{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,3]],"date-time":"2026-09-03T09:14:02Z","timestamp":1788426842694,"version":"build-2803163510"},"reference-count":77,"publisher":"Wiley","issue":"4","license":[{"start":{"date-parts":[[2026,8,23]],"date-time":"2026-08-23T00:00:00Z","timestamp":1787443200000},"content-version":"vor","delay-in-days":53,"URL":"http:\/\/onlinelibrary.wiley.com\/termsAndConditions#vor"},{"start":{"date-parts":[[2026,7,1]],"date-time":"2026-07-01T00:00:00Z","timestamp":1782864000000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/doi.wiley.com\/10.1002\/tdm_license_1.1"}],"content-domain":{"domain":["onlinelibrary.wiley.com"],"crossmark-restriction":true},"short-container-title":["Physiologia Plantarum"],"published-print":{"date-parts":[[2026,7]]},"abstract":"<jats:title>ABSTRACT<\/jats:title>\n                  <jats:p>\n                    Salinity is a major constraint on rice (\n                    <jats:styled-content style=\"fixed-case\">\n                      <jats:italic>Oryza sativa<\/jats:italic>\n                    <\/jats:styled-content>\n                    L.) production, yet the regulatory hubs that distinguish tolerant from susceptible genotypes remain largely unknown. Using a computational and experimental pipeline combining time\u2010series meta\u2010transcriptomics, weighted gene co\u2010expression network analysis (WGCNA), fuzzy clustering, network centrality metrics, promoter analysis, and molecular and physicochemical evaluations, we identified genotype\u2010specific hub genes associated with salinity tolerance in rice. Analysis of RNA\u2010Seq data from tolerant (Pokkali) and susceptible (IR29) genotypes across five time points after salinity treatment yielded 3369 meta\u2010differentially expressed genes. WGCNA revealed a salinity\u2010responsive co\u2010expression module, within which fuzzy clustering uncovered a cluster of 48 genes showing striking opposite temporal patterns between genotypes. Multi\u2010metric centrality ranking prioritized\n                    <jats:italic>Trehalase1<\/jats:italic>\n                    (\n                    <jats:italic>TRE1<\/jats:italic>\n                    ), encoding a trehalase enzyme, among the identified hub genes. Promoter analysis of\n                    <jats:italic>TRE1<\/jats:italic>\n                    revealed the presence of stress\u2010related cis\u2010elements (ABRE, TGACG\u2010motif, MYB\/MYC, DRE). Independent greenhouse validation confirmed the opposite expression pattern of\n                    <jats:italic>TRE1<\/jats:italic>\n                    between Pokkali and IR29 under salinity, correlating with increased trehalose accumulation in Pokkali and trehalose depletion in IR29. Physicochemical assessments showed that Pokkali exhibited lower oxidative stress markers, higher relative water content, better photosynthetic performance, and a more favorable K\n                    <jats:sup>+<\/jats:sup>\n                    \/Na\n                    <jats:sup>+<\/jats:sup>\n                    ratio than IR29. Principal component analysis distinctly separated the two genotypes, with\n                    <jats:italic>TRE1<\/jats:italic>\n                    expression clustering with susceptibility\u2010associated traits, while trehalose clustered with tolerance\u2010associated traits. Our network\u2010based discovery and experimental validation together indicate that the contrasting regulation of the hub gene\n                    <jats:italic>TRE1<\/jats:italic>\n                    links trehalose metabolism to salinity tolerance in rice, highlighting\n                    <jats:italic>TRE1<\/jats:italic>\n                    as a possible target for further functional analysis to enhance salinity tolerance.\n                  <\/jats:p>","DOI":"10.1111\/ppl.71081","type":"journal-article","created":{"date-parts":[[2026,8,24]],"date-time":"2026-08-24T00:20:48Z","timestamp":1787530848000},"update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Integrative Multi\u2010Scale Analysis Identifies the Hub Gene\n                    <scp>\n                      <i>TRE1<\/i>\n                    <\/scp>\n                    Associating Trehalose Metabolism With Salinity Tolerance in Rice"],"prefix":"10.1111","volume":"178","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-6449-305X","authenticated-orcid":false,"given":"Roohollah","family":"Shamloo\u2010Dashtpagerdi","sequence":"first","affiliation":[{"name":"Department of Agriculture and Natural Resources Higher Education Center of Eghlid  Eghlid Iran"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sirous","family":"Tahmasebi","sequence":"additional","affiliation":[{"name":"Department of Seed and Plant Improvement Research, Fars Agriculture and Natural Resources Research and Education Center Agricultural Research, Education and Extension Organization (AREEO)  Shiraz Iran"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"311","published-online":{"date-parts":[[2026,8,23]]},"reference":[{"key":"e_1_2_12_2_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-025-92527-2"},{"key":"e_1_2_12_3_1","doi-asserted-by":"publisher","DOI":"10.1515\/ijb-2023-0125"},{"key":"e_1_2_12_4_1","doi-asserted-by":"publisher","DOI":"10.1080\/07352689.2022.2065136"},{"key":"e_1_2_12_5_1","doi-asserted-by":"publisher","DOI":"10.1111\/ppl.13126"},{"key":"e_1_2_12_6_1","doi-asserted-by":"publisher","DOI":"10.3390\/plants11162145"},{"key":"e_1_2_12_7_1","doi-asserted-by":"publisher","DOI":"10.3390\/ijms20081975"},{"key":"e_1_2_12_8_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.plaphy.2014.02.001"},{"key":"e_1_2_12_9_1","doi-asserted-by":"publisher","DOI":"10.1111\/jac.12387"},{"key":"e_1_2_12_10_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.plaphy.2021.06.017"},{"key":"e_1_2_12_11_1","doi-asserted-by":"publisher","DOI":"10.1186\/s12870-026-08802-5"},{"key":"e_1_2_12_12_1","doi-asserted-by":"publisher","DOI":"10.1007\/s00299-025-03685-6"},{"key":"e_1_2_12_13_1","doi-asserted-by":"publisher","DOI":"10.1111\/nph.70533"},{"key":"e_1_2_12_14_1","doi-asserted-by":"publisher","DOI":"10.3389\/fpls.2018.00204"},{"key":"e_1_2_12_15_1","doi-asserted-by":"publisher","DOI":"10.1007\/s00344-025-11898-y"},{"key":"e_1_2_12_16_1","doi-asserted-by":"publisher","DOI":"10.1186\/s12870-021-03406-7"},{"key":"e_1_2_12_17_1","doi-asserted-by":"publisher","DOI":"10.1007\/s00344-022-10851-7"},{"key":"e_1_2_12_18_1","doi-asserted-by":"publisher","DOI":"10.3390\/plants13243506"},{"key":"e_1_2_12_19_1","doi-asserted-by":"publisher","DOI":"10.1016\/0003-9861(68)90654-1"},{"key":"e_1_2_12_20_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.gene.2018.10.071"},{"key":"e_1_2_12_21_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.plantsci.2023.111728"},{"key":"e_1_2_12_22_1","doi-asserted-by":"publisher","DOI":"10.1093\/plphys\/kiad585"},{"key":"e_1_2_12_23_1","doi-asserted-by":"publisher","DOI":"10.1093\/jxb\/erz462"},{"key":"e_1_2_12_24_1","doi-asserted-by":"publisher","DOI":"10.1111\/ppl.13702"},{"key":"e_1_2_12_25_1","doi-asserted-by":"publisher","DOI":"10.3389\/fpls.2021.660303"},{"key":"e_1_2_12_26_1","doi-asserted-by":"crossref","unstructured":"Kawahara Y. 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