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By integrating differential expression, weighted gene co-expression network analysis (WGCNA), and alternative splicing (AS) profiling, a phase-dependent regulatory model was proposed. Quantitatively, the network was initially resolved into 17 co-expression modules, which were subsequently consolidated into 10 final modules. A core set of 147 transcription factors (predominantly AP2\/ERF and NAC families) was consistently associated with the response across time points. During the early shock phase (6 h), the broad repression of energy-associated transcripts suggests rapid intracellular stabilization. The transition phase (12 h) was characterized by transcriptomic shifts suggestive of chromatin-level regulation and post-transcriptional adjustments. By late acclimation (24 h), the reorganization of stress-associated modules indicates a progression toward a stabilized regulatory state. Furthermore, the identification of dynamic AS events across multiple regulatory families suggests that isoform diversification is a crucial parallel regulatory layer. Moving beyond static expression profiling, this study provides a comprehensive temporal framework of sorghum cold acclimation and identifies phase-specific candidate genes for future experimental validation in C4 crops.<\/jats:p>","DOI":"10.3390\/biology15070560","type":"journal-article","created":{"date-parts":[[2026,4,2]],"date-time":"2026-04-02T11:51:03Z","timestamp":1775130663000},"page":"560","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":1,"title":["A Phase-Dependent Model of Sorghum (Sorghum bicolor) Cold Acclimation: Integrating Multi-Layered Networks and Alternative Splicing Signatures"],"prefix":"10.3390","volume":"15","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-0172-1953","authenticated-orcid":false,"given":"Firat","family":"Kurt","sequence":"first","affiliation":[{"name":"Department of Plant Production and Technologies, Faculty of Applied Sciences, Mu\u015f Alparslan University, 49250 Mu\u015f, T\u00fcrkiye"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2026,3,31]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","unstructured":"Ogbaga, C.C., Stepien, P., Dyson, B.C., Rattray, N.J.W., Ellis, D.I., Goodacre, R., and Johnson, G.N. (2016). Biochemical Analyses of Sorghum Varieties Reveal Differential Responses to Drought. PLoS ONE, 11.","DOI":"10.1371\/journal.pone.0154423"},{"key":"ref_2","doi-asserted-by":"crossref","unstructured":"Ali, A.E.E., Husselmann, L.H., Tabb, D.L., and Ludidi, N. (2023). Comparative Proteomics Analysis between Maize and Sorghum Uncovers Important Proteins and Metabolic Pathways Mediating Drought Tolerance. Life, 13.","DOI":"10.3390\/life13010170"},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1094\/CM-2010-1109-01-RV","article-title":"Grain Sorghum Water Requirement and Responses to Drought Stress: A Review","volume":"9","author":"Assefa","year":"2010","journal-title":"Crop Manag."},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"589","DOI":"10.4236\/ajps.2011.24070","article-title":"Recent Advances in Sorghum Genetic Enhancement Research at ICRISAT","volume":"2","author":"Kumar","year":"2011","journal-title":"Am. J. Plant Sci."},{"key":"ref_5","doi-asserted-by":"crossref","unstructured":"Zhou, B., Zheng, B., and Wu, W. (2023). The ncRNAs Involved in the Regulation of Abiotic Stress-Induced Anthocyanin Biosynthesis in Plants. Antioxidants, 13.","DOI":"10.3390\/antiox13010055"},{"key":"ref_6","doi-asserted-by":"crossref","unstructured":"Vera Hern\u00e1ndez, P.F., Mendoza Onofre, L.E., and Rosas C\u00e1rdenas, F.D.F. (2023). Responses of Sorghum to Cold Stress: A Review Focused on Molecular Breeding. Front. Plant Sci., 14.","DOI":"10.3389\/fpls.2023.1124335"},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"1711","DOI":"10.1111\/ppl.13373","article-title":"Abiotic Stress-induced Anthocyanins in Plants: Their Role in Tolerance to Abiotic Stresses","volume":"172","author":"Naing","year":"2021","journal-title":"Physiol. Plant."},{"key":"ref_8","doi-asserted-by":"crossref","unstructured":"Luo, Y., Jiao, W., Huang, K., Li, X., Li, J., Wang, M., Zhang, R., and Cao, X. (2025). Comprehensive Analysis of Sorghum CNGC Genes Reveals Their Potential Roles in Abiotic Stress Responses. Genes, 16.","DOI":"10.3390\/genes16121405"},{"key":"ref_9","doi-asserted-by":"crossref","unstructured":"Lou, Q., Wang, P., Yu, M., Xie, Z., Xu, C., Chen, S., Yu, H., Zhang, R., Tian, G., and Hao, D. (2025). Transcriptome Analysis Reveals the Pivotal Genes and Regulation Pathways Under Cold Stress and Identifies SbERF027, an AP2\/ERF Gene That Confers Cold Tolerance in Sorghum. Plants, 14.","DOI":"10.3390\/plants14060879"},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"876","DOI":"10.1007\/s40502-025-00906-8","article-title":"Transcriptomic Analysis Reveals Time-of-Day-Specific Genes and Gene Regulatory Networks in Response to Chilling Stress in Sorghum","volume":"30","author":"Laosuntisuk","year":"2025","journal-title":"Plant Physiol. Rep."},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"100401","DOI":"10.1016\/j.stress.2024.100401","article-title":"Ethanol-mediated cold stress tolerance in sorghum seedlings through photosynthetic adaptation, antioxidant defense, and osmoprotectant enhancement","volume":"11","author":"Ghosh","year":"2024","journal-title":"Plant Stress"},{"key":"ref_12","doi-asserted-by":"crossref","unstructured":"Tu, M., Du, C., Yu, B., Wang, G., Deng, Y., Wang, Y., Chen, M., Chang, J., Yang, G., and He, G. (2023). Current Advances in the Molecular Regulation of Abiotic Stress Tolerance in Sorghum via Transcriptomic, Proteomic, and Metabolomic Approaches. Front. Plant Sci., 14.","DOI":"10.3389\/fpls.2023.1147328"},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"496","DOI":"10.1111\/jipb.13451","article-title":"The Battle of Crops against Drought: Genetic Dissection and Improvement","volume":"65","author":"Yang","year":"2023","journal-title":"J. Integr. Plant Biol."},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"D19","DOI":"10.1093\/nar\/gkq1019","article-title":"The Sequence Read Archive","volume":"39","author":"Leinonen","year":"2011","journal-title":"Nucleic Acids Res."},{"key":"ref_15","doi-asserted-by":"crossref","unstructured":"The Galaxy Community, Abueg, L.A.L., Afgan, E., Allart, O., Awan, A.H., Bacon, W.A., Baker, D., Bassetti, M., Batut, B., and Bernt, M. (2024). The Galaxy Platform for Accessible, Reproducible, and Collaborative Data Analyses: 2024 Update. Nucleic Acids Res., 52, W83\u2013W94.","DOI":"10.1093\/nar\/gkae410"},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"1874","DOI":"10.12688\/f1000research.21142.2","article-title":"Falco: High-Speed FastQC Emulation for Quality Control of Sequencing Data","volume":"8","author":"Smith","year":"2021","journal-title":"F1000Research"},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"3047","DOI":"10.1093\/bioinformatics\/btw354","article-title":"MultiQC: Summarize Analysis Results for Multiple Tools and Samples in a Single Report","volume":"32","author":"Ewels","year":"2016","journal-title":"Bioinformatics"},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"i884","DOI":"10.1093\/bioinformatics\/bty560","article-title":"Fastp: An Ultra-Fast All-in-One FASTQ Preprocessor","volume":"34","author":"Chen","year":"2018","journal-title":"Bioinformatics"},{"key":"ref_19","unstructured":"Edwards, D. (2016). Ensembl Plants: Integrating Tools for Visualizing, Mining, and Analyzing Plant Genomics Data. Plant Bioinformatics: Methods and Protocols, Springer."},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"D689","DOI":"10.1093\/nar\/gkz890","article-title":"Ensembl Genomes 2020\u2014Enabling Non-Vertebrate Genomic Research","volume":"48","author":"Howe","year":"2020","journal-title":"Nucleic Acids Res."},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"996","DOI":"10.1101\/gr.229102","article-title":"The Human Genome Browser at UCSC","volume":"6","author":"Kent","year":"2002","journal-title":"Genome Res."},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"2184","DOI":"10.1093\/bioinformatics\/bts356","article-title":"RSeQC: Quality Control of RNA-Seq Experiments","volume":"28","author":"Wang","year":"2012","journal-title":"Bioinformatics"},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"15","DOI":"10.1093\/bioinformatics\/bts635","article-title":"STAR: Ultrafast Universal RNA-Seq Aligner","volume":"29","author":"Dobin","year":"2013","journal-title":"Bioinformatics"},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"923","DOI":"10.1093\/bioinformatics\/btt656","article-title":"featureCounts: An Efficient General Purpose Program for Assigning Sequence Reads to Genomic Features","volume":"30","author":"Liao","year":"2014","journal-title":"Bioinformatics"},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"550","DOI":"10.1186\/s13059-014-0550-8","article-title":"Moderated Estimation of Fold Change and Dispersion for RNA-Seq Data with DESeq2","volume":"15","author":"Love","year":"2014","journal-title":"Genome Biol."},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"2811","DOI":"10.1093\/bioinformatics\/btu393","article-title":"Circlize Implements and Enhances Circular Visualization in R","volume":"30","author":"Gu","year":"2014","journal-title":"Bioinformatics"},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"D1178","DOI":"10.1093\/nar\/gkr944","article-title":"Phytozome: A Comparative Platform for Green Plant Genomics","volume":"40","author":"Goodstein","year":"2012","journal-title":"Nucleic Acids Res."},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"D891","DOI":"10.1093\/nar\/gkad1049","article-title":"Ensembl 2024","volume":"52","author":"Harrison","year":"2024","journal-title":"Nucleic Acids Res."},{"key":"ref_29","unstructured":"R Core Team (2024). R: A Language and Environment for Statistical Computing, R Foundation for Statistical Computing."},{"key":"ref_30","unstructured":"Ushey, K., Allaire, J.J., Wickham, H., and Ritchie, G. (2025, December 16). rstudioapi: Safely Access the RStudio API; R Package Version 0.16.0, 2024. Available online: https:\/\/cran.r-project.org\/package=rstudioapi."},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"35","DOI":"10.1007\/s00425-022-03821-6","article-title":"SorghumBase: A Web-Based Portal for Sorghum Genetic Information and Community Advancement","volume":"255","author":"Gladman","year":"2022","journal-title":"Planta"},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"1667","DOI":"10.1016\/j.molp.2016.09.014","article-title":"iTAK: A Program for Genome-Wide Prediction and Classification of Plant Transcription Factors, Transcriptional Regulators, and Protein Kinases","volume":"9","author":"Zheng","year":"2016","journal-title":"Mol. Plant"},{"key":"ref_33","doi-asserted-by":"crossref","unstructured":"The UniProt Consortium (2019). UniProt: A Worldwide Hub of Protein Knowledge. Nucleic Acids Res., 47, D506\u2013D515.","DOI":"10.1093\/nar\/gky1049"},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"bar030","DOI":"10.1093\/database\/bar030","article-title":"Ensembl BioMarts: A Hub for Data Retrieval across Taxonomic Space","volume":"2011","author":"Kinsella","year":"2011","journal-title":"Database"},{"key":"ref_35","doi-asserted-by":"crossref","unstructured":"Langfelder, P., and Horvath, S. (2008). WGCNA: An R Package for Weighted Correlation Network Analysis. BMC Bioinform., 9.","DOI":"10.1186\/1471-2105-9-559"},{"key":"ref_36","doi-asserted-by":"crossref","unstructured":"Zhang, B., and Horvath, S. (2005). A General Framework for Weighted Gene Co-Expression Network Analysis. Stat. Appl. Genet. Mol. Biol., 4.","DOI":"10.2202\/1544-6115.1128"},{"key":"ref_37","doi-asserted-by":"crossref","unstructured":"Chen, H., and Boutros, P.C. (2011). VennDiagram: A Package for the Generation of Highly-Customizable Venn and Euler Diagrams in R. BMC Bioinform., 12.","DOI":"10.1186\/1471-2105-12-35"},{"key":"ref_38","doi-asserted-by":"crossref","first-page":"2938","DOI":"10.1093\/bioinformatics\/btx364","article-title":"UpSetR: An R Package for the Visualization of Intersecting Sets and Their Properties","volume":"33","author":"Conway","year":"2017","journal-title":"Bioinformatics"},{"key":"ref_39","doi-asserted-by":"crossref","first-page":"2498","DOI":"10.1101\/gr.1239303","article-title":"Cytoscape: A Software Environment for Integrated Models of Biomolecular Interaction Networks","volume":"13","author":"Shannon","year":"2003","journal-title":"Genome Res."},{"key":"ref_40","doi-asserted-by":"crossref","first-page":"E5593","DOI":"10.1073\/pnas.1419161111","article-title":"rMATS: Robust and Flexible Detection of Differential Alternative Splicing from Replicate RNA-Seq Data","volume":"111","author":"Shen","year":"2014","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_41","doi-asserted-by":"crossref","first-page":"1686","DOI":"10.21105\/joss.01686","article-title":"Welcome to the Tidyverse","volume":"4","author":"Wickham","year":"2019","journal-title":"J. Open Source Softw."},{"key":"ref_42","doi-asserted-by":"crossref","first-page":"24","DOI":"10.1038\/nbt.1754","article-title":"Integrative Genomics Viewer","volume":"29","author":"Robinson","year":"2011","journal-title":"Nat. Biotechnol."},{"key":"ref_43","doi-asserted-by":"crossref","unstructured":"Heberle, H., Meirelles, G.V., Da Silva, F.R., Telles, G.P., and Minghim, R. (2015). InteractiVenn: A Web-Based Tool for the Analysis of Sets through Venn Diagrams. BMC Bioinform., 16.","DOI":"10.1186\/s12859-015-0611-3"},{"key":"ref_44","doi-asserted-by":"crossref","first-page":"2628","DOI":"10.1093\/bioinformatics\/btz931","article-title":"ShinyGO: A Graphical Gene-Set Enrichment Tool for Animals and Plants","volume":"36","author":"Ge","year":"2020","journal-title":"Bioinformatics"},{"key":"ref_45","doi-asserted-by":"crossref","unstructured":"Lokdarshi, A., Morgan, P.W., Franks, M., Emert, Z., Emanuel, C., and Von Arnim, A.G. (2020). Light-Dependent Activation of the GCN2 Kinase Under Cold and Salt Stress Is Mediated by the Photosynthetic Status of the Chloroplast. Front. Plant Sci., 11.","DOI":"10.3389\/fpls.2020.00431"},{"key":"ref_46","doi-asserted-by":"crossref","first-page":"217","DOI":"10.1080\/07352689.2017.1375836","article-title":"Responses of the Mitochondrial Respiratory System to Low Temperature in Plants","volume":"36","author":"Heidarvand","year":"2017","journal-title":"Crit. Rev. Plant Sci."},{"key":"ref_47","doi-asserted-by":"crossref","unstructured":"Han, B., Sun, K., Zhou, J., Xu, J., Feng, A., and Zhao, X. (2025). Genome-Wide Identification and Expression Analysis of Adenylate Kinase Family Members in Pepper Under Abiotic Stress. Int. J. Mol. Sci., 26.","DOI":"10.3390\/ijms262010213"},{"key":"ref_48","doi-asserted-by":"crossref","first-page":"56","DOI":"10.1111\/pce.12826","article-title":"The Inhibition of Protein Translation Mediated by AtGCN1 Is Essential for Cold Tolerance in Arabidopsis thaliana","volume":"40","author":"Wang","year":"2017","journal-title":"Plant Cell Environ."},{"key":"ref_49","doi-asserted-by":"crossref","unstructured":"Johnson, S.M., Lim, F.-L., Finkler, A., Fromm, H., Slabas, A.R., and Knight, M.R. (2014). Transcriptomic Analysis of Sorghum Bicolor Responding to Combined Heat and Drought Stress. BMC Genom., 15.","DOI":"10.1186\/1471-2164-15-456"},{"key":"ref_50","doi-asserted-by":"crossref","first-page":"2117","DOI":"10.1093\/plcell\/koae039","article-title":"Pan-Transcriptomic Analysis Reveals Alternative Splicing Control of Cold Tolerance in Rice","volume":"36","author":"Zhong","year":"2024","journal-title":"Plant Cell"},{"key":"ref_51","doi-asserted-by":"crossref","unstructured":"Peng, C., Hua, W., and Liu, J. (2025). Unraveling the Signaling Pathways of Plant Cold Stress: Current Insights and Future Directions. Front. Plant Sci., 16.","DOI":"10.3389\/fpls.2025.1666852"},{"key":"ref_52","unstructured":"Villarreal, A.S. (2010). Genomic and Physiological Characterization of the Mutant Time for Coffee Within the Arabidopsis Thaliana Circadian Clock. [Ph.D. Thesis, Universit\u00e4t zu K\u00f6ln]."},{"key":"ref_53","doi-asserted-by":"crossref","unstructured":"Yu, G.-H., Jiang, L.-L., Ma, X.-F., Xu, Z.-S., Liu, M.-M., Shan, S.-G., and Cheng, X.-G. (2014). A Soybean C2H2-Type Zinc Finger Gene GmZF1 Enhanced Cold Tolerance in Transgenic Arabidopsis. PLoS ONE, 9.","DOI":"10.1371\/journal.pone.0109399"},{"key":"ref_54","doi-asserted-by":"crossref","first-page":"43","DOI":"10.1146\/annurev-genet-111523-102226","article-title":"Regulatory Networks Underlying Plant Responses and Adaptation to Cold Stress","volume":"58","author":"Ding","year":"2024","journal-title":"Annu. Rev. Genet."},{"key":"ref_55","doi-asserted-by":"crossref","unstructured":"Zhang, R., Yang, L., Zhang, H., Yang, Y., Wen, L., Yin, A., and Fu, L. (2025). Molecular Networks Governing Plant Responses to Heat and Cold Stress. Plants, 14.","DOI":"10.3390\/plants14132073"},{"key":"ref_56","doi-asserted-by":"crossref","unstructured":"Qian, Z., He, L., and Li, F. (2024). Understanding Cold Stress Response Mechanisms in Plants: An Overview. Front. Plant Sci., 15.","DOI":"10.3389\/fpls.2024.1443317"},{"key":"ref_57","doi-asserted-by":"crossref","unstructured":"Ramirez, V.E., and Poppenberger, B. (2020). Modes of Brassinosteroid Activity in Cold Stress Tolerance. Front. Plant Sci., 11.","DOI":"10.3389\/fpls.2020.583666"},{"key":"ref_58","doi-asserted-by":"crossref","unstructured":"Manghwar, H., Hussain, A., Ali, Q., and Liu, F. (2022). Brassinosteroids (BRs) Role in Plant Development and Coping with Different Stresses. Int. J. Mol. Sci., 23.","DOI":"10.3390\/ijms23031012"},{"key":"ref_59","doi-asserted-by":"crossref","unstructured":"Liu, X., Zhang, C., Lamlom, S.F., Zhao, K., Abdelghany, A.M., Wang, X., Zhang, F., Yuan, R., Han, D., and Zha, B. (2024). Genetic Adaptations of Soybean to Cold Stress Reveal Key Insights Through Transcriptomic Analysis. Biology, 13.","DOI":"10.3390\/biology13110856"},{"key":"ref_60","doi-asserted-by":"crossref","first-page":"410","DOI":"10.1111\/aab.12938","article-title":"Integration of Transcriptional Responses in Cold Contrasting Sorghum Genotypes under Low Temperatures","volume":"185","year":"2024","journal-title":"Ann. Appl. Biol."},{"key":"ref_61","doi-asserted-by":"crossref","unstructured":"Dugas, D.V., Monaco, M.K., Olson, A., Klein, R.R., Kumari, S., Ware, D., and Klein, P.E. (2011). Functional Annotation of the Transcriptome of Sorghum Bicolor in Response to Osmotic Stress and Abscisic Acid. BMC Genom., 12.","DOI":"10.1186\/1471-2164-12-514"},{"key":"ref_62","doi-asserted-by":"crossref","unstructured":"Yang, T., Zhuang, Z., Bian, J., Ren, Z., Ta, W., and Peng, Y. (2025). Mechanisms of Exogenous Brassinosteroids and Abscisic Acid in Regulating Maize Cold Stress Tolerance. Int. J. Mol. Sci., 26.","DOI":"10.3390\/ijms26073326"},{"key":"ref_63","doi-asserted-by":"crossref","first-page":"a032870","DOI":"10.1101\/cshperspect.a032870","article-title":"Role of eIF2\u03b1 Kinases in Translational Control and Adaptation to Cellular Stress","volume":"10","author":"Wek","year":"2018","journal-title":"Cold Spring Harb. Perspect. Biol."},{"key":"ref_64","doi-asserted-by":"crossref","unstructured":"Han, J., Wang, Q., Qian, B., Liu, Q., Wang, Z., Liu, Y., Chen, Z., Wu, W., Zhang, C., and Yin, Y. (2024). Exploring the Roles of the Swi2\/Snf2 Gene Family in Maize Abiotic Stress Responses. Int. J. Mol. Sci., 25.","DOI":"10.3390\/ijms25179686"},{"key":"ref_65","first-page":"117","article-title":"Genome-Wide Identification of Chromatin Regulators in Sorghum Bicolor","volume":"12","author":"Hu","year":"2022","journal-title":"3Biotech"},{"key":"ref_66","doi-asserted-by":"crossref","first-page":"992","DOI":"10.1016\/j.tcb.2024.02.005","article-title":"Epigenetic Control of Circadian Clocks by Environmental Signals","volume":"34","author":"Liu","year":"2024","journal-title":"Trends Cell Biol."},{"key":"ref_67","doi-asserted-by":"crossref","first-page":"100081","DOI":"10.1016\/j.stress.2022.100081","article-title":"Cold Stress in Plants: Strategies to Improve Cold Tolerance in Forage Species","volume":"4","author":"Adhikari","year":"2022","journal-title":"Plant Stress"},{"key":"ref_68","doi-asserted-by":"crossref","first-page":"e19124","DOI":"10.7717\/peerj.19124","article-title":"Mining of Co-Expression Genes in Response to Cold Stress at Maize (Zea mays L.) Germination and Sprouting Stages by Weighted Gene Co-Expression Networks Analysis","volume":"13","author":"Shi","year":"2025","journal-title":"PeerJ"},{"key":"ref_69","doi-asserted-by":"crossref","first-page":"1081","DOI":"10.1111\/tpj.16467","article-title":"Time of Day and Genotype Sensitivity Adjust Molecular Responses to Temperature Stress in Sorghum","volume":"116","author":"Bonnot","year":"2023","journal-title":"Plant J."},{"key":"ref_70","doi-asserted-by":"crossref","unstructured":"Jang, J., Lee, S., Kim, J.-I., Lee, S., and Kim, J. (2024). The Roles of Circadian Clock Genes in Plant Temperature Stress Responses. Int. J. Mol. Sci., 25.","DOI":"10.3390\/ijms25020918"},{"key":"ref_71","doi-asserted-by":"crossref","first-page":"1424","DOI":"10.1105\/tpc.18.00177","article-title":"Rapid and Dynamic Alternative Splicing Impacts the Arabidopsis Cold Response Transcriptome","volume":"30","author":"Calixto","year":"2018","journal-title":"Plant Cell"},{"key":"ref_72","doi-asserted-by":"crossref","unstructured":"Pu, X., Fu, Y., Xu, C., Li, X., Wang, W., De, K., Wei, X., and Yao, X. (2024). Transcriptomic Analyses Provide Molecular Insight into the Cold Stress Response of Cold-Tolerant Alfalfa. BMC Plant Biol., 24.","DOI":"10.1186\/s12870-024-05136-y"},{"key":"ref_73","doi-asserted-by":"crossref","first-page":"35","DOI":"10.1007\/s13562-024-00923-y","article-title":"The Long-Noncoding RNAs: Effective Players in Plant Development and Stress Responses","volume":"34","author":"Bhat","year":"2025","journal-title":"J. Plant Biochem. Biotechnol."},{"key":"ref_74","doi-asserted-by":"crossref","first-page":"11583","DOI":"10.1038\/s41598-023-38571-2","article-title":"Identification of Genes Associated with the Regulation of Cold Tolerance and the RNA Movement in the Grafted Apple","volume":"13","author":"Lee","year":"2023","journal-title":"Sci. Rep."},{"key":"ref_75","doi-asserted-by":"crossref","unstructured":"Seth, D., Kumari, P., Pramanik, S., Das, A., and Madhusudhana, R. (2025). Role of Omics for Enhancing Abiotic Stress Resilience in Sorghum (Sorghum bicolor L. Moench). J. Plant Biochem. Biotechnol.","DOI":"10.1007\/s13562-025-00994-5"},{"key":"ref_76","doi-asserted-by":"crossref","unstructured":"Gao, J., Zhu, J., Lan, Z., He, F., and Dong, X. (2025). Genome-Wide Analysis of NAC Gene Family and Its Cold-Responsive Transcriptional Dynamics in Coffea Arabica. Agronomy, 15.","DOI":"10.3390\/agronomy15102394"},{"key":"ref_77","doi-asserted-by":"crossref","first-page":"143","DOI":"10.1007\/s00425-025-04847-2","article-title":"Alternative Splicing in Plant Stress Responses: Potential Application for Crop Improvement","volume":"262","author":"Toh","year":"2025","journal-title":"Planta"},{"key":"ref_78","doi-asserted-by":"crossref","first-page":"231","DOI":"10.1016\/j.bbamcr.2017.10.010","article-title":"The Rice Cold-Responsive Calcium-Dependent Protein Kinase OsCPK17 Is Regulated by Alternative Splicing and Post-Translational Modifications","volume":"1865","author":"Almadanim","year":"2018","journal-title":"Biochim. Biophys. Acta (BBA)-Mol. Cell Res."},{"key":"ref_79","doi-asserted-by":"crossref","first-page":"687","DOI":"10.1146\/annurev-arplant-083123-090055","article-title":"Alternative Splicing Dynamics in Plant Adaptive Responses to Stress","volume":"76","author":"Alhabsi","year":"2025","journal-title":"Annu. Rev. Plant Biol."},{"key":"ref_80","doi-asserted-by":"crossref","unstructured":"Liu, J., Chen, H., Li, C., Du, K., and Yang, J. (2025). Genome-Wide Identification and Expression Analysis of GRAS Transcription Factors under Cold Stress in Diploid and Triploid Eucalyptus. Front. Genet., 16.","DOI":"10.3389\/fgene.2025.1436285"},{"key":"ref_81","doi-asserted-by":"crossref","unstructured":"Dolgikh, A.V., Kirienko, A.N., Tikhonovich, I.A., Foo, E., and Dolgikh, E.A. (2019). The DELLA Proteins Influence the Expression of Cytokinin Biosynthesis and Response Genes During Nodulation. Front. Plant Sci., 10.","DOI":"10.3389\/fpls.2019.00432"},{"key":"ref_82","doi-asserted-by":"crossref","unstructured":"Feng, Y., Li, Z., Kong, X., Khan, A., Ullah, N., and Zhang, X. (2025). Plant Coping with Cold Stress: Molecular and Physiological Adaptive Mechanisms with Future Perspectives. Cells, 14.","DOI":"10.3390\/cells14020110"},{"key":"ref_83","doi-asserted-by":"crossref","unstructured":"Chopra, R., Burow, G., Hayes, C., Emendack, Y., Xin, Z., and Burke, J. (2015). Transcriptome Profiling and Validation of Gene Based Single Nucleotide Polymorphisms (SNPs) in Sorghum Genotypes with Contrasting Responses to Cold Stress. BMC Genom., 16.","DOI":"10.1186\/s12864-015-2268-8"}],"container-title":["Biology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/2079-7737\/15\/7\/560\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,4,2]],"date-time":"2026-04-02T12:13:10Z","timestamp":1775131990000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/2079-7737\/15\/7\/560"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,3,31]]},"references-count":83,"journal-issue":{"issue":"7","published-online":{"date-parts":[[2026,4]]}},"alternative-id":["biology15070560"],"URL":"https:\/\/doi.org\/10.3390\/biology15070560","relation":{},"ISSN":["2079-7737"],"issn-type":[{"value":"2079-7737","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,3,31]]}}}