{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,27]],"date-time":"2026-09-27T04:58:54Z","timestamp":1790485134538,"version":"4.1.0"},"reference-count":158,"publisher":"Elsevier BV","license":[{"start":{"date-parts":[[2026,10,1]],"date-time":"2026-10-01T00:00:00Z","timestamp":1790812800000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/tdm\/userlicense\/1.0\/"},{"start":{"date-parts":[[2026,10,1]],"date-time":"2026-10-01T00:00:00Z","timestamp":1790812800000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/legal\/tdmrep-license"},{"start":{"date-parts":[[2026,10,1]],"date-time":"2026-10-01T00:00:00Z","timestamp":1790812800000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-017"},{"start":{"date-parts":[[2026,10,1]],"date-time":"2026-10-01T00:00:00Z","timestamp":1790812800000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-037"},{"start":{"date-parts":[[2026,10,1]],"date-time":"2026-10-01T00:00:00Z","timestamp":1790812800000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-012"},{"start":{"date-parts":[[2026,10,1]],"date-time":"2026-10-01T00:00:00Z","timestamp":1790812800000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-029"},{"start":{"date-parts":[[2026,10,1]],"date-time":"2026-10-01T00:00:00Z","timestamp":1790812800000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-004"}],"funder":[{"DOI":"10.13039\/501100007129","name":"Shandong Province Natural Science Foundation","doi-asserted-by":"publisher","award":["ZR2025QC302"],"award-info":[{"award-number":["ZR2025QC302"]}],"id":[{"id":"10.13039\/501100007129","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["elsevier.com","sciencedirect.com"],"crossmark-restriction":true},"short-container-title":["Journal of Plant Physiology"],"published-print":{"date-parts":[[2026,10]]},"DOI":"10.1016\/j.jplph.2026.154868","type":"journal-article","created":{"date-parts":[[2026,8,26]],"date-time":"2026-08-26T14:53:00Z","timestamp":1787755980000},"page":"154868","update-policy":"https:\/\/doi.org\/10.1016\/elsevier_cm_policy","source":"Crossref","is-referenced-by-count":0,"special_numbering":"C","title":["Intron retention as a hub for splicing regulation in plant environmental adaptation and developmental programming"],"prefix":"10.1016","volume":"325","author":[{"ORCID":"https:\/\/orcid.org\/0009-0004-9435-2783","authenticated-orcid":false,"given":"Weibo","family":"Xu","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Meng","family":"Wang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0002-1481-7065","authenticated-orcid":false,"given":"Like","family":"Liu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"78","reference":[{"key":"10.1016\/j.jplph.2026.154868_bib1","doi-asserted-by":"crossref","first-page":"355","DOI":"10.1007\/s11103-016-0473-8","article-title":"Intron retention and rhythmic diel pattern regulation of carotenoid cleavage dioxygenase 2 during crocetin biosynthesis in saffron","volume":"91","author":"Ahrazem","year":"2016","journal-title":"Plant Mol. Biol."},{"key":"10.1016\/j.jplph.2026.154868_bib2","doi-asserted-by":"crossref","DOI":"10.1007\/s11295-016-1035-6","article-title":"PtFCA from precocious trifoliate orange is regulated by alternative splicing and affects flowering time and root development in transgenic arabidopsis","volume":"12","author":"Ai","year":"2016","journal-title":"Tree Genet. Genomes"},{"key":"10.1016\/j.jplph.2026.154868_bib3","doi-asserted-by":"crossref","DOI":"10.1016\/j.xplc.2022.100495","article-title":"ABA signaling prevents phosphodegradation of the SR45 splicing factor to alleviate inhibition of early seedling development in Arabidopsis","volume":"4","author":"Albuquerque-Martins","year":"2023","journal-title":"Plant Commun."},{"key":"10.1016\/j.jplph.2026.154868_bib4","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":"10.1016\/j.jplph.2026.154868_bib5","first-page":"457","article-title":"MADS-box gene evolution beyond flowers: expression in pollen, endosperm, guard cells, roots and trichomes","volume":"24","author":"Alvarez-Buylla","year":"2000","journal-title":"Plant J."},{"key":"10.1016\/j.jplph.2026.154868_bib6","doi-asserted-by":"crossref","first-page":"474","DOI":"10.1016\/j.tplants.2008.06.006","article-title":"Convergent energy and stress signaling","volume":"13","author":"Baena-Gonz\u00e1lez","year":"2008","journal-title":"Trends Plant Sci."},{"key":"10.1016\/j.jplph.2026.154868_bib7","doi-asserted-by":"crossref","first-page":"1035","DOI":"10.1016\/j.molcel.2021.12.010","article-title":"Systematic mapping of nuclear domain-associated transcripts reveals speckles and lamina as hubs of functionally distinct retained introns","volume":"82","author":"Barutcu","year":"2022","journal-title":"Mol Cell"},{"key":"10.1016\/j.jplph.2026.154868_bib8","doi-asserted-by":"crossref","first-page":"22","DOI":"10.1038\/nsmb1030","article-title":"The human SWI\/SNF subunit Brm is a regulator of alternative splicing","volume":"13","author":"Batsch\u00e9","year":"2006","journal-title":"Nat. Struct. Mol. Biol."},{"key":"10.1016\/j.jplph.2026.154868_bib9","doi-asserted-by":"crossref","first-page":"63","DOI":"10.1101\/gad.247361.114","article-title":"Detained introns are a novel, widespread class of post-transcriptionally spliced introns","volume":"29","author":"Boutz","year":"2015","journal-title":"Genes Dev."},{"key":"10.1016\/j.jplph.2026.154868_bib10","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1002\/wrna.100","article-title":"Evolution of SR protein and hnRNP splicing regulatory factors","volume":"3","author":"Busch","year":"2012","journal-title":"Wiley Interdiscip. Rev. RNA"},{"key":"10.1016\/j.jplph.2026.154868_bib11","doi-asserted-by":"crossref","first-page":"377","DOI":"10.1111\/tpj.15675","article-title":"Alternative splicing of an exitron determines the subnuclear localization of the Arabidopsis DNA glycosylase MBD4L under heat stress","volume":"110","author":"Cecchini","year":"2022","journal-title":"Plant J."},{"key":"10.1016\/j.jplph.2026.154868_bib12","doi-asserted-by":"crossref","first-page":"916","DOI":"10.1111\/tpj.14671","article-title":"Wide-ranging transcriptome remodelling mediated by alternative polyadenylation in response to abiotic stresses in Sorghum","volume":"102","author":"Chakrabarti","year":"2020","journal-title":"Plant J."},{"key":"10.1016\/j.jplph.2026.154868_bib13","doi-asserted-by":"crossref","first-page":"3476","DOI":"10.1016\/j.ygeno.2021.08.006","article-title":"Epigenetic differences in an identical genetic background modulate alternative splicing in A. thaliana","volume":"113","author":"Chaudhary","year":"2021","journal-title":"Genomics"},{"key":"10.1016\/j.jplph.2026.154868_bib14","doi-asserted-by":"crossref","first-page":"708","DOI":"10.3389\/fpls.2019.00708","article-title":"Alternative splicing and protein diversity: plants versus animals","volume":"10","author":"Chaudhary","year":"2019","journal-title":"Front. Plant Sci."},{"key":"10.1016\/j.jplph.2026.154868_bib15","doi-asserted-by":"crossref","first-page":"22376","DOI":"10.1073\/pnas.1906244116","article-title":"Highly ABA-Induced 1 (HAI1)-Interacting protein HIN1 and drought acclimation-enhanced splicing efficiency at intron retention sites","volume":"116","author":"Chong","year":"2019","journal-title":"Proc Natl Acad Sci U S A"},{"key":"10.1016\/j.jplph.2026.154868_bib16","doi-asserted-by":"crossref","first-page":"689","DOI":"10.3389\/fpls.2019.00689","article-title":"Expanding alternative splicing identification by integrating multiple sources of transcription data in tomato","volume":"10","author":"Clark","year":"2019","journal-title":"Front. Plant Sci."},{"key":"10.1016\/j.jplph.2026.154868_bib17","doi-asserted-by":"crossref","first-page":"393","DOI":"10.1016\/j.bbagrm.2015.12.008","article-title":"Rice phytochrome-interacting factor protein OsPIF14 represses OsDREB1B gene expression through an extended N-box and interacts preferentially with the active form of phytochrome B","volume":"1859","author":"Cordeiro","year":"2016","journal-title":"Biochim. Biophys. Acta"},{"key":"10.1016\/j.jplph.2026.154868_bib18","doi-asserted-by":"crossref","first-page":"16160","DOI":"10.1073\/pnas.1419030111","article-title":"Antisense COOLAIR mediates the coordinated switching of chromatin states at FLC during vernalization","volume":"111","author":"Csorba","year":"2014","journal-title":"Proc Natl Acad Sci U S A"},{"key":"10.1016\/j.jplph.2026.154868_bib19","doi-asserted-by":"crossref","first-page":"2838","DOI":"10.1105\/tpc.18.00244","article-title":"The U1 snRNP subunit LUC7 modulates plant development and stress responses via regulation of alternative splicing","volume":"30","author":"de Francisco Amorim","year":"2018","journal-title":"Plant Cell"},{"key":"10.1016\/j.jplph.2026.154868_bib20","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pgen.1003867","article-title":"Transcription termination and chimeric RNA formation controlled by Arabidopsis thaliana FPA","volume":"9","author":"Duc","year":"2013","journal-title":"PLoS Genet."},{"key":"10.1016\/j.jplph.2026.154868_bib21","doi-asserted-by":"crossref","DOI":"10.1177\/00368504241301533","article-title":"HXK, SnRK1, and TOR signaling in plants: unraveling mechanisms of stress response and secondary metabolism","volume":"107","author":"Eom","year":"2024","journal-title":"Sci. Prog."},{"key":"10.1016\/j.jplph.2026.154868_bib22","doi-asserted-by":"crossref","first-page":"96","DOI":"10.1261\/rna.037044.112","article-title":"Position-dependent splicing activation and repression by SR and hnRNP proteins rely on common mechanisms","volume":"19","author":"Erkelenz","year":"2013","journal-title":"Rna"},{"key":"10.1016\/j.jplph.2026.154868_bib23","doi-asserted-by":"crossref","first-page":"2280","DOI":"10.1093\/jxb\/erae002","article-title":"The arabidopsis SR45 splicing factor bridges the splicing machinery and the exon-exon junction complex","volume":"75","author":"Fanara","year":"2024","journal-title":"J. Exp. Bot."},{"key":"10.1016\/j.jplph.2026.154868_bib24","doi-asserted-by":"crossref","first-page":"207","DOI":"10.1016\/j.molp.2014.10.011","article-title":"Environmental stresses modulate abundance and timing of alternatively spliced circadian transcripts in arabidopsis","volume":"8","author":"Filichkin","year":"2015","journal-title":"Mol. Plant"},{"key":"10.1016\/j.jplph.2026.154868_bib25","doi-asserted-by":"crossref","DOI":"10.1016\/j.pbi.2021.102049","article-title":"Regulation of flowering time: when and where?","volume":"63","author":"Freytes","year":"2021","journal-title":"Curr. Opin. Plant Biol."},{"key":"10.1016\/j.jplph.2026.154868_bib26","doi-asserted-by":"crossref","first-page":"54","DOI":"10.1007\/s00438-004-1095-4","article-title":"Large deletions within the first intron in VRN-1 are associated with spring growth habit in barley and wheat","volume":"273","author":"Fu","year":"2005","journal-title":"Mol. Genet. Genom."},{"key":"10.1016\/j.jplph.2026.154868_bib27","doi-asserted-by":"crossref","first-page":"128","DOI":"10.1111\/tpj.13351","article-title":"Alternative splicing provides a proactive mechanism for the diurnal CONSTANS dynamics in Arabidopsis photoperiodic flowering","volume":"89","author":"Gil","year":"2017","journal-title":"Plant J."},{"key":"10.1016\/j.jplph.2026.154868_bib28","doi-asserted-by":"crossref","first-page":"309","DOI":"10.3389\/fpls.2019.00309","article-title":"Alternative splicing and transcription elongation in plants","volume":"10","author":"Godoy Herz","year":"2019","journal-title":"Front. Plant Sci."},{"key":"10.1016\/j.jplph.2026.154868_bib29","doi-asserted-by":"crossref","first-page":"1066","DOI":"10.1016\/j.molcel.2018.12.005","article-title":"Light regulates plant alternative splicing through the control of transcriptional elongation","volume":"73","author":"Godoy Herz","year":"2019","journal-title":"Mol Cell"},{"key":"10.1016\/j.jplph.2026.154868_bib30","doi-asserted-by":"crossref","first-page":"754","DOI":"10.1105\/tpc.113.118075","article-title":"Imaging of endogenous messenger RNA splice variants in living cells reveals nuclear retention of transcripts inaccessible to nonsense-mediated decay in Arabidopsis","volume":"26","author":"G\u00f6hring","year":"2014","journal-title":"Plant Cell"},{"key":"10.1016\/j.jplph.2026.154868_bib31","doi-asserted-by":"crossref","first-page":"473","DOI":"10.1016\/0092-8674(89)90428-5","article-title":"The AU-rich sequences present in the introns of plant nuclear pre-mRNAs are required for splicing","volume":"58","author":"Goodall","year":"1989","journal-title":"Cell"},{"key":"10.1016\/j.jplph.2026.154868_bib32","doi-asserted-by":"crossref","first-page":"67","DOI":"10.1016\/j.gde.2020.11.002","article-title":"Nuclear mechanisms of gene expression control: pre-mrna splicing as a life or death decision","volume":"67","author":"Gordon","year":"2021","journal-title":"Curr. Opin. Genet. Dev."},{"key":"10.1016\/j.jplph.2026.154868_bib33","doi-asserted-by":"crossref","first-page":"105","DOI":"10.1016\/j.bbaexp.2005.01.004","article-title":"Two novel arginine\/serine (SR) proteins in maize are differentially spliced and utilize non-canonical splice sites","volume":"1728","author":"Gupta","year":"2005","journal-title":"Biochim. Biophys. Acta"},{"key":"10.1016\/j.jplph.2026.154868_bib34","doi-asserted-by":"crossref","first-page":"1624","DOI":"10.1101\/gr.278659.123","article-title":"Contrasting and combining transcriptome complexity captured by short and long RNA sequencing reads","volume":"34","author":"Han","year":"2024","journal-title":"Genome Res."},{"key":"10.1016\/j.jplph.2026.154868_bib35","doi-asserted-by":"crossref","first-page":"107","DOI":"10.1007\/s00438-009-0449-3","article-title":"Regions associated with repression of the barley (Hordeum vulgare) VERNALIZATION1 gene are not required for cold induction","volume":"282","author":"Hemming","year":"2009","journal-title":"Mol. Genet. Genom."},{"key":"10.1016\/j.jplph.2026.154868_bib36","doi-asserted-by":"crossref","first-page":"203","DOI":"10.1016\/j.devcel.2009.12.009","article-title":"The spen family protein FPA controls alternative cleavage and polyadenylation of RNA","volume":"18","author":"Hornyik","year":"2010","journal-title":"Dev. Cell"},{"key":"10.1016\/j.jplph.2026.154868_bib37","doi-asserted-by":"crossref","first-page":"2245","DOI":"10.1111\/pbi.13913","article-title":"Epitranscriptomic mRNA modifications governing plant stress responses: underlying mechanism and potential application","volume":"20","author":"Hu","year":"2022","journal-title":"Plant Biotechnol. J."},{"key":"10.1016\/j.jplph.2026.154868_bib38","doi-asserted-by":"crossref","DOI":"10.1016\/j.plantsci.2026.113031","article-title":"Multiple-layered fine-tuning of flowering locus C --- flowering control and beyond","volume":"365","author":"Huang","year":"2026","journal-title":"Plant Sci."},{"key":"10.1016\/j.jplph.2026.154868_bib39","doi-asserted-by":"crossref","first-page":"88","DOI":"10.1111\/nph.20204","article-title":"Biomolecular condensation programs floral transition to orchestrate flowering time and inflorescence architecture","volume":"245","author":"Huang","year":"2025","journal-title":"New Phytol."},{"key":"10.1016\/j.jplph.2026.154868_bib40","doi-asserted-by":"crossref","first-page":"780","DOI":"10.1038\/s41477-020-0688-1","article-title":"Post-transcriptional splicing of nascent RNA contributes to widespread intron retention in plants","volume":"6","author":"Jia","year":"2020","journal-title":"Nat. Plants"},{"key":"10.1016\/j.jplph.2026.154868_bib41","doi-asserted-by":"crossref","DOI":"10.3390\/ijms231710147","article-title":"Regulatory network of Serine\/Arginine-Rich (SR) proteins: the molecular mechanism and physiological function in plants","volume":"23","author":"Jin","year":"2022","journal-title":"Int. J. Mol. Sci."},{"key":"10.1016\/j.jplph.2026.154868_bib42","doi-asserted-by":"crossref","DOI":"10.1093\/plcell\/koaf117","article-title":"PROTEIN PHOSPHATASE 2A B'\u03b7 drives spliceosome subunit dephosphorylation to mediate alternative splicing following heat stress","volume":"37","author":"Jo","year":"2025","journal-title":"Plant Cell"},{"key":"10.1016\/j.jplph.2026.154868_bib43","doi-asserted-by":"crossref","first-page":"2454","DOI":"10.1093\/nar\/gkr932","article-title":"Alternative splicing and nonsense-mediated decay modulate expression of important regulatory genes in Arabidopsis","volume":"40","author":"Kalyna","year":"2012","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.jplph.2026.154868_bib44","doi-asserted-by":"crossref","DOI":"10.1017\/qpb.2022.9","article-title":"How alternative splicing changes the properties of plant proteins","volume":"3","author":"Kashkan","year":"2022","journal-title":"Quant Plant Biol"},{"key":"10.1016\/j.jplph.2026.154868_bib45","doi-asserted-by":"crossref","DOI":"10.1073\/pnas.2214565119","article-title":"SWAP1-SFPS-RRC1 splicing factor complex modulates pre-mRNA splicing to promote photomorphogenesis in Arabidopsis","volume":"119","author":"Kathare","year":"2022","journal-title":"Proc Natl Acad Sci U S A"},{"key":"10.1016\/j.jplph.2026.154868_bib46","doi-asserted-by":"crossref","first-page":"6147","DOI":"10.1093\/nar\/gkl737","article-title":"Both introns and long 3'-UTRs operate as cis-acting elements to trigger nonsense-mediated decay in plants","volume":"34","author":"Kert\u00e9sz","year":"2006","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.jplph.2026.154868_bib47","doi-asserted-by":"crossref","first-page":"1231","DOI":"10.1007\/s00438-018-1455-0","article-title":"Single nucleotide polymorphisms in a regulatory site of VRN-A1 first intron are associated with differences in vernalization requirement in winter wheat","volume":"293","author":"Kippes","year":"2018","journal-title":"Mol. Genet. Genom."},{"key":"10.1016\/j.jplph.2026.154868_bib48","first-page":"2757","article-title":"Active 5' splice sites regulate the biogenesis efficiency of Arabidopsis microRNAs derived from intron-containing genes","volume":"45","author":"Knop","year":"2017","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.jplph.2026.154868_bib49","doi-asserted-by":"crossref","first-page":"326","DOI":"10.1007\/s00122-003-1250-z","article-title":"A new AOX homologous gene OsIM1 from rice (Oryza sativa L.) with an alternative splicing mechanism under salt stress","volume":"107","author":"Kong","year":"2003","journal-title":"Theor. Appl. Genet."},{"key":"10.1016\/j.jplph.2026.154868_bib50","doi-asserted-by":"crossref","first-page":"644","DOI":"10.1261\/rna.079294.122","article-title":"PABPN1 prevents the nuclear export of an unspliced RNA with a constitutive transport element and controls human gene expression via intron retention","volume":"29","author":"Kwiatek","year":"2023","journal-title":"Rna"},{"key":"10.1016\/j.jplph.2026.154868_bib51","doi-asserted-by":"crossref","first-page":"140","DOI":"10.1016\/j.tplants.2017.09.019","article-title":"Alternative splicing control of abiotic stress responses","volume":"23","author":"Laloum","year":"2018","journal-title":"Trends Plant Sci."},{"key":"10.1016\/j.jplph.2026.154868_bib52","doi-asserted-by":"crossref","first-page":"1638","DOI":"10.1093\/emboj\/19.7.1638","article-title":"UBP1, a novel hnRNP-like protein that functions at multiple steps of higher plant nuclear pre-mRNA maturation","volume":"19","author":"Lambermon","year":"2000","journal-title":"EMBO J."},{"key":"10.1016\/j.jplph.2026.154868_bib53","doi-asserted-by":"crossref","DOI":"10.3389\/fpls.2022.869870","article-title":"Ubiquitination and ubiquitin-like modifications as mediators of alternative Pre-mRNA splicing in Arabidopsis thaliana","volume":"13","author":"Lan","year":"2022","journal-title":"Front. Plant Sci."},{"key":"10.1016\/j.jplph.2026.154868_bib54","doi-asserted-by":"crossref","first-page":"823","DOI":"10.1007\/s11103-005-8105-8","article-title":"Conservation and divergence of FCA function between Arabidopsis and rice","volume":"58","author":"Lee","year":"2005","journal-title":"Plant Mol. Biol."},{"key":"10.1016\/j.jplph.2026.154868_bib55","doi-asserted-by":"crossref","first-page":"3181","DOI":"10.1016\/j.apsb.2023.05.022","article-title":"Towards understandings of serine\/arginine-rich splicing factors","volume":"13","author":"Li","year":"2023","journal-title":"Acta Pharm. Sin. B"},{"key":"10.1016\/j.jplph.2026.154868_bib56","doi-asserted-by":"crossref","first-page":"7714","DOI":"10.1111\/pce.70066","article-title":"Phosphorylation of wild soybean (Glycine soja) splicing factor GsSCL30a by GsSnRK1 regulates soybean tolerance to alkali stress","volume":"48","author":"Li","year":"2025","journal-title":"Plant Cell Environ."},{"key":"10.1016\/j.jplph.2026.154868_bib57","doi-asserted-by":"crossref","first-page":"14699","DOI":"10.1073\/pnas.1212977109","article-title":"Splice variant of the SND1 transcription factor is a dominant negative of SND1 members and their regulation in Populus trichocarpa","volume":"109","author":"Li","year":"2012","journal-title":"Proc Natl Acad Sci U S A"},{"key":"10.1016\/j.jplph.2026.154868_bib58","doi-asserted-by":"crossref","first-page":"641","DOI":"10.1111\/nph.17175","article-title":"Dual roles of the serine\/arginine-rich splicing factor SR45a in promoting and interacting with nuclear cap-binding complex to modulate the salt-stress response in Arabidopsis","volume":"230","author":"Li","year":"2021","journal-title":"New Phytol."},{"key":"10.1016\/j.jplph.2026.154868_bib59","doi-asserted-by":"crossref","first-page":"731","DOI":"10.1105\/tpc.019331","article-title":"A new Arabidopsis gene, FLK, encodes an RNA binding protein with K homology motifs and regulates flowering time via FLOWERING LOCUS C","volume":"16","author":"Lim","year":"2004","journal-title":"Plant Cell"},{"key":"10.1016\/j.jplph.2026.154868_bib60","doi-asserted-by":"crossref","first-page":"E9722","DOI":"10.1073\/pnas.1714422114","article-title":"Reciprocal cross-regulation of VND and SND multigene TF families for wood formation in Populus trichocarpa","volume":"114","author":"Lin","year":"2017","journal-title":"Proc Natl Acad Sci U S A"},{"key":"10.1016\/j.jplph.2026.154868_bib61","doi-asserted-by":"crossref","first-page":"2659","DOI":"10.1093\/jxb\/ery062","article-title":"Thermopriming triggers splicing memory in Arabidopsis","volume":"69","author":"Ling","year":"2018","journal-title":"J. Exp. Bot."},{"key":"10.1016\/j.jplph.2026.154868_bib62","doi-asserted-by":"crossref","first-page":"512","DOI":"10.1104\/pp.112.205864","article-title":"An autoregulatory loop controlling Arabidopsis HsfA2 expression: role of heat shock-induced alternative splicing","volume":"162","author":"Liu","year":"2013","journal-title":"Plant Physiol"},{"key":"10.1016\/j.jplph.2026.154868_bib63","doi-asserted-by":"crossref","first-page":"116","DOI":"10.1016\/j.molp.2025.11.007","article-title":"Pathogen-induced H(2)O(2) triggers phosphorylation of the RNA-binding protein RRM2R to suppress OsMAPKKK18 intron retention for orchestrating rice immunity and growth","volume":"19","author":"Lu","year":"2026","journal-title":"Mol. Plant"},{"key":"10.1016\/j.jplph.2026.154868_bib64","doi-asserted-by":"crossref","first-page":"7020","DOI":"10.1111\/pce.15678","article-title":"Molecular mechanisms of temperature-mediated flowering regulation: from arabidopsis to short-day crops","volume":"48","author":"Luo","year":"2025","journal-title":"Plant Cell Environ."},{"key":"10.1016\/j.jplph.2026.154868_bib65","doi-asserted-by":"crossref","DOI":"10.7554\/eLife.22114","article-title":"Natural haplotypes of FLM non-coding sequences fine-tune flowering time in ambient spring temperatures in Arabidopsis","volume":"6","author":"Lutz","year":"2017","journal-title":"eLife"},{"key":"10.1016\/j.jplph.2026.154868_bib66","doi-asserted-by":"crossref","first-page":"662","DOI":"10.1111\/jipb.13006","article-title":"The pre-mRNA splicing factor RDM16 regulates root stem cell maintenance in Arabidopsis","volume":"63","author":"Lv","year":"2021","journal-title":"J. Integr. Plant Biol."},{"key":"10.1016\/j.jplph.2026.154868_bib67","doi-asserted-by":"crossref","DOI":"10.1016\/j.ijbiomac.2024.133393","article-title":"The CONSTANS-LIKE gene PeCOL13 regulates flowering through intron-retained alternative splicing in Phyllostachys edulis","volume":"274","author":"Ma","year":"2024","journal-title":"Int. J. Biol. Macromol."},{"key":"10.1016\/j.jplph.2026.154868_bib68","doi-asserted-by":"crossref","first-page":"115","DOI":"10.1111\/nph.70846","article-title":"Regulation of alternative splicing in the ABA signaling pathway of plants","volume":"250","author":"Ma","year":"2026","journal-title":"New Phytol."},{"key":"10.1016\/j.jplph.2026.154868_bib69","doi-asserted-by":"crossref","first-page":"1064","DOI":"10.1126\/science.1172408","article-title":"Regulators of PP2C phosphatase activity function as abscisic acid sensors","volume":"324","author":"Ma","year":"2009","journal-title":"Science"},{"key":"10.1016\/j.jplph.2026.154868_bib70","doi-asserted-by":"crossref","first-page":"877","DOI":"10.1105\/tpc.010456","article-title":"Functional significance of the alternative transcript processing of the Arabidopsis floral promoter FCA","volume":"14","author":"Macknight","year":"2002","journal-title":"Plant Cell"},{"key":"10.1016\/j.jplph.2026.154868_bib71","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pgen.1005924","article-title":"BRR2a affects flowering time via FLC splicing","volume":"12","author":"Mahrez","year":"2016","journal-title":"PLoS Genet."},{"key":"10.1016\/j.jplph.2026.154868_bib72","doi-asserted-by":"crossref","first-page":"190","DOI":"10.1093\/plphys\/kiae109","article-title":"Flowering time: from physiology, through genetics to mechanism","volume":"195","author":"Maple","year":"2024","journal-title":"Plant Physiol"},{"key":"10.1016\/j.jplph.2026.154868_bib73","doi-asserted-by":"crossref","first-page":"242","DOI":"10.1038\/s41580-022-00545-z","article-title":"The physiology of alternative splicing","volume":"24","author":"Marasco","year":"2023","journal-title":"Nat. Rev. Mol. Cell Biol."},{"key":"10.1016\/j.jplph.2026.154868_bib74","doi-asserted-by":"crossref","first-page":"1654","DOI":"10.1093\/plcell\/koac309","article-title":"Cotranscriptional RNA processing and modification in plants","volume":"35","author":"Marquardt","year":"2023","journal-title":"Plant Cell"},{"key":"10.1016\/j.jplph.2026.154868_bib75","doi-asserted-by":"crossref","first-page":"1184","DOI":"10.1101\/gr.134106.111","article-title":"Transcriptome survey reveals increased complexity of the alternative splicing landscape in Arabidopsis","volume":"22","author":"Marquez","year":"2012","journal-title":"Genome Res."},{"key":"10.1016\/j.jplph.2026.154868_bib76","doi-asserted-by":"crossref","first-page":"995","DOI":"10.1101\/gr.186585.114","article-title":"Unmasking alternative splicing inside protein-coding exons defines exitrons and their role in proteome plasticity","volume":"25","author":"Marquez","year":"2015","journal-title":"Genome Res."},{"key":"10.1016\/j.jplph.2026.154868_bib77","doi-asserted-by":"crossref","first-page":"35","DOI":"10.1186\/s13059-020-02258-y","article-title":"Alternative splicing landscapes in Arabidopsis thaliana across tissues and stress conditions highlight major functional differences with animals","volume":"22","author":"Mart\u00edn","year":"2021","journal-title":"Genome Biol."},{"key":"10.1016\/j.jplph.2026.154868_bib78","doi-asserted-by":"crossref","first-page":"694","DOI":"10.3389\/fpls.2017.00694","article-title":"A comprehensive analysis of alternative splicing in paleopolyploid maize","volume":"8","author":"Mei","year":"2017","journal-title":"Front. Plant Sci."},{"key":"10.1016\/j.jplph.2026.154868_bib79","doi-asserted-by":"crossref","first-page":"4873","DOI":"10.1093\/nar\/gkp471","article-title":"Stochastic noise in splicing machinery","volume":"37","author":"Melamud","year":"2009","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.jplph.2026.154868_bib80","doi-asserted-by":"crossref","first-page":"949","DOI":"10.1105\/tpc.11.5.949","article-title":"FLOWERING LOCUS C encodes a novel MADS domain protein that acts as a repressor of flowering","volume":"11","author":"Michaels","year":"1999","journal-title":"Plant Cell"},{"key":"10.1016\/j.jplph.2026.154868_bib81","first-page":"11497","article-title":"The changing paradigm of intron retention: regulation, ramifications and recipes","volume":"47","author":"Monteuuis","year":"2019","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.jplph.2026.154868_bib82","doi-asserted-by":"crossref","first-page":"227","DOI":"10.2174\/138920208784533629","article-title":"Plant spliceosomal introns: not only cut and paste","volume":"9","author":"Morello","year":"2008","journal-title":"Curr Genomics"},{"issue":"Suppl. l","key":"10.1016\/j.jplph.2026.154868_bib83","doi-asserted-by":"crossref","first-page":"S111","DOI":"10.1105\/tpc.001362","article-title":"Control of flowering time: interacting pathways as a basis for diversity","volume":"14","author":"Mouradov","year":"2002","journal-title":"Plant Cell"},{"key":"10.1016\/j.jplph.2026.154868_bib84","doi-asserted-by":"crossref","first-page":"165","DOI":"10.1146\/annurev-biochem-060614-034242","article-title":"Regulation of alternative splicing through coupling with transcription and chromatin structure","volume":"84","author":"Naftelberg","year":"2015","journal-title":"Annu. Rev. Biochem."},{"key":"10.1016\/j.jplph.2026.154868_bib85","doi-asserted-by":"crossref","first-page":"3370","DOI":"10.1016\/j.febslet.2015.08.002","article-title":"Chromatin, DNA structure and alternative splicing","volume":"589","author":"Nieto Moreno","year":"2015","journal-title":"FEBS Lett."},{"key":"10.1016\/j.jplph.2026.154868_bib86","doi-asserted-by":"crossref","first-page":"457","DOI":"10.1038\/nature08909","article-title":"Expansion of the eukaryotic proteome by alternative splicing","volume":"463","author":"Nilsen","year":"2010","journal-title":"Nature"},{"key":"10.1016\/j.jplph.2026.154868_bib87","doi-asserted-by":"crossref","first-page":"102","DOI":"10.1186\/s13059-017-1235-x","article-title":"Histone H3 lysine 36 methylation affects temperature-induced alternative splicing and flowering in plants","volume":"18","author":"Pajoro","year":"2017","journal-title":"Genome Biol."},{"key":"10.1016\/j.jplph.2026.154868_bib88","doi-asserted-by":"crossref","first-page":"421","DOI":"10.1093\/pcp\/pcv010","article-title":"Differential recruitment of splice variants from SR pre-mRNAs to polysomes during development and in response to stresses","volume":"56","author":"Palusa","year":"2015","journal-title":"Plant Cell Physiol."},{"key":"10.1016\/j.jplph.2026.154868_bib89","doi-asserted-by":"crossref","first-page":"3564","DOI":"10.1016\/j.febslet.2015.09.023","article-title":"Genome-wide analysis of alternative splicing events in Hordeum vulgare: highlighting retention of intron-based splicing and its possible function through network analysis","volume":"589","author":"Panahi","year":"2015","journal-title":"FEBS Lett."},{"key":"10.1016\/j.jplph.2026.154868_bib90","doi-asserted-by":"crossref","first-page":"1068","DOI":"10.1126\/science.1173041","article-title":"Abscisic acid inhibits type 2C protein phosphatases via the PYR\/PYL family of START proteins","volume":"324","author":"Park","year":"2009","journal-title":"Science"},{"key":"10.1016\/j.jplph.2026.154868_bib91","doi-asserted-by":"crossref","first-page":"824","DOI":"10.1016\/j.cell.2017.05.003","article-title":"The U6 snRNA m(6)A methyltransferase METTL16 regulates SAM synthetase Intron retention","volume":"169","author":"Pendleton","year":"2017","journal-title":"Cell"},{"key":"10.1016\/j.jplph.2026.154868_bib92","doi-asserted-by":"crossref","first-page":"1752","DOI":"10.1093\/plcell\/koad009","article-title":"Do not panic: an intron-centric guide to alternative splicing","volume":"35","author":"Petrillo","year":"2023","journal-title":"Plant Cell"},{"key":"10.1016\/j.jplph.2026.154868_bib93","doi-asserted-by":"crossref","DOI":"10.3390\/genes16080986","article-title":"Intron retention: a reemerging paradigm in RNA biology and post-transcriptional gene regulation","volume":"16","author":"Porras-Tobias","year":"2025","journal-title":"Genes"},{"key":"10.1016\/j.jplph.2026.154868_bib94","doi-asserted-by":"crossref","DOI":"10.1016\/j.pbi.2024.102590","article-title":"Mechanisms of heat stress-induced transcriptional memory","volume":"81","author":"Pratx","year":"2024","journal-title":"Curr. Opin. Plant Biol."},{"key":"10.1016\/j.jplph.2026.154868_bib95","doi-asserted-by":"crossref","DOI":"10.1038\/s41467-025-66651-6","article-title":"Conserved heat shock factors HvHSFA2 and HvHSFA3 control barley heat stress memory through diverged mechanisms","volume":"16","author":"Pratx","year":"2025","journal-title":"Nat. Commun."},{"key":"10.1016\/j.jplph.2026.154868_bib96","doi-asserted-by":"crossref","first-page":"265","DOI":"10.1104\/pp.107.109561","article-title":"Discrete developmental roles for temperate cereal grass VERNALIZATION1\/FRUITFULL-like genes in flowering competency and the transition to flowering","volume":"146","author":"Preston","year":"2008","journal-title":"Plant Physiol"},{"key":"10.1016\/j.jplph.2026.154868_bib97","doi-asserted-by":"crossref","first-page":"433","DOI":"10.1016\/j.molcel.2017.06.006","article-title":"Body temperature cycles control rhythmic alternative splicing in mammals","volume":"67","author":"Preu\u00dfner","year":"2017","journal-title":"Mol Cell"},{"key":"10.1016\/j.jplph.2026.154868_bib98","doi-asserted-by":"crossref","first-page":"1625","DOI":"10.3389\/fpls.2019.01625","article-title":"RNA splicing of FLC modulates the transition to flowering","volume":"10","author":"Qi","year":"2019","journal-title":"Front. Plant Sci."},{"key":"10.1016\/j.jplph.2026.154868_bib99","doi-asserted-by":"crossref","first-page":"3142","DOI":"10.1093\/emboj\/cdg305","article-title":"Autoregulation of FCA pre-mRNA processing controls Arabidopsis flowering time","volume":"22","author":"Quesada","year":"2003","journal-title":"EMBO J."},{"key":"10.1016\/j.jplph.2026.154868_bib100","doi-asserted-by":"crossref","first-page":"3657","DOI":"10.1105\/tpc.113.117523","article-title":"Complexity of the alternative splicing landscape in plants","volume":"25","author":"Reddy","year":"2013","journal-title":"Plant Cell"},{"key":"10.1016\/j.jplph.2026.154868_bib101","doi-asserted-by":"crossref","first-page":"1651","DOI":"10.1101\/gr.153510.112","article-title":"The maize methylome influences mRNA splice sites and reveals widespread paramutation-like switches guided by small RNA","volume":"23","author":"Regulski","year":"2013","journal-title":"Genome Res."},{"key":"10.1016\/j.jplph.2026.154868_bib102","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pgen.1004375","article-title":"Intron retention in the 5'UTR of the novel ZIF2 transporter enhances translation to promote zinc tolerance in arabidopsis","volume":"10","author":"Remy","year":"2014","journal-title":"PLoS Genet."},{"key":"10.1016\/j.jplph.2026.154868_bib103","doi-asserted-by":"crossref","DOI":"10.1093\/aobpla\/plae014","article-title":"Exitrons: offering new roles to retained introns-the novel regulators of protein diversity and utility","volume":"16","author":"Shamnas","year":"2024","journal-title":"AoB Plants"},{"key":"10.1016\/j.jplph.2026.154868_bib104","doi-asserted-by":"crossref","first-page":"373","DOI":"10.1111\/ppl.13163","article-title":"The molecular mechanism of vernalization in Arabidopsis and cereals: role of flowering locus C and its homologs","volume":"170","author":"Sharma","year":"2020","journal-title":"Physiol Plant"},{"key":"10.1016\/j.jplph.2026.154868_bib105","doi-asserted-by":"crossref","first-page":"2703","DOI":"10.1093\/plphys\/kiad223","article-title":"Complexity and regulation of age-dependent alternative splicing in Brachypodium distachyon","volume":"192","author":"Shen","year":"2023","journal-title":"Plant Physiol"},{"key":"10.1016\/j.jplph.2026.154868_bib106","doi-asserted-by":"crossref","first-page":"74","DOI":"10.1038\/nature10442","article-title":"CTCF-Promoted RNA polymerase II pausing links DNA methylation to splicing","volume":"479","author":"Shukla","year":"2011","journal-title":"Nature"},{"key":"10.1016\/j.jplph.2026.154868_bib107","doi-asserted-by":"crossref","first-page":"285","DOI":"10.1126\/science.296.5566.285","article-title":"Arabidopsis, the Rosetta stone of flowering time?","volume":"296","author":"Simpson","year":"2002","journal-title":"Science"},{"key":"10.1016\/j.jplph.2026.154868_bib108","doi-asserted-by":"crossref","first-page":"441","DOI":"10.1146\/annurev-arplant-043014-115555","article-title":"Photoperiodic flowering: time measurement mechanisms in leaves","volume":"66","author":"Song","year":"2015","journal-title":"Annu. Rev. Plant Biol."},{"key":"10.1016\/j.jplph.2026.154868_bib109","doi-asserted-by":"crossref","first-page":"2402","DOI":"10.1111\/nph.20377","article-title":"Stress resilience in plants: the complex interplay between heat stress memory and resetting","volume":"245","author":"Staacke","year":"2025","journal-title":"New Phytol."},{"key":"10.1016\/j.jplph.2026.154868_bib110","doi-asserted-by":"crossref","DOI":"10.3390\/ijms222212284","article-title":"In-Depth sequence analysis of bread wheat VRN1 genes","volume":"22","author":"Strej\u010dkov\u00e1","year":"2021","journal-title":"Int. J. Mol. Sci."},{"key":"10.1016\/j.jplph.2026.154868_bib111","doi-asserted-by":"crossref","first-page":"642","DOI":"10.1105\/tpc.108.062596","article-title":"The cytosolic protein response as a subcomponent of the wider heat shock response in Arabidopsis","volume":"21","author":"Sugio","year":"2009","journal-title":"Plant Cell"},{"key":"10.1016\/j.jplph.2026.154868_bib112","doi-asserted-by":"crossref","first-page":"3729","DOI":"10.1093\/plcell\/koae189","article-title":"Alternative splicing of a potato disease resistance gene maintains homeostasis between growth and immunity","volume":"36","author":"Sun","year":"2024","journal-title":"Plant Cell"},{"key":"10.1016\/j.jplph.2026.154868_bib113","doi-asserted-by":"crossref","first-page":"2093","DOI":"10.1111\/nph.19699","article-title":"Regulation of plant resistance to salt stress by the SnRK1-dependent splicing factor SRRM1L","volume":"242","author":"Sun","year":"2024","journal-title":"New Phytol."},{"key":"10.1016\/j.jplph.2026.154868_bib114","doi-asserted-by":"crossref","first-page":"799","DOI":"10.1038\/nature08618","article-title":"Cold-induced silencing by long antisense transcripts of an Arabidopsis Polycomb target","volume":"462","author":"Swiezewski","year":"2009","journal-title":"Nature"},{"key":"10.1016\/j.jplph.2026.154868_bib115","doi-asserted-by":"crossref","first-page":"616","DOI":"10.1016\/j.tplants.2012.06.001","article-title":"Alternative splicing in plants--coming of age","volume":"17","author":"Syed","year":"2012","journal-title":"Trends Plant Sci."},{"key":"10.1016\/j.jplph.2026.154868_bib116","doi-asserted-by":"crossref","DOI":"10.1016\/j.xplc.2023.100552","article-title":"Photoperiodic flowering in Arabidopsis: multilayered regulatory mechanisms of CONSTANS and the florigen FLOWERING LOCUS T","volume":"4","author":"Takagi","year":"2023","journal-title":"Plant Commun."},{"key":"10.1016\/j.jplph.2026.154868_bib117","doi-asserted-by":"crossref","first-page":"592","DOI":"10.1038\/s41467-024-44859-2","article-title":"Molecular switching in transcription through splicing and proline-isomerization regulates stress responses in plants","volume":"15","author":"Theisen","year":"2024","journal-title":"Nat. Commun."},{"key":"10.1016\/j.jplph.2026.154868_bib118","doi-asserted-by":"crossref","first-page":"50","DOI":"10.1126\/science.abm4245","article-title":"Structural basis of branch site recognition by the human spliceosome","volume":"375","author":"Tholen","year":"2022","journal-title":"Science"},{"key":"10.1016\/j.jplph.2026.154868_bib119","doi-asserted-by":"crossref","DOI":"10.1016\/j.celrep.2022.111784","article-title":"Chromatin-associated YTHDC1 coordinates heat-induced reprogramming of gene expression","volume":"41","author":"Timcheva","year":"2022","journal-title":"Cell Rep."},{"key":"10.1016\/j.jplph.2026.154868_bib120","doi-asserted-by":"crossref","first-page":"2251","DOI":"10.1093\/jxb\/erac431","article-title":"Alternative splicing in plants: current knowledge and future directions for assessing the biological relevance of splice variants","volume":"74","author":"Tognacca","year":"2023","journal-title":"J. Exp. Bot."},{"key":"10.1016\/j.jplph.2026.154868_bib121","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":"10.1016\/j.jplph.2026.154868_bib122","doi-asserted-by":"crossref","DOI":"10.1002\/wrna.70030","article-title":"Comprehensive overview of computational tools for alternative splicing analysis","volume":"16","author":"Tran","year":"2025","journal-title":"Wiley Interdiscip. Rev. RNA"},{"key":"10.1016\/j.jplph.2026.154868_bib123","doi-asserted-by":"crossref","first-page":"352","DOI":"10.1016\/j.tplants.2007.06.010","article-title":"The molecular basis of vernalization-induced flowering in cereals","volume":"12","author":"Trevaskis","year":"2007","journal-title":"Trends Plant Sci."},{"key":"10.1016\/j.jplph.2026.154868_bib124","doi-asserted-by":"crossref","first-page":"882","DOI":"10.1093\/plphys\/kiac271","article-title":"HISTONE DEACETYLASE 15 and MOS4-associated complex subunits 3A\/3B coregulate intron retention of ABA-responsive genes","volume":"190","author":"Tu","year":"2022","journal-title":"Plant Physiol"},{"key":"10.1016\/j.jplph.2026.154868_bib125","doi-asserted-by":"crossref","first-page":"21","DOI":"10.1186\/s12864-017-4393-z","article-title":"Exploring the relationship between intron retention and chromatin accessibility in plants","volume":"19","author":"Ullah","year":"2018","journal-title":"BMC Genom."},{"key":"10.1016\/j.jplph.2026.154868_bib126","doi-asserted-by":"crossref","first-page":"14","DOI":"10.1016\/j.ymeth.2019.06.001","article-title":"Next-generation transcriptome assembly and analysis: impact of ploidy","volume":"176","author":"Voshall","year":"2020","journal-title":"Methods"},{"key":"10.1016\/j.jplph.2026.154868_bib127","doi-asserted-by":"crossref","DOI":"10.1002\/pro.4624","article-title":"A splicing variant of EDS1 from Vitis vinifera forms homodimers but no heterodimers with PAD4","volume":"32","author":"Voss","year":"2023","journal-title":"Protein Sci."},{"key":"10.1016\/j.jplph.2026.154868_bib128","article-title":"CLK2 condensates reorganize nuclear speckles and induce intron retention","volume":"11","author":"Wang","year":"2024","journal-title":"Adv. Sci. (Weinh.)"},{"key":"10.1016\/j.jplph.2026.154868_bib129","doi-asserted-by":"crossref","first-page":"7175","DOI":"10.1073\/pnas.0602039103","article-title":"Genomewide comparative analysis of alternative splicing in plants","volume":"103","author":"Wang","year":"2006","journal-title":"Proc Natl Acad Sci U S A"},{"key":"10.1016\/j.jplph.2026.154868_bib130","doi-asserted-by":"crossref","first-page":"1229","DOI":"10.1093\/plphys\/kiaa103","article-title":"The Physcomitrella patens chromatin adaptor PpMRG1 interacts with H3K36me3 and regulates light-responsive alternative splicing","volume":"185","author":"Wang","year":"2021","journal-title":"Plant Physiol"},{"key":"10.1016\/j.jplph.2026.154868_bib131","doi-asserted-by":"crossref","first-page":"66","DOI":"10.1038\/s41477-023-01605-8","article-title":"Regulation of micro- and small-exon retention and other splicing processes by GRP20 for flower development","volume":"10","author":"Wang","year":"2024","journal-title":"Nat. Plants"},{"key":"10.1016\/j.jplph.2026.154868_bib132","doi-asserted-by":"crossref","first-page":"718","DOI":"10.1111\/pce.14537","article-title":"Two environmental signal-driven RNA metabolic processes: alternative splicing and translation","volume":"46","author":"Wang","year":"2023","journal-title":"Plant Cell Environ."},{"key":"10.1016\/j.jplph.2026.154868_bib133","first-page":"751","article-title":"Regulation of flowering transition by alternative splicing: the role of the U2 auxiliary factor","volume":"71","author":"Wang","year":"2020","journal-title":"J. Exp. Bot."},{"key":"10.1016\/j.jplph.2026.154868_bib134","doi-asserted-by":"crossref","DOI":"10.1038\/ncomms15134","article-title":"Intron retention is regulated by altered MeCP2-mediated splicing factor recruitment","volume":"8","author":"Wong","year":"2017","journal-title":"Nat. Commun."},{"key":"10.1016\/j.jplph.2026.154868_bib135","doi-asserted-by":"crossref","first-page":"2124","DOI":"10.1104\/pp.15.01279","article-title":"Evolution of VRN2\/Ghd7-Like genes in vernalization-mediated repression of grass flowering","volume":"170","author":"Woods","year":"2016","journal-title":"Plant Physiol"},{"key":"10.1016\/j.jplph.2026.154868_bib136","doi-asserted-by":"crossref","first-page":"3539","DOI":"10.1242\/dev.02521","article-title":"Temporal regulation of shoot development in Arabidopsis thaliana by miR156 and its target SPL3","volume":"133","author":"Wu","year":"2006","journal-title":"Development"},{"key":"10.1016\/j.jplph.2026.154868_bib137","doi-asserted-by":"crossref","first-page":"151","DOI":"10.1186\/1471-2229-12-151","article-title":"A naturally occurring InDel variation in BraA.FLC.b (BrFLC2) associated with flowering time variation in Brassica rapa","volume":"12","author":"Wu","year":"2012","journal-title":"BMC Plant Biol."},{"key":"10.1016\/j.jplph.2026.154868_bib138","doi-asserted-by":"crossref","DOI":"10.3390\/horticulturae11091064","article-title":"Insights into loquat flowering regulation through analysis of alternative splicing of flowering-time genes and functions of EjCO1 isoforms","volume":"11","author":"Wu","year":"2025","journal-title":"Horticulturae"},{"key":"10.1016\/j.jplph.2026.154868_bib139","doi-asserted-by":"crossref","first-page":"27","DOI":"10.1104\/pp.19.01009","article-title":"Autonomous pathway: FLOWERING LOCUS C repression through an antisense-mediated chromatin-silencing mechanism","volume":"182","author":"Wu","year":"2020","journal-title":"Plant Physiol"},{"key":"10.1016\/j.jplph.2026.154868_bib140","doi-asserted-by":"crossref","first-page":"757","DOI":"10.1007\/s00122-016-2848-2","article-title":"The alternative splicing of EAM8 contributes to early flowering and short-season adaptation in a landrace barley from the Qinghai-Tibetan Plateau","volume":"130","author":"Xia","year":"2017","journal-title":"Theor. Appl. Genet."},{"key":"10.1016\/j.jplph.2026.154868_bib141","doi-asserted-by":"crossref","first-page":"280","DOI":"10.1104\/pp.106.084475","article-title":"Genomic organization, differential expression, and interaction of SQUAMOSA promoter-binding-like transcription factors and microRNA156 in rice","volume":"142","author":"Xie","year":"2006","journal-title":"Plant Physiol"},{"key":"10.1016\/j.jplph.2026.154868_bib142","doi-asserted-by":"crossref","first-page":"277","DOI":"10.1111\/nph.15756","article-title":"AtU2AF65b functions in abscisic acid mediated flowering via regulating the precursor messenger RNA splicing of ABI5 and FLC in Arabidopsis","volume":"223","author":"Xiong","year":"2019","journal-title":"New Phytol."},{"key":"10.1016\/j.jplph.2026.154868_bib143","article-title":"Unraveling branch point-driven SR45a splicing dynamics in heat stress for plant adaptation","volume":"12","author":"Xu","year":"2026","journal-title":"Sci. Adv."},{"key":"10.1016\/j.jplph.2026.154868_bib144","doi-asserted-by":"crossref","first-page":"710","DOI":"10.1111\/nph.19168","article-title":"Intronic microRNA-directed regulation of mitochondrial reactive oxygen species enhances plant stress tolerance in Arabidopsis","volume":"240","author":"Xu","year":"2023","journal-title":"New Phytol."},{"key":"10.1016\/j.jplph.2026.154868_bib145","doi-asserted-by":"crossref","first-page":"268","DOI":"10.1016\/j.devcel.2009.06.007","article-title":"The microRNA-regulated SBP-Box transcription factor SPL3 is a direct upstream activator of LEAFY, FRUITFULL, and APETALA1","volume":"17","author":"Yamaguchi","year":"2009","journal-title":"Dev. Cell"},{"key":"10.1016\/j.jplph.2026.154868_bib146","doi-asserted-by":"crossref","first-page":"40623","DOI":"10.1074\/jbc.M201531200","article-title":"Identification of a cis element for tissue-specific alternative splicing of chloroplast ascorbate peroxidase pre-mRNA in higher plants","volume":"277","author":"Yoshimura","year":"2002","journal-title":"J. Biol. Chem."},{"key":"10.1016\/j.jplph.2026.154868_bib147","doi-asserted-by":"crossref","DOI":"10.1016\/j.celrep.2025.115501","article-title":"The Exserohilum turcicum effector EtEC81 reprograms alternative splicing in maize and activates immunity","volume":"44","author":"Yu","year":"2025","journal-title":"Cell Rep."},{"key":"10.1016\/j.jplph.2026.154868_bib148","doi-asserted-by":"crossref","first-page":"131","DOI":"10.1007\/s00299-018-2354-x","article-title":"The chromatin remodeler ZmCHB101 impacts alternative splicing contexts in response to osmotic stress","volume":"38","author":"Yu","year":"2019","journal-title":"Plant Cell Rep."},{"key":"10.1016\/j.jplph.2026.154868_bib149","doi-asserted-by":"crossref","first-page":"1299","DOI":"10.1093\/jxb\/erp010","article-title":"A naturally occurring splicing site mutation in the Brassica rapa FLC1 gene is associated with variation in flowering time","volume":"60","author":"Yuan","year":"2009","journal-title":"J. Exp. Bot."},{"key":"10.1016\/j.jplph.2026.154868_bib150","doi-asserted-by":"crossref","DOI":"10.1016\/j.plantsci.2019.110256","article-title":"Maize NAC-domain retained splice variants act as dominant negatives to interfere with the full-length NAC counterparts","volume":"289","author":"Zhang","year":"2019","journal-title":"Plant Sci."},{"key":"10.1016\/j.jplph.2026.154868_bib151","doi-asserted-by":"crossref","first-page":"7985","DOI":"10.1038\/s41467-024-52391-6","article-title":"Variation of C-terminal domain governs RNA polymerase II genomic locations and alternative splicing in eukaryotic transcription","volume":"15","author":"Zhang","year":"2024","journal-title":"Nat. Commun."},{"key":"10.1016\/j.jplph.2026.154868_bib152","doi-asserted-by":"crossref","first-page":"1577","DOI":"10.1104\/pp.107.108720","article-title":"Alternative splicing and mRNA levels of the disease resistance gene RPS4 are induced during defense responses","volume":"145","author":"Zhang","year":"2007","journal-title":"Plant Physiol"},{"key":"10.1016\/j.jplph.2026.154868_bib153","article-title":"Phase separation of HRLP regulates flowering time in Arabidopsis","volume":"8","author":"Zhang","year":"2022","journal-title":"Sci. Adv."},{"key":"10.1016\/j.jplph.2026.154868_bib154","doi-asserted-by":"crossref","first-page":"1280","DOI":"10.1007\/s11427-023-2466-7","article-title":"A repertoire of intronic lariat RNAs reveals tissue-specific regulation and target mimicry potential in plants","volume":"67","author":"Zhang","year":"2024","journal-title":"Sci. China Life Sci."},{"key":"10.1016\/j.jplph.2026.154868_bib155","doi-asserted-by":"crossref","first-page":"63","DOI":"10.1093\/mp\/ssr066","article-title":"A novel rice gene, NRR responds to macronutrient deficiency and regulates root growth","volume":"5","author":"Zhang","year":"2012","journal-title":"Mol. Plant"},{"key":"10.1016\/j.jplph.2026.154868_bib156","doi-asserted-by":"crossref","DOI":"10.3390\/ijms21010299","article-title":"The temperature-dependent retention of introns in GPI8 transcripts contributes to a drooping and fragile shoot phenotype in rice","volume":"21","author":"Zhao","year":"2019","journal-title":"Int. J. Mol. Sci."},{"key":"10.1016\/j.jplph.2026.154868_bib157","doi-asserted-by":"crossref","first-page":"253","DOI":"10.3389\/fgene.2019.00253","article-title":"Analysis of transcriptome and epitranscriptome in plants using PacBio Iso-Seq and nanopore-based direct RNA sequencing","volume":"10","author":"Zhao","year":"2019","journal-title":"Front. Genet."},{"key":"10.1016\/j.jplph.2026.154868_bib158","doi-asserted-by":"crossref","first-page":"5130","DOI":"10.1038\/s41467-024-49571-9","article-title":"Light regulates nuclear detainment of intron-retained transcripts through COP1-spliceosome to modulate photomorphogenesis","volume":"15","author":"Zhou","year":"2024","journal-title":"Nat. Commun."}],"container-title":["Journal of Plant Physiology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S0176161726001811?httpAccept=text\/xml","content-type":"text\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S0176161726001811?httpAccept=text\/plain","content-type":"text\/plain","content-version":"vor","intended-application":"text-mining"}],"deposited":{"date-parts":[[2026,9,27]],"date-time":"2026-09-27T04:25:58Z","timestamp":1790483158000},"score":1,"resource":{"primary":{"URL":"https:\/\/linkinghub.elsevier.com\/retrieve\/pii\/S0176161726001811"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,10]]},"references-count":158,"alternative-id":["S0176161726001811"],"URL":"https:\/\/doi.org\/10.1016\/j.jplph.2026.154868","relation":{},"ISSN":["0176-1617"],"issn-type":[{"value":"0176-1617","type":"print"}],"subject":[],"published":{"date-parts":[[2026,10]]},"assertion":[{"value":"Elsevier","name":"publisher","label":"This article is maintained by"},{"value":"Intron retention as a hub for splicing regulation in plant environmental adaptation and developmental programming","name":"articletitle","label":"Article Title"},{"value":"Journal of Plant Physiology","name":"journaltitle","label":"Journal Title"},{"value":"https:\/\/doi.org\/10.1016\/j.jplph.2026.154868","name":"articlelink","label":"CrossRef DOI link to publisher maintained version"},{"value":"article","name":"content_type","label":"Content Type"},{"value":"\u00a9 2026 Elsevier GmbH. All rights are reserved, including those for text and data mining, AI training, and similar technologies.","name":"copyright","label":"Copyright"}],"article-number":"154868"}}