{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,30]],"date-time":"2026-07-30T17:48:50Z","timestamp":1785433730094,"version":"3.56.0"},"reference-count":23,"publisher":"MDPI AG","issue":"3","license":[{"start":{"date-parts":[[2026,7,24]],"date-time":"2026-07-24T00:00:00Z","timestamp":1784851200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"University of Nari\u00f1o","award":["098"],"award-info":[{"award-number":["098"]}]},{"award":["098"],"award-info":[{"award-number":["098"]}],"id":[{"id":"https:\/\/ror.org\/050bg0846","id-type":"ROR","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Epigenomes"],"abstract":"<jats:p>Background: Glutathione peroxidases (GPXs) regulate peroxide detoxification and redox signaling, but their relationship with DNA methylation remains unclear in Oryza sativa. This study evaluated whether silencing mitochondrial GPX1 and GPX3 is associated with changes in growth, antioxidant activity, and DNA methylation-related profiles. Methods: Non-transformed plants (NT) and five GPX-silenced lines were evaluated in a randomized complete block design. Morphophysiological traits, antioxidant enzyme activities, total 5-methylcytosine content, and methylation-sensitive restriction profiles were analyzed. Results: GPX silencing impaired early establishment and significantly affected flowering time and leaf, root, seed, and total biomass. Total dry biomass decreased by 62.1% in the most affected GPX1 lines and by 29.2% in GPX3 lines relative to NT plants. Root biomass declined by up to 86.1%, and flowering was delayed by up to 30.7 days. Genotype significantly affected GPX-associated and glutathione reductase activities, whereas no significant genotype effects were detected for catalase, ascorbate peroxidase, or superoxide dismutase activities. GPX-associated and glutathione reductase activities were strongly correlated (r = 0.85, p &lt; 0.001), consistent with selective alteration of GPX-associated and glutathione-linked redox metabolism. Total 5-methylcytosine content decreased by 41\u201342% in GPX-silenced groups. However, increased McrBC digestion and unchanged HpaII\/MspI profiles indicated that methylation-related changes were nonuniform and depended on the genomic sites recognized by each enzymatic assay. Conclusions: These findings show that mitochondrial GPX knockdown is associated with impaired rice growth and reproductive development, as well as with altered total 5-methylcytosine content and restriction-sensitive methylation profiles, suggesting a potential relationship among redox homeostasis, developmental regulation, and epigenetic plasticity that requires further validation using locus-resolved and mechanistic approaches.<\/jats:p>","DOI":"10.3390\/epigenomes10030049","type":"journal-article","created":{"date-parts":[[2026,7,24]],"date-time":"2026-07-24T07:36:13Z","timestamp":1784878573000},"page":"49","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["GPX Knockdown Is Associated with Altered Redox Homeostasis, Plant Development, and DNA Methylation-Related Profiles in Rice"],"prefix":"10.3390","volume":"10","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-7564-4519","authenticated-orcid":false,"given":"Pedro Alexander","family":"Velasquez-Vasconez","sequence":"first","affiliation":[{"name":"Department of Production and Plant Protection, University of Nari\u00f1o, Pasto 520001, Colombia"},{"name":"School of Basic Sciences, Technology and Engineering, National Open and Distance University, Pasto 520001, Colombia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6110-2700","authenticated-orcid":false,"given":"Marina de Lima","family":"Nogueira","sequence":"additional","affiliation":[{"name":"Department of Biological and Health Sciences, Federal University of Amap\u00e1, Macap\u00e1 68903-419, AP, Brazil"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Carlos Betancourth","family":"Garc\u00eda","sequence":"additional","affiliation":[{"name":"Department of Production and Plant Protection, University of Nari\u00f1o, Pasto 520001, Colombia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Claudia Elizabeth","family":"Salazar-Gonz\u00e1lez","sequence":"additional","affiliation":[{"name":"Department of Production and Plant Protection, University of Nari\u00f1o, Pasto 520001, Colombia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0005-1754-6311","authenticated-orcid":false,"given":"Angie Fernanda","family":"Riascos-Espa\u00f1a","sequence":"additional","affiliation":[{"name":"Faculty of Exact and Natural Sciences\/Biology Program, University of Nari\u00f1o, Pasto 520001, Colombia"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2026,7,24]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","unstructured":"Chai, Y.-C., and Mieyal, J.J. (2023). Glutathione and Glutaredoxin\u2014Key Players in Cellular Redox Homeostasis and Signaling. Antioxidants, 12.","DOI":"10.3390\/antiox12081553"},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"3903","DOI":"10.1093\/plcell\/koae094","article-title":"Plastid Retrograde Signaling: A Developmental Perspective","volume":"36","author":"Loudya","year":"2024","journal-title":"Plant Cell"},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"375","DOI":"10.1007\/s10535-014-0394-9","article-title":"Chloroplastic and Mitochondrial GPX Genes Play a Critical Role in Rice Development","volume":"58","author":"Passaia","year":"2014","journal-title":"Biol. Plant."},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"22","DOI":"10.1016\/j.plantsci.2015.01.017","article-title":"Glutathione Peroxidases as Redox Sensor Proteins in Plant Cells","volume":"234","author":"Passaia","year":"2015","journal-title":"Plant Sci."},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"1596","DOI":"10.1093\/pcp\/pcs100","article-title":"The Involvement of Arabidopsis Glutathione Peroxidase 8 in the Suppression of Oxidative Damage in the Nucleus and Cytosol","volume":"53","author":"Gaber","year":"2012","journal-title":"Plant Cell Physiol."},{"key":"ref_6","doi-asserted-by":"crossref","unstructured":"Sun, M., Yang, Z., Liu, L., and Duan, L. (2022). DNA Methylation in Plant Responses and Adaption to Abiotic Stresses. Int. J. Mol. Sci., 23.","DOI":"10.3390\/ijms23136910"},{"key":"ref_7","doi-asserted-by":"crossref","unstructured":"Parrilla-Doblas, J.T., Rold\u00e1n-Arjona, T., Ariza, R.R., and C\u00f3rdoba-Ca\u00f1ero, D. (2019). Active DNA Demethylation in Plants. Int. J. Mol. Sci., 20.","DOI":"10.3390\/ijms20194683"},{"key":"ref_8","doi-asserted-by":"crossref","unstructured":"Lee, J., Lee, S., Park, K., Shin, S.-Y., Frost, J.M., Hsieh, P.-H., Shin, C., Fischer, R.L., Hsieh, T.-F., and Choi, Y. (2023). Distinct Regulatory Pathways Contribute to Dynamic CHH Methylation Patterns in Transposable Elements throughout Arabidopsis Embryogenesis. Front. Plant Sci., 14.","DOI":"10.3389\/fpls.2023.1204279"},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"4941","DOI":"10.1038\/s41467-021-25128-y","article-title":"Pre-Meiotic 21-Nucleotide Reproductive PhasiRNAs Emerged in Seed Plants and Diversified in Flowering Plants","volume":"12","author":"Pokhrel","year":"2021","journal-title":"Nat. Commun."},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"663","DOI":"10.1007\/s12298-026-01709-3","article-title":"Cadmium\u2013Drought Interaction Modulates Oxidative Stress, Antioxidant Defense, and Stress-Responsive Gene in Rice Sprouts","volume":"32","author":"Singh","year":"2026","journal-title":"Physiol. Mol. Biol. Plants"},{"key":"ref_11","doi-asserted-by":"crossref","unstructured":"Tavu, L.E.J., and Redillas, M.C.F.R. (2025). Oxidative Stress in Rice (Oryza Sativa): Mechanisms, Impact, and Adaptive Strategies. Plants, 14.","DOI":"10.3390\/plants14101463"},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"21386","DOI":"10.1021\/acs.est.5c05890","article-title":"Plant Cell Wall Remodeling under Toxic Metal Stress: Structural Adaptation and Functional Implications","volume":"59","author":"Anjitha","year":"2025","journal-title":"Environ. Sci. Technol."},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"141838","DOI":"10.1016\/j.foodchem.2024.141838","article-title":"H2O2-Mediated Cell Wall Remodeling and Pectin Demethylesterification Are Involved in Maintaining Postharvest Texture of Table Grape by Sulfur Dioxide","volume":"464","author":"Li","year":"2025","journal-title":"Food Chem."},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"12","DOI":"10.1016\/j.envexpbot.2018.10.027","article-title":"Mitochondrial Glutathione Peroxidase (OsGPX3) Has a Crucial Role in Rice Protection against Salt Stress","volume":"158","author":"Paiva","year":"2019","journal-title":"Environ. Exp. Bot."},{"key":"ref_15","doi-asserted-by":"crossref","unstructured":"Gao, Y., Feng, B., Gao, C., Zhang, H., Wen, F., Tao, L., Fu, G., and Xiong, J. (2022). The Evolution and Functional Roles of MiR408 and Its Targets in Plants. Int. J. Mol. Sci., 23.","DOI":"10.3390\/ijms23010530"},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"148378","DOI":"10.1016\/j.gene.2024.148378","article-title":"Revisiting the Role and Mechanism of ELF3 in Circadian Clock Modulation","volume":"913","author":"Zhu","year":"2024","journal-title":"Gene"},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"100327","DOI":"10.1016\/j.stress.2023.100327","article-title":"Roles and Regulation of the RBOHD Enzyme in Initiating ROS-Mediated Systemic Signaling during Biotic and Abiotic Stress","volume":"11","author":"Rivas","year":"2024","journal-title":"Plant Stress"},{"key":"ref_18","doi-asserted-by":"crossref","unstructured":"Giustarini, D., Milzani, A., Dalle-Donne, I., and Rossi, R. (2023). How to Increase Cellular Glutathione. Antioxidants, 12.","DOI":"10.3390\/antiox12051094"},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"4333","DOI":"10.1007\/s00344-024-11402-y","article-title":"Exogenous Glutathione Enhances Salt Tolerance in Kenaf by Mediating Modulation of Oxidative Stress Response and DNA Methylation","volume":"43","author":"Cao","year":"2024","journal-title":"J. Plant Growth Regul."},{"key":"ref_20","doi-asserted-by":"crossref","unstructured":"Akinmusola, R.Y., Wilkins, C.-A., and Doughty, J. (2023). DDM1-Mediated TE Silencing in Plants. Plants, 12.","DOI":"10.3390\/plants12030437"},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"e05255","DOI":"10.7554\/eLife.05255","article-title":"DNA Methylation in Arabidopsis Has a Genetic Basis and Shows Evidence of Local Adaptation","volume":"4","author":"Dubin","year":"2015","journal-title":"Elife"},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"461","DOI":"10.1016\/j.cell.2008.12.038","article-title":"Epigenetic Reprogramming and Small RNA Silencing of Transposable Elements in Pollen","volume":"136","author":"Slotkin","year":"2009","journal-title":"Cell"},{"key":"ref_23","unstructured":"R Core Team (2020). R: A Language and Environment for Statistical Computing, R Foundation for Statistical Computing."}],"container-title":["Epigenomes"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/2075-4655\/10\/3\/49\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,7,24]],"date-time":"2026-07-24T08:09:02Z","timestamp":1784880542000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/2075-4655\/10\/3\/49"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,7,24]]},"references-count":23,"journal-issue":{"issue":"3","published-online":{"date-parts":[[2026,9]]}},"alternative-id":["epigenomes10030049"],"URL":"https:\/\/doi.org\/10.3390\/epigenomes10030049","relation":{},"ISSN":["2075-4655"],"issn-type":[{"value":"2075-4655","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,7,24]]}}}