{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,2]],"date-time":"2026-06-02T13:54:15Z","timestamp":1780408455631,"version":"3.54.1"},"reference-count":87,"publisher":"Wiley","issue":"4","license":[{"start":{"date-parts":[[2023,2,9]],"date-time":"2023-02-09T00:00:00Z","timestamp":1675900800000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/onlinelibrary.wiley.com\/termsAndConditions#vor"}],"content-domain":{"domain":["onlinelibrary.wiley.com"],"crossmark-restriction":true},"short-container-title":["Plant Cell &amp; Environment"],"published-print":{"date-parts":[[2023,4]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>Plant height (PH) in rice (<jats:italic>Oryza sativa<\/jats:italic>) is an important trait for its adaptation and agricultural performance. Discovery of the<jats:italic>semi\u2010dwarf1<\/jats:italic>(<jats:italic>SD1<\/jats:italic>) mutation initiated the Green Revolution, boosting rice yield and fitness, but the underlying genetic regulation of PH in rice remains largely unknown. Here, we performed genome\u2010wide association study (GWAS) and identified 12 non\u2010repetitive QTL\/genes regulating PH variation in 619 Asian cultivated rice accessions. One of these was an<jats:italic>SD1<\/jats:italic>structural variant, not normally detected in standard GWAS analyses. Given the strong effect of<jats:italic>SD1<\/jats:italic>on PH, we also divided 619 accessions into subgroups harbouring distinct<jats:italic>SD1<\/jats:italic>haplotypes, and found a further 85 QTL\/genes for PH, revealing genetic heterogeneity that may be missed by analysing a broad, diverse population. Moreover, we uncovered two epistatic interaction networks of PH\u2010associated QTL\/genes in the<jats:italic>japonica<\/jats:italic>(<jats:italic>Geng<\/jats:italic>)\u2010dominant<jats:italic>SD1<\/jats:italic><jats:sup><jats:italic>NIP<\/jats:italic><\/jats:sup>subgroup. In one of them, the hub QTL\/gene<jats:italic>qphSN1.4\/GAMYB<\/jats:italic>interacted with<jats:italic>qphSN3.1\/OsINO80<\/jats:italic>,<jats:italic>qphSN3.4\/HD16\/EL1<\/jats:italic>,<jats:italic>qphSN6.2\/LOC_Os06g11130<\/jats:italic>, and<jats:italic>qphSN10.2\/MADS56<\/jats:italic>. Sequence variations in<jats:italic>GAMYB<\/jats:italic>and<jats:italic>MADS56<\/jats:italic>were associated with their expression levels and PH variations, and MADS56 was shown to physically interact with MADS57 to coregulate expression of gibberellin (GA) metabolic genes<jats:italic>OsGA2ox3<\/jats:italic>and<jats:italic>Elongated Uppermost Internode1<\/jats:italic>(<jats:italic>EUI1<\/jats:italic>). Our study uncovered the multifaceted genetic architectures of rice PH, and provided novel and abundant genetic resources for breeding semi\u2010dwarf rice and new candidates for further mechanistic studies on regulation of PH in rice.<\/jats:p>","DOI":"10.1111\/pce.14557","type":"journal-article","created":{"date-parts":[[2023,2,3]],"date-time":"2023-02-03T10:39:41Z","timestamp":1675420781000},"page":"1295-1311","update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":20,"title":["Combined genome\u2010wide association study and epistasis analysis reveal multifaceted genetic architectures of plant height in Asian cultivated rice"],"prefix":"10.1111","volume":"46","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-2407-1973","authenticated-orcid":false,"given":"Jun","family":"Hong","sequence":"first","affiliation":[{"name":"Joint International Research Laboratory of Metabolic and Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Yazhou Bay Institute of Deepsea Sci\u2010Tech Shanghai Jiao Tong University Shanghai China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Su","family":"Su","sequence":"additional","affiliation":[{"name":"Joint International Research Laboratory of Metabolic and Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Yazhou Bay Institute of Deepsea Sci\u2010Tech Shanghai Jiao Tong University Shanghai China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Li","family":"Wang","sequence":"additional","affiliation":[{"name":"Joint International Research Laboratory of Metabolic and Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Yazhou Bay Institute of Deepsea Sci\u2010Tech Shanghai Jiao Tong University Shanghai China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shaoxing","family":"Bai","sequence":"additional","affiliation":[{"name":"Joint International Research Laboratory of Metabolic and Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Yazhou Bay Institute of Deepsea Sci\u2010Tech Shanghai Jiao Tong University Shanghai China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jianlong","family":"Xu","sequence":"additional","affiliation":[{"name":"Institute of Crop Sciences Chinese Academy of Agricultural Sciences Beijing China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zhikang","family":"Li","sequence":"additional","affiliation":[{"name":"Institute of Crop Sciences Chinese Academy of Agricultural Sciences Beijing China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Natalie","family":"Betts","sequence":"additional","affiliation":[{"name":"School of Agriculture, Food and Wine University of Adelaide Urrbrae South Australia Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Wanqi","family":"Liang","sequence":"additional","affiliation":[{"name":"Joint International Research Laboratory of Metabolic and Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Yazhou Bay Institute of Deepsea Sci\u2010Tech Shanghai Jiao Tong University Shanghai China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Wensheng","family":"Wang","sequence":"additional","affiliation":[{"name":"Institute of Crop Sciences Chinese Academy of Agricultural Sciences Beijing China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7717-0863","authenticated-orcid":false,"given":"Jianxin","family":"Shi","sequence":"additional","affiliation":[{"name":"Joint International Research Laboratory of Metabolic and Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Yazhou Bay Institute of Deepsea Sci\u2010Tech Shanghai Jiao Tong University Shanghai China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dabing","family":"Zhang","sequence":"additional","affiliation":[{"name":"Joint International Research Laboratory of Metabolic and Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Yazhou Bay Institute of Deepsea Sci\u2010Tech Shanghai Jiao Tong University Shanghai China"},{"name":"School of Agriculture, Food and Wine University of Adelaide Urrbrae South Australia Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"311","published-online":{"date-parts":[[2023,2,9]]},"reference":[{"key":"e_1_2_8_2_1","doi-asserted-by":"publisher","DOI":"10.1038\/nmeth0410-248"},{"key":"e_1_2_8_3_1","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gku1039"},{"key":"e_1_2_8_4_1","doi-asserted-by":"publisher","DOI":"10.1007\/s00438-008-0406-6"},{"key":"e_1_2_8_5_1","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.1019490108"},{"key":"e_1_2_8_6_1","doi-asserted-by":"publisher","DOI":"10.1111\/nph.15901"},{"key":"e_1_2_8_7_1","doi-asserted-by":"publisher","DOI":"10.1105\/tpc.108.062935"},{"key":"e_1_2_8_8_1","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/bth457"},{"key":"e_1_2_8_9_1","doi-asserted-by":"publisher","DOI":"10.1007\/s00122-020-03699-6"},{"key":"e_1_2_8_10_1","doi-asserted-by":"publisher","DOI":"10.1186\/s12284-019-0298-6"},{"key":"e_1_2_8_11_1","doi-asserted-by":"crossref","DOI":"10.1002\/tpg2.20077","article-title":"Status and prospects of genome\u2010wide association studies in plants","volume":"14","author":"Cortes L.T.","year":"2021","journal-title":"Plant Genome"},{"key":"e_1_2_8_12_1","doi-asserted-by":"publisher","DOI":"10.1038\/emboj.2010.75"},{"key":"e_1_2_8_13_1","doi-asserted-by":"publisher","DOI":"10.1105\/tpc.19.00023"},{"key":"e_1_2_8_14_1","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-017-1289-9"},{"key":"e_1_2_8_15_1","doi-asserted-by":"publisher","DOI":"10.1007\/s11240-009-9541-y"},{"key":"e_1_2_8_16_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.tplants.2020.05.009"},{"key":"e_1_2_8_17_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.celrep.2022.111235"},{"key":"e_1_2_8_18_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2021.02.001"},{"key":"e_1_2_8_19_1","doi-asserted-by":"crossref","unstructured":"Hong J. Rosental L. Xu Y. Xu D. Orf I. Wang W.et al. (2022)Genetic architecture of seed glycerolipids in Asian cultivated rice.Plant Cell & Environment.https:\/\/doi.org\/10.1111\/pce.14378","DOI":"10.1111\/pce.14378"},{"key":"e_1_2_8_20_1","doi-asserted-by":"publisher","DOI":"10.1105\/tpc.105.030973"},{"key":"e_1_2_8_21_1","doi-asserted-by":"publisher","DOI":"10.1111\/tpj.12268"},{"key":"e_1_2_8_22_1","doi-asserted-by":"publisher","DOI":"10.1038\/ng.695"},{"key":"e_1_2_8_23_1","doi-asserted-by":"publisher","DOI":"10.1038\/ng.1018"},{"key":"e_1_2_8_24_1","doi-asserted-by":"publisher","DOI":"10.1111\/j.1365-3040.2009.02106.x"},{"key":"e_1_2_8_25_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-020-16482-4"},{"key":"e_1_2_8_26_1","doi-asserted-by":"publisher","DOI":"10.1104\/pp.104.052274"},{"key":"e_1_2_8_27_1","doi-asserted-by":"publisher","DOI":"10.1002\/j.1460-2075.1987.tb02730.x"},{"key":"e_1_2_8_28_1","doi-asserted-by":"publisher","DOI":"10.1186\/s12284-019-0324-8"},{"key":"e_1_2_8_29_1","doi-asserted-by":"publisher","DOI":"10.1534\/genetics.114.163931"},{"key":"e_1_2_8_30_1","doi-asserted-by":"publisher","DOI":"10.1038\/nature12870"},{"key":"e_1_2_8_31_1","doi-asserted-by":"publisher","DOI":"10.1111\/j.1365-313X.2011.04877.x"},{"key":"e_1_2_8_32_1","doi-asserted-by":"publisher","DOI":"10.1007\/s00299-018-2260-2"},{"key":"e_1_2_8_33_1","doi-asserted-by":"publisher","DOI":"10.1105\/tpc.017327"},{"key":"e_1_2_8_34_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.gene.2004.12.014"},{"key":"e_1_2_8_35_1","doi-asserted-by":"publisher","DOI":"10.1111\/tpj.15705"},{"key":"e_1_2_8_36_1","doi-asserted-by":"publisher","DOI":"10.1093\/molbev\/msaa185"},{"key":"e_1_2_8_37_1","doi-asserted-by":"publisher","DOI":"10.1080\/15592324.2015.1046667"},{"key":"e_1_2_8_38_1","doi-asserted-by":"publisher","DOI":"10.1111\/pce.12134"},{"key":"e_1_2_8_39_1","doi-asserted-by":"publisher","DOI":"10.1111\/jipb.12603"},{"key":"e_1_2_8_40_1","doi-asserted-by":"publisher","DOI":"10.1007\/s00439-011-1118-2"},{"key":"e_1_2_8_41_1","doi-asserted-by":"publisher","DOI":"10.1038\/nmeth.1681"},{"key":"e_1_2_8_42_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.molp.2017.12.004"},{"key":"e_1_2_8_43_1","doi-asserted-by":"publisher","DOI":"10.1007\/s00425-017-2798-1"},{"key":"e_1_2_8_44_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.molp.2022.02.011"},{"key":"e_1_2_8_45_1","doi-asserted-by":"publisher","DOI":"10.1111\/j.1744-7909.2010.00959.x"},{"key":"e_1_2_8_46_1","doi-asserted-by":"publisher","DOI":"10.1111\/pbi.12681"},{"key":"e_1_2_8_47_1","doi-asserted-by":"publisher","DOI":"10.1093\/molbev\/msab208"},{"key":"e_1_2_8_48_1","doi-asserted-by":"publisher","DOI":"10.3389\/fpls.2016.01801"},{"key":"e_1_2_8_49_1","doi-asserted-by":"publisher","DOI":"10.1017\/S0016672305007780"},{"key":"e_1_2_8_50_1","doi-asserted-by":"publisher","DOI":"10.1111\/nph.16439"},{"key":"e_1_2_8_51_1","doi-asserted-by":"publisher","DOI":"10.1111\/pbi.13023"},{"key":"e_1_2_8_52_1","doi-asserted-by":"publisher","DOI":"10.1111\/pbi.13516"},{"key":"e_1_2_8_53_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41586-020-2501-8"},{"key":"e_1_2_8_54_1","doi-asserted-by":"publisher","DOI":"10.1086\/519795"},{"key":"e_1_2_8_55_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2021.04.046"},{"key":"e_1_2_8_56_1","doi-asserted-by":"publisher","DOI":"10.1111\/j.1365-3040.2009.02008.x"},{"key":"e_1_2_8_57_1","doi-asserted-by":"publisher","DOI":"10.1104\/pp.103.033696"},{"key":"e_1_2_8_58_1","doi-asserted-by":"publisher","DOI":"10.1038\/416701a"},{"key":"e_1_2_8_59_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41422-022-00685-z"},{"key":"e_1_2_8_60_1","doi-asserted-by":"publisher","DOI":"10.1038\/ng.3518"},{"key":"e_1_2_8_61_1","doi-asserted-by":"publisher","DOI":"10.1146\/annurev-genet-050720-122916"},{"key":"e_1_2_8_62_1","doi-asserted-by":"publisher","DOI":"10.1111\/pbi.13661"},{"key":"e_1_2_8_63_1","doi-asserted-by":"publisher","DOI":"10.3390\/ijms21218106"},{"key":"e_1_2_8_64_1","doi-asserted-by":"publisher","DOI":"10.1111\/j.1365-313X.2012.04989.x"},{"key":"e_1_2_8_65_1","doi-asserted-by":"publisher","DOI":"10.3389\/fpls.2015.00084"},{"key":"e_1_2_8_66_1","doi-asserted-by":"publisher","DOI":"10.1038\/nature04028"},{"key":"e_1_2_8_67_1","doi-asserted-by":"publisher","DOI":"10.1007\/s00299-022-02904-8"},{"key":"e_1_2_8_68_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41586-018-0063-9"},{"key":"e_1_2_8_69_1","doi-asserted-by":"publisher","DOI":"10.1186\/s12870-021-02857-2"},{"key":"e_1_2_8_70_1","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pgen.1006386"},{"key":"e_1_2_8_71_1","doi-asserted-by":"publisher","DOI":"10.1093\/jxb\/ery243"},{"key":"e_1_2_8_72_1","doi-asserted-by":"publisher","DOI":"10.1186\/s12284-022-00576-2"},{"key":"e_1_2_8_73_1","doi-asserted-by":"publisher","DOI":"10.1007\/s11103-017-0595-7"},{"key":"e_1_2_8_74_1","doi-asserted-by":"publisher","DOI":"10.1105\/tpc.18.00375"},{"key":"e_1_2_8_75_1","doi-asserted-by":"publisher","DOI":"10.1038\/ncomms6087"},{"key":"e_1_2_8_76_1","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.1904964116"},{"key":"e_1_2_8_77_1","doi-asserted-by":"publisher","DOI":"10.1038\/ng.3596"},{"key":"e_1_2_8_78_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-020-66604-7"},{"key":"e_1_2_8_79_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.cub.2022.04.028"},{"key":"e_1_2_8_80_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.jgg.2022.01.008"},{"key":"e_1_2_8_81_1","doi-asserted-by":"publisher","DOI":"10.1186\/s12863-021-00995-y"},{"key":"e_1_2_8_82_1","doi-asserted-by":"publisher","DOI":"10.1111\/tpj.13069"},{"key":"e_1_2_8_83_1","doi-asserted-by":"publisher","DOI":"10.1038\/ncomms1467"},{"key":"e_1_2_8_84_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41588-018-0041-z"},{"key":"e_1_2_8_85_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.plantsci.2013.10.003"},{"key":"e_1_2_8_86_1","doi-asserted-by":"publisher","DOI":"10.1038\/nature12878"},{"key":"e_1_2_8_87_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.molp.2018.11.010"},{"key":"e_1_2_8_88_1","doi-asserted-by":"publisher","DOI":"10.1105\/tpc.105.038455"}],"container-title":["Plant, Cell &amp; Environment"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/pdf\/10.1111\/pce.14557","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/full-xml\/10.1111\/pce.14557","content-type":"application\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/pdf\/10.1111\/pce.14557","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,12,6]],"date-time":"2023-12-06T05:08:49Z","timestamp":1701839329000},"score":1,"resource":{"primary":{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/10.1111\/pce.14557"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2023,2,9]]},"references-count":87,"journal-issue":{"issue":"4","published-print":{"date-parts":[[2023,4]]}},"alternative-id":["10.1111\/pce.14557"],"URL":"https:\/\/doi.org\/10.1111\/pce.14557","archive":["Portico"],"relation":{},"ISSN":["0140-7791","1365-3040"],"issn-type":[{"value":"0140-7791","type":"print"},{"value":"1365-3040","type":"electronic"}],"subject":[],"published":{"date-parts":[[2023,2,9]]},"assertion":[{"value":"2022-10-25","order":0,"name":"received","label":"Received","group":{"name":"publication_history","label":"Publication History"}},{"value":"2023-02-01","order":1,"name":"accepted","label":"Accepted","group":{"name":"publication_history","label":"Publication History"}},{"value":"2023-02-09","order":2,"name":"published","label":"Published","group":{"name":"publication_history","label":"Publication History"}}]}}