{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,30]],"date-time":"2026-07-30T16:01:39Z","timestamp":1785427299190,"version":"3.56.0"},"reference-count":153,"publisher":"MDPI AG","issue":"7","license":[{"start":{"date-parts":[[2026,7,15]],"date-time":"2026-07-15T00:00:00Z","timestamp":1784073600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100019644","name":"Ministry of Agriculture of the Republic of Kazakhstan","doi-asserted-by":"crossref","award":["IRN BR22883587"],"award-info":[{"award-number":["IRN BR22883587"]}],"id":[{"id":"10.13039\/100019644","id-type":"DOI","asserted-by":"crossref"}]},{"award":["IRN BR22883587"],"award-info":[{"award-number":["IRN BR22883587"]}],"id":[{"id":"https:\/\/ror.org\/03577hm03","id-type":"ROR","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["CIMB"],"abstract":"<jats:p>Salinity stress affects not only the survival and productivity of halophytic plants, but also the composition, structure and processability of their biomass. In Salicornia spp., salt-induced regulation of ion transport, osmotic adjustment, reactive oxygen species signaling, antioxidant defense, and cell wall remodeling can directly influence residual salinity, water retention, texture, extractability, drying behavior, and oxidative stability of plant biomass. However, most existing transcriptomic studies of Salicornia and related halophytes have focused mainly on salt tolerance mechanisms, whereas the connection between stress-regulated molecular networks and processing-related biomass traits remains insufficiently systematized. This review addresses this gap by proposing a mechanistic framework that links salinity perception, ROS-mediated signaling, ABA and MAPK pathways, antioxidant gene families, transcription factor networks and processing-oriented quality traits. Special attention is given to enzymatic antioxidant systems, including SOD, CAT, APX, POD and components of the ascorbate-glutathione cycle, as well as to non-enzymatic defense mechanisms involving ascorbate, glutathione, phenolic compounds, carotenoids, proline and glycine betaine. The review also discusses the regulatory roles of WRKY, DREB\/CBF, NAC, bZIP and MYB transcription factor families as molecular control points connecting salinity stress responses with downstream metabolic and structural traits. Network-based approaches, including WGCNA, pathway signatures and transcript panels, are considered more informative than single-gene markers for predicting complex quality traits in Salicornia biomass. In addition, recent genomic and computational strategies, including CRISPR\/Cas-mediated functional validation, GWAS, genomic selection, multi-omics integration and AI-assisted modeling, are discussed as emerging tools for candidate-gene prioritization and predictive assessment of stress-dependent biomass quality. Overall, this review shifts the interpretation of Salicornia transcriptomics from a descriptive salt-tolerance model toward a mechanistic and application-oriented framework for improving halophytic raw materials for food, feed and bioprocessing applications.<\/jats:p>","DOI":"10.3390\/cimb48070719","type":"journal-article","created":{"date-parts":[[2026,7,16]],"date-time":"2026-07-16T06:49:36Z","timestamp":1784184576000},"page":"719","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["ROS-Centered Transcriptomic Regulatory Networks Linking Salinity Stress, Antioxidant Defense and Processability Traits in Salicornia spp."],"prefix":"10.3390","volume":"48","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-8185-714X","authenticated-orcid":false,"given":"Nurtai","family":"Gubaidullin","sequence":"first","affiliation":[{"name":"Institute of Animal Science and Veterinary Medicine, Saken Seifullin Kazakh Agrotechnical University, Astana 010000, Kazakhstan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6043-4658","authenticated-orcid":false,"given":"Gulnazym","family":"Ospankulova","sequence":"additional","affiliation":[{"name":"Institute of Engineering and Food Technology, Saken Seifullin Kazakh Agrotechnical University, Astana 010000, Kazakhstan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Aisarat","family":"Gajimuradova","sequence":"additional","affiliation":[{"name":"Engineering Center for Organic Agricultural Technology, Saken Seifullin Kazakh Agrotechnical University, Astana 010000, Kazakhstan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alfiya","family":"Syzdykova","sequence":"additional","affiliation":[{"name":"Institute of Animal Science and Veterinary Medicine, Saken Seifullin Kazakh Agrotechnical University, Astana 010000, Kazakhstan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8661-7348","authenticated-orcid":false,"given":"Aibek","family":"Zhumalin","sequence":"additional","affiliation":[{"name":"Institute of Animal Science and Veterinary Medicine, Saken Seifullin Kazakh Agrotechnical University, Astana 010000, Kazakhstan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0006-4487-4625","authenticated-orcid":false,"given":"Kalamkas","family":"Dairova","sequence":"additional","affiliation":[{"name":"Institute of Engineering and Food Technology, Saken Seifullin Kazakh Agrotechnical University, Astana 010000, Kazakhstan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Damilya","family":"Konysbayeva","sequence":"additional","affiliation":[{"name":"Institute of Agriculture and Forestry, Saken Seifullin Kazakh Agrotechnical University, Astana 010000, Kazakhstan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Viktoriya","family":"Gorbulya","sequence":"additional","affiliation":[{"name":"Institute of Agriculture and Forestry, Saken Seifullin Kazakh Agrotechnical University, Astana 010000, Kazakhstan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4128-6482","authenticated-orcid":false,"given":"Kadyrzhan","family":"Makangali","sequence":"additional","affiliation":[{"name":"Engineering Center for Organic Agricultural Technology, Saken Seifullin Kazakh Agrotechnical University, Astana 010000, Kazakhstan"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2026,7,15]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"313","DOI":"10.1016\/j.cell.2016.08.029","article-title":"Abiotic stress signaling and responses in plants","volume":"167","author":"Zhu","year":"2016","journal-title":"Cell"},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"651","DOI":"10.1146\/annurev.arplant.59.032607.092911","article-title":"Mechanisms of salinity tolerance","volume":"59","author":"Munns","year":"2008","journal-title":"Annu. Rev. Plant Biol."},{"key":"ref_3","doi-asserted-by":"crossref","unstructured":"Zhao, S., Cao, R., Sun, L., Zhuang, D., Zhong, M., Zhao, F., Jiao, G., Chen, P., Li, X., and Duan, Y. (2024). An Integrative Analysis of the Transcriptome and Proteome of Rice Grain Chalkiness Formation Under High Temperature. Plants, 13.","DOI":"10.3390\/plants13233309"},{"key":"ref_4","doi-asserted-by":"crossref","unstructured":"Nirmal, R.C., Furtado, A., Wrigley, C., and Henry, R.J. (2016). Influence of gene expression on hardness in wheat. PLoS ONE, 11.","DOI":"10.1371\/journal.pone.0164746"},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"100906","DOI":"10.1016\/j.crfs.2024.100906","article-title":"Techno-functional, rheological, and chemical properties of plant-based protein ingredients obtained with dry fractionation and wet extraction","volume":"9","author":"Latrofa","year":"2024","journal-title":"Curr. Res. Food Sci."},{"key":"ref_6","doi-asserted-by":"crossref","unstructured":"Gan, J., Qiu, Y., Tao, Y., Zhang, L., Okita, T.W., Yan, Y., and Tian, L. (2024). RNA-seq analysis reveals transcriptome reprogramming and alternative splicing during early response to salt stress in tomato root. Front. Plant Sci., 15.","DOI":"10.3389\/fpls.2024.1394223"},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"70","DOI":"10.1007\/s11306-022-01926-3","article-title":"Quality assurance and quality control reporting in untargeted metabolic phenotyping: mQACC recommendations for analytical quality management","volume":"18","author":"Kirwan","year":"2022","journal-title":"Metabolomics"},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"110577","DOI":"10.1016\/j.plaphy.2025.110577","article-title":"Development of multi-sensing technologies for high-throughput morphological, physiological, and biochemical phenotyping of drought-stressed watermelon plants","volume":"229","author":"Faqeerzada","year":"2025","journal-title":"Plant Physiol. Biochem."},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"205","DOI":"10.1007\/s00122-025-04984-y","article-title":"Integration of crop modeling and sensing into molecular breeding for nutritional quality and stress tolerance","volume":"138","author":"Berlingeri","year":"2025","journal-title":"Theor. Appl. Genet."},{"key":"ref_10","doi-asserted-by":"crossref","unstructured":"Upton, R.N., Correr, F.H., Lile, J., Reynolds, G.L., Falaschi, K., Cook, J.P., and Lachowiec, J. (2023). Design, execution, and interpretation of plant RNA seq analyses. Front. Plant Sci., 14.","DOI":"10.3389\/fpls.2023.1135455"},{"key":"ref_11","doi-asserted-by":"crossref","unstructured":"Butardo, V.M., Luo, J., Li, Z., Gidley, M.J., Bird, A.R., Tetlow, I.J., Fitzgerald, M., Jobling, S.A., and Rahman, S. (2020). Functional genomic validation of the roles of soluble starch synthase IIa in Japonica rice endosperm. Front. Genet., 11.","DOI":"10.3389\/fgene.2020.00289"},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"32846","DOI":"10.1021\/acs.jafc.5c14669","article-title":"Metabolic and starch biosynthetic networks underlying yam waxiness formation revealed by integrated transcriptomics and proteomics","volume":"73","author":"Li","year":"2025","journal-title":"J. Agric. Food Chem."},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"3434","DOI":"10.1080\/10408398.2025.2597286","article-title":"Mechanistic analysis of starch gelatinization properties regulated by biomolecules: A protein, non-starch polysaccharides and lipids perspective","volume":"66","author":"Song","year":"2025","journal-title":"Crit. Rev. Food Sci. Nutr."},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"227","DOI":"10.1038\/nrg3185","article-title":"Insights into the regulation of protein abundance from proteomic and transcriptomic analyses","volume":"13","author":"Vogel","year":"2012","journal-title":"Nat. Rev. Genet."},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"391","DOI":"10.1038\/nrm1939","article-title":"Interpreting the protein language using proteomics","volume":"7","author":"Jensen","year":"2006","journal-title":"Nat. Rev. Mol. Cell Biol."},{"key":"ref_16","doi-asserted-by":"crossref","unstructured":"Moskal, K., Puchta-Jasi\u0144ska, M., Bolc, P., Motor, A., Frankowski, R., Pietrusi\u0144ska-Radzio, A., Ruci\u0144ska, A., Tomiczak, K., and Boczkowska, M. (2025). Why \u201cWhere\u201d Matters as Much as \u201cHow Much\u201d: Single-Cell and Spatial Transcriptomics in Plants. Int. J. Mol. Sci., 26.","DOI":"10.3390\/ijms262411819"},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"24","DOI":"10.1007\/s12038-022-00253-y","article-title":"Emerging landscape of molecular interaction networks: Opportunities, challenges and prospects","volume":"47","author":"Panditrao","year":"2022","journal-title":"J. Biosci."},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"5040","DOI":"10.1039\/D5RA07499A","article-title":"Rheological analysis in food processing: Factors, applications, and future outlooks with machine learning integration","volume":"16","author":"Chen","year":"2026","journal-title":"RSC Adv."},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"e287792","DOI":"10.1590\/1519-6984.287792","article-title":"Advancements in green extraction technologies for pectin enhancing efficiency, sustainability, and functional properties: A systematic review","volume":"85","year":"2025","journal-title":"Braz. J. Biol."},{"key":"ref_20","doi-asserted-by":"crossref","unstructured":"Spinardi, A., Cola, G., Gardana, C.S., and Mignani, I. (2019). Variation of anthocyanin content and profile throughout fruit development and ripening of highbush blueberry cultivars grown at two different altitudes. Front. Plant Sci., 10.","DOI":"10.3389\/fpls.2019.01045"},{"key":"ref_21","doi-asserted-by":"crossref","unstructured":"Xie, M., Wang, J., Wang, F., Wang, J., Yan, Y., Feng, K., and Chen, B. (2025). A review of genomic, transcriptomic, and proteomic applications in edible fungi biology: Current status and future directions. J. Fungi, 11.","DOI":"10.3390\/jof11060422"},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"6908","DOI":"10.1080\/10408398.2021.1908221","article-title":"\u03b2-glucan, \u201cthe knight of health sector\u201d: Critical insights on physiochemical heterogeneities, action mechanisms and health implications","volume":"62","author":"Muthuramalingam","year":"2022","journal-title":"Crit. Rev. Food Sci. Nutr."},{"key":"ref_23","doi-asserted-by":"crossref","unstructured":"Desai, N., Rana, D., Salave, S., Gupta, R., Patel, P., Karunakaran, B., Sharma, A., Giri, J., Benival, D., and Kommineni, N. (2023). Chitosan: A potential biopolymer in drug delivery and biomedical applications. Pharmaceutics, 15.","DOI":"10.3390\/pharmaceutics15041313"},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"43","DOI":"10.1038\/s41392-025-02554-8","article-title":"Region-resolved proteomic map of the human brain: Functional interconnections and neurological implications","volume":"11","author":"Zhang","year":"2026","journal-title":"Signal Transduct. Target. Ther."},{"key":"ref_25","doi-asserted-by":"crossref","unstructured":"Zhan, C., Tang, T., Wu, E., Zhang, Y., He, M., Wu, R., Bi, C., Wang, J., Zhang, Y., and Shen, B. (2023). From multi-omics approaches to personalized medicine in myocardial infarction. Front. Cardiovasc. Med., 10.","DOI":"10.3389\/fcvm.2023.1250340"},{"key":"ref_26","doi-asserted-by":"crossref","unstructured":"Huo, J., Yu, M., Feng, N., Zheng, D., Zhang, R., Xue, Y., Khan, A., Zhou, H., Mei, W., and Du, X. (2024). Integrated transcriptome and metabolome analysis of salinity tolerance in response to foliar application of choline chloride in rice (Oryza sativa L.). Front. Plant Sci., 15.","DOI":"10.3389\/fpls.2024.1440663"},{"key":"ref_27","doi-asserted-by":"crossref","unstructured":"Satrio, R.D., Fendiyanto, M.H., and Miftahudin, M. (2024). Tools and techniques used at global scale through genomics, transcriptomics, proteomics, and metabolomics to investigate plant stress responses at the molecular level. Molecular Dynamics of Plant Stress and Its Management, Springer Nature.","DOI":"10.1007\/978-981-97-1699-9_25"},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"foac025","DOI":"10.1093\/femsyr\/foac025","article-title":"Post-transcriptional regulation during stress","volume":"22","author":"Sunnerhagen","year":"2022","journal-title":"FEMS Yeast Res."},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"2406318","DOI":"10.1002\/advs.202406318","article-title":"Post-translational modifications of RNA-modifying proteins in cellular dynamics and disease progression","volume":"11","author":"Lin","year":"2024","journal-title":"Adv. Sci."},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"98","DOI":"10.1016\/j.cels.2022.12.009","article-title":"Spatial self-organization of metabolism in microbial systems: A matter of enzymes and chemicals","volume":"14","author":"Ackermann","year":"2023","journal-title":"Cell Syst."},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"3648","DOI":"10.1021\/acs.biomac.2c00546","article-title":"Probing crowdedness of artificial organelles by clustering polymersomes for spatially controlled and pH-triggered enzymatic reactions","volume":"23","author":"Wang","year":"2022","journal-title":"Biomacromolecules"},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"14088","DOI":"10.1021\/acs.chemrev.0c01333","article-title":"Deconstruction and reassembly of renewable polymers and biocolloids into next generation structured materials","volume":"121","author":"Tardy","year":"2021","journal-title":"Chem. Rev."},{"key":"ref_33","doi-asserted-by":"crossref","unstructured":"Arrigo, R., Malucelli, G., and Mantia, F.P.L. (2021). Effect of the elongational flow on the morphology and properties of polymer systems: A brief review. Polymers, 13.","DOI":"10.3390\/polym13203529"},{"key":"ref_34","doi-asserted-by":"crossref","unstructured":"Oyinloye, T.M., Lee, C.J., and Yoon, W.B. (2025). Integration of nonlinear rheology and CFD simulation to elucidate the influence of saturated oil on soy protein concentrate behavior during high-moisture extrusion. Gels, 11.","DOI":"10.3390\/gels11121003"},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"939","DOI":"10.1104\/pp.110.162545","article-title":"Suppression of the vacuolar invertase gene prevents cold-induced sweetening in potato","volume":"154","author":"Bhaskar","year":"2010","journal-title":"Plant Physiol."},{"key":"ref_36","doi-asserted-by":"crossref","unstructured":"Liu, T., Zhou, T., Cui, G., Liu, X., and Song, B. (Hortic. Plant J., 2025). Advances in understanding cold-induced sweetening in potato tubers, Hortic. Plant J., in press.","DOI":"10.1016\/j.hpj.2025.08.015"},{"key":"ref_37","doi-asserted-by":"crossref","unstructured":"Wang, Q., Li, Y., Sun, F., Li, X., Wang, P., Yang, G., and He, G. (2019). Expression of Puroindoline a in durum wheat affects milling and pasting properties. Front. Plant Sci., 10.","DOI":"10.3389\/fpls.2019.00482"},{"key":"ref_38","doi-asserted-by":"crossref","first-page":"100348","DOI":"10.1016\/j.fochms.2025.100348","article-title":"Transcriptional networks shaping malting quality in barley: From grain development to brewing performance","volume":"12","author":"Panahi","year":"2025","journal-title":"Food Chem. Mol. Sci."},{"key":"ref_39","unstructured":"Held, S.T. (2022). Effects of Mash Style on \u03b2-Glucan Concentration and \u03b2-Glucanase Activity in the Production of Quality Wort for Beer Brewing. [Master\u2019s Thesis, University of California]."},{"key":"ref_40","unstructured":"Fox, G.P. (2025). Variation in Barley Quality and Its Impact on Malting and Brewing. [Ph.D. Thesis, Stellenbosch University]."},{"key":"ref_41","doi-asserted-by":"crossref","unstructured":"Amirebrahimi, F.F., Saidi, A., and Ahmadikhah, A. (2025). Genome-wide association study (GWAS) and transcription analysis of candidate genes for rice grain eating and cooking quality traits. BMC Genom., 27.","DOI":"10.1186\/s12864-025-12354-7"},{"key":"ref_42","doi-asserted-by":"crossref","unstructured":"Zhao, Y., Zhao, J., Hu, M., Sun, L., Liu, Q., Zhang, Y., Li, Q., Wang, P., Ma, W., and Li, H. (2023). Transcriptome and proteome analysis revealed the influence of high-molecular-weight glutenin subunits deficiency on expression of storage substances and the potential regulatory mechanism of HMW-GSs. Foods, 12.","DOI":"10.3390\/foods12020361"},{"key":"ref_43","doi-asserted-by":"crossref","first-page":"142205","DOI":"10.1016\/j.foodchem.2024.142205","article-title":"Investigating the molecular mechanism of high-molecular-weight glutenin subunit affects gluten aggregation during dough mixing: Experimental characterizations and computational simulations","volume":"466","author":"Yang","year":"2025","journal-title":"Food Chem."},{"key":"ref_44","doi-asserted-by":"crossref","first-page":"1460","DOI":"10.1016\/j.cj.2025.06.002","article-title":"TaIAA10-6D orchestrates processing quality and grain yield by modulating glutenin\u2013gliadin ratio and plant morphogenesis in wheat","volume":"13","author":"Liu","year":"2025","journal-title":"Crop J."},{"key":"ref_45","doi-asserted-by":"crossref","first-page":"1952","DOI":"10.1111\/pbi.14103","article-title":"Efficient proteome-wide identification of transcription factors targeting Glu-1: A case study for functional validation of TaB3-2A1 in wheat","volume":"21","author":"Xie","year":"2023","journal-title":"Plant Biotechnol. J."},{"key":"ref_46","doi-asserted-by":"crossref","unstructured":"Merlino, M., Gaudin, J.C., Dardevet, M., Martre, P., Ravel, C., and Boudet, J. (2023). Wheat DOF transcription factors TaSAD and WPBF regulate glutenin gene expression in cooperation with SPA. PLoS ONE, 18.","DOI":"10.1371\/journal.pone.0287645"},{"key":"ref_47","doi-asserted-by":"crossref","unstructured":"Li, C., Mur, L.A., Wang, Q., Hou, X., Zhao, C., Chen, Z., Wu, J., and Guo, Q. (2022). ROS scavenging and ion homeostasis is required for the adaptation of halophyte Karelinia caspia to high salinity. Front. Plant Sci., 13.","DOI":"10.3389\/fpls.2022.979956"},{"key":"ref_48","doi-asserted-by":"crossref","unstructured":"Wang, X., Wang, T., Yu, P., Li, Y., and Lv, X. (2024). NO enhances the adaptability to high-salt environments by regulating osmotic balance, antioxidant defense, and ion homeostasis in eelgrass based on transcriptome and metabolome analysis. Front. Plant Sci., 15.","DOI":"10.3389\/fpls.2024.1343154"},{"key":"ref_49","doi-asserted-by":"crossref","first-page":"12","DOI":"10.1016\/j.ejsobi.2011.08.006","article-title":"Shifts in microbial community function and structure along the successional gradient of coastal wetlands in Yellow River Estuary","volume":"49","author":"Yu","year":"2012","journal-title":"Eur. J. Soil Biol."},{"key":"ref_50","doi-asserted-by":"crossref","first-page":"111","DOI":"10.1146\/annurev-arplant-070122-030236","article-title":"cis-Regulatory elements in plant development, adaptation, and evolution","volume":"74","author":"Marand","year":"2023","journal-title":"Annu. Rev. Plant Biol."},{"key":"ref_51","doi-asserted-by":"crossref","first-page":"e31","DOI":"10.1093\/nar\/gkx1279","article-title":"TF2Network: Predicting transcription factor regulators and gene regulatory networks in Arabidopsis using publicly available binding site information","volume":"46","author":"Kulkarni","year":"2018","journal-title":"Nucleic Acids Res."},{"key":"ref_52","doi-asserted-by":"crossref","first-page":"489","DOI":"10.1146\/annurev-arplant-050718-100334","article-title":"MicroRNAs and their regulatory roles in plant\u2013environment interactions","volume":"70","author":"Song","year":"2019","journal-title":"Annu. Rev. Plant Biol."},{"key":"ref_53","doi-asserted-by":"crossref","unstructured":"Zeng, Z., Zhang, S., Li, W., Chen, B., and Li, W. (2022). Gene-coexpression network analysis identifies specific modules and hub genes related to cold stress in rice. BMC Genom., 23.","DOI":"10.1186\/s12864-022-08438-3"},{"key":"ref_54","doi-asserted-by":"crossref","unstructured":"Yu, T., Zhang, J., Cao, J., Ma, X., Li, W., and Yang, G. (2023). Hub gene mining and co-expression network construction of low-temperature response in maize of seedling by WGCNA. Genes, 14.","DOI":"10.3390\/genes14081598"},{"key":"ref_55","first-page":"D1104","article-title":"PlantRegMap: Charting functional regulatory maps in plants","volume":"48","author":"Tian","year":"2020","journal-title":"Nucleic Acids Res."},{"key":"ref_56","doi-asserted-by":"crossref","unstructured":"Hussey, S.G., Mizrachi, E., Creux, N.M., and Myburg, A.A. (2013). Navigating the transcriptional roadmap regulating plant secondary cell wall deposition. Front. Plant Sci., 4.","DOI":"10.3389\/fpls.2013.00325"},{"key":"ref_57","doi-asserted-by":"crossref","first-page":"789","DOI":"10.1093\/aob\/mcae189","article-title":"Lipid metabolism improves salt tolerance of Salicornia europaea","volume":"135","author":"Yang","year":"2025","journal-title":"Ann. Bot."},{"key":"ref_58","doi-asserted-by":"crossref","first-page":"1598","DOI":"10.1111\/pbi.70424","article-title":"The Zma-miRNA319-ZmMYB74 module regulates maize resistance to stalk rot disease by modulating lignin deposition","volume":"24","author":"Cao","year":"2026","journal-title":"Plant Biotechnol. J."},{"key":"ref_59","doi-asserted-by":"crossref","unstructured":"Arshad, K.T., Li, C., Li, L., Wang, J., Chen, J., and Zhao, Y. (2025). Genome-wide identification and expression profiling of bHLH transcription factors associated with ferulic acid biosynthesis in Angelica sinensis. Front. Plant Sci., 16.","DOI":"10.3389\/fpls.2025.1718585"},{"key":"ref_60","doi-asserted-by":"crossref","unstructured":"Qiao, X., Jian, B., Qiu, J., Singh, J., Kaur, I., Hao, R., Singh, J., Singh, L., Zhang, H., and Yin, X. (2025). Transcriptomics in solanaceous crop improvement: Advances and opportunities. Front. Plant Sci., 16.","DOI":"10.3389\/fpls.2025.1750317"},{"key":"ref_61","doi-asserted-by":"crossref","unstructured":"Zhu, Z., Jiang, L., and Ding, X. (2023). Advancing breast cancer heterogeneity analysis: Insights from genomics, transcriptomics and proteomics at bulk and single-cell levels. Cancers, 15.","DOI":"10.3390\/cancers15164164"},{"key":"ref_62","doi-asserted-by":"crossref","first-page":"337","DOI":"10.1016\/j.tplants.2025.10.005","article-title":"Advances in plant spatial multi-omics data analysis","volume":"31","author":"Yao","year":"2025","journal-title":"Trends Plant Sci."},{"key":"ref_63","doi-asserted-by":"crossref","first-page":"21","DOI":"10.1146\/annurev-arplant-070122-035226","article-title":"Plant small RNAs: Their biogenesis, regulatory roles, and functions","volume":"74","author":"Zhan","year":"2023","journal-title":"Annu. Rev. Plant Biol."},{"key":"ref_64","doi-asserted-by":"crossref","first-page":"330","DOI":"10.1186\/s12935-025-03964-y","article-title":"Integrating bulk RNA-seq, scRNA-seq and spatial transcriptomics data to identify novel post-translational modification-related molecular subtypes and therapeutic responses in hepatocellular carcinoma","volume":"25","author":"Chen","year":"2025","journal-title":"Cancer Cell Int."},{"key":"ref_65","doi-asserted-by":"crossref","first-page":"107124","DOI":"10.1016\/j.isci.2023.107124","article-title":"SCING: Inference of robust, interpretable gene regulatory networks from single-cell and spatial transcriptomics","volume":"26","author":"Littman","year":"2023","journal-title":"iScience"},{"key":"ref_66","doi-asserted-by":"crossref","first-page":"lqae184","DOI":"10.1093\/nargab\/lqae184","article-title":"Phenotype prediction in plants is improved by integrating large-scale transcriptomic datasets","volume":"6","author":"Wu","year":"2024","journal-title":"NAR Genom. Bioinform."},{"key":"ref_67","doi-asserted-by":"crossref","first-page":"1841","DOI":"10.1104\/pp.111.187898","article-title":"Gene expression biomarkers provide sensitive indicators of in planta nitrogen status in maize","volume":"157","author":"Yang","year":"2011","journal-title":"Plant Physiol."},{"key":"ref_68","doi-asserted-by":"crossref","first-page":"915","DOI":"10.1111\/tpj.13959","article-title":"Spatial analysis of lipid metabolites and expressed genes reveals tissue-specific heterogeneity of lipid metabolism in high- and low-oil Brassica napus seeds","volume":"94","author":"Lu","year":"2018","journal-title":"Plant J."},{"key":"ref_69","doi-asserted-by":"crossref","first-page":"759","DOI":"10.1038\/s41597-025-05115-4","article-title":"A spatio-temporal transcriptomic and proteomic dataset of developing Brassica napus seeds","volume":"12","author":"Knoch","year":"2025","journal-title":"Sci. Data"},{"key":"ref_70","doi-asserted-by":"crossref","first-page":"149718","DOI":"10.1016\/j.gene.2025.149718","article-title":"Single-cell transcriptome sequencing reveals dynamic gene expression trajectories regulating vascular cell senescence in Hylocereus undatus","volume":"966","author":"Wang","year":"2025","journal-title":"Gene"},{"key":"ref_71","doi-asserted-by":"crossref","unstructured":"Yao, Y., Xiong, E., Qu, X., Li, J., Liu, H., Quan, L., Lu, W., Zhu, X., Chen, M., and Li, K. (2023). WGCNA and transcriptome profiling reveal hub genes for key development stage seed size\/oil content between wild and cultivated soybean. BMC Genom., 24.","DOI":"10.1186\/s12864-023-09617-6"},{"key":"ref_72","doi-asserted-by":"crossref","first-page":"29","DOI":"10.1186\/s13578-024-01204-w","article-title":"Transcriptome-wide association studies associated with Crohn\u2019s disease: Challenges and perspectives","volume":"14","author":"Jia","year":"2024","journal-title":"Cell Biosci."},{"key":"ref_73","doi-asserted-by":"crossref","unstructured":"Yasir, M., Kanwal, H.H., Hussain, Q., Riaz, M.W., Sajjad, M., Rong, J., and Jiang, Y. (2022). Status and prospects of genome-wide association studies in cotton. Front. Plant Sci., 13.","DOI":"10.3389\/fpls.2022.1019347"},{"key":"ref_74","doi-asserted-by":"crossref","first-page":"112023","DOI":"10.1016\/j.postharvbio.2022.112023","article-title":"RNA-seq based analysis of transcriptomic changes associated with ABA-induced postharvest cold tolerance in zucchini fruit","volume":"192","author":"Benitez","year":"2022","journal-title":"Postharvest Biol. Technol."},{"key":"ref_75","doi-asserted-by":"crossref","first-page":"733","DOI":"10.1038\/nrg2825","article-title":"Tackling the widespread and critical impact of batch effects in high-throughput data","volume":"11","author":"Leek","year":"2010","journal-title":"Nat. Rev. Genet."},{"key":"ref_76","doi-asserted-by":"crossref","first-page":"839","DOI":"10.1261\/rna.053959.115","article-title":"How many biological replicates are needed in an RNA-seq experiment and which differential expression tool should you use?","volume":"22","author":"Schurch","year":"2016","journal-title":"RNA"},{"key":"ref_77","doi-asserted-by":"crossref","first-page":"301","DOI":"10.1093\/bioinformatics\/btt688","article-title":"RNA-seq differential expression studies: More sequence or more replication?","volume":"30","author":"Liu","year":"2014","journal-title":"Bioinformatics"},{"key":"ref_78","first-page":"11","article-title":"Isolation of total RNA from tissues rich in polyphenols and polysaccharides of mangrove plants","volume":"14","year":"2011","journal-title":"Electron. J. Biotechnol."},{"key":"ref_79","doi-asserted-by":"crossref","first-page":"78","DOI":"10.1016\/j.ejbt.2020.09.008","article-title":"An easy and robust method for the isolation of high quality RNA from coconut tissues","volume":"48","author":"Iqbal","year":"2020","journal-title":"Electron. J. Biotechnol."},{"key":"ref_80","doi-asserted-by":"crossref","first-page":"144","DOI":"10.21638\/spbu03.2021.205","article-title":"Isolation of high-quality RNA from plant seeds","volume":"66","author":"Mishko","year":"2021","journal-title":"Biol. Commun."},{"key":"ref_81","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_82","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_83","doi-asserted-by":"crossref","first-page":"525","DOI":"10.1038\/nbt.3519","article-title":"Near-optimal probabilistic RNA-seq quantification","volume":"34","author":"Bray","year":"2016","journal-title":"Nat. Biotechnol."},{"key":"ref_84","doi-asserted-by":"crossref","first-page":"1521","DOI":"10.12688\/f1000research.7563.2","article-title":"Differential analyses for RNA-seq: Transcript-level estimates improve gene-level inferences","volume":"4","author":"Soneson","year":"2016","journal-title":"F1000Research"},{"key":"ref_85","doi-asserted-by":"crossref","unstructured":"Zhao, L., Zhang, H., Kohnen, M.V., Prasad, K.V., Gu, L., and Reddy, A.S. (2019). Analysis of transcriptome and epitranscriptome in plants using PacBio Iso-Seq and nanopore-based direct RNA sequencing. Front. Genet., 10.","DOI":"10.3389\/fgene.2019.00253"},{"key":"ref_86","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_87","doi-asserted-by":"crossref","first-page":"R25","DOI":"10.1186\/gb-2010-11-3-r25","article-title":"A scaling normalization method for differential expression analysis of RNA-seq data","volume":"11","author":"Robinson","year":"2010","journal-title":"Genome Biol."},{"key":"ref_88","doi-asserted-by":"crossref","first-page":"13","DOI":"10.1186\/s13059-016-0881-8","article-title":"A survey of best practices for RNA-seq data analysis","volume":"17","author":"Conesa","year":"2016","journal-title":"Genome Biol."},{"key":"ref_89","doi-asserted-by":"crossref","first-page":"281","DOI":"10.1007\/s12064-012-0162-3","article-title":"Measurement of mRNA abundance using RNA-seq data: RPKM measure is inconsistent among samples","volume":"131","author":"Wagner","year":"2012","journal-title":"Theory Biosci."},{"key":"ref_90","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_91","doi-asserted-by":"crossref","unstructured":"The Gene Ontology Consortium (2021). The Gene Ontology resource: Enriching a GOld mine. Nucleic Acids Res., 49, D325\u2013D334.","DOI":"10.1093\/nar\/gkaa1113"},{"key":"ref_92","doi-asserted-by":"crossref","first-page":"27","DOI":"10.1093\/nar\/28.1.27","article-title":"KEGG: Kyoto encyclopedia of genes and genomes","volume":"28","author":"Kanehisa","year":"2000","journal-title":"Nucleic Acids Res."},{"key":"ref_93","doi-asserted-by":"crossref","first-page":"879","DOI":"10.1016\/j.molp.2019.01.003","article-title":"MapMan4: A refined protein classification and annotation framework applicable to multi-omics data analysis","volume":"12","author":"Schwacke","year":"2019","journal-title":"Mol. Plant"},{"key":"ref_94","doi-asserted-by":"crossref","first-page":"15545","DOI":"10.1073\/pnas.0506580102","article-title":"Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles","volume":"102","author":"Subramanian","year":"2005","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_95","doi-asserted-by":"crossref","first-page":"284","DOI":"10.1089\/omi.2011.0118","article-title":"clusterProfiler: An R package for comparing biological themes among gene clusters","volume":"16","author":"Yu","year":"2012","journal-title":"OMICS A J. Integr. Biol."},{"key":"ref_96","doi-asserted-by":"crossref","first-page":"btaf365","DOI":"10.1093\/bioinformatics\/btaf365","article-title":"Annotation matters: The effect of structural gene annotation on orthology inference","volume":"41","author":"Nevers","year":"2025","journal-title":"Bioinformatics"},{"key":"ref_97","doi-asserted-by":"crossref","first-page":"1447","DOI":"10.1093\/molbev\/msaa302","article-title":"Degree of functional divergence in duplicates is associated with distinct roles in plant evolution","volume":"38","author":"Ezoe","year":"2021","journal-title":"Mol. Biol. Evol."},{"key":"ref_98","doi-asserted-by":"crossref","first-page":"308","DOI":"10.1016\/j.tig.2023.01.003","article-title":"Interpreting omics data with pathway enrichment analysis","volume":"39","author":"Zhao","year":"2023","journal-title":"Trends Genet."},{"key":"ref_99","doi-asserted-by":"crossref","first-page":"410","DOI":"10.1093\/sysbio\/syab044","article-title":"A new pipeline for removing paralogs in target enrichment data","volume":"71","author":"Zhou","year":"2022","journal-title":"Syst. Biol."},{"key":"ref_100","doi-asserted-by":"crossref","first-page":"D1456","DOI":"10.1093\/nar\/gkab794","article-title":"PlantGSAD: A comprehensive gene set annotation database for plant species","volume":"50","author":"Ma","year":"2022","journal-title":"Nucleic Acids Res."},{"key":"ref_101","doi-asserted-by":"crossref","first-page":"238","DOI":"10.1186\/s13059-019-1832-y","article-title":"OrthoFinder: Phylogenetic orthology inference for comparative genomics","volume":"20","author":"Emms","year":"2019","journal-title":"Genome Biol."},{"key":"ref_102","doi-asserted-by":"crossref","first-page":"D309","DOI":"10.1093\/nar\/gky1085","article-title":"eggNOG 5.0: A hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses","volume":"47","author":"Szklarczyk","year":"2019","journal-title":"Nucleic Acids Res."},{"key":"ref_103","doi-asserted-by":"crossref","first-page":"160018","DOI":"10.1038\/sdata.2016.18","article-title":"The FAIR guiding principles for scientific data management and stewardship","volume":"3","author":"Wilkinson","year":"2016","journal-title":"Sci. Data"},{"key":"ref_104","doi-asserted-by":"crossref","unstructured":"Clough, E., and Barrett, T. (2016). The gene expression omnibus database. Statistical Genomics: Methods and Protocols, Springer.","DOI":"10.1007\/978-1-4939-3578-9_5"},{"key":"ref_105","first-page":"D1145","article-title":"The Proteo-meXchange consortium in 2020: Enabling big data approaches in proteomics","volume":"48","author":"Deutsch","year":"2020","journal-title":"Nucleic Acids Res."},{"key":"ref_106","doi-asserted-by":"crossref","first-page":"163","DOI":"10.1016\/j.plaphy.2019.11.001","article-title":"Tuber transcriptome profiling of eight potato cultivars with different cold-induced sweetening responses","volume":"146","author":"Tai","year":"2020","journal-title":"Plant Physiol. Biochem."},{"key":"ref_107","doi-asserted-by":"crossref","unstructured":"Hadish, J.A., Hargarten, H.L., Zhang, H., Mattheis, J.P., Honaas, L.A., and Ficklin, S.P. (2024). Towards identification of post-harvest fruit quality transcriptomic markers in Malus domestica. PLoS ONE, 19, Correction in PLoS ONE 2024, 21, 0306187.","DOI":"10.1371\/journal.pone.0306187"},{"key":"ref_108","doi-asserted-by":"crossref","first-page":"10258","DOI":"10.1038\/s41598-020-66986-8","article-title":"ssGSEA score-based Ras dependency indexes derived from gene expression data reveal potential Ras addiction mechanisms with possible clinical implications","volume":"10","author":"Yi","year":"2020","journal-title":"Sci. Rep."},{"key":"ref_109","doi-asserted-by":"crossref","first-page":"139","DOI":"10.1105\/tpc.19.00332","article-title":"Transcriptome-based prediction of complex traits in maize","volume":"32","author":"Azodi","year":"2020","journal-title":"Plant Cell"},{"key":"ref_110","doi-asserted-by":"crossref","first-page":"102670","DOI":"10.1016\/j.pbi.2024.102670","article-title":"Evolving best practices for transcriptome-wide association studies accelerate discovery of gene\u2013phenotype links","volume":"83","author":"Li","year":"2025","journal-title":"Curr. Opin. Plant Biol."},{"key":"ref_111","doi-asserted-by":"crossref","first-page":"23","DOI":"10.1186\/s12284-025-00782-8","article-title":"Comprehensive GWAS and transcriptome analysis discovered candidate gene associated with starch pasting properties of temperate japonica rice (Oryza sativa L.)","volume":"18","author":"Lee","year":"2025","journal-title":"Rice"},{"key":"ref_112","doi-asserted-by":"crossref","first-page":"254","DOI":"10.1186\/s13059-024-03401-9","article-title":"Assessing and mitigating batch effects in large-scale omics studies","volume":"25","author":"Yu","year":"2024","journal-title":"Genome Biol."},{"key":"ref_113","doi-asserted-by":"crossref","first-page":"201","DOI":"10.1186\/s13059-023-03047-z","article-title":"Correcting batch effects in large-scale multiomics studies using a reference-material-based ratio method","volume":"24","author":"Yu","year":"2023","journal-title":"Genome Biol."},{"key":"ref_114","doi-asserted-by":"crossref","first-page":"1029","DOI":"10.1016\/j.tibtech.2022.02.005","article-title":"Are batch effects still relevant in the age of big data?","volume":"40","author":"Goh","year":"2022","journal-title":"Trends Biotechnol."},{"key":"ref_115","doi-asserted-by":"crossref","first-page":"101","DOI":"10.1016\/j.csbj.2025.12.015","article-title":"Designing RNA sequencing experiments: A practical guide to reproducible gene expression analysis","volume":"31","author":"Antoszewski","year":"2025","journal-title":"Comput. Struct. Biotechnol. J."},{"key":"ref_116","doi-asserted-by":"crossref","unstructured":"Sun, H., Li, C., Li, S., Ma, J., Li, S., Li, X., Gao, C., Yang, R., Ma, N., and Yang, J. (2024). Identification and validation of stable reference genes for RT-qPCR analyses of Kobresia littledalei seedlings. BMC Plant Biol., 24.","DOI":"10.1186\/s12870-024-04924-w"},{"key":"ref_117","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_118","doi-asserted-by":"crossref","first-page":"1280","DOI":"10.1016\/j.cell.2016.04.038","article-title":"Cistrome and epicistrome features shape the regulatory DNA landscape","volume":"165","author":"Huang","year":"2016","journal-title":"Cell"},{"key":"ref_119","doi-asserted-by":"crossref","unstructured":"Huynh-Thu, V.A., Irrthum, A., Wehenkel, L., and Geurts, P. (2010). Inferring regulatory networks from expression data using tree-based methods. PLoS ONE, 5.","DOI":"10.1371\/journal.pone.0012776"},{"key":"ref_120","doi-asserted-by":"crossref","first-page":"259","DOI":"10.1111\/j.1365-3040.2011.02336.x","article-title":"ROS and redox signalling in the response of plants to abiotic stress","volume":"35","author":"Suzuki","year":"2012","journal-title":"Plant Cell Environ."},{"key":"ref_121","doi-asserted-by":"crossref","first-page":"1229","DOI":"10.1093\/jxb\/ert375","article-title":"ROS as key players in plant stress signalling","volume":"65","author":"Baxter","year":"2014","journal-title":"J. Exp. Bot."},{"key":"ref_122","doi-asserted-by":"crossref","unstructured":"Nadarajah, K.K. (2020). ROS homeostasis in abiotic stress tolerance in plants. Int. J. Mol. Sci., 21.","DOI":"10.3390\/ijms21155208"},{"key":"ref_123","doi-asserted-by":"crossref","unstructured":"Rai, G.K., Mishra, S., Chouhan, R., Mushtaq, M., Chowdhary, A.A., Rai, P.K., Kumar, R.R., Kumar, P., Perez-Alfocea, F., and Colla, G. (2023). Plant salinity stress, sensing, and its mitigation through WRKY. Front. Plant Sci., 14.","DOI":"10.3389\/fpls.2023.1238507"},{"key":"ref_124","doi-asserted-by":"crossref","first-page":"414","DOI":"10.1111\/j.1399-3054.2009.01326.x","article-title":"ROS in biotic interactions","volume":"138","author":"Torres","year":"2010","journal-title":"Physiol. Plant."},{"key":"ref_125","doi-asserted-by":"crossref","unstructured":"Kurusu, T., Kuchitsu, K., and Tada, Y. (2015). Plant signaling networks involving Ca2+ and Rboh\/Nox-mediated ROS production under salinity stress. Front. Plant Sci., 6.","DOI":"10.3389\/fpls.2015.00427"},{"key":"ref_126","doi-asserted-by":"crossref","unstructured":"Hasanuzzaman, M., Bhuyan, M.H.M.B., Zulfiqar, F., Raza, A., Mohsin, S.M., Mahmud, J.A., Fujita, M., and Fotopoulos, V. (2020). Reactive oxygen species and antioxidant defense in plants under abiotic stress: Revisiting the crucial role of a universal defense regulator. Antioxidants, 9.","DOI":"10.3390\/antiox9080681"},{"key":"ref_127","doi-asserted-by":"crossref","unstructured":"Mishra, N., Jiang, C., Chen, L., Paul, A., Chatterjee, A., and Shen, G. (2023). Achieving abiotic stress tolerance in plants through antioxidative defense mechanisms. Front. Plant Sci., 14.","DOI":"10.3389\/fpls.2023.1110622"},{"key":"ref_128","doi-asserted-by":"crossref","first-page":"1011","DOI":"10.1590\/S1415-47572012000600016","article-title":"Plant responses to stresses: Role of ascorbate peroxidase in the antioxidant protection","volume":"35","author":"Caverzan","year":"2012","journal-title":"Genet. Mol. Biol."},{"key":"ref_129","doi-asserted-by":"crossref","unstructured":"Homayouni, H., Razi, H., Izadi, M., Alemzadeh, A., Kazemeini, S.A., Niazi, A., and Vicente, O. (2024). Temporal changes in biochemical responses to salt stress in three Salicornia species. Plants, 13.","DOI":"10.3390\/plants13070979"},{"key":"ref_130","doi-asserted-by":"crossref","first-page":"1261","DOI":"10.1007\/s11738-010-0656-x","article-title":"Effect of salt stress on physiological and antioxidative responses in two species of Salicornia (S. persica and S. europaea)","volume":"33","author":"Aghaleh","year":"2011","journal-title":"Acta Physiol. Plant."},{"key":"ref_131","doi-asserted-by":"crossref","unstructured":"Szyma\u0144ska, K.P., Polkowska-Kowalczyk, L., Lichocka, M., Maszkowska, J., and Dobrowolska, G. (2019). SNF1-related protein kinases SnRK2.4 and SnRK2.10 modulate ROS homeostasis in plant response to salt stress. Int. J. Mol. Sci., 20.","DOI":"10.3390\/ijms20010143"},{"key":"ref_132","doi-asserted-by":"crossref","unstructured":"Hussain, Q., Asim, M., Zhang, R., Khan, R., Farooq, S., and Wu, J. (2021). Transcription factors interact with ABA through gene expression and signaling pathways to mitigate drought and salinity stress. Biomolecules, 11.","DOI":"10.3390\/biom11081159"},{"key":"ref_133","doi-asserted-by":"crossref","unstructured":"Golldack, D., Li, C., Mohan, H., and Probst, N. (2014). Tolerance to drought and salt stress in plants: Unraveling the signaling networks. Front. Plant Sci., 5.","DOI":"10.3389\/fpls.2014.00151"},{"key":"ref_134","doi-asserted-by":"crossref","first-page":"2277","DOI":"10.1111\/pce.14606","article-title":"Revisiting the role of MAPK signalling pathway in plants and its manipulation for crop improvement","volume":"46","author":"Manna","year":"2023","journal-title":"Plant Cell Environ."},{"key":"ref_135","doi-asserted-by":"crossref","unstructured":"Khoso, M.A., Hussain, A., Ritonga, F.N., Ali, Q., Channa, M.M., Alshegaihi, R.M., Meng, Q., Ali, M., Zaman, W., and Brohi, R.D. (2022). WRKY transcription factors (TFs): Molecular switches to regulate drought, temperature, and salinity stresses in plants. Front. Plant Sci., 13.","DOI":"10.3389\/fpls.2022.1039329"},{"key":"ref_136","doi-asserted-by":"crossref","first-page":"510","DOI":"10.1111\/jipb.13854","article-title":"Multiple roles of NAC transcription factors in plant development and stress responses","volume":"67","author":"Xiong","year":"2025","journal-title":"J. Integr. Plant Biol."},{"key":"ref_137","doi-asserted-by":"crossref","first-page":"1613131","DOI":"10.1080\/15592324.2019.1613131","article-title":"Research advances of MYB transcription factors in plant stress resistance and breeding","volume":"14","author":"Li","year":"2019","journal-title":"Plant Signal. Behav."},{"key":"ref_138","doi-asserted-by":"crossref","first-page":"2169","DOI":"10.1007\/s00344-020-10134-z","article-title":"RNA-seq transcriptome profiling of the halophyte Salicornia persica in response to salinity","volume":"40","author":"Aliakbari","year":"2021","journal-title":"J. Plant Growth Regul."},{"key":"ref_139","doi-asserted-by":"crossref","unstructured":"Fan, P., Nie, L., Jiang, P., Feng, J., Lv, S., Chen, X., Bao, H., Guo, J., Tai, F., and Wang, J. (2013). Transcriptome analysis of Salicornia europaea under saline conditions revealed the adaptive primary metabolic pathways as early events to facilitate salt adaptation. PLoS ONE, 8.","DOI":"10.1371\/journal.pone.0080595"},{"key":"ref_140","doi-asserted-by":"crossref","unstructured":"Ma, J., Zhang, M., Xiao, X., You, J., Wang, J., Wang, T., Yao, Y., Tian, C., and Li, C. (2013). Global transcriptome profiling of Salicornia europaea L. shoots under NaCl treatment. PLoS ONE, 8.","DOI":"10.1371\/journal.pone.0065877"},{"key":"ref_141","doi-asserted-by":"crossref","unstructured":"Mendis, C.L., Padmathilake, R.E., Attanayake, R.N., and Perera, D. (2025). Learning from Salicornia: Physiological, biochemical, and molecular mechanisms of salinity tolerance. Int. J. Mol. Sci., 26.","DOI":"10.3390\/ijms26135936"},{"key":"ref_142","doi-asserted-by":"crossref","unstructured":"Alfheeaid, H.A., Raheem, D., Ahmed, F., Alhodieb, F.S., Alsharari, Z.D., Alhaji, J.H., BinMowyna, M.N., Saraiva, A., and Raposo, A. (2022). Salicornia bigelovii, S. brachiata and S. herbacea: Their nutritional characteristics and an evaluation of their potential as salt substitutes. Foods, 11.","DOI":"10.3390\/foods11213402"},{"key":"ref_143","doi-asserted-by":"crossref","first-page":"964","DOI":"10.1038\/s41598-025-30480-w","article-title":"Cell wall remodeling and polarized light analysis reveal ecotype-specific strategies in Salicornia europaea L. with biotechnological applications","volume":"16","author":"Strzelecki","year":"2025","journal-title":"Sci. Rep."},{"key":"ref_144","doi-asserted-by":"crossref","first-page":"105606","DOI":"10.1016\/j.envexpbot.2023.105606","article-title":"Salinity-driven changes in Salicornia cell wall nanomechanics and lignin composition","volume":"218","author":"Perez","year":"2024","journal-title":"Environ. Exp. Bot."},{"key":"ref_145","doi-asserted-by":"crossref","first-page":"3331","DOI":"10.1021\/pr801083a","article-title":"Comparative proteomic analysis of differentially expressed proteins in shoots of Salicornia europaea under different salinity","volume":"8","author":"Wang","year":"2009","journal-title":"J. Proteome Res."},{"key":"ref_146","doi-asserted-by":"crossref","first-page":"1177","DOI":"10.1007\/s00425-017-2762-0","article-title":"The V-ATPase subunit A is essential for salt tolerance through participating in vacuolar Na+ compartmentalization in Salicornia europaea","volume":"246","author":"Lv","year":"2017","journal-title":"Planta"},{"key":"ref_147","first-page":"100511","article-title":"Halophytes as holobionts: Disentangling the contribution of plant genotype and environmental factors to the associated microbiome of hydro- and xerohalophytes","volume":"9","author":"Pajuelo","year":"2025","journal-title":"Curr. Res. Microb. Sci."},{"key":"ref_148","doi-asserted-by":"crossref","first-page":"47","DOI":"10.1007\/s11032-019-0954-y","article-title":"Enhanced rice salinity tolerance via CRISPR\/Cas9-targeted mutagenesis of the OsRR22 gene","volume":"39","author":"Zhang","year":"2019","journal-title":"Mol. Breed."},{"key":"ref_149","doi-asserted-by":"crossref","first-page":"70","DOI":"10.1007\/s10142-024-01347-6","article-title":"CRISPR\/Cas9 targeted mutations of OsDSG1 gene enhanced salt tolerance in rice","volume":"24","author":"Ly","year":"2024","journal-title":"Funct. Integr. Genom."},{"key":"ref_150","doi-asserted-by":"crossref","unstructured":"Wang, T., Xun, H., Wang, W., Ding, X., Tian, H., Hussain, S., Dong, Q., Li, Y., Cheng, Y., and Wang, C. (2021). Mutation of GmAITR genes by CRISPR\/Cas9 genome editing results in enhanced salinity stress tolerance in soybean. Front. Plant Sci., 12.","DOI":"10.3389\/fpls.2021.779598"},{"key":"ref_151","doi-asserted-by":"crossref","first-page":"3550","DOI":"10.1038\/s41467-023-39167-0","article-title":"Genome-wide association studies identify OsWRKY53 as a key regulator of salt tolerance in rice","volume":"14","author":"Yu","year":"2023","journal-title":"Nat. Commun."},{"key":"ref_152","doi-asserted-by":"crossref","unstructured":"Hazzouri, K.M., Khraiwesh, B., Amiri, K.M.A., Pauli, D., Blake, T., Shahid, M., Mullath, S.K., Nelson, D., Mansour, A.L., and Salehi-Ashtiani, K. (2018). Mapping of HKT1;5 gene in barley using GWAS approach and its implication in salt tolerance mechanism. Front. Plant Sci., 9.","DOI":"10.3389\/fpls.2018.00156"},{"key":"ref_153","doi-asserted-by":"crossref","unstructured":"Duan, H., Tiika, R.J., Tian, F., Lu, Y., Zhang, Q., Hu, Y., Cui, G., and Yang, H. (2023). Metabolomics analysis unveils important changes involved in the salt tolerance of Salicornia europaea. Front. Plant Sci., 13.","DOI":"10.3389\/fpls.2022.1097076"}],"container-title":["Current Issues in Molecular Biology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/1467-3045\/48\/7\/719\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,7,17]],"date-time":"2026-07-17T04:24:50Z","timestamp":1784262290000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/1467-3045\/48\/7\/719"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,7,15]]},"references-count":153,"journal-issue":{"issue":"7","published-online":{"date-parts":[[2026,7]]}},"alternative-id":["cimb48070719"],"URL":"https:\/\/doi.org\/10.3390\/cimb48070719","relation":{},"ISSN":["1467-3045"],"issn-type":[{"value":"1467-3045","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,7,15]]}}}