{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,8]],"date-time":"2026-09-08T11:08:35Z","timestamp":1788865715058,"version":"build-2803163510"},"reference-count":194,"publisher":"Wiley","license":[{"start":{"date-parts":[[2026,9,8]],"date-time":"2026-09-08T00:00:00Z","timestamp":1788825600000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"},{"start":{"date-parts":[[2026,9,8]],"date-time":"2026-09-08T00:00:00Z","timestamp":1788825600000},"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":["JIPB"],"abstract":"<jats:title>ABSTRACT<\/jats:title>\n                  <jats:p>\n                    <jats:italic>Cis<\/jats:italic>\n                    \u2010regulatory elements (CREs) orchestrate the spatiotemporal precision of gene expression that underlies plant development, adaptation, and domestication. Decoding the\n                    <jats:italic>cis<\/jats:italic>\n                    \u2010regulatory grammar of plant genomes remains a central challenge in modern biology, with profound implications for programmable crop engineering. Here, recent conceptual and technological advances are synthesized to reshape our understanding of plant CREs. This review first argues that CRE function is not only an intrinsic property of DNA sequence alone but also emerges from a multidimensional context, including chromatin accessibility, histone modifications, three\u2010dimensional genome topology, and cell type\u2010specific regulatory landscapes. Furthermore, the convergence of single\u2010cell epigenomics, high\u2010throughput functional assays, and CRISPR\u2010based dissection has begun to unravel this contextual grammar, revealing the computational principles governing transcriptional regulation. Critically, we propose that artificial intelligence (AI) platforms are catalyzing an ongoing transition from descriptive discovery to predictive engineering, wherein these platforms outperform natural evolution in designing synthetic CREs. Finally, a roadmap is outlined toward a plant regulatory grammar foundation model, which will enable truly predictive engineering of gene expression when fine\u2010tuned for specific tasks. Collectively, the integration of single\u2010cell resolution maps, precise genome editing, AI\u2010driven design, and regulatory\u2010compliant delivery systems promises to transform our ability to reprogram plant gene regulation for next\u2010generation agriculture, bridging the gap between foundational regulatory biology and tangible crop improvement.\n                  <\/jats:p>","DOI":"10.1111\/jipb.70386","type":"journal-article","created":{"date-parts":[[2026,9,8]],"date-time":"2026-09-08T10:23:55Z","timestamp":1788863035000},"update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Plant\n                    <i>cis<\/i>\n                    \u2010regulatory grammar: Decoding the multidimensional code of transcriptional regulation for programmable crop engineering"],"prefix":"10.1111","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-6419-5562","authenticated-orcid":false,"given":"Libin","family":"Zhang","sequence":"first","affiliation":[{"name":"Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology Huazhong University of Science and Technology Wuhan 430074 China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1655-9637","authenticated-orcid":false,"given":"Maoteng","family":"Li","sequence":"additional","affiliation":[{"name":"Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology Huazhong University of Science and Technology Wuhan 430074 China"},{"name":"Biological Seed Industry Research Institute, Xianghu Laboratory Hangzhou 311231 China"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"311","published-online":{"date-parts":[[2026,9,8]]},"reference":[{"key":"e_1_2_11_2_1","doi-asserted-by":"crossref","first-page":"183","DOI":"10.1080\/21645698.2015.1129937","article-title":"Genome editing for crop improvement: Challenges and opportunities","volume":"6","author":"Abdallah N.A.","year":"2015","journal-title":"GM Crops Food"},{"key":"e_1_2_11_3_1","doi-asserted-by":"crossref","first-page":"382","DOI":"10.1126\/science.aax7063","article-title":"A cytosine deaminase for programmable single\u2010base RNA editing","volume":"365","author":"Abudayyeh O.O.","year":"2019","journal-title":"Science"},{"key":"e_1_2_11_4_1","doi-asserted-by":"crossref","first-page":"5895","DOI":"10.1093\/nar\/gkae345","article-title":"Prokaryotic Argonaute nuclease cooperates with co\u2010encoded RNase to acquire guide RNAs and target invader DNA","volume":"52","author":"Agapov A.","year":"2024","journal-title":"Nucleic Acids Res."},{"key":"e_1_2_11_5_1","doi-asserted-by":"crossref","first-page":"831","DOI":"10.1038\/nbt.3300","article-title":"Predicting the sequence specificities of DNA\u2010 and RNA\u2010binding proteins by deep learning","volume":"33","author":"Alipanahi B.","year":"2015","journal-title":"Nat. Biotechnol."},{"key":"e_1_2_11_6_1","doi-asserted-by":"crossref","DOI":"10.1126\/science.adt8983","article-title":"A deep\u2010time landscape of plant cis\u2010regulatory sequence evolution","volume":"12","author":"Amundson K.R.","year":"2026","journal-title":"Science"},{"key":"e_1_2_11_7_1","doi-asserted-by":"crossref","first-page":"149","DOI":"10.1038\/s41586-019-1711-4","article-title":"Search\u2010and\u2010replace genome editing without double\u2010strand breaks or donor DNA","volume":"576","author":"Anzalone A.V.","year":"2019","journal-title":"Nature"},{"key":"e_1_2_11_8_1","doi-asserted-by":"crossref","first-page":"1065","DOI":"10.1016\/j.omtn.2019.12.042","article-title":"Novel engineered programmable systems for ADAR\u2010mediated RNA editing","volume":"19","author":"Aquino\u2010Jarquin G.","year":"2020","journal-title":"Mol. Ther. Nucleic Acids"},{"key":"e_1_2_11_9_1","doi-asserted-by":"crossref","first-page":"1074","DOI":"10.1126\/science.1232542","article-title":"Genome\u2010wide quantitative enhancer activity maps identified by STARR\u2010seq","volume":"339","author":"Arnold C.D.","year":"2013","journal-title":"Science"},{"key":"e_1_2_11_10_1","doi-asserted-by":"crossref","first-page":"98","DOI":"10.1007\/s00299-024-03183-1","article-title":"Crop bioengineering via gene editing: Reshaping the future of agriculture","volume":"43","author":"Atia M.","year":"2024","journal-title":"Plant Cell Rep."},{"key":"e_1_2_11_11_1","doi-asserted-by":"crossref","first-page":"W202","DOI":"10.1093\/nar\/gkp335","article-title":"MEME SUITE: Tools for motif discovery and searching","volume":"37","author":"Bailey T.L.","year":"2009","journal-title":"Nucleic Acids Res."},{"key":"e_1_2_11_12_1","doi-asserted-by":"crossref","first-page":"461","DOI":"10.1093\/pcp\/pcae121","article-title":"Enhancers in plant development, adaptation and evolution","volume":"66","author":"Beernink B.M.","year":"2025","journal-title":"Plant Cell Physiol."},{"key":"e_1_2_11_13_1","doi-asserted-by":"crossref","first-page":"269","DOI":"10.1007\/s11240-016-1057-7","article-title":"Cis\u2010regulatory elements used to control gene expression in plants","volume":"127","author":"Bi\u0142as R.","year":"2016","journal-title":"Plant Cell Tissue Organ Cult."},{"key":"e_1_2_11_14_1","doi-asserted-by":"crossref","first-page":"46","DOI":"10.1002\/biot.201200120","article-title":"Promoter engineering: Recent advances in controlling transcription at the most fundamental level","volume":"8","author":"Blazeck J.","year":"2013","journal-title":"Biotechnol. J."},{"key":"e_1_2_11_15_1","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0033279","article-title":"Rational diversification of a promoter providing fine\u2010tuned expression and orthogonal regulation for synthetic biology","volume":"7","author":"Blount B.A.","year":"2012","journal-title":"PLoS ONE"},{"key":"e_1_2_11_16_1","doi-asserted-by":"crossref","first-page":"419","DOI":"10.1146\/annurev-phyto-080508-081936","article-title":"Xanthomonas AvrBs3 family\u2010type III effectors: Discovery and function","volume":"48","author":"Boch J.","year":"2010","journal-title":"Annu. Rev. Phytopathol."},{"key":"e_1_2_11_17_1","doi-asserted-by":"crossref","first-page":"1509","DOI":"10.1126\/science.1178811","article-title":"Breaking the code of DNA binding specificity of TAL\u2010type III effectors","volume":"326","author":"Boch J.","year":"2009","journal-title":"Science"},{"key":"e_1_2_11_18_1","doi-asserted-by":"crossref","first-page":"41","DOI":"10.1016\/j.biotechadv.2014.12.006","article-title":"The CRISPR\/Cas9 system for plant genome editing and beyond","volume":"33","author":"Bortesi L.","year":"2015","journal-title":"Biotechnol. Adv."},{"key":"e_1_2_11_19_1","doi-asserted-by":"crossref","first-page":"31","DOI":"10.1016\/j.bbagrm.2016.07.005","article-title":"Combinatorial control of plant gene expression","volume":"1860","author":"Brkljacic J.","year":"2017","journal-title":"Biochim. Biophys. Acta Gene Regul. Mech."},{"key":"e_1_2_11_20_1","doi-asserted-by":"crossref","DOI":"10.34133\/bdr.0013","article-title":"Plant promoters and terminators for high\u2010precision bioengineering","volume":"5","author":"Brooks E.G.","year":"2023","journal-title":"Biodes. Res."},{"key":"e_1_2_11_21_1","doi-asserted-by":"crossref","first-page":"508","DOI":"10.1038\/nmeth.2926","article-title":"Principles of genetic circuit design","volume":"11","author":"Brophy J.A.","year":"2014","journal-title":"Nat. Methods"},{"key":"e_1_2_11_22_1","doi-asserted-by":"crossref","first-page":"1213","DOI":"10.1038\/nmeth.2688","article-title":"Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA\u2010binding proteins and nucleosome position","volume":"10","author":"Buenrostro J.D.","year":"2013","journal-title":"Nat. Methods"},{"key":"e_1_2_11_23_1","doi-asserted-by":"crossref","first-page":"486","DOI":"10.1038\/nature14590","article-title":"Single\u2010cell chromatin accessibility reveals principles of regulatory variation","volume":"523","author":"Buenrostro J.D.","year":"2015","journal-title":"Nature"},{"key":"e_1_2_11_24_1","doi-asserted-by":"crossref","first-page":"2370","DOI":"10.1111\/pbi.13399","article-title":"Engineering herbicide resistance via prime editing in rice","volume":"18","author":"Butt H.","year":"2020","journal-title":"Plant Biotechnol. J."},{"key":"e_1_2_11_25_1","doi-asserted-by":"crossref","DOI":"10.1038\/s41467-024-55195-w","article-title":"MaizeCODE reveals bi\u2010directionally expressed enhancers that harbor molecular signatures of maize domestication","volume":"15","author":"Cahn J.","year":"2024","journal-title":"Nat. Commun."},{"key":"e_1_2_11_26_1","doi-asserted-by":"crossref","first-page":"719","DOI":"10.1038\/s41467-021-20940-y","article-title":"H3K27me3\u2010rich genomic regions can function as silencers to repress gene expression via chromatin interactions","volume":"12","author":"Cai Y.","year":"2021","journal-title":"Nat. Commun."},{"key":"e_1_2_11_27_1","doi-asserted-by":"crossref","first-page":"11845","DOI":"10.1093\/nar\/gkaa682","article-title":"Rational design of minimal synthetic promoters for plants","volume":"48","author":"Cai Y.M.","year":"2020","journal-title":"Nucleic Acids Res."},{"key":"e_1_2_11_28_1","doi-asserted-by":"crossref","first-page":"1386","DOI":"10.1038\/s41597-024-04243-7","article-title":"The FLAIR\u2010GG federated network of FAIR germplasm data resources","volume":"11","author":"C\u00e1mara Ballesteros A.","year":"2024","journal-title":"Sci. Data"},{"key":"e_1_2_11_29_1","doi-asserted-by":"crossref","DOI":"10.1016\/j.isci.2025.114062","article-title":"Plant domestication revisited: Genomic insights into origins, mechanisms, and convergent evolution","volume":"29","author":"Cao Y.","year":"2025","journal-title":"iScience"},{"key":"e_1_2_11_30_1","doi-asserted-by":"crossref","first-page":"703","DOI":"10.1016\/j.molp.2025.03.005","article-title":"A comprehensive omics resource and genetic tools for functional genomics research and genetic improvement of sorghum","volume":"18","author":"Chen C.","year":"2025","journal-title":"Mol. Plant"},{"key":"e_1_2_11_31_1","doi-asserted-by":"crossref","first-page":"1221","DOI":"10.1038\/s41588-023-01419-6","article-title":"A complete telomere\u2010to\u2010telomere assembly of the maize genome","volume":"55","author":"Chen J.","year":"2023","journal-title":"Nat. Genet."},{"key":"e_1_2_11_32_1","doi-asserted-by":"crossref","first-page":"667","DOI":"10.1146\/annurev-arplant-050718-100049","article-title":"CRISPR\/Cas genome editing and precision plant breeding in agriculture","volume":"70","author":"Chen K.","year":"2019","journal-title":"Annu. Rev. Plant Biol."},{"key":"e_1_2_11_33_1","doi-asserted-by":"crossref","first-page":"2240","DOI":"10.1093\/plphys\/kiad652","article-title":"Genetic dissection of cis\u2010regulatory control of ZmWUSCHEL1 expression by type B RESPONSE REGULATORS","volume":"194","author":"Chen Z.","year":"2024","journal-title":"Plant Physiol."},{"key":"e_1_2_11_34_1","doi-asserted-by":"crossref","DOI":"10.1111\/tpj.70416","article-title":"Chromatin accessibility analysis reveals functional cis\u2010regulatory regions related to fruit development and domestication in tomato","volume":"123","author":"Cheng Y.J.","year":"2025","journal-title":"Plant J."},{"key":"e_1_2_11_35_1","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pgen.1011174","article-title":"Extreme restructuring of cis\u2010regulatory regions controlling a deeply conserved plant stem cell regulator","volume":"20","author":"Ciren D.","year":"2024","journal-title":"PLoS Genet."},{"key":"e_1_2_11_36_1","doi-asserted-by":"crossref","first-page":"16","DOI":"10.1111\/pbi.14191","article-title":"Coordinated gene upregulation in maize through CRISPR\/Cas\u2010mediated enhancer insertion","volume":"22","author":"Claeys H.","year":"2024","journal-title":"Plant Biotechnol. J."},{"key":"e_1_2_11_37_1","doi-asserted-by":"crossref","first-page":"1014","DOI":"10.1111\/tpj.13517","article-title":"Accurate measurement of transgene copy number in crop plants using droplet digital PCR","volume":"90","author":"Collier R.","year":"2017","journal-title":"Plant J."},{"key":"e_1_2_11_38_1","doi-asserted-by":"crossref","first-page":"123","DOI":"10.1101\/gr.4074106","article-title":"Genome\u2010wide mapping of DNase hypersensitive sites using massively parallel signature sequencing (MPSS)","volume":"16","author":"Crawford G.E.","year":"2006","journal-title":"Genome Res."},{"key":"e_1_2_11_39_1","doi-asserted-by":"crossref","first-page":"124","DOI":"10.1007\/s11103-025-01642-1","article-title":"cis\u2010 and trans\u2010elements for the transcriptional regulation of sugar responsive genes: From current knowledge to future applications","volume":"115","author":"Cruz\u2010L\u00f3pez M.I.","year":"2025","journal-title":"Plant Mol. Biol."},{"key":"e_1_2_11_40_1","doi-asserted-by":"crossref","first-page":"743","DOI":"10.1111\/jipb.70120","article-title":"Population\u2010scale landscape of TE insertion polymorphisms reveal their roles in gene expression regulation, adaptation, and agronomic traits in Brassica napus","volume":"68","author":"Cui X.","year":"2026","journal-title":"J. Integr. Plant Biol."},{"key":"e_1_2_11_41_1","doi-asserted-by":"crossref","first-page":"181","DOI":"10.1186\/s13059-023-03018-4","article-title":"3D organization of regulatory elements for transcriptional regulation in Arabidopsis","volume":"24","author":"Deng L.","year":"2023","journal-title":"Genome Biol."},{"key":"e_1_2_11_42_1","doi-asserted-by":"crossref","DOI":"10.1093\/plcell\/koaf236","article-title":"Decoding tissue\u2010specific enhancers in plants using massively parallel assays and deep learning","volume":"37","author":"Deng Y.","year":"2025","journal-title":"Plant Cell"},{"key":"e_1_2_11_43_1","doi-asserted-by":"crossref","first-page":"201","DOI":"10.1111\/jipb.12809","article-title":"Tissue\u2010specific Hi\u2010C analyses of rice, foxtail millet and maize suggest non\u2010canonical function of plant chromatin domains","volume":"62","author":"Dong P.","year":"2020","journal-title":"J. Integr. Plant Biol."},{"key":"e_1_2_11_44_1","doi-asserted-by":"crossref","first-page":"276","DOI":"10.1038\/s41587-020-0439-x","article-title":"The nf\u2010core framework for community\u2010curated bioinformatics pipelines","volume":"38","author":"Ewels P.A.","year":"2020","journal-title":"Nat. Biotechnol."},{"key":"e_1_2_11_45_1","doi-asserted-by":"crossref","first-page":"W273","DOI":"10.1093\/nar\/gkh458","article-title":"VISTA: Computational tools for comparative genomics","volume":"32","author":"Frazer K.A.","year":"2004","journal-title":"Nucleic Acids Res."},{"key":"e_1_2_11_46_1","doi-asserted-by":"crossref","first-page":"3666","DOI":"10.1093\/nar\/gkg540","article-title":"Cluster\u2010Buster: Finding dense clusters of motifs in DNA sequences","volume":"31","author":"Frith M.C.","year":"2003","journal-title":"Nucleic Acids Res."},{"key":"e_1_2_11_47_1","doi-asserted-by":"crossref","first-page":"1664","DOI":"10.1038\/s41588-019-0538-0","article-title":"Activity\u2010by\u2010contact model of enhancer\u2010promoter regulation from thousands of CRISPR perturbations","volume":"51","author":"Fulco C.P.","year":"2019","journal-title":"Nat. Genet."},{"key":"e_1_2_11_48_1","doi-asserted-by":"crossref","first-page":"1205","DOI":"10.1038\/s41477-025-02007-8","article-title":"Transcription factor binding divergence drives transcriptional and phenotypic variation in maize","volume":"11","author":"Galli M.","year":"2025","journal-title":"Nat. Plants"},{"key":"e_1_2_11_49_1","doi-asserted-by":"crossref","first-page":"1621","DOI":"10.1016\/j.cell.2021.01.005","article-title":"Genome engineering for crop improvement and future agriculture","volume":"184","author":"Gao C.","year":"2021","journal-title":"Cell"},{"key":"e_1_2_11_50_1","doi-asserted-by":"crossref","first-page":"208","DOI":"10.1111\/jipb.13620","article-title":"Increased long\u2010distance and homo\u2010trans interactions related to H3K27me3 in Arabidopsis hybrids","volume":"66","author":"Gao Z.","year":"2024","journal-title":"J. Integr. Plant Biol."},{"key":"e_1_2_11_51_1","doi-asserted-by":"crossref","first-page":"464","DOI":"10.1038\/nature24644","article-title":"Programmable base editing of A\u00b7T to G\u00b7C in genomic DNA without DNA cleavage","volume":"551","author":"Gaudelli N.M.","year":"2017","journal-title":"Nature"},{"key":"e_1_2_11_52_1","doi-asserted-by":"crossref","first-page":"512","DOI":"10.1038\/s41477-018-0210-1","article-title":"Demography and its effects on genomic variation in crop domestication","volume":"4","author":"Gaut B.S.","year":"2018","journal-title":"Nat. Plants"},{"key":"e_1_2_11_53_1","doi-asserted-by":"crossref","first-page":"647","DOI":"10.1016\/j.cell.2014.09.029","article-title":"Genome\u2010scale CRISPR\u2010mediated control of gene repression and activation","volume":"159","author":"Gilbert L.A.","year":"2014","journal-title":"Cell"},{"key":"e_1_2_11_54_1","doi-asserted-by":"crossref","DOI":"10.1093\/nargab\/lqag034","article-title":"T\u2010ChroNet: Time\u2010aware chromatin network reconstruction to detect dynamic regulatory programs in longitudinal epigenetic dataset","volume":"8","author":"Giovenale S.","year":"2026","journal-title":"NAR Genom. Bioinform."},{"key":"e_1_2_11_55_1","doi-asserted-by":"crossref","first-page":"9308","DOI":"10.1038\/s41467-024-53760-x","article-title":"Mutations of PDS5 genes enhance TAD\u2010like domain formation Arabidopsis thaliana","volume":"15","author":"G\u00f6bel A.M.","year":"2024","journal-title":"Nat. Commun."},{"key":"e_1_2_11_56_1","first-page":"38","article-title":"Using morphogenic genes to improve recovery and regeneration of transgenic plants","volume":"8","author":"Gordon\u2010Kamm B.","year":"2019","journal-title":"Plants (Basel)"},{"key":"e_1_2_11_57_1","doi-asserted-by":"crossref","first-page":"1017","DOI":"10.1093\/bioinformatics\/btr064","article-title":"FIMO: Scanning for occurrences of a given motif","volume":"27","author":"Grant C.E.","year":"2011","journal-title":"Bioinformatics"},{"key":"e_1_2_11_58_1","doi-asserted-by":"crossref","first-page":"1203","DOI":"10.1111\/tpj.15873","article-title":"TDTHub, a web server tool for the analysis of transcription factor binding sites in plants","volume":"111","author":"Grau J.","year":"2022","journal-title":"Plant J."},{"key":"e_1_2_11_59_1","doi-asserted-by":"crossref","first-page":"109","DOI":"10.1016\/j.plantsci.2013.12.007","article-title":"Identification and validation of promoters and cis\u2010acting regulatory elements","volume":"217","author":"Hernandez\u2010Garcia C.M.","year":"2014","journal-title":"Plant Sci."},{"key":"e_1_2_11_60_1","doi-asserted-by":"crossref","DOI":"10.1002\/biot.201600173","article-title":"Targeted modification of plant genomes for precision crop breeding","volume":"12","author":"Hilscher J.","year":"2017","journal-title":"Biotechnol. J."},{"key":"e_1_2_11_61_1","first-page":"783","article-title":"From gene knockouts to genome remodeling: Large DNA fragment deletion technologies in plants","volume":"15","author":"Hou J.","year":"2026","journal-title":"Plants (Basel)"},{"key":"e_1_2_11_62_1","doi-asserted-by":"crossref","first-page":"627","DOI":"10.1016\/j.molp.2018.02.007","article-title":"Precise A\u00b7T to G\u00b7C base editing in the rice genome","volume":"11","author":"Hua K.","year":"2018","journal-title":"Mol. Plant"},{"key":"e_1_2_11_63_1","doi-asserted-by":"crossref","DOI":"10.1002\/bies.202400121","article-title":"Pushing the TAD boundary: Decoding insulator codes of clustered CTCF sites in 3D genomes","volume":"46","author":"Huang H.","year":"2024","journal-title":"BioEssays"},{"key":"e_1_2_11_64_1","doi-asserted-by":"crossref","first-page":"531","DOI":"10.1146\/annurev-arplant-050213-035715","article-title":"Natural variations and genome\u2010wide association studies in crop plants","volume":"65","author":"Huang X.","year":"2014","journal-title":"Annu. Rev. Plant Biol."},{"key":"e_1_2_11_65_1","doi-asserted-by":"crossref","first-page":"961","DOI":"10.1038\/ng.695","article-title":"Genome\u2010wide association studies of 14 agronomic traits in rice landraces","volume":"42","author":"Huang X.","year":"2010","journal-title":"Nat. Genet."},{"key":"e_1_2_11_66_1","doi-asserted-by":"crossref","first-page":"808","DOI":"10.1038\/ng.2309","article-title":"Comparative population genomics of maize domestication and improvement","volume":"44","author":"Hufford M.B.","year":"2012","journal-title":"Nat. Genet."},{"key":"e_1_2_11_67_1","doi-asserted-by":"crossref","DOI":"10.1111\/tpj.70254","article-title":"Engineering an RNA\/protein\u2010binding module for higher transgene protein production and improved long\u2010term durability","volume":"122","author":"Hung Y.H.","year":"2025","journal-title":"Plant J."},{"key":"e_1_2_11_68_1","doi-asserted-by":"crossref","first-page":"985","DOI":"10.3389\/fpls.2018.00985","article-title":"CRISPR for crop improvement: An update review","volume":"9","author":"Jaganathan D.","year":"2018","journal-title":"Front. Plant Sci."},{"key":"e_1_2_11_69_1","doi-asserted-by":"crossref","first-page":"284","DOI":"10.1038\/s41586-020-2947-8","article-title":"The barley pan\u2010genome reveals the hidden legacy of mutation breeding","volume":"588","author":"Jayakodi M.","year":"2020","journal-title":"Nature"},{"key":"e_1_2_11_70_1","doi-asserted-by":"crossref","first-page":"257","DOI":"10.1186\/s13059-020-02170-5","article-title":"Prime editing efficiently generates W542L and S621I double mutations in two ALS genes in maize","volume":"21","author":"Jiang Y.Y.","year":"2020","journal-title":"Genome Biol."},{"key":"e_1_2_11_71_1","doi-asserted-by":"crossref","first-page":"541","DOI":"10.1038\/ng.591","article-title":"Regulation of OsSPL14 by OsmiR156 defines ideal plant architecture in rice","volume":"42","author":"Jiao Y.","year":"2010","journal-title":"Nat. Genet."},{"key":"e_1_2_11_72_1","doi-asserted-by":"crossref","first-page":"637","DOI":"10.1111\/nph.70232","article-title":"Single\u2010cell transcriptomes reveal spatiotemporal heat stress response in pearl millet leaves","volume":"247","author":"Jin Y.","year":"2025","journal-title":"New Phytol."},{"key":"e_1_2_11_73_1","doi-asserted-by":"crossref","DOI":"10.1093\/bfgp\/elaf025","article-title":"Bioinformatics insights into plant genomic imprinting: Approaches, challenges, and future perspectives","volume":"25","author":"Jing X.","year":"2026","journal-title":"Brief Funct. Genomics"},{"key":"e_1_2_11_74_1","doi-asserted-by":"crossref","first-page":"1497","DOI":"10.1126\/science.1141319","article-title":"Genome\u2010wide mapping of in vivo protein\u2010DNA interactions","volume":"316","author":"Johnson D.S.","year":"2007","journal-title":"Science"},{"key":"e_1_2_11_75_1","doi-asserted-by":"crossref","first-page":"42","DOI":"10.1016\/j.pbi.2019.12.008","article-title":"Identification and evolution of gene regulatory networks: Insights from comparative studies in plants","volume":"54","author":"Jones D.M.","year":"2020","journal-title":"Curr. Opin. Plant Biol."},{"key":"e_1_2_11_76_1","doi-asserted-by":"crossref","first-page":"2120","DOI":"10.1105\/tpc.20.00155","article-title":"Identification of plant enhancers and their constituent elements by STARR\u2010seq in tobacco leaves","volume":"32","author":"Jores T.","year":"2020","journal-title":"Plant Cell"},{"key":"e_1_2_11_77_1","doi-asserted-by":"crossref","DOI":"10.1093\/plcell\/koaf084","article-title":"Small DNA elements that act as both insulators and silencers in plants","volume":"37","author":"Jores T.","year":"2025","journal-title":"Plant Cell"},{"key":"e_1_2_11_78_1","doi-asserted-by":"crossref","first-page":"842","DOI":"10.1038\/s41477-021-00932-y","article-title":"Synthetic promoter designs enabled by a comprehensive analysis of plant core promoters","volume":"7","author":"Jores T.","year":"2021","journal-title":"Nat. Plants"},{"key":"e_1_2_11_79_1","doi-asserted-by":"crossref","DOI":"10.1126\/sciadv.adu6565","article-title":"TAC\u2010C uncovers open chromatin interaction in crops and SPL\u2010mediated photosynthesis regulation","volume":"11","author":"Kang J.","year":"2025","journal-title":"Sci. Adv."},{"key":"e_1_2_11_80_1","doi-asserted-by":"crossref","first-page":"1930","DOI":"10.1038\/s41467-019-09982-5","article-title":"CUT&Tag for efficient epigenomic profiling of small samples and single cells","volume":"10","author":"Kaya\u2010Okur H.S.","year":"2019","journal-title":"Nat. Commun."},{"key":"e_1_2_11_81_1","doi-asserted-by":"crossref","first-page":"2147","DOI":"10.1111\/nph.70348","article-title":"Precise knock\u2010in of stress\u2010responsive cis\u2010regulatory elements using gene targeting for improving abiotic stress tolerance in plants","volume":"247","author":"Ke Y.","year":"2025","journal-title":"New Phytol."},{"key":"e_1_2_11_82_1","doi-asserted-by":"crossref","first-page":"416","DOI":"10.1038\/s41587-024-02236-w","article-title":"CRISPRi\u2010based circuits to control gene expression in plants","volume":"43","author":"Khan M.A.","year":"2025","journal-title":"Nat. Biotechnol."},{"key":"e_1_2_11_83_1","doi-asserted-by":"crossref","first-page":"373","DOI":"10.1016\/j.molcel.2022.12.032","article-title":"Deciphering the multi\u2010scale, quantitative cis\u2010regulatory code","volume":"83","author":"Kim S.","year":"2023","journal-title":"Mol. Cell"},{"key":"e_1_2_11_84_1","doi-asserted-by":"crossref","first-page":"2235","DOI":"10.1093\/plcell\/koab117","article-title":"Endosperm\u2010based incompatibilities in hybrid monkeyflowers","volume":"33","author":"Kinser T.J.","year":"2021","journal-title":"Plant Cell"},{"key":"e_1_2_11_85_1","doi-asserted-by":"crossref","first-page":"8","DOI":"10.1086\/426833","article-title":"Long\u2010range control of gene expression: Emerging mechanisms and disruption in disease","volume":"76","author":"Kleinjan D.A.","year":"2005","journal-title":"Am. J. Hum. Genet."},{"key":"e_1_2_11_86_1","doi-asserted-by":"crossref","first-page":"420","DOI":"10.1038\/nature17946","article-title":"Programmable editing of a target base in genomic DNA without double\u2010stranded DNA cleavage","volume":"533","author":"Komor A.C.","year":"2016","journal-title":"Nature"},{"key":"e_1_2_11_87_1","doi-asserted-by":"crossref","first-page":"983","DOI":"10.1038\/s41592-024-02260-3","article-title":"Multiplex profiling of developmental cis\u2010regulatory elements with quantitative single\u2010cell expression reporters","volume":"21","author":"Lalanne J.B.","year":"2024","journal-title":"Nat. Methods"},{"key":"e_1_2_11_88_1","doi-asserted-by":"crossref","first-page":"16","DOI":"10.1016\/j.copbio.2017.07.003","article-title":"Synthetic genetic circuits in crop plants","volume":"49","author":"Lange O.","year":"2018","journal-title":"Curr. Opin. Biotechnol."},{"key":"e_1_2_11_89_1","doi-asserted-by":"crossref","first-page":"6139","DOI":"10.1073\/pnas.1323964111","article-title":"Current perspectives and the future of domestication studies","volume":"111","author":"Larson G.","year":"2014","journal-title":"Proc. Natl. Acad. Sci. U.S.A."},{"key":"e_1_2_11_90_1","doi-asserted-by":"crossref","first-page":"1482","DOI":"10.1038\/s41588-024-01758-y","article-title":"High\u2010resolution genome\u2010wide mapping of chromosome\u2010arm\u2010scale truncations induced by CRISPR\u2010Cas9 editing","volume":"56","author":"Lazar N.H.","year":"2024","journal-title":"Nat. Genet."},{"key":"e_1_2_11_91_1","doi-asserted-by":"crossref","first-page":"766","DOI":"10.1038\/s41477-018-0259-x","article-title":"Rapid improvement of domestication traits in an orphan crop by genome editing","volume":"4","author":"Lemmon Z.H.","year":"2018","journal-title":"Nat. Plants"},{"key":"e_1_2_11_92_1","doi-asserted-by":"crossref","first-page":"59","DOI":"10.1186\/s13059-018-1443-z","article-title":"Expanded base editing in rice and wheat using a Cas9\u2010adenosine deaminase fusion","volume":"19","author":"Li C.","year":"2018","journal-title":"Genome Biol."},{"key":"e_1_2_11_93_1","doi-asserted-by":"crossref","first-page":"671","DOI":"10.1016\/j.molp.2020.03.011","article-title":"Precise modifications of both exogenous and endogenous genes in rice by prime editing","volume":"13","author":"Li H.","year":"2020","journal-title":"Mol. Plant"},{"key":"e_1_2_11_94_1","doi-asserted-by":"crossref","first-page":"510","DOI":"10.1007\/s42994-025-00237-0","article-title":"Cis\u2010regulatory elements: Systematic identification and horticultural applications","volume":"6","author":"Li T.","year":"2025","journal-title":"aBIOTECH"},{"key":"e_1_2_11_95_1","doi-asserted-by":"crossref","first-page":"984","DOI":"10.1016\/j.tig.2025.02.005","article-title":"Cis\u2010regulatory dynamics in plant domestication","volume":"41","author":"Li X.","year":"2025","journal-title":"Trends Genet."},{"key":"e_1_2_11_96_1","doi-asserted-by":"crossref","DOI":"10.1016\/j.xplc.2023.100596","article-title":"Synthetic dual hormone\u2010responsive promoters enable engineering of plants with broad\u2010spectrum resistance","volume":"4","author":"Li X.","year":"2023","journal-title":"Plant Commun."},{"key":"e_1_2_11_97_1","doi-asserted-by":"crossref","first-page":"357","DOI":"10.1146\/annurev-arplant-080720-090632","article-title":"Natural variation in crops: Realized understanding, continuing promise","volume":"72","author":"Liang Y.","year":"2021","journal-title":"Annu. Rev. Plant Biol."},{"key":"e_1_2_11_98_1","doi-asserted-by":"crossref","first-page":"289","DOI":"10.1126\/science.1181369","article-title":"Comprehensive mapping of long\u2010range interactions reveals folding principles of the human genome","volume":"326","author":"Lieberman\u2010Aiden E.","year":"2009","journal-title":"Science"},{"key":"e_1_2_11_99_1","doi-asserted-by":"crossref","first-page":"582","DOI":"10.1038\/s41587-020-0455-x","article-title":"Prime genome editing in rice and wheat","volume":"38","author":"Lin Q.","year":"2020","journal-title":"Nat. Biotechnol."},{"key":"e_1_2_11_100_1","doi-asserted-by":"crossref","first-page":"49","DOI":"10.1038\/nrg3374","article-title":"How important are transposons for plant evolution?","volume":"14","author":"Lisch D.","year":"2013","journal-title":"Nat. Rev. Genet."},{"key":"e_1_2_11_101_1","doi-asserted-by":"crossref","first-page":"303","DOI":"10.1007\/s11105-013-0667-z","article-title":"Critical cis\u2010acting elements and interacting transcription factors: Key players associated with abiotic stress responses in plants","volume":"32","author":"Liu J.","year":"2014","journal-title":"Plant Mol. Biol. Rep."},{"key":"e_1_2_11_102_1","doi-asserted-by":"crossref","DOI":"10.1016\/j.xplc.2025.101427","article-title":"Programmable genome engineering and gene modifications for plant biodesign","volume":"6","author":"Liu J.","year":"2025","journal-title":"Plant Commun."},{"key":"e_1_2_11_103_1","doi-asserted-by":"crossref","DOI":"10.1093\/hr\/uhaf228","article-title":"Pangenomics and single\u2010cell transcriptomics uncover the genetic basis of continuous bearing trait in grapevine","volume":"12","author":"Liu Y.","year":"2025","journal-title":"Hortic. Res."},{"key":"e_1_2_11_104_1","doi-asserted-by":"crossref","DOI":"10.1111\/tpj.70090","article-title":"The switch\u2010liker's guide to plant synthetic gene circuits","volume":"121","author":"Lloyd J.P.B.","year":"2025","journal-title":"Plant J."},{"key":"e_1_2_11_105_1","doi-asserted-by":"crossref","first-page":"2540","DOI":"10.3390\/ijms27062540","article-title":"Design and testing of root\u2010specific synthetic promoters by machine learning","volume":"27","author":"Lu C.","year":"2026","journal-title":"Int. J. Mol. Sci."},{"key":"e_1_2_11_106_1","doi-asserted-by":"crossref","first-page":"523","DOI":"10.1016\/j.molp.2016.11.013","article-title":"Precise editing of a target base in the rice genome using a modified CRISPR\/Cas9 system","volume":"10","author":"Lu Y.","year":"2017","journal-title":"Mol. Plant"},{"key":"e_1_2_11_107_1","doi-asserted-by":"crossref","first-page":"1250","DOI":"10.1038\/s41477-019-0548-z","article-title":"The prevalence, evolution and chromatin signatures of plant regulatory elements","volume":"5","author":"Lu Z.","year":"2019","journal-title":"Nat. Plants"},{"key":"e_1_2_11_108_1","doi-asserted-by":"crossref","first-page":"784","DOI":"10.1038\/s41477-018-0249-z","article-title":"Genome encode analyses reveal the basis of convergent evolution of fleshy fruit ripening","volume":"4","author":"L\u00fc P.","year":"2018","journal-title":"Nat. Plants"},{"key":"e_1_2_11_109_1","doi-asserted-by":"crossref","first-page":"961","DOI":"10.1016\/j.molp.2016.04.009","article-title":"CRISPR\/Cas9 platforms for genome editing in plants: Developments and applications","volume":"9","author":"Ma X.","year":"2016","journal-title":"Mol. Plant"},{"key":"e_1_2_11_110_1","doi-asserted-by":"crossref","first-page":"15","DOI":"10.1105\/tpc.17.00581","article-title":"Profiling of accessible chromatin regions across multiple plant species and cell types reveals common gene regulatory principles and new control modules","volume":"30","author":"Maher K.A.","year":"2018","journal-title":"Plant Cell"},{"key":"e_1_2_11_111_1","doi-asserted-by":"crossref","first-page":"1514","DOI":"10.1038\/s41477-024-01796-8","article-title":"The Arabidopsis U1 snRNP regulates mRNA 3\u2032\u2010end processing","volume":"10","author":"Mangilet A.F.","year":"2024","journal-title":"Nat. Plants"},{"key":"e_1_2_11_112_1","doi-asserted-by":"crossref","first-page":"131","DOI":"10.1016\/j.bbagrm.2016.06.006","article-title":"Towards genome\u2010wide prediction and characterization of enhancers in plants","volume":"1860","author":"Marand A.P.","year":"2017","journal-title":"Biochim. Biophys. Acta Gene Regul. Mech."},{"key":"e_1_2_11_113_1","doi-asserted-by":"crossref","first-page":"111","DOI":"10.1146\/annurev-arplant-070122-030236","article-title":"cis\u2010regulatory elements in plant development, adaptation, and evolution","volume":"74","author":"Marand A.P.","year":"2023","journal-title":"Annu. Rev. Plant Biol."},{"key":"e_1_2_11_114_1","doi-asserted-by":"crossref","DOI":"10.1126\/science.ads6601","article-title":"The genetic architecture of cell type\u2010specific cis regulation in maize","volume":"388","author":"Marand A.P.","year":"2025","journal-title":"Science"},{"key":"e_1_2_11_115_1","doi-asserted-by":"crossref","first-page":"394","DOI":"10.1038\/nrg3683","article-title":"RNA\u2010directed DNA methylation: An epigenetic pathway of increasing complexity","volume":"15","author":"Matzke M.A.","year":"2014","journal-title":"Nat. Rev. Genet."},{"key":"e_1_2_11_116_1","doi-asserted-by":"crossref","first-page":"271","DOI":"10.1038\/nbt.2137","article-title":"Systematic dissection and optimization of inducible enhancers in human cells using a massively parallel reporter assay","volume":"30","author":"Melnikov A.","year":"2012","journal-title":"Nat. Biotechnol."},{"key":"e_1_2_11_117_1","doi-asserted-by":"crossref","first-page":"1486","DOI":"10.1111\/tpj.16351","article-title":"Exploring plant cis\u2010regulatory elements at single\u2010cell resolution: Overcoming biological and computational challenges to advance plant research","volume":"115","author":"Mendieta J.P.","year":"2023","journal-title":"Plant J."},{"key":"e_1_2_11_118_1","doi-asserted-by":"crossref","DOI":"10.1073\/pnas.2402781121","article-title":"Investigating the cis\u2010regulatory basis of C3 and C4 photosynthesis in grasses at single\u2010cell resolution","volume":"121","author":"Mendieta J.P.","year":"2024","journal-title":"Proc. Natl. Acad. Sci. U.S.A."},{"key":"e_1_2_11_119_1","doi-asserted-by":"crossref","first-page":"1997","DOI":"10.1093\/plcell\/koab093","article-title":"Genomic editing of intronic enhancers unveils their role in fine\u2010tuning tissue\u2010specific gene expression in Arabidopsis thaliana","volume":"33","author":"Meng F.","year":"2021","journal-title":"Plant Cell"},{"key":"e_1_2_11_120_1","doi-asserted-by":"crossref","first-page":"2551","DOI":"10.1038\/s41592-025-02900-2","article-title":"FX\u2010Cell: A method for single\u2010cell RNA sequencing on difficult\u2010to\u2010digest and cryopreserved plant samples","volume":"22","author":"Ming X.","year":"2025","journal-title":"Nat. Methods"},{"key":"e_1_2_11_121_1","doi-asserted-by":"crossref","first-page":"679","DOI":"10.1038\/s41592-022-01488-1","article-title":"ColabFold: Making protein folding accessible to all","volume":"19","author":"Mirdita M.","year":"2022","journal-title":"Nat. Methods"},{"key":"e_1_2_11_122_1","doi-asserted-by":"crossref","first-page":"545","DOI":"10.1038\/ng.592","article-title":"OsSPL14 promotes panicle branching and higher grain productivity in rice","volume":"42","author":"Miura K.","year":"2010","journal-title":"Nat. Genet."},{"key":"e_1_2_11_123_1","doi-asserted-by":"crossref","first-page":"215","DOI":"10.1186\/gb-2010-11-12-219","article-title":"Silencing signals in plants: A long journey for small RNAs","volume":"12","author":"Molnar A.","year":"2011","journal-title":"Genome Biol."},{"key":"e_1_2_11_124_1","doi-asserted-by":"crossref","first-page":"919","DOI":"10.1038\/nmeth.3999","article-title":"HiChIP: Efficient and sensitive analysis of protein\u2010directed genome architecture","volume":"13","author":"Mumbach M.R.","year":"2016","journal-title":"Nat. Methods"},{"key":"e_1_2_11_125_1","doi-asserted-by":"crossref","first-page":"1047","DOI":"10.1186\/1471-2164-15-1047","article-title":"De novo prediction of cis\u2010regulatory elements and modules through integrative analysis of a large number of ChIP datasets","volume":"15","author":"Niu M.","year":"2014","journal-title":"BMC Genomics"},{"key":"e_1_2_11_126_1","doi-asserted-by":"crossref","first-page":"137","DOI":"10.1186\/s13059-017-1273-4","article-title":"Genome\u2010wide mapping of transcriptional enhancer candidates using DNA and chromatin features in maize","volume":"18","author":"Oka R.","year":"2017","journal-title":"Genome Biol."},{"key":"e_1_2_11_127_1","doi-asserted-by":"crossref","DOI":"10.1016\/j.celrep.2023.112350","article-title":"Haplotype mapping of H3K27me3\u2010associated chromatin interactions defines topological regulation of gene silencing in rice","volume":"42","author":"Ouyang W.","year":"2023","journal-title":"Cell Rep."},{"key":"e_1_2_11_128_1","doi-asserted-by":"crossref","first-page":"3488","DOI":"10.1038\/s41467-024-47744-0","article-title":"Deep learning the cis\u2010regulatory code for gene expression in selected model plants","volume":"15","author":"Peleke F.F.","year":"2024","journal-title":"Nat. Commun."},{"key":"e_1_2_11_129_1","doi-asserted-by":"crossref","first-page":"2632","DOI":"10.1038\/s41467-019-10602-5","article-title":"Chromatin interaction maps reveal genetic regulation for quantitative traits in maize","volume":"10","author":"Peng Y.","year":"2019","journal-title":"Nat. Commun."},{"key":"e_1_2_11_130_1","doi-asserted-by":"crossref","DOI":"10.7554\/eLife.03198","article-title":"Natural epigenetic polymorphisms lead to intraspecific variation in Arabidopsis gene imprinting","volume":"3","author":"Pignatta D.","year":"2014","journal-title":"eLife"},{"key":"e_1_2_11_131_1","doi-asserted-by":"crossref","first-page":"3","DOI":"10.1016\/j.plantsci.2018.03.035","article-title":"From plant metabolic engineering to plant synthetic biology: The evolution of the design\/build\/test\/learn cycle","volume":"273","author":"Pouvreau B.","year":"2018","journal-title":"Plant Sci."},{"key":"e_1_2_11_132_1","doi-asserted-by":"crossref","first-page":"21","DOI":"10.1038\/s41576-022-00509-1","article-title":"Characterizing cis\u2010regulatory elements using single\u2010cell epigenomics","volume":"24","author":"Preissl S.","year":"2023","journal-title":"Nat. Rev. Genet."},{"key":"e_1_2_11_133_1","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1016\/j.pbi.2016.11.011","article-title":"Applying CRISPR\/Cas for genome engineering in plants: The best is yet to come","volume":"36","author":"Puchta H.","year":"2017","journal-title":"Curr. Opin. Plant Biol."},{"key":"e_1_2_11_134_1","doi-asserted-by":"crossref","first-page":"R705","DOI":"10.1016\/j.cub.2019.05.053","article-title":"Evolutionary insights into the nature of plant domestication","volume":"29","author":"Purugganan M.D.","year":"2019","journal-title":"Curr. Biol."},{"key":"e_1_2_11_135_1","doi-asserted-by":"crossref","first-page":"663","DOI":"10.1016\/j.tree.2022.04.006","article-title":"What is domestication?","volume":"37","author":"Purugganan M.D.","year":"2022","journal-title":"Trends. Ecol. Evol."},{"key":"e_1_2_11_136_1","doi-asserted-by":"crossref","first-page":"D174","DOI":"10.1093\/nar\/gkad1059","article-title":"JASPAR 2024: 20th anniversary of the open\u2010access database of transcription factor binding profiles","volume":"52","author":"Rauluseviciute I.","year":"2024","journal-title":"Nucleic Acids Res."},{"key":"e_1_2_11_137_1","doi-asserted-by":"crossref","first-page":"1237","DOI":"10.1038\/s41477-019-0547-0","article-title":"Widespread long\u2010range cis\u2010regulatory elements in the maize genome","volume":"5","author":"Ricci W.A.","year":"2019","journal-title":"Nat. Plants"},{"key":"e_1_2_11_138_1","doi-asserted-by":"crossref","first-page":"470","DOI":"10.1016\/j.cell.2017.08.030","article-title":"Engineering quantitative trait variation for crop improvement by genome editing","volume":"171","author":"Rodriguez\u2010Leal D.","year":"2017","journal-title":"Cell"},{"key":"e_1_2_11_139_1","doi-asserted-by":"crossref","DOI":"10.1016\/j.heliyon.2024.e41135","article-title":"Critical considerations and computational tools in plant genome editing","volume":"11","author":"Saha D.","year":"2024","journal-title":"Heliyon"},{"key":"e_1_2_11_140_1","doi-asserted-by":"crossref","first-page":"218","DOI":"10.1016\/j.pbi.2018.04.013","article-title":"Towards a more predictable plant breeding pipeline with CRISPR\/Cas\u2010induced allelic series to optimize quantitative and qualitative traits","volume":"45","author":"Scheben A.","year":"2018","journal-title":"Curr. Opin. Plant Biol."},{"key":"e_1_2_11_141_1","doi-asserted-by":"crossref","first-page":"1954","DOI":"10.1002\/1873-3468.13073","article-title":"Transforming plant biology and breeding with CRISPR\/Cas9, Cas12 and Cas13","volume":"592","author":"Schindele P.","year":"2018","journal-title":"FEBS Lett."},{"key":"e_1_2_11_142_1","doi-asserted-by":"crossref","first-page":"407","DOI":"10.1093\/plcell\/koab281","article-title":"Cis\u2010regulatory sequences in plants: Their importance, discovery, and future challenges","volume":"34","author":"Schmitz R.J.","year":"2022","journal-title":"Plant Cell"},{"key":"e_1_2_11_143_1","doi-asserted-by":"crossref","first-page":"361","DOI":"10.1016\/bs.mie.2016.03.004","article-title":"Libraries of synthetic TALE\u2010activated promoters: Methods and applications","volume":"576","author":"Schreiber T.","year":"2016","journal-title":"Methods Enzymol."},{"key":"e_1_2_11_144_1","doi-asserted-by":"crossref","first-page":"114","DOI":"10.3389\/fpls.2019.00114","article-title":"Plant genome engineering for targeted improvement of crop traits","volume":"10","author":"Sedeek K.E.","year":"2019","journal-title":"Front. Plant Sci."},{"key":"e_1_2_11_145_1","doi-asserted-by":"crossref","first-page":"878","DOI":"10.1038\/s41422-022-00685-z","article-title":"A super pan\u2010genomic landscape of rice","volume":"32","author":"Shang L.","year":"2022","journal-title":"Cell Res."},{"key":"e_1_2_11_146_1","doi-asserted-by":"crossref","first-page":"1403","DOI":"10.1038\/s41587-022-01281-7","article-title":"Targeting a gene regulatory element enhances rice grain yield by decoupling panicle number and size","volume":"40","author":"Song X.","year":"2022","journal-title":"Nat. Biotechnol."},{"key":"e_1_2_11_147_1","doi-asserted-by":"crossref","DOI":"10.1016\/j.xplc.2025.101376","article-title":"A map of integrated cis\u2010regulatory elements enhances gene\u2010regulatory analysis in maize","volume":"6","author":"Staut J.","year":"2025","journal-title":"Plant Commun."},{"key":"e_1_2_11_148_1","doi-asserted-by":"crossref","first-page":"1160","DOI":"10.1038\/ng.942","article-title":"Identification of a functional transposon insertion in the maize domestication gene tb1","volume":"43","author":"Studer A.","year":"2011","journal-title":"Nat. Genet."},{"key":"e_1_2_11_149_1","doi-asserted-by":"crossref","first-page":"140","DOI":"10.1016\/j.gpb.2018.11.003","article-title":"Global quantitative mapping of enhancers in rice by STARR\u2010seq","volume":"17","author":"Sun J.","year":"2019","journal-title":"Genomics Proteomics Bioinformatics"},{"key":"e_1_2_11_150_1","doi-asserted-by":"crossref","first-page":"1966","DOI":"10.1111\/jipb.13502","article-title":"Conserved H3K27me3\u2010associated chromatin looping mediates physical interactions of gene clusters in plants","volume":"65","author":"Sun L.","year":"2023","journal-title":"J. Integr. Plant Biol."},{"key":"e_1_2_11_151_1","doi-asserted-by":"crossref","first-page":"35","DOI":"10.1038\/s41467-023-44347-z","article-title":"Mapping nucleosome\u2010resolution chromatin organization and enhancer\u2010promoter loops in plants using Micro\u2010C\u2010XL","volume":"15","author":"Sun L.","year":"2024","journal-title":"Nat. Commun."},{"key":"e_1_2_11_152_1","doi-asserted-by":"crossref","first-page":"506","DOI":"10.1016\/j.tplants.2016.01.014","article-title":"Lessons from domestication: Targeting Cis\u2010regulatory elements for crop improvement","volume":"21","author":"Swinnen G.","year":"2016","journal-title":"Trends Plant Sci."},{"key":"e_1_2_11_153_1","doi-asserted-by":"crossref","first-page":"868","DOI":"10.1111\/nph.19020","article-title":"Beyond knockouts: Fine\u2010tuning regulation of gene expression in plants with CRISPR\u2010Cas\u2010based promoter editing","volume":"239","author":"Tang X.","year":"2023","journal-title":"New Phytol."},{"key":"e_1_2_11_154_1","doi-asserted-by":"crossref","DOI":"10.1016\/j.xplc.2022.100308","article-title":"A combinatorial indexing strategy for low\u2010cost epigenomic profiling of plant single cells","volume":"3","author":"Tu X.","year":"2022","journal-title":"Plant Commun."},{"key":"e_1_2_11_155_1","doi-asserted-by":"crossref","first-page":"33","DOI":"10.1016\/j.plantsci.2018.02.024","article-title":"DNA assembly standards: Setting the low\u2010level programming code for plant biotechnology","volume":"273","author":"Vazquez\u2010Vilar M.","year":"2018","journal-title":"Plant Sci."},{"key":"e_1_2_11_156_1","doi-asserted-by":"crossref","DOI":"10.1016\/j.copbio.2024.103140","article-title":"Sourcing DNA parts for synthetic biology applications in plants","volume":"87","author":"Vollen K.","year":"2024","journal-title":"Curr. Opin. Biotechnol."},{"key":"e_1_2_11_157_1","doi-asserted-by":"crossref","first-page":"1805","DOI":"10.1111\/nph.20280","article-title":"Towards targeted engineering of promoters via deletion of repressive cis\u2010regulatory elements","volume":"245","author":"Wang F.Z.","year":"2025","journal-title":"New Phytol."},{"key":"e_1_2_11_158_1","doi-asserted-by":"crossref","first-page":"1242","DOI":"10.1261\/rna.071209.119","article-title":"Novel mRNAs 3\u2032 end\u2010associated cis\u2010regulatory elements with epigenomic signatures of mammalian enhancers in the Arabidopsis genome","volume":"25","author":"Wang H.V.","year":"2019","journal-title":"RNA"},{"key":"e_1_2_11_159_1","doi-asserted-by":"crossref","first-page":"215","DOI":"10.1186\/s13059-017-1346-4","article-title":"The interplay of demography and selection during maize domestication and expansion","volume":"18","author":"Wang L.","year":"2017","journal-title":"Genome Biol."},{"key":"e_1_2_11_160_1","doi-asserted-by":"crossref","DOI":"10.1073\/pnas.2602740123","article-title":"A phosphorylation cascade involving ZmSnRK2.10\u2010ZmRIPK2\u2010ZmWRKY38 attenuates drought response by derepressing ZmSUS2 in maize","volume":"123","author":"Wang T.","year":"2026","journal-title":"Proc. Natl. Acad. Sci. U.S.A."},{"key":"e_1_2_11_161_1","doi-asserted-by":"crossref","first-page":"722","DOI":"10.1038\/s41586-025-09251-0","article-title":"A single\u2010cell multi\u2010omics atlas of rice","volume":"644","author":"Wang X.","year":"2025","journal-title":"Nature"},{"key":"e_1_2_11_162_1","doi-asserted-by":"crossref","DOI":"10.1038\/sdata.2016.18","article-title":"The FAIR guiding principles for scientific data management and stewardship","volume":"3","author":"Wilkinson M.D.","year":"2016","journal-title":"Sci. Data"},{"key":"e_1_2_11_163_1","doi-asserted-by":"crossref","first-page":"59","DOI":"10.1038\/nrg3095","article-title":"Cis\u2010regulatory elements: Molecular mechanisms and evolutionary processes underlying divergence","volume":"13","author":"Wittkopp P.J.","year":"2011","journal-title":"Nat. Rev. Genet."},{"key":"e_1_2_11_164_1","doi-asserted-by":"crossref","first-page":"23","DOI":"10.1007\/978-1-4939-8657-6_2","article-title":"Application of CRISPR\/Cas to understand Cis\u2010 and Trans\u2010regulatory elements in plants","volume":"1830","author":"Wolter F.","year":"2018","journal-title":"Methods Mol. Biol."},{"key":"e_1_2_11_165_1","doi-asserted-by":"crossref","first-page":"3573","DOI":"10.15252\/embj.201798004","article-title":"Topologically associating domains and chromatin loops depend on cohesin and are regulated by CTCF, WAPL, and PDS5 proteins","volume":"36","author":"Wutz G.","year":"2017","journal-title":"EMBO J."},{"key":"e_1_2_11_166_1","doi-asserted-by":"crossref","DOI":"10.1016\/j.xplc.2026.101851","article-title":"TargetGAN: A generative AI framework for the design of plant core promoters with targeted activity","volume":"7","author":"Xiang X.","year":"2026","journal-title":"Plant Commun."},{"key":"e_1_2_11_167_1","doi-asserted-by":"crossref","DOI":"10.1016\/j.pbi.2025.102786","article-title":"Fine\u2010scale 3D chromatin architectures and their regulatory mechanisms in plants","volume":"88","author":"Xiao S.","year":"2025","journal-title":"Curr. Opin. Plant Biol."},{"key":"e_1_2_11_168_1","doi-asserted-by":"crossref","first-page":"2272","DOI":"10.1093\/plcell\/koae064","article-title":"Identification and functional characterization of conserved cis\u2010regulatory elements responsible for early fruit development in cucurbit crops","volume":"36","author":"Xin H.","year":"2024","journal-title":"Plant Cell"},{"key":"e_1_2_11_169_1","doi-asserted-by":"crossref","DOI":"10.1016\/j.xplc.2020.100043","article-title":"Development of plant prime\u2010editing systems for precise genome editing","volume":"1","author":"Xu R.","year":"2020","journal-title":"Plant Commun."},{"key":"e_1_2_11_170_1","doi-asserted-by":"crossref","first-page":"890","DOI":"10.1186\/s12864-025-12115-6","article-title":"Linkage: An interactive web application for linking of DNA regulatory peaks to genes","volume":"26","author":"Xu S.","year":"2025","journal-title":"BMC Genomics"},{"key":"e_1_2_11_171_1","doi-asserted-by":"crossref","first-page":"3456","DOI":"10.1111\/pbi.14466","article-title":"Comparative evaluation of gene copy number estimation techniques in genetically modified crops: Insights from Southern blotting, qPCR, dPCR and NGS","volume":"22","author":"Xu W.","year":"2024","journal-title":"Plant Biotechnol. J."},{"key":"e_1_2_11_172_1","doi-asserted-by":"crossref","first-page":"507","DOI":"10.1038\/s41588-023-01302-4","article-title":"Pangenomic analysis identifies structural variation associated with heat tolerance in pearl millet","volume":"55","author":"Yan H.","year":"2023","journal-title":"Nat. Genet."},{"key":"e_1_2_11_173_1","doi-asserted-by":"crossref","first-page":"2050","DOI":"10.1038\/s41477-025-02106-6","article-title":"A single\u2010cell rice atlas integrates multi\u2010species data to reveal cis\u2010regulatory evolution","volume":"11","author":"Yan H.","year":"2025","journal-title":"Nat. Plants"},{"key":"e_1_2_11_174_1","doi-asserted-by":"crossref","first-page":"1116","DOI":"10.1038\/s41477-026-02289-6","article-title":"Single\u2010cell chromatin accessibility and cis\u2010regulatory element analyses in plants using the scPlantReg platform","volume":"12","author":"Yan H.","year":"2026","journal-title":"Nat. Plants"},{"key":"e_1_2_11_175_1","doi-asserted-by":"crossref","first-page":"11","DOI":"10.1016\/j.tig.2012.09.007","article-title":"Deciphering the transcriptional cis\u2010regulatory code","volume":"29","author":"Y\u00e1\u00f1ez\u2010Cuna J.O.","year":"2013","journal-title":"Trends Genet."},{"key":"e_1_2_11_176_1","doi-asserted-by":"crossref","DOI":"10.1002\/advs.202512036","article-title":"A pan\u2010TE map reveals the important role of transposable elements in gene expression and phenotypic diversity in 2,311 rapeseed accessions","volume":"13","author":"Yang Z.","year":"2026","journal-title":"Adv. Sci. (Weinh)"},{"key":"e_1_2_11_177_1","doi-asserted-by":"crossref","first-page":"1472","DOI":"10.1016\/j.molp.2024.07.009","article-title":"Efficient and multiplex gene upregulation in plants through CRISPR\u2010Cas\u2010mediated knockin of enhancers","volume":"17","author":"Yao Q.","year":"2024","journal-title":"Mol. Plant"},{"key":"e_1_2_11_178_1","doi-asserted-by":"crossref","DOI":"10.1002\/advs.202516600","article-title":"From natural discovery to AI\u2010guided design: A curated collection of compact enhancers for crop engineering","volume":"13","author":"Yao Q.","year":"2026","journal-title":"Adv. Sci. (Weinh)"},{"key":"e_1_2_11_179_1","doi-asserted-by":"crossref","DOI":"10.3389\/fpls.2026.1768521","article-title":"Synthetic promoter design in plants: Integration of computational and experimental approaches","volume":"17","author":"Yaschenko A.E.","year":"2026","journal-title":"Front. Plant Sci."},{"key":"e_1_2_11_180_1","doi-asserted-by":"crossref","DOI":"10.1016\/j.xplc.2023.100558","article-title":"Designing artificial synthetic promoters for accurate, smart, and versatile gene expression in plants","volume":"4","author":"Yasmeen E.","year":"2023","journal-title":"Plant Commun."},{"key":"e_1_2_11_181_1","doi-asserted-by":"crossref","first-page":"27","DOI":"10.1016\/j.molp.2020.12.013","article-title":"Orphan crops and their wild relatives in the genomic era","volume":"14","author":"Ye C.Y.","year":"2021","journal-title":"Mol. Plant"},{"key":"e_1_2_11_182_1","doi-asserted-by":"crossref","DOI":"10.1016\/j.pbi.2021.102139","article-title":"Current status and future perspectives on the evolution of cis\u2010regulatory elements in plants","volume":"65","author":"Yocca A.E.","year":"2022","journal-title":"Curr. Opin. Plant Biol."},{"key":"e_1_2_11_183_1","doi-asserted-by":"crossref","DOI":"10.1111\/tpj.17193","article-title":"Unlocking regeneration potential: Harnessing morphogenic regulators and small peptides for enhanced plant engineering","volume":"121","author":"Youngstrom C.","year":"2025","journal-title":"Plant J."},{"key":"e_1_2_11_184_1","doi-asserted-by":"crossref","DOI":"10.1016\/j.xplc.2022.100508","article-title":"Single\u2010cell and spatial multi\u2010omics in the plant sciences: Technical advances, applications, and perspectives","volume":"4","author":"Yu X.","year":"2023","journal-title":"Plant Commun."},{"key":"e_1_2_11_185_1","doi-asserted-by":"crossref","DOI":"10.1111\/tpj.70795","article-title":"BnLEA4 and BnMYB96 target BnLTP2 to enhance drought tolerance and oil accumulation in Brassica napus L","volume":"125","author":"Yuan G.","year":"2026","journal-title":"Plant J."},{"key":"e_1_2_11_186_1","doi-asserted-by":"crossref","first-page":"550","DOI":"10.1016\/j.cell.2024.10.050","article-title":"A spatially resolved multi\u2010omic single\u2010cell atlas of soybean development","volume":"188","author":"Zhang X.","year":"2025","journal-title":"Cell"},{"key":"e_1_2_11_187_1","doi-asserted-by":"crossref","first-page":"778","DOI":"10.1038\/s41477-019-0461-5","article-title":"The emerging and uncultivated potential of CRISPR technology in plant science","volume":"5","author":"Zhang Y.","year":"2019","journal-title":"Nat. Plants"},{"key":"e_1_2_11_188_1","doi-asserted-by":"crossref","first-page":"4454","DOI":"10.1111\/pbi.70647","article-title":"Single\u2010cell CRISPR: An efficient strategy for decoding plant cis\u2010regulatory complexity","volume":"24","author":"Zhang Y.","year":"2026","journal-title":"Plant Biotechnol. J."},{"key":"e_1_2_11_189_1","doi-asserted-by":"crossref","first-page":"24","DOI":"10.1186\/s13059-020-1927-5","article-title":"Genome\u2010wide MNase hypersensitivity assay unveils distinct classes of open chromatin associated with H3K27me3 and DNA methylation in Arabidopsis thaliana","volume":"21","author":"Zhao H.","year":"2020","journal-title":"Genome Biol."},{"key":"e_1_2_11_190_1","doi-asserted-by":"crossref","first-page":"467","DOI":"10.1038\/ncomms1467","article-title":"Genome\u2010wide association mapping reveals a rich genetic architecture of complex traits in Oryza sativa","volume":"2","author":"Zhao K.","year":"2011","journal-title":"Nat. Commun."},{"key":"e_1_2_11_191_1","doi-asserted-by":"crossref","DOI":"10.1016\/j.xgen.2025.100982","article-title":"Endogenous fine\u2010mapping and prioritization of functional regulatory elements in complex genetic loci","volume":"5","author":"Zhao K.","year":"2025","journal-title":"Cell Genom."},{"key":"e_1_2_11_192_1","doi-asserted-by":"crossref","first-page":"661","DOI":"10.1038\/s41580-020-00288-9","article-title":"Applications of CRISPR\u2010Cas in agriculture and plant biotechnology","volume":"21","author":"Zhu H.","year":"2020","journal-title":"Nat. Rev. Mol. Cell Biol."},{"key":"e_1_2_11_193_1","doi-asserted-by":"crossref","DOI":"10.1016\/j.copbio.2025.103418","article-title":"Functional cereal pan\u2010genomics: Harnessing structural and regulatory variation for precision crop design","volume":"97","author":"Zhu Z.","year":"2026","journal-title":"Curr. Opin. Biotechnol"},{"key":"e_1_2_11_194_1","doi-asserted-by":"crossref","first-page":"438","DOI":"10.1038\/nbt.3811","article-title":"Precise base editing in rice, wheat and maize with a Cas9\u2010cytidine deaminase fusion","volume":"35","author":"Zong Y.","year":"2017","journal-title":"Nat. Biotechnol."},{"key":"e_1_2_11_195_1","doi-asserted-by":"crossref","first-page":"1211","DOI":"10.1038\/nbt.4272","article-title":"De novo domestication of wild tomato using genome editing","volume":"36","author":"Zs\u00f6g\u00f6n A.","year":"2018","journal-title":"Nat. Biotechnol."}],"container-title":["Journal of Integrative Plant Biology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/pdf\/10.1111\/jipb.70386","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/full-xml\/10.1111\/jipb.70386","content-type":"application\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/pdf\/10.1111\/jipb.70386","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,9,8]],"date-time":"2026-09-08T10:24:19Z","timestamp":1788863059000},"score":1,"resource":{"primary":{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/10.1111\/jipb.70386"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,9,8]]},"references-count":194,"alternative-id":["10.1111\/jipb.70386"],"URL":"https:\/\/doi.org\/10.1111\/jipb.70386","archive":["Portico"],"relation":{},"ISSN":["1672-9072","1744-7909"],"issn-type":[{"value":"1672-9072","type":"print"},{"value":"1744-7909","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,9,8]]},"assertion":[{"value":"2026-07-06","order":0,"name":"received","label":"Received","group":{"name":"publication_history","label":"Publication History"}},{"value":"2026-08-24","order":2,"name":"accepted","label":"Accepted","group":{"name":"publication_history","label":"Publication History"}},{"value":"2026-09-08","order":3,"name":"published","label":"Published","group":{"name":"publication_history","label":"Publication History"}}],"article-number":"jipb.70386"}}