that this age dependent effect persists across successive generations. Using a set of detector lines carrying the mutated uidA gene, we examined if a particular parental age maintained across five consecutive generations affected the rates of base substitution (BSR), intrachromosomal recombination (ICR), frameshift mutation (FS), and transposition. The frequency of functional GUS reversions were assessed in seedlings as a function of identical/different parental ages across generations. In the context of a fixed parental age, BSR/ICR rates were unaffected in the first three generations, then dropped significantly in the 4th and increased in most instances in the 5th generation (e.g. BSR (F1 38 = 0.9, F2 38 = 1.14, F3 38 = 1.02, F4 38 = 0.5, F5 38 = 0.76)). On the other hand, with advancing parental ages, BSR/ICR rates remained high in the first two/three generations, with a striking resemblance in the pattern of mutation rates (BSR (F1 38 = 0.9, F1 43 = 0.53, F1 48 = 0.79, F1 53 = 0.83 and F2 38 = 1.14, F2 43 = 0.57, F2 48 = 0.64, F2 53 = 0.94). We adopted a novel approach of identifying and tagging flowers pollinated on a particular day, thereby avoiding biases due to potential emasculation induced stress responses. Our results suggest a time component in counting the number of generations a plant has passed through self-fertilization at a particular age in determining the somatic mutation rates.
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Affiliation(s)
- Shashi Bhushan
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology-Madras, Chennai, 600 036, India
| | - Amit Kumar Singh
- Department of Plant Molecular Biology, University of Delhi South Campus, Benito Juarez Road, New Delhi, 110021, India
- Institut de Biologie Moléculaire des Plantes, UPR2357 CNRS, Université de Strasbourg, 12 rue du Général Zimmer, Strasbourg Cédex, 67084, France
| | - Yogendra Thakur
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology-Madras, Chennai, 600 036, India
| | - Ramamurthy Baskar
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology-Madras, Chennai, 600 036, India.
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Zhu D, Shao Y, Fang C, Li M, Yu Y, Qin Y. Effect of storage time on chemical compositions, physiological and cooking quality characteristics of different rice types. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2023; 103:2077-2087. [PMID: 36239993 DOI: 10.1002/jsfa.12275] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 09/18/2022] [Accepted: 10/14/2022] [Indexed: 06/16/2023]
Abstract
BACKGROUND Storage affects rice quality significantly. The aim of this study was to investigate the changes in the chemical composition and in the physiological and cooking quality characteristics of three rice types after 1 year storage at 25 °C. RESULTS Two japonica, two indica, and two indica-japonica hybrid rice varieties were selected. After storage, the total starch content decreased. The amylose content of japonica, indica, and indica-japonica hybrid rice increased by 9.63%-11.65%, 2.99%-4.67%, and 8.07%-8.97%, respectively, and the fat content decreased by 60.00%-65.00%, 37.21%-46.51%, and 41.67%-42.42%, respectively. The abscisic acid (ABA) and raffinose content decreased after 1 year's storage; the former decreased gradually during the storage and the latter increased by 19.35%-45.45%, 7.02%-10.77%, and 16.13%-28.13%, respectively, after 4 months' storage and then decreased to the lowest level after 1 year's storage. The activity of antioxidant enzymes deceased, which resulted in the increases in fatty acid value and malondialdehyde (MDA). The changes in chemical composition after 1 year storage led to the deterioration of rice cooking quality, which was reflected in the decrease in viscosity and increases in gelatinization temperature and cooked rice hardness. CONCLUSION After 1 year's storage, the rice chemical composition changed and physiological and cooking quality characteristics decreased. Compared with japonica and indica-japonica hybrid rice, indica rice was more stable during 1 year storage. This may be due to the higher content of ABA and raffinose in fresh rice. Our findings will provide information for the identification and breeding of storable rice cultivars. © 2022 Society of Chemical Industry.
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Affiliation(s)
- Dawei Zhu
- Rice Product Quality Supervision and Inspection Center, Ministry of Agriculture and Rural Affairs, China National Rice Research Institute, Hangzhou, China
| | - Yafang Shao
- Rice Product Quality Supervision and Inspection Center, Ministry of Agriculture and Rural Affairs, China National Rice Research Institute, Hangzhou, China
| | - Changyun Fang
- Rice Product Quality Supervision and Inspection Center, Ministry of Agriculture and Rural Affairs, China National Rice Research Institute, Hangzhou, China
| | - Min Li
- Rice Research Institute of Guizhou Province, Guiyang, China
| | - Yonghong Yu
- Rice Product Quality Supervision and Inspection Center, Ministry of Agriculture and Rural Affairs, China National Rice Research Institute, Hangzhou, China
| | - Yebo Qin
- Argo-Technical Extension Service Center of Zhejiang Province, Hangzhou, China
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6
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Choudhary P, Pramitha L, Aggarwal PR, Rana S, Vetriventhan M, Muthamilarasan M. Biotechnological interventions for improving the seed longevity in cereal crops: progress and prospects. Crit Rev Biotechnol 2023; 43:309-325. [PMID: 35443842 DOI: 10.1080/07388551.2022.2027863] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Seed longevity is a measure of the viability of seeds during long-term storage and is crucial for germplasm conservation and crop improvement programs. Also, longevity is an important trait for ensuring food and nutritional security. Thus, a better understanding of various factors regulating seed longevity is requisite to improve this trait and to minimize the genetic drift during the regeneration of germplasm. In particular, seed deterioration of cereal crops during storage adversely affects agricultural productivity and food security. The irreversible process of seed deterioration involves a complex interplay between different genes and regulatory pathways leading to: loss of DNA integrity, membrane damage, inactivation of storage enzymes and mitochondrial dysfunction. Identifying the genetic determinants of seed longevity and manipulating them using biotechnological tools hold the key to ensuring prolonged seed storage. Genetics and genomics approaches had identified several genomic regions regulating the longevity trait in major cereals such as: rice, wheat, maize and barley. However, very few studies are available in other Poaceae members, including millets. Deploying omics tools, including genomics, proteomics, metabolomics, and phenomics, and integrating the datasets will pinpoint the precise molecular determinants affecting the survivability of seeds. Given this, the present review enumerates the genetic factors regulating longevity and demonstrates the importance of integrated omics strategies to dissect the molecular machinery underlying seed deterioration. Further, the review provides a roadmap for deploying biotechnological approaches to manipulate the genes and genomic regions to develop improved cultivars with prolonged storage potential.
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Affiliation(s)
- Pooja Choudhary
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad, India
| | - Lydia Pramitha
- School of Agriculture and Biosciences, Karunya Institute of Technology and Sciences, Coimbatore, India
| | - Pooja Rani Aggarwal
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad, India
| | - Sumi Rana
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad, India
| | - Mani Vetriventhan
- International Crops Research Institute for the Semi-Arid Tropics, Patancheru, India
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Identification of DNA Methylation Changes in European Beech Seeds during Desiccation and Storage. Int J Mol Sci 2023; 24:ijms24043557. [PMID: 36834975 PMCID: PMC9968092 DOI: 10.3390/ijms24043557] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Revised: 02/06/2023] [Accepted: 02/08/2023] [Indexed: 02/12/2023] Open
Abstract
Ageing and deterioration of seeds is a major problem for the maintenance of seed quality and viability during long-term storage. Prediction of early stages of seed deterioration in order to point out the plantlets' regeneration time is a major challenge of successful storage. In preserved seeds, damages accumulate within cells at the rate mainly related to their moisture content and temperature of storage. Current research reveals global alterations in DNA methylation in lipid-rich intermediate seeds during desiccation and storage at various regimes covering nonoptimal and optimal conditions. We show for the first time that monitoring of 5-methylcytosine (m5C) level in seeds can be used as a truly universal viability marker regardless of postharvest category of seeds and their composition. For seeds stored up to three years, in varied conditions, moisture content, temperature, and time of storage had significant influence on seedling emergence and DNA methylation (p < 0.05). Similarities among lipid-rich intermediate and orthodox seeds regarding different reactions of embryonic axes and cotyledons to desiccation are newly revealed. Along with previous studies on seeds dramatically different in desiccation tolerance (recalcitrant vs. orthodox), results regarding lipid-rich seeds positioned in-between (intermediate) prove that maintaining global DNA methylation status is crucial for maintaining seed viability.
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Trusiak M, Plitta-Michalak BP, Michalak M. Choosing the Right Path for the Successful Storage of Seeds. PLANTS (BASEL, SWITZERLAND) 2022; 12:72. [PMID: 36616200 PMCID: PMC9823941 DOI: 10.3390/plants12010072] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Revised: 12/19/2022] [Accepted: 12/21/2022] [Indexed: 06/17/2023]
Abstract
Seeds are the most commonly used source of storage material to preserve the genetic diversity of plants. However, prior to the deposition of seeds in gene banks, several questions need to be addressed. Here, we illustrate the scheme that can be used to ensure that the most optimal conditions are identified to enable the long-term storage of seeds. The main questions that need to be answered pertain to the production of viable seeds by plants, the availability of proper protocols for dormancy alleviation and germination, seed tolerance to desiccation and cold storage at -20 °C. Finally, it is very important to fully understand the capability or lack thereof for seeds or their explants to tolerate cryogenic conditions. The proper storage regimes for orthodox, intermediate and recalcitrant seeds are discussed.
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Affiliation(s)
- Magdalena Trusiak
- Department of Plant Physiology, Genetics and Biotechnology, University of Warmia and Mazury in Olsztyn, M. Oczapowskiego 1A, 10-721 Olsztyn, Poland
| | | | - Marcin Michalak
- Department of Plant Physiology, Genetics and Biotechnology, University of Warmia and Mazury in Olsztyn, M. Oczapowskiego 1A, 10-721 Olsztyn, Poland
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Alves S, Braga Â, Parreira D, Alhinho AT, Silva H, Ramos MJN, Costa MMR, Morais‐Cecílio L. Genome-wide identification, phylogeny, and gene duplication of the epigenetic regulators in Fagaceae. PHYSIOLOGIA PLANTARUM 2022; 174:e13788. [PMID: 36169620 PMCID: PMC9828519 DOI: 10.1111/ppl.13788] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Revised: 09/16/2022] [Accepted: 09/21/2022] [Indexed: 05/04/2023]
Abstract
Epigenetic regulators are proteins involved in controlling gene expression. Information about the epigenetic regulators within the Fagaceae, a relevant family of trees and shrubs of the northern hemisphere ecosystems, is scarce. With the intent to characterize these proteins in Fagaceae, we searched for orthologs of DNA methyltransferases (DNMTs) and demethylases (DDMEs) and Histone modifiers involved in acetylation (HATs), deacetylation (HDACs), methylation (HMTs), and demethylation (HDMTs) in Fagus, Quercus, and Castanea genera. Blast searches were performed in the available genomes, and freely available RNA-seq data were used to de novo assemble transcriptomes. We identified homologs of seven DNMTs, three DDMEs, six HATs, 11 HDACs, 32 HMTs, and 21 HDMTs proteins. Protein analysis showed that most of them have the putative characteristic domains found in these protein families, which suggests their conserved function. Additionally, to elucidate the evolutionary history of these genes within Fagaceae, paralogs were identified, and phylogenetic analyses were performed with DNA and histone modifiers. We detected duplication events in all species analyzed with higher frequency in Quercus and Castanea and discuss the evidence of transposable elements adjacent to paralogs and their involvement in gene duplication. The knowledge gathered from this work is a steppingstone to upcoming studies concerning epigenetic regulation in this economically important family of Fagaceae.
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Affiliation(s)
- Sofia Alves
- LEAF—Linking Landscape, Environment, Agriculture and FoodInstituto Superior de Agronomia, University of LisbonLisboaPortugal
| | - Ângelo Braga
- Instituto Superior de Agronomia, University of LisbonLisboaPortugal
| | - Denise Parreira
- Instituto Superior de Agronomia, University of LisbonLisboaPortugal
| | - Ana Teresa Alhinho
- Centre of Molecular and Environmental Biology (CBMA)University of MinhoBragaPortugal
| | - Helena Silva
- Centre of Molecular and Environmental Biology (CBMA)University of MinhoBragaPortugal
| | - Miguel Jesus Nunes Ramos
- LEAF—Linking Landscape, Environment, Agriculture and FoodInstituto Superior de Agronomia, University of LisbonLisboaPortugal
- Present address:
GenoMed, Diagnósticos de Medicina MolecularLisboaPortugal
| | | | - Leonor Morais‐Cecílio
- LEAF—Linking Landscape, Environment, Agriculture and FoodInstituto Superior de Agronomia, University of LisbonLisboaPortugal
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Triticale doubled haploid plant regeneration factors linked by structural equation modeling. J Appl Genet 2022; 63:677-690. [PMID: 36018540 PMCID: PMC9637073 DOI: 10.1007/s13353-022-00719-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Revised: 08/10/2022] [Accepted: 08/11/2022] [Indexed: 11/26/2022]
Abstract
Triticale regeneration via anther culture faces many difficulties, e.g., a low percentage of regenerated plants and the presence of albinos. Plant regeneration may be affected by abiotic stresses and by ingredients added to the induction medium. The latter influences biochemical pathways and plant regeneration efficiency. Among such ingredients, copper and silver ions acting as cofactors for enzymatic reactions are of interest. However, their role in plant tissue cultures and relationships with biochemical pathways has not been studied yet. The study evaluated relationships between DNA methylation, changes in DNA sequence variation, and green plant regeneration efficiency influenced by copper and silver ions during triticale plant regeneration. For this purpose, a biological model based on donor plants and their regenerants, a methylation-sensitive amplified fragment length polymorphism, and structural equation modeling were employed. The green plant regeneration efficiency varied from 0.71 to 6.06 green plants per 100 plated anthers. The values for the components of tissue culture-induced variation related to cytosine methylation in a CHH sequence context (where H is A, C, or T) were 8.65% for sequence variation, 0.76% for DNA demethylation, and 0.58% for de novo methylation. The proposed model states that copper ions affect the regeneration efficiency through cytosine methylation and may induce mutations through, e.g., oxidative processes, which may interfere with the green plant regeneration efficiency. The linear regression confirms that the plant regeneration efficiency rises with increasing copper ion concentration in the absence of Ag ions in the induction medium. The least absolute shrinkage and selection operator regression shows that de novo methylation, demethylation, and copper ions may be involved in the green plant regeneration efficiency. According to structural equation modeling, copper ions play a central role in the model determining the regeneration efficiency.
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Szuba A, Kalemba EM, Wawrzyniak MK, Suszka J, Chmielarz P. Deterioration in the Quality of Recalcitrant Quercus robur Seeds during Six Months of Storage at Subzero Temperatures: Ineffective Activation of Prosurvival Mechanisms and Evidence of Freezing Stress from an Untargeted Metabolomic Study. Metabolites 2022; 12:756. [PMID: 36005628 PMCID: PMC9413681 DOI: 10.3390/metabo12080756] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 08/09/2022] [Accepted: 08/15/2022] [Indexed: 11/25/2022] Open
Abstract
Pedunculate oak (Quercus robur L.) is an economically important forest-forming species in Poland that produces seeds that are sensitive to desiccation; therefore, short-lived seeds are classified as recalcitrant. Such seeds display active metabolism throughout storage. Acorns stored under controlled conditions (moisture content of 40%, temperature -3 °C) maintain viability for up to 1.5-2 years. Meanwhile, oaks only produce large numbers of seeds every few years during so-called mast years. This results in a scarcity of good-quality seeds for continuous nursery production and restoration. The recalcitrant storage behavior and the requirements of foresters make it necessary to develop a new protocol for longer acorn storage at lower temperatures. Two storage temperatures were tested: -3 °C (currently used in forest practice) and -7 °C. Our results showed that acorns stored for six months exhibited deterioration and reduced germination capacity, as well as reduced seedling performance, particularly when acorns were stored at -7 °C. To elucidate the decrease in quality during storage, an untargeted metabolomics study was performed for the first time and supported with the analysis of carbohydrates and percentages of carbon (C) and nitrogen (N). Embryonic axes were characterized by a lower C:N ratio and higher hydration. A total of 1985 metabolites were detected, and 303 were successfully identified and quantified, revealing 44 known metabolites that displayed significantly up- or downregulated abundance. We demonstrated for the first time that the significant deterioration of seed germination potential, particularly in seeds stored at -7 °C, was accompanied by an increased abundance of phenolic compounds and carbohydrates but also amino acids and phosphorylated monosaccharides, particularly in the embryonic axes. The increased abundance of defense-related metabolites (1,2,4-Benzenetriol; BTO), products of ascorbic acid degradation (threonic and isothreonic acid), as well as antifreezing compounds (sugar alcohols, predominantly threitol), was reported in seed stored at -7 °C. We hypothesize that seed deterioration was caused by freezing stress experienced during six months of storage at -7 °C, a decline in antioxidative potential and the unsuccessful rerouting of the energy-production pathways. Additionally, our data are a good example of the application of high-throughput metabolomic tools in forest management.
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Affiliation(s)
- Agnieszka Szuba
- Polish Academy of Sciences, Institute of Dendrology, Parkowa 5, PL-62035 Kórnik, Poland
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12
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Michalak M, Plitta-Michalak BP, Naskręt-Barciszewska MZ, Barciszewski J, Chmielarz P. DNA Methylation as an Early Indicator of Aging in Stored Seeds of “Exceptional” Species Populus nigra L. Cells 2022; 11:cells11132080. [PMID: 35805164 PMCID: PMC9265770 DOI: 10.3390/cells11132080] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Revised: 06/27/2022] [Accepted: 06/28/2022] [Indexed: 01/27/2023] Open
Abstract
Ex situ preservation of genetic resources is an essential strategy for the conservation of plant biodiversity. In this regard, seed storage is the most convenient and efficient way of preserving germplasm for future plant breeding efforts. A better understanding of the molecular changes that occur during seed desiccation and aging is necessary to improve conservation protocols, as well as real-time methods for monitoring seed quality. In the present study, we assessed changes in the level of genomic 5-methylcytosine (5mC) in seeds of Populus nigra L. by 2D-TLC. Epigenetic changes were characterized in response to several seed storage regimes. Our results demonstrate that P. nigra seeds represent an intermediate type of post-harvest behavior, falling between recalcitrant and orthodox seeds. This was also true for the epigenetic response of P. nigra seeds to external factors. A crucial question is whether aging in seeds is initiated by a decline in the level of 5mC, or if epigenetic changes induce a process that leads to deterioration. In our study, we demonstrate for the first time that 5mC levels decrease during storage and that the decline can be detected before any changes in seed germination are evident. Once P. nigra seeds reached an 8–10% reduction in the level of 5mC, a substantial decrease in germination occurred. The decline in the level of 5mC appears to be a critical parameter underlying the rapid deterioration of intermediate seeds. Thus, the measurement of 5mC can be a fast, real-time method for assessing asymptomatic aging in stored seeds.
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Affiliation(s)
- Marcin Michalak
- Department of Plant Physiology, Genetics and Biotechnology, University of Warmia and Mazury in Olsztyn, M Oczapowskiego 1A, 10-721 Olsztyn, Poland;
- Correspondence: ; Tel.: +48-89-523-44-55
| | - Beata Patrycja Plitta-Michalak
- Department of Plant Physiology, Genetics and Biotechnology, University of Warmia and Mazury in Olsztyn, M Oczapowskiego 1A, 10-721 Olsztyn, Poland;
- Department of Chemistry, University of Warmia and Mazury in Olsztyn, Plac Łódzki 4, 10-719 Olsztyn, Poland
| | | | - Jan Barciszewski
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Z. Noskowskiego 12/14, 61-704 Poznan, Poland; (M.Z.N.-B.); (J.B.)
- NanoBioMedical Centre, Adam Mickiewicz University, Wszechnicy Piastowskiej 3, 61-614 Poznan, Poland
| | - Paweł Chmielarz
- Institute of Dendrology, Polish Academy of Sciences, Parkowa 5, 62-035 Kornik, Poland;
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Epigenetic Marks, DNA Damage Markers, or Both? The Impact of Desiccation and Accelerated Aging on Nucleobase Modifications in Plant Genomic DNA. Cells 2022; 11:cells11111748. [PMID: 35681443 PMCID: PMC9179523 DOI: 10.3390/cells11111748] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Revised: 05/15/2022] [Accepted: 05/24/2022] [Indexed: 02/04/2023] Open
Abstract
Modifications of DNA nucleobases are present in all forms of life. The purpose of these modifications in eukaryotic cells, however, is not always clear. Although the role of 5-methylcytosine (m5C) in epigenetic regulation and the maintenance of stability in plant genomes is becoming better understood, knowledge pertaining to the origin and function of oxidized nucleobases is still scarce. The formation of 5-hydroxymetylcytosine (hm5C) in plant genomes is especially debatable. DNA modifications, functioning as regulatory factors or serving as DNA injury markers, may have an effect on DNA structure and the interaction of genomic DNA with proteins. Thus, these modifications can influence plant development and adaptation to environmental stress. Here, for the first time, the changes in DNA global levels of m5C, hm5C, and 8-oxo-7,8-dihydroguanine (8-oxoG) measured by ELISA have been documented in recalcitrant embryonic axes subjected to desiccation and accelerated aging. We demonstrated that tissue desiccation induces a similar trend in changes in the global level of hm5C and 8-oxoG, which may suggest that they both originate from the activity of reactive oxygen species (ROS). Our study supports the premise that m5C can serve as a marker of plant tissue viability whereas oxidized nucleobases, although indicating a cellular redox state, cannot.
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14
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Gomez-Cabellos S, Toorop PE, Cañal MJ, Iannetta PPM, Fernández-Pascual E, Pritchard HW, Visscher AM. Global DNA methylation and cellular 5-methylcytosine and H4 acetylated patterns in primary and secondary dormant seeds of Capsella bursa-pastoris (L.) Medik. (shepherd's purse). PROTOPLASMA 2022; 259:595-614. [PMID: 34212249 PMCID: PMC9010400 DOI: 10.1007/s00709-021-01678-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Accepted: 06/01/2021] [Indexed: 05/06/2023]
Abstract
Despite the importance of dormancy and dormancy cycling for plants' fitness and life cycle phenology, a comprehensive characterization of the global and cellular epigenetic patterns across space and time in different seed dormancy states is lacking. Using Capsella bursa-pastoris (L.) Medik. (shepherd's purse) seeds with primary and secondary dormancy, we investigated the dynamics of global genomic DNA methylation and explored the spatio-temporal distribution of 5-methylcytosine (5-mC) and histone H4 acetylated (H4Ac) epigenetic marks. Seeds were imbibed at 30 °C in a light regime to maintain primary dormancy, or in darkness to induce secondary dormancy. An ELISA-based method was used to quantify DNA methylation, in relation to total genomic cytosines. Immunolocalization of 5-mC and H4Ac within whole seeds (i.e., including testa) was assessed with reference to embryo anatomy. Global DNA methylation levels were highest in prolonged (14 days) imbibed primary dormant seeds, with more 5-mC marked nuclei present only in specific parts of the seed (e.g., SAM and cotyledons). In secondary dormant seeds, global methylation levels and 5-mC signal where higher at 3 and 7 days than 1 or 14 days. With respect to acetylation, seeds had fewer H4Ac marked nuclei (e.g., SAM) in deeper dormant states, for both types of dormancy. However, the RAM still showed signal after 14 days of imbibition under dormancy-inducing conditions, suggesting a central role for the radicle/RAM in the response to perceived ambient changes and the adjustment of the seed dormancy state. Thus, we show that seed dormancy involves extensive cellular remodeling of DNA methylation and H4 acetylation.
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Affiliation(s)
- Sara Gomez-Cabellos
- Department of Comparative Plant and Fungal Biology, Royal Botanic Gardens, Kew, Wakehurst Place, Ardingly, RH17 6TN West Sussex UK
- Departamento de Biología de Organismos y Sistemas, Universidad de Oviedo, C/Catedrático Rodrigo Uría, 33006 Oviedo, Spain
| | - Peter E. Toorop
- Department of Comparative Plant and Fungal Biology, Royal Botanic Gardens, Kew, Wakehurst Place, Ardingly, RH17 6TN West Sussex UK
| | - María Jesús Cañal
- Departamento de Biología de Organismos y Sistemas, Universidad de Oviedo, C/Catedrático Rodrigo Uría, 33006 Oviedo, Spain
| | | | - Eduardo Fernández-Pascual
- Departamento de Biología de Organismos y Sistemas, Universidad de Oviedo, C/Catedrático Rodrigo Uría, 33006 Oviedo, Spain
| | - Hugh W. Pritchard
- Department of Comparative Plant and Fungal Biology, Royal Botanic Gardens, Kew, Wakehurst Place, Ardingly, RH17 6TN West Sussex UK
| | - Anne M. Visscher
- Department of Comparative Plant and Fungal Biology, Royal Botanic Gardens, Kew, Wakehurst Place, Ardingly, RH17 6TN West Sussex UK
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15
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Rodell R, Tsao N, Ganguly A, Mosammaparast N. Use of High-Performance Liquid Chromatography-Mass Spectrometry (HPLC-MS) to Quantify Modified Nucleosides. Methods Mol Biol 2022; 2444:125-140. [PMID: 35290635 PMCID: PMC9426999 DOI: 10.1007/978-1-0716-2063-2_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] [Indexed: 06/14/2023]
Abstract
Physiological and chemically induced modifications to nucleosides are common in both DNA and RNA. Physiological forms of these modifications play critical roles in gene expression, yet aberrant marks, if left unrepaired, may be associated with increased genome instability. Due to the low prevalence of these marks in most samples of interest, a highly sensitive method is needed for their detection and quantitation. High-performance liquid chromatography, coupled to mass spectrometry (HPLC-MS), provides this high degree of sensitivity while also being adaptable to nearly any modified nucleoside of interest and still maintaining exquisite specificity. In this chapter, we demonstrate how to use HPLC-MS to analyze the catalytic activity of a nucleic acid demethylase, to quantify the prevalence of N6-methyladenosine from RNA, and to determine the kinetics of alkylation damage repair.
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Affiliation(s)
- Rebecca Rodell
- Department of Pathology and Immunology, Washington University in St. Louis School of Medicine, St. Louis, MO, USA
| | - Ning Tsao
- Department of Pathology and Immunology, Washington University in St. Louis School of Medicine, St. Louis, MO, USA
| | - Adit Ganguly
- Department of Pathology and Immunology, Washington University in St. Louis School of Medicine, St. Louis, MO, USA
| | - Nima Mosammaparast
- Department of Pathology and Immunology, Washington University in St. Louis School of Medicine, St. Louis, MO, USA.
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16
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Can Forest Trees Cope with Climate Change?-Effects of DNA Methylation on Gene Expression and Adaptation to Environmental Change. Int J Mol Sci 2021; 22:ijms222413524. [PMID: 34948318 PMCID: PMC8703565 DOI: 10.3390/ijms222413524] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Revised: 12/09/2021] [Accepted: 12/12/2021] [Indexed: 12/13/2022] Open
Abstract
Epigenetic modifications, including chromatin modifications and DNA methylation, play key roles in regulating gene expression in both plants and animals. Transmission of epigenetic markers is important for some genes to maintain specific expression patterns and preserve the status quo of the cell. This article provides a review of existing research and the current state of knowledge about DNA methylation in trees in the context of global climate change, along with references to the potential of epigenome editing tools and the possibility of their use for forest tree research. Epigenetic modifications, including DNA methylation, are involved in evolutionary processes, developmental processes, and environmental interactions. Thus, the implications of epigenetics are important for adaptation and phenotypic plasticity because they provide the potential for tree conservation in forest ecosystems exposed to adverse conditions resulting from global warming and regional climate fluctuations.
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17
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Michalak M, Plitta-Michalak BP, Nadarajan J, Colville L. Volatile signature indicates viability of dormant orthodox seeds. PHYSIOLOGIA PLANTARUM 2021; 173:788-804. [PMID: 34008870 DOI: 10.1111/ppl.13465] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Revised: 05/11/2021] [Indexed: 06/12/2023]
Abstract
All seeds eventually die even under optimal storage conditions. The moment of viability loss is difficult to predict and detect. In order to differentiate between dead and viable dormant orthodox seeds, GC-MS analysis was used to non-invasively evaluate the volatile signature of seeds of Pyrus communis L. and Sorbus aucuparia L. Dormant seeds are capable of extended metabolic depression. However, their low metabolic rate remains largely unquantified, and there are no measurements of metabolites, i.e. volatile organic compounds (VOC) for physiologically dormant seeds during storage. Therefore, to address this issue, seeds were stored at a broad range of moisture content (MC) ranging from 2 to 30% under cryogenic (-196°C), cool (5°C) and elevated (40°C) temperatures. Volatile emission was highly dependent on seed MC and storage temperature and was higher under conditions associated with seed viability loss. However, changes in the emission of volatiles entrapped in seeds and released during 24 h after storage were detected for all conditions, providing insight into the processes occurring in dry dormant seeds. Among the 36 volatiles identified, three (acetaldehyde, ethanol, ethyl acetate) were highly correlated with seed germinability and show potential for the non-invasive screening of viability. Significantly, all three VOC are derived mostly from glycolysis and peroxidation and were detected even under very low moisture and temperature storage conditions. This is the first study to report on VOC accumulation and emission from physiologically dormant seeds and provide a broader view into their viability.
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Affiliation(s)
- Marcin Michalak
- Department of Plant Physiology, Genetics and Biotechnology, University of Warmia and Mazury in Olsztyn, Olsztyn, Poland
- Institute of Dendrology, Polish Academy of Sciences, Kórnik, Poland
| | - Beata P Plitta-Michalak
- Department of Plant Physiology, Genetics and Biotechnology, University of Warmia and Mazury in Olsztyn, Olsztyn, Poland
- Institute of Dendrology, Polish Academy of Sciences, Kórnik, Poland
| | - Jayanthi Nadarajan
- Comparative Plant and Fungal Biology, Royal Botanic Gardens, Kew, Wakehurst Place, Ardingly, UK
- The New Zealand Institute for Plant and Food Research Limited, Food Industry Science Centre, Fitzherbert Science Centre, Palmerston North, New Zealand
| | - Louise Colville
- Comparative Plant and Fungal Biology, Royal Botanic Gardens, Kew, Wakehurst Place, Ardingly, UK
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18
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Kakoulidou I, Avramidou EV, Baránek M, Brunel-Muguet S, Farrona S, Johannes F, Kaiserli E, Lieberman-Lazarovich M, Martinelli F, Mladenov V, Testillano PS, Vassileva V, Maury S. Epigenetics for Crop Improvement in Times of Global Change. BIOLOGY 2021; 10:766. [PMID: 34439998 PMCID: PMC8389687 DOI: 10.3390/biology10080766] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 08/04/2021] [Accepted: 08/06/2021] [Indexed: 12/15/2022]
Abstract
Epigenetics has emerged as an important research field for crop improvement under the on-going climatic changes. Heritable epigenetic changes can arise independently of DNA sequence alterations and have been associated with altered gene expression and transmitted phenotypic variation. By modulating plant development and physiological responses to environmental conditions, epigenetic diversity-naturally, genetically, chemically, or environmentally induced-can help optimise crop traits in an era challenged by global climate change. Beyond DNA sequence variation, the epigenetic modifications may contribute to breeding by providing useful markers and allowing the use of epigenome diversity to predict plant performance and increase final crop production. Given the difficulties in transferring the knowledge of the epigenetic mechanisms from model plants to crops, various strategies have emerged. Among those strategies are modelling frameworks dedicated to predicting epigenetically controlled-adaptive traits, the use of epigenetics for in vitro regeneration to accelerate crop breeding, and changes of specific epigenetic marks that modulate gene expression of traits of interest. The key challenge that agriculture faces in the 21st century is to increase crop production by speeding up the breeding of resilient crop species. Therefore, epigenetics provides fundamental molecular information with potential direct applications in crop enhancement, tolerance, and adaptation within the context of climate change.
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Affiliation(s)
- Ioanna Kakoulidou
- Department of Molecular Life Sciences, Technical University of Munich, Liesel-Beckmann-Str. 2, 85354 Freising, Germany; (I.K.); (F.J.)
| | - Evangelia V. Avramidou
- Laboratory of Forest Genetics and Biotechnology, Institute of Mediterranean Forest Ecosystems, Hellenic Agricultural Organization-Dimitra (ELGO-DIMITRA), 11528 Athens, Greece;
| | - Miroslav Baránek
- Faculty of Horticulture, Mendeleum—Institute of Genetics, Mendel University in Brno, Valtická 334, 69144 Lednice, Czech Republic;
| | - Sophie Brunel-Muguet
- UMR 950 Ecophysiologie Végétale, Agronomie et Nutritions N, C, S, UNICAEN, INRAE, Normandie Université, CEDEX, F-14032 Caen, France;
| | - Sara Farrona
- Plant and AgriBiosciences Centre, Ryan Institute, National University of Ireland (NUI) Galway, H91 TK33 Galway, Ireland;
| | - Frank Johannes
- Department of Molecular Life Sciences, Technical University of Munich, Liesel-Beckmann-Str. 2, 85354 Freising, Germany; (I.K.); (F.J.)
- Institute for Advanced Study, Technical University of Munich, Lichtenberg Str. 2a, 85748 Garching, Germany
| | - Eirini Kaiserli
- Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, Bower Building, University of Glasgow, Glasgow G12 8QQ, UK;
| | - Michal Lieberman-Lazarovich
- Institute of Plant Sciences, Agricultural Research Organization, Volcani Center, Rishon LeZion 7505101, Israel;
| | - Federico Martinelli
- Department of Biology, University of Florence, 50019 Sesto Fiorentino, Italy;
| | - Velimir Mladenov
- Faculty of Agriculture, University of Novi Sad, Sq. Dositeja Obradovića 8, 21000 Novi Sad, Serbia;
| | - Pilar S. Testillano
- Pollen Biotechnology of Crop Plants Group, Centro de Investigaciones Biológicas Margarita Salas-(CIB-CSIC), Ramiro Maeztu 9, 28040 Madrid, Spain;
| | - Valya Vassileva
- Department of Molecular Biology and Genetics, Institute of Plant Physiology and Genetics, Bulgarian Academy of Sciences, Acad. Georgi Bonchev Str., Bldg. 21, 1113 Sofia, Bulgaria;
| | - Stéphane Maury
- Laboratoire de Biologie des Ligneux et des Grandes Cultures, INRAE, EA1207 USC1328, Université d’Orléans, F-45067 Orléans, France
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19
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Epigenetic Integrity of Orthodox Seeds Stored under Conventional and Cryogenic Conditions. FORESTS 2021. [DOI: 10.3390/f12030288] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
The level of 5-methylcytosine (m5C) in DNA has been observed to change in plants in response to biotic and abiotic stress factors. Little information has been reported on alterations in DNA methylation in orthodox tree seeds in response to storage conditions. In the current study, epigenetic integrity was analyzed in seeds of Pyrus communis L. in response to conventional and cryogenic storage. The results indicate that conventional storage under optimal conditions resulted in a significant increase in m5C. In contrast, a decrease in m5C level after cryostorage at high water content (WC) was observed, not only in seeds but also in 3-month-old seedlings which were smaller than seedlings obtained from seeds cryostored at optimal WC. This shows that non-optimal cryostorage conditions increase epigenetic instability in seeds and seedlings. Optimal procedures for germplasm conservation are very important for germplasm banking since they have serious implications for the quality of stored collections. Maintaining epigenetic integrity during WC adjustment and optimal storage is a characteristic feature of orthodox seeds. The current results underline the importance of proper protocols and techniques for conventional storage and particularly cryopreservation as a method for conservation of true-to-type germplasm for long periods.
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20
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Engels JMM, Thormann I. Main Challenges and Actions Needed to Improve Conservation and Sustainable Use of Our Crop Wild Relatives. PLANTS 2020; 9:plants9080968. [PMID: 32751715 PMCID: PMC7463933 DOI: 10.3390/plants9080968] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/05/2020] [Revised: 07/25/2020] [Accepted: 07/27/2020] [Indexed: 12/14/2022]
Abstract
Crop wild relatives (CWR, plural CWRs) are those wild species that are regarded as the ancestors of our cultivated crops. It was only at the end of the last century that they were accorded a high priority for their conservation and, thus, for many genebanks, they are a new and somewhat unknown set of plant genetic resources for food and agriculture. After defining and characterizing CWR and their general threat status, providing an assessment of biological peculiarities of CWR with respect to conservation management, illustrating the need for prioritization and addressing the importance of data and information, we made a detailed assessment of specific aspects of CWRs of direct relevance for their conservation and use. This assessment was complemented by an overview of the current status of CWRs conservation and use, including facts and figures on the in situ conservation, on the ex situ conservation in genebanks and botanic gardens, as well as of the advantages of a combination of in situ and ex situ conservation, the so-called complementary conservation approach. In addition, a brief assessment of the situation with respect to the use of CWRs was made. From these assessments we derived the needs for action in order to achieve a more effective and efficient conservation and use, specifically with respect to the documentation of CWRs, their in situ and ex situ, as well as their complementarity conservation, and how synergies between these components can be obtained. The review was concluded with suggestions on how use can be strengthened, as well as the conservation system at large at the local, national, and regional/international level. Finally, based on the foregoing assessments, a number of recommendations were elaborated on how CWRs can be better conserved and used in order to exploit their potential benefits more effectively.
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Affiliation(s)
- Johannes M. M. Engels
- Alliance of Bioversity International and CIAT, Maccarese, 00054 Rome, Italy
- Correspondence:
| | - Imke Thormann
- Federal Office for Agriculture and Food, 53179 Bonn, Germany;
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21
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Dissecting the Seed Maturation and Germination Processes in the Non-Orthodox Quercus ilex Species Based on Protein Signatures as Revealed by 2-DE Coupled to MALDI-TOF/TOF Proteomics Strategy. Int J Mol Sci 2020; 21:ijms21144870. [PMID: 32660160 PMCID: PMC7402289 DOI: 10.3390/ijms21144870] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Revised: 07/06/2020] [Accepted: 07/07/2020] [Indexed: 12/15/2022] Open
Abstract
Unlike orthodox species, seed recalcitrance is poorly understood, especially at the molecular level. In this regard, seed maturation and germination were studied in the non-orthodox Quercus ilex by using a proteomics strategy based on two-dimensional gel electrophoresis coupled to matrix-assisted laser desorption ionization/time of flight (2-DE-MALDI-TOF).Cotyledons and embryo/radicle were sampled at different developmental stages, including early (M1–M3), middle (M4–M7), and late (M8–M9) seed maturation, and early (G1–G3) and late (G4–G5) germination. Samples corresponding to non-germinating, inviable, seeds were also included. Protein extracts were subjected to 2-dimensional gel electrophoresis (2-DE) and changes in the protein profiles were analyzed. Identified variable proteins were grouped according to their function, being the energy, carbohydrate, lipid, and amino acid metabolisms, together with protein fate, redox homeostasis, and response to stress are the most represented groups. Beyond the visual aspect, morphometry, weight, and water content, each stage had a specific protein signature. Clear tendencies for the different protein groups throughout the maturation and germination stages were observed for, respectively, cotyledon and the embryo axis. Proteins related to metabolism, translation, legumins, proteases, proteasome, and those stress related were less abundant in non-germinating seeds, it related to the loss of viability. Cotyledons were enriched with reserve proteins and protein-degrading enzymes, while the embryo axis was enriched with proteins of cell defense and rescue, including heat-shock proteins (HSPs) and antioxidants. The peaks of enzyme proteins occurred at the middle stages (M6–M7) in cotyledons and at late ones (M8–M9) in the embryo axis. Unlike orthodox seeds, proteins associated with glycolysis, tricarboxylic acid cycle, carbohydrate, amino acid and lipid metabolism are present at high levels in the mature seed and were maintained throughout the germination stages. The lack of desiccation tolerance in Q. ilex seeds may be associated with the repression of some genes, late embryogenesis abundant proteins being one of the candidates.
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22
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Katsuya-Gaviria K, Caro E, Carrillo-Barral N, Iglesias-Fernández R. Reactive Oxygen Species (ROS) and Nucleic Acid Modifications During Seed Dormancy. PLANTS (BASEL, SWITZERLAND) 2020; 9:E679. [PMID: 32471221 PMCID: PMC7356579 DOI: 10.3390/plants9060679] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Revised: 05/24/2020] [Accepted: 05/26/2020] [Indexed: 12/15/2022]
Abstract
The seed is the propagule of higher plants and allows its dissemination and the survival of the species. Seed dormancy prevents premature germination under favourable conditions. Dormant seeds are only able to germinate in a narrow range of conditions. During after-ripening (AR), a mechanism of dormancy release, seeds gradually lose dormancy through a period of dry storage. This review is mainly focused on how chemical modifications of mRNA and genomic DNA, such as oxidation and methylation, affect gene expression during late stages of seed development, especially during dormancy. The oxidation of specific nucleotides produced by reactive oxygen species (ROS) alters the stability of the seed stored mRNAs, being finally degraded or translated into non-functional proteins. DNA methylation is a well-known epigenetic mechanism of controlling gene expression. In Arabidopsis thaliana, while there is a global increase in CHH-context methylation through embryogenesis, global DNA methylation levels remain stable during seed dormancy, decreasing when germination occurs. The biological significance of nucleic acid oxidation and methylation upon seed development is discussed.
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Affiliation(s)
- Kai Katsuya-Gaviria
- Centro de Biotecnología y Genómica de Plantas-Severo Ochoa (CBGP, UPM-INIA), Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), 28223-Pozuelo de Alarcón, Spain; (K.K.-G.); (E.C.)
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, UPM, 28040-Madrid, Spain
| | - Elena Caro
- Centro de Biotecnología y Genómica de Plantas-Severo Ochoa (CBGP, UPM-INIA), Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), 28223-Pozuelo de Alarcón, Spain; (K.K.-G.); (E.C.)
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, UPM, 28040-Madrid, Spain
| | - Néstor Carrillo-Barral
- Departamento de Fisiología Vegetal, Facultad de Ciencias, Universidad da Coruña (UdC), 15008-A Coruña, Spain;
| | - Raquel Iglesias-Fernández
- Centro de Biotecnología y Genómica de Plantas-Severo Ochoa (CBGP, UPM-INIA), Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), 28223-Pozuelo de Alarcón, Spain; (K.K.-G.); (E.C.)
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, UPM, 28040-Madrid, Spain
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Pirredda M, González-Benito ME, Martín C, Mira S. Genetic and Epigenetic Stability in Rye Seeds under Different Storage Conditions: Ageing and Oxygen Effect. PLANTS 2020; 9:plants9030393. [PMID: 32210066 PMCID: PMC7154831 DOI: 10.3390/plants9030393] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Revised: 03/16/2020] [Accepted: 03/19/2020] [Indexed: 02/01/2023]
Abstract
Seed ageing is a complex process and can be described as the loss of viability or quality with time. It is important to elucidate whether genetic and epigenetic stability is altered in stored seeds and in seedlings produced from them. Non-stored and stored rye seeds at different stages of ageing were compared, as well as the seedlings obtained from them. Seeds were stored at 35 °C and 15% water content, under vacuum or air atmosphere. DNA of seeds and seedlings was isolated at three stages of the deterioration curve: P75 (13 days), P20 (29 days), and P0 (36 days). Genetic stability was assessed by RAPD technique, and epigenetic changes by MSAP markers. While seeds showed genetic stability after storage, the similarity of seedlings obtained from seeds stored for 29 days was lower (95%) when compared to seedlings from control seeds. Epigenetic changes were between 15% and 30% (both de novo methylation and demethylation) in the stored seeds compared to control seeds, with no differences between 13 and 29 days of storage with either air or vacuum atmospheres. In seedlings, epigenetic changes significantly increased with storage time. In conclusion, ageing increased epigenetic instability in both seeds and seedlings, when compared to controls.
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Affiliation(s)
| | | | | | - Sara Mira
- Correspondence: ; Tel.: +34-91-06-70888
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24
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Ebone LA, Caverzan A, Chavarria G. Physiologic alterations in orthodox seeds due to deterioration processes. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2019; 145:34-42. [PMID: 31665665 DOI: 10.1016/j.plaphy.2019.10.028] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2019] [Revised: 10/17/2019] [Accepted: 10/18/2019] [Indexed: 05/22/2023]
Abstract
Seed deterioration is a partially elucidated phenomenon that happen during the life of the seed. This review describes the processes that lead to seed deterioration, including loss of seed protection capacity against reactive oxygen species (ROS), damage to the plasma membrane, consumption of reserves, and damage to genetic material. A hypothesis of how seed deterioration occurs was also addressed; in this hypothesis, seed deterioration was divided into three phases. The first is the beginning of deterioration, with a slight reduction of vigor caused by the reactions of reducing sugars with antioxidant enzymes and genetic material. In the second, the cell shows oxidative damages, causing lipid peroxidation, which leads to the leaching of solutes, the formation of malondialdehyde, and, consequently, an increase in damages to genetic material. In the third phase, there is cell collapse with mitochondrial membrane deconstruction and a high accumulation of reactive oxygen species, malondialdehyde, and reducing sugars.
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Affiliation(s)
- Luciano Antônio Ebone
- Laboratory of Plant Physiology, Agronomy Post-Graduate Program, University of Passo Fundo, Passo Fundo, Rio Grande do Sul, Brazil.
| | - Andréia Caverzan
- Laboratory of Plant Physiology, Agronomy Post-Graduate Program, University of Passo Fundo, Passo Fundo, Rio Grande do Sul, Brazil.
| | - Geraldo Chavarria
- Laboratory of Plant Physiology, Agronomy Post-Graduate Program, University of Passo Fundo, Passo Fundo, Rio Grande do Sul, Brazil.
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25
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Fleming MB, Hill LM, Walters C. The kinetics of ageing in dry-stored seeds: a comparison of viability loss and RNA degradation in unique legacy seed collections. ANNALS OF BOTANY 2019; 123:1133-1146. [PMID: 30566591 PMCID: PMC6613187 DOI: 10.1093/aob/mcy217] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Accepted: 11/29/2018] [Indexed: 05/05/2023]
Abstract
BACKGROUND AND AIMS Determining seed longevity by identifying chemical changes that precede, and may be linked to, seed mortality, is an important but difficult task. The standard assessment, germination proportion, reveals seed longevity by showing that germination proportion declines, but cannot be used to predict when germination will be significantly compromised. Assessment of molecular integrity, such as RNA integrity, may be more informative about changes in seed health that precede viability loss, and has been shown to be useful in soybean. METHODS A collection of seeds stored at 5 °C and 35-50 % relative humidity for 1-30 years was used to test how germination proportion and RNA integrity are affected by storage time. Similarly, a collection of seeds stored at temperatures from -12 to +32 °C for 59 years was used to manipulate ageing rate. RNA integrity was calculated using total RNA extracted from one to five seeds per sample, analysed on an Agilent Bioanalyzer. RESULTS Decreased RNA integrity was usually observed before viability loss. Correlation of RNA integrity with storage time or storage temperature was negative and significant for most species tested. Exceptions were watermelon, for which germination proportion and storage time were poorly correlated, and tomato, which showed electropherogram anomalies that affected RNA integrity number calculation. Temperature dependencies of ageing reactions were not significantly different across species or mode of detection. The overall correlation between germination proportion and RNA integrity, across all experiments, was positive and significant. CONCLUSIONS Changes in RNA integrity when ageing is asymptomatic can be used to predict onset of viability decline. RNA integrity appears to be a metric of seed ageing that is broadly applicable across species. Time and molecular mobility of the substrate affect both the progress of seed ageing and loss of RNA integrity.
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Affiliation(s)
- Margaret B Fleming
- USDA-ARS, National Laboratory for Genetic Resource Preservation, Fort Collins, CO, USA
| | - Lisa M Hill
- USDA-ARS, National Laboratory for Genetic Resource Preservation, Fort Collins, CO, USA
| | - Christina Walters
- USDA-ARS, National Laboratory for Genetic Resource Preservation, Fort Collins, CO, USA
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26
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Fleming MB, Hill LM, Walters C. The kinetics of ageing in dry-stored seeds: a comparison of viability loss and RNA degradation in unique legacy seed collections. ANNALS OF BOTANY 2019; 123:1133-1146. [PMID: 30566591 DOI: 10.1093/aob/mcy1217] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Accepted: 11/29/2018] [Indexed: 05/22/2023]
Abstract
BACKGROUND AND AIMS Determining seed longevity by identifying chemical changes that precede, and may be linked to, seed mortality, is an important but difficult task. The standard assessment, germination proportion, reveals seed longevity by showing that germination proportion declines, but cannot be used to predict when germination will be significantly compromised. Assessment of molecular integrity, such as RNA integrity, may be more informative about changes in seed health that precede viability loss, and has been shown to be useful in soybean. METHODS A collection of seeds stored at 5 °C and 35-50 % relative humidity for 1-30 years was used to test how germination proportion and RNA integrity are affected by storage time. Similarly, a collection of seeds stored at temperatures from -12 to +32 °C for 59 years was used to manipulate ageing rate. RNA integrity was calculated using total RNA extracted from one to five seeds per sample, analysed on an Agilent Bioanalyzer. RESULTS Decreased RNA integrity was usually observed before viability loss. Correlation of RNA integrity with storage time or storage temperature was negative and significant for most species tested. Exceptions were watermelon, for which germination proportion and storage time were poorly correlated, and tomato, which showed electropherogram anomalies that affected RNA integrity number calculation. Temperature dependencies of ageing reactions were not significantly different across species or mode of detection. The overall correlation between germination proportion and RNA integrity, across all experiments, was positive and significant. CONCLUSIONS Changes in RNA integrity when ageing is asymptomatic can be used to predict onset of viability decline. RNA integrity appears to be a metric of seed ageing that is broadly applicable across species. Time and molecular mobility of the substrate affect both the progress of seed ageing and loss of RNA integrity.
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Affiliation(s)
- Margaret B Fleming
- USDA-ARS, National Laboratory for Genetic Resource Preservation, Fort Collins, CO, USA
| | - Lisa M Hill
- USDA-ARS, National Laboratory for Genetic Resource Preservation, Fort Collins, CO, USA
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27
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Kurek K, Plitta-Michalak B, Ratajczak E. Reactive Oxygen Species as Potential Drivers of the Seed Aging Process. PLANTS (BASEL, SWITZERLAND) 2019; 8:E174. [PMID: 31207940 PMCID: PMC6630744 DOI: 10.3390/plants8060174] [Citation(s) in RCA: 69] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Revised: 05/24/2019] [Accepted: 05/30/2019] [Indexed: 12/27/2022]
Abstract
Seeds are an important life cycle stage because they guarantee plant survival in unfavorable environmental conditions and the transfer of genetic information from parents to offspring. However, similar to every organ, seeds undergo aging processes that limit their viability and ultimately cause the loss of their basic property, i.e., the ability to germinate. Seed aging is a vital economic and scientific issue that is related to seed resistance to an array of factors, both internal (genetic, structural, and physiological) and external (mainly storage conditions: temperature and humidity). Reactive oxygen species (ROS) are believed to initiate seed aging via the degradation of cell membrane phospholipids and the structural and functional deterioration of proteins and genetic material. Researchers investigating seed aging claim that the effective protection of genetic resources requires an understanding of the reasons for senescence of seeds with variable sensitivity to drying and long-term storage. Genomic integrity considerably affects seed viability and vigor. The deterioration of nucleic acids inhibits transcription and translation and exacerbates reductions in the activity of antioxidant system enzymes. All of these factors significantly limit seed viability.
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Affiliation(s)
- Katarzyna Kurek
- Institute of Dendrology, Polish Academy of Sciences, Parkowa 5, 62-035 Kórnik, Poland.
| | | | - Ewelina Ratajczak
- Institute of Dendrology, Polish Academy of Sciences, Parkowa 5, 62-035 Kórnik, Poland.
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28
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Plitta-Michalak BP, Naskret-Barciszewska MZ, Kotlarski S, Tomaszewski D, Tylkowski T, Barciszewski J, Chmielarz P, Michalak M. Changes in genomic 5-methylcytosine level mirror the response of orthodox (Acer platanoides L.) and recalcitrant (Acer pseudoplatanus L.) seeds to severe desiccation. TREE PHYSIOLOGY 2018; 38:617-629. [PMID: 29121348 DOI: 10.1093/treephys/tpx134] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2017] [Accepted: 09/26/2017] [Indexed: 06/07/2023]
Abstract
Poor storability of recalcitrant seeds is due to their inability to tolerate low moisture content. Understanding the processes underlying their recalcitrance is a prerequisite to developing a maintenance strategy and prolonging their lifespan. Multiple studies have investigated the differences between orthodox (desiccation-tolerant) and recalcitrant (desiccation-sensitive) seeds. Information on epigenetic regulation, however, is lacking and thus limits our understanding of the processes defining the physiology of seeds. In the present comparative study, changes in the global levels of 5-methylcytosine (m5C) in orthodox and recalcitrant seeds of Acer platanoides L. and Acer pseudoplatanus L. were characterized during progressive stages of severe drying. Concomitant with their differential sensitivity to desiccation stress, we demonstrate variation in the response of embryonic axes and cotyledons to water deficit at the level of DNA methylation. Results indicate that desiccation-induced changes in m5C are both tissue- and seed category-specific and are highly correlated with recalcitrant seed viability. Moreover, we demonstrate that m5C global changes in response to desiccation are not retained in DNA isolated from seedlings, except in seedlings that are derived from strongly desiccated orthodox seeds (moisture content of 3.5%). Finally, the potential utilization of m5C status as a universal seed viability marker is discussed.
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Affiliation(s)
| | | | - Szymon Kotlarski
- Institute of Dendrology, Polish Academy of Sciences, Parkowa 5, 62-035 Kórnik, Poland
| | - Dominik Tomaszewski
- Institute of Dendrology, Polish Academy of Sciences, Parkowa 5, 62-035 Kórnik, Poland
| | - Tadeusz Tylkowski
- Institute of Dendrology, Polish Academy of Sciences, Parkowa 5, 62-035 Kórnik, Poland
| | - Jan Barciszewski
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Z. Noskowskiego 12/14, 61-704 Poznan, Poland
| | - Pawel Chmielarz
- Institute of Dendrology, Polish Academy of Sciences, Parkowa 5, 62-035 Kórnik, Poland
| | - Marcin Michalak
- Institute of Dendrology, Polish Academy of Sciences, Parkowa 5, 62-035 Kórnik, Poland
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29
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Großkinsky DK, Syaifullah SJ, Roitsch T. Integration of multi-omics techniques and physiological phenotyping within a holistic phenomics approach to study senescence in model and crop plants. JOURNAL OF EXPERIMENTAL BOTANY 2018; 69:825-844. [PMID: 29444308 DOI: 10.1093/jxb/erx333] [Citation(s) in RCA: 75] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
The study of senescence in plants is complicated by diverse levels of temporal and spatial dynamics as well as the impact of external biotic and abiotic factors and crop plant management. Whereas the molecular mechanisms involved in developmentally regulated leaf senescence are very well understood, in particular in the annual model plant species Arabidopsis, senescence of other organs such as the flower, fruit, and root is much less studied as well as senescence in perennials such as trees. This review addresses the need for the integration of multi-omics techniques and physiological phenotyping into holistic phenomics approaches to dissect the complex phenomenon of senescence. That became feasible through major advances in the establishment of various, complementary 'omics' technologies. Such an interdisciplinary approach will also need to consider knowledge from the animal field, in particular in relation to novel regulators such as small, non-coding RNAs, epigenetic control and telomere length. Such a characterization of phenotypes via the acquisition of high-dimensional datasets within a systems biology approach will allow us to systematically characterize the various programmes governing senescence beyond leaf senescence in Arabidopsis and to elucidate the underlying molecular processes. Such a multi-omics approach is expected to also spur the application of results from model plants to agriculture and their verification for sustainable and environmentally friendly improvement of crop plant stress resilience and productivity and contribute to improvements based on postharvest physiology for the food industry and the benefit of its customers.
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Affiliation(s)
- Dominik K Großkinsky
- Department of Plant and Environmental Sciences, Copenhagen Plant Science Centre, University of Copenhagen, Højbakkegård Allé, Taastrup, Denmark
| | - Syahnada Jaya Syaifullah
- Department of Plant and Environmental Sciences, Copenhagen Plant Science Centre, University of Copenhagen, Højbakkegård Allé, Taastrup, Denmark
| | - Thomas Roitsch
- Department of Plant and Environmental Sciences, Copenhagen Plant Science Centre, University of Copenhagen, Højbakkegård Allé, Taastrup, Denmark
- Department of Adaptive Biotechnologies, Global Change Research Institute, CAS, v.v.i., Drásov, Czech Republic
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30
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Varga S, Soulsbury CD. Paternal arbuscular mycorrhizal fungal status affects DNA methylation in seeds. Biol Lett 2017; 13:rsbl.2017.0407. [PMID: 28931731 DOI: 10.1098/rsbl.2017.0407] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Accepted: 08/29/2017] [Indexed: 11/12/2022] Open
Abstract
Most land plants grow in association with arbuscular mycorrhizal fungi (AMF) in their roots and these fungi can cause transgenerational effects on plants' offspring. These may be caused by changes in DNA methylation of the offspring. In this study, we compared the amount of global DNA methylation in seeds of the gynodioecious plant Geranium sylvaticum in relation to the gender and the AMF status of the parents producing the seeds. The amount of DNA methylated was positively related to seed mass. Seeds produced by females had a similar proportion of methylated DNA regardless of the AMF status of the father siring the seed. By contrast, seeds from hermaphrodites had higher DNA methylation when sired by AMF fathers. We show to the best of our knowledge for the first time, that the AMF status of fathers can affect DNA methylation in seeds and that these changes in DNA methylation are further dependent on the gender of the mother producing the seeds.
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Affiliation(s)
- Sandra Varga
- School of Life Sciences, University of Lincoln, Joseph Banks Laboratories, Lincoln LN6 7TS, UK
| | - Carl D Soulsbury
- School of Life Sciences, University of Lincoln, Joseph Banks Laboratories, Lincoln LN6 7TS, UK
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31
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Gianoglio S, Moglia A, Acquadro A, Comino C, Portis E. The genome-wide identification and transcriptional levels of DNA methyltransferases and demethylases in globe artichoke. PLoS One 2017; 12:e0181669. [PMID: 28746368 PMCID: PMC5529103 DOI: 10.1371/journal.pone.0181669] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2017] [Accepted: 07/05/2017] [Indexed: 11/19/2022] Open
Abstract
Changes to the cytosine methylation status of DNA, driven by the activity of C5 methyltransferases (C5-MTases) and demethylases, exert an important influence over development, transposon movement, gene expression and imprinting. Three groups of C5-MTase enzymes have been identified in plants, namely MET (methyltransferase 1), CMT (chromomethyltransferases) and DRM (domains rearranged methyltransferases). Here the repertoire of genes encoding C5-MTase and demethylase by the globe artichoke (Cynara cardunculus var. scolymus) is described, based on sequence homology, a phylogenetic analysis and a characterization of their functional domains. A total of ten genes encoding C5-MTase (one MET, five CMTs and four DRMs) and five demethylases was identified. An analysis of their predicted product's protein structure suggested an extensive level of conservation has been retained by the C5-MTases. Transcriptional profiling based on quantitative real time PCR revealed a number of differences between the genes encoding maintenance and de novo methyltransferases, sometimes in a tissue- or development-dependent manner, which implied a degree of functional specialization.
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Affiliation(s)
- Silvia Gianoglio
- Department of Agricultural, Forest and Food Sciences, University of Torino, Grugliasco, Italy
| | - Andrea Moglia
- Department of Agricultural, Forest and Food Sciences, University of Torino, Grugliasco, Italy
| | - Alberto Acquadro
- Department of Agricultural, Forest and Food Sciences, University of Torino, Grugliasco, Italy
| | - Cinzia Comino
- Department of Agricultural, Forest and Food Sciences, University of Torino, Grugliasco, Italy
| | - Ezio Portis
- Department of Agricultural, Forest and Food Sciences, University of Torino, Grugliasco, Italy
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32
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Dou L, Jia X, Wei H, Fan S, Wang H, Guo Y, Duan S, Pang C, Yu S. Global analysis of DNA methylation in young (J1) and senescent (J2) Gossypium hirsutum L. cotyledons by MeDIP-Seq. PLoS One 2017; 12:e0179141. [PMID: 28715427 PMCID: PMC5513416 DOI: 10.1371/journal.pone.0179141] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2016] [Accepted: 05/24/2017] [Indexed: 11/18/2022] Open
Abstract
DNA methylation is an important epigenetic modification regulating gene expression, genomic imprinting, transposon silencing and chromatin structure in plants and plays an important role in leaf senescence. However, the DNA methylation pattern during Gossypium hirsutum L. cotyledon senescence is poorly understood. In this study, global DNA methylation patterns were compared between two cotyledon development stages, young (J1) and senescence (J2), using methylated DNA immunoprecipitation (MeDIP-Seq). Methylated cytosine occurred mostly in repeat elements, especially LTR/Gypsy in both J1 and J2. When comparing J1 against J2, there were 1222 down-methylated genes and 623 up-methylated genes. Methylated genes were significantly enriched in carbohydrate metabolism, biosynthesis of other secondary metabolites and amino acid metabolism pathways. The global DNA methylation level decreased from J1 to J2, especially in gene promoters, transcriptional termination regions and regions around CpG islands. We further investigated the expression patterns of 9 DNA methyltransferase-associated genes and 2 DNA demethyltransferase-associated genes from young to senescent cotyledons, which were down-regulated during cotyledon development. In this paper, we first reported that senescent cotton cotyledons exhibited lower DNA methylation levels, primarily due to decreased DNA methyltransferase activity and which also play important role in regulating secondary metabolite process.
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Affiliation(s)
- Lingling Dou
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of CAAS, Anyang, Henan, P. R. China
- Weinan Institute of Agricultural Sciences, Weinan, Shaanxi, P. R. China
| | - Xiaoyun Jia
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of CAAS, Anyang, Henan, P. R. China
| | - Hengling Wei
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of CAAS, Anyang, Henan, P. R. China
| | - Shuli Fan
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of CAAS, Anyang, Henan, P. R. China
| | - Hantao Wang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of CAAS, Anyang, Henan, P. R. China
| | - Yaning Guo
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of CAAS, Anyang, Henan, P. R. China
| | - Shan Duan
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of CAAS, Anyang, Henan, P. R. China
| | - Chaoyou Pang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of CAAS, Anyang, Henan, P. R. China
- * E-mail: (CP); (SY)
| | - Shuxun Yu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of CAAS, Anyang, Henan, P. R. China
- * E-mail: (CP); (SY)
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34
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Affiliation(s)
| | - Joseph Sherma
- Department of Chemistry, Lafayette College, Easton, PA, USA
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