{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,22]],"date-time":"2026-09-22T17:09:21Z","timestamp":1790096961305,"version":"4.0.1"},"reference-count":34,"publisher":"MDPI AG","issue":"18","license":[{"start":{"date-parts":[[2026,9,20]],"date-time":"2026-09-20T00:00:00Z","timestamp":1789862400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100004608","name":"Natural Science Foundation of Jiangsu Province","doi-asserted-by":"publisher","award":["BK20220307"],"award-info":[{"award-number":["BK20220307"]}],"id":[{"id":"10.13039\/501100004608","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100007540","name":"Jiangsu Agricultural Science and Technology Innovation Fund","doi-asserted-by":"publisher","award":["CX(23)3087"],"award-info":[{"award-number":["CX(23)3087"]}],"id":[{"id":"10.13039\/100007540","id-type":"DOI","asserted-by":"publisher"}]},{"award":["CX(23)3087"],"award-info":[{"award-number":["CX(23)3087"]}],"id":[{"id":"https:\/\/ror.org\/0335n2618","id-type":"ROR","asserted-by":"publisher"}]},{"name":"Core Provenance Project in Jiangsu Province","award":["JBGS[2021]009"],"award-info":[{"award-number":["JBGS[2021]009"]}]},{"name":"Zhongshan Biological Breeding Laboratory","award":["ZSBBL-KY2023-01-01"],"award-info":[{"award-number":["ZSBBL-KY2023-01-01"]}]},{"name":"Key R&D Program of Yangzhou Modern Agriculture","award":["YZ2024053"],"award-info":[{"award-number":["YZ2024053"]}]},{"name":"Special Fund for Scientific Research Development of the Institute of Agricultural Sciences for Lixiahe Region in Jiangsu","award":["SJ(22)107"],"award-info":[{"award-number":["SJ(22)107"]}]},{"name":"Special Fund for Scientific Research Development of the Institute of Agricultural Sciences for Lixiahe Region in Jiangsu","award":["SJ(22)109"],"award-info":[{"award-number":["SJ(22)109"]}]},{"name":"Earmarked Fund for the China Agricultural Research System","award":["CARS-01-78"],"award-info":[{"award-number":["CARS-01-78"]}],"id":[{"id":"https:\/\/ror.org\/03p5eky76","id-type":"ROR","asserted-by":"crossref"}]},{"award":["CARS-01-78"],"award-info":[{"award-number":["CARS-01-78"]}],"id":[{"id":"https:\/\/ror.org\/03p5eky76","id-type":"ROR","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Int. J. Mol. Sci.","IJMS"],"abstract":"<jats:p>Amylose content (AC) is primarily regulated by the Wx gene and acts as a key determinant of rice eating and cooking quality. Natural low-AC alleles are limited in fine-tuning effects across genetic backgrounds, and studies exploiting natural allelic variation are nearing saturation. Here, we employed prime editing (PE) to generate precise promoter deletions near the transcription start site (TSS) of Wx in japonica rice Huaidao 5, obtaining two homozygous mutant lines: Wx5d harboring the designed 5 bp deletion and Wx32d carrying an unintended 32 bp promoter deletion. Compared with the wild-type, AC was significantly reduced by 3.95 and 2.77 percentage points, respectively, with no obvious changes in grain transparency or the eight major agronomic traits evaluated in this study. The edited lines showed higher taste values measured by a Satake cooked rice taste analyzer, with Wx32d achieving the highest score (76.6 versus 72.6 for the wild-type). Gel consistency was correspondingly longer in both edited lines, and Rapid Visco Analyser (RVA) pasting profiles showed higher breakdown viscosity and more negative setback, most prominently in Wx32d. Reduced AC was accompanied by decreased Wx transcript accumulation and lower granule-bound starch synthase I (OsGBSSI) protein abundance. These two alleles were absent in 3032 natural rice accessions. This study illustrates that PE-mediated promoter editing can efficiently generate valuable low-amylose rice germplasm with minimal agronomic trade-offs among the traits evaluated under the tested environment, providing valuable intermediate materials for rice quality breeding.<\/jats:p>","DOI":"10.3390\/ijms27188386","type":"journal-article","created":{"date-parts":[[2026,9,22]],"date-time":"2026-09-22T13:32:12Z","timestamp":1790083932000},"page":"8386","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Generation and Characterization of Novel Low-Amylose Rice Germplasm via Prime Editing of the Wx Promoter"],"prefix":"10.3390","volume":"27","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-0148-6666","authenticated-orcid":false,"given":"Jianju","family":"Liu","sequence":"first","affiliation":[{"name":"Institute of Agricultural Sciences for Lixiahe Region in Jiangsu, Yangzhou Rice Experiment Station of the China Agricultural Research System, Yangzhou 225009, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yue","family":"Cai","sequence":"additional","affiliation":[{"name":"Institute of Agricultural Sciences for Lixiahe Region in Jiangsu, Yangzhou Rice Experiment Station of the China Agricultural Research System, Yangzhou 225009, China"},{"name":"Collaborative Innovation Center for Modern Crop Production Co-Sponsored by Province and Ministry, Nanjing 210095, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zichun","family":"Chen","sequence":"additional","affiliation":[{"name":"Institute of Agricultural Sciences for Lixiahe Region in Jiangsu, Yangzhou Rice Experiment Station of the China Agricultural Research System, Yangzhou 225009, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yunyu","family":"Wu","sequence":"additional","affiliation":[{"name":"Institute of Agricultural Sciences for Lixiahe Region in Jiangsu, Yangzhou Rice Experiment Station of the China Agricultural Research System, Yangzhou 225009, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Peng","family":"Gao","sequence":"additional","affiliation":[{"name":"Institute of Agricultural Sciences for Lixiahe Region in Jiangsu, Yangzhou Rice Experiment Station of the China Agricultural Research System, Yangzhou 225009, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ling","family":"Yu","sequence":"additional","affiliation":[{"name":"Institute of Agricultural Sciences for Lixiahe Region in Jiangsu, Yangzhou Rice Experiment Station of the China Agricultural Research System, Yangzhou 225009, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Wei","family":"Shi","sequence":"additional","affiliation":[{"name":"Institute of Agricultural Sciences for Lixiahe Region in Jiangsu, Yangzhou Rice Experiment Station of the China Agricultural Research System, Yangzhou 225009, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zhiping","family":"Wang","sequence":"additional","affiliation":[{"name":"Institute of Agricultural Sciences for Lixiahe Region in Jiangsu, Yangzhou Rice Experiment Station of the China Agricultural Research System, Yangzhou 225009, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shuhao","family":"Zhu","sequence":"additional","affiliation":[{"name":"Institute of Agricultural Sciences for Lixiahe Region in Jiangsu, Yangzhou Rice Experiment Station of the China Agricultural Research System, Yangzhou 225009, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Cunhong","family":"Pan","sequence":"additional","affiliation":[{"name":"Institute of Agricultural Sciences for Lixiahe Region in Jiangsu, Yangzhou Rice Experiment Station of the China Agricultural Research System, Yangzhou 225009, China"},{"name":"Collaborative Innovation Center for Modern Crop Production Co-Sponsored by Province and Ministry, Nanjing 210095, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Niansheng","family":"Huang","sequence":"additional","affiliation":[{"name":"Institute of Agricultural Sciences for Lixiahe Region in Jiangsu, Yangzhou Rice Experiment Station of the China Agricultural Research System, Yangzhou 225009, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yuhong","family":"Li","sequence":"additional","affiliation":[{"name":"Institute of Agricultural Sciences for Lixiahe Region in Jiangsu, Yangzhou Rice Experiment Station of the China Agricultural Research System, Yangzhou 225009, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xiaoxiang","family":"Zhang","sequence":"additional","affiliation":[{"name":"Institute of Agricultural Sciences for Lixiahe Region in Jiangsu, Yangzhou Rice Experiment Station of the China Agricultural Research System, Yangzhou 225009, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hongjuan","family":"Ji","sequence":"additional","affiliation":[{"name":"Institute of Agricultural Sciences for Lixiahe Region in Jiangsu, Yangzhou Rice Experiment Station of the China Agricultural Research System, Yangzhou 225009, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jianhua","family":"Zhao","sequence":"additional","affiliation":[{"name":"Institute of Agricultural Sciences for Lixiahe Region in Jiangsu, Yangzhou Rice Experiment Station of the China Agricultural Research System, Yangzhou 225009, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ning","family":"Xiao","sequence":"additional","affiliation":[{"name":"Institute of Agricultural Sciences for Lixiahe Region in Jiangsu, Yangzhou Rice Experiment Station of the China Agricultural Research System, Yangzhou 225009, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Aihong","family":"Li","sequence":"additional","affiliation":[{"name":"Institute of Agricultural Sciences for Lixiahe Region in Jiangsu, Yangzhou Rice Experiment Station of the China Agricultural Research System, Yangzhou 225009, China"},{"name":"Zhongshan Biological Breeding Laboratory, Nanjing 210014, China"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2026,9,20]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"13","DOI":"10.1093\/jxb\/err248","article-title":"Improving crop productivity and resource use efficiency to ensure food security and environmental quality in China","volume":"63","author":"Fan","year":"2012","journal-title":"J. Exp. Bot."},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"165","DOI":"10.1023\/A:1009692221152","article-title":"Analysis of quantitative trait loci which contribute to anther culturability in rice (Oryza sativa L.)","volume":"4","author":"He","year":"1998","journal-title":"Mol. Breed."},{"key":"ref_3","first-page":"1663","article-title":"Strategies for developing green super rice","volume":"104","author":"Zhang","year":"2007","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"21760","DOI":"10.1073\/pnas.0912396106","article-title":"Allelic diversities in rice starch biosynthesis lead to a diverse array of rice eating and cooking qualities","volume":"106","author":"Tian","year":"2009","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"283","DOI":"10.1093\/nsr\/nww006","article-title":"Breeding high-yield superior quality hybrid super rice by rational design","volume":"3","author":"Qian","year":"2016","journal-title":"Natl. Sci. Rev."},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"1297","DOI":"10.1111\/pbi.12228","article-title":"Modulation of amylose content by structure-based modification of OsGBSS1 activity in rice (Oryza sativa L.)","volume":"12","author":"Liu","year":"2014","journal-title":"Plant Biotechnol. J."},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"133","DOI":"10.1046\/j.1365-313X.1998.00189.x","article-title":"A naturally occurring functional allele of the rice waxy locus has a GT to TT mutation at the 5\u2032 splice site of the first intron","volume":"15","author":"Isshiki","year":"1998","journal-title":"Plant J."},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"1193","DOI":"10.1016\/S0168-9452(03)00326-1","article-title":"Duplicated coding sequence in the waxy allele of tropical glutinous rice (Oryza sativa L.)","volume":"165","author":"Wanchana","year":"2003","journal-title":"Plant Sci."},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"217","DOI":"10.1007\/s00122-007-0557-6","article-title":"A novel Wx mutation caused by insertion of a retrotransposon-like sequence in a glutinous cultivar of rice (Oryza sativa)","volume":"115","author":"Hori","year":"2007","journal-title":"Theor. Appl. Genet."},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"889","DOI":"10.1111\/jipb.13010","article-title":"A rare Waxy allele coordinately improves rice eating and cooking quality and grain transparency","volume":"63","author":"Zhang","year":"2021","journal-title":"J. Integr. Plant Biol."},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"878","DOI":"10.1111\/jipb.13011","article-title":"The origin of Wxla provides new insights into the improvement of grain quality in rice","volume":"63","author":"Zhou","year":"2021","journal-title":"J. Integr. Plant Biol."},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"613","DOI":"10.1046\/j.1365-313X.1995.7040613.x","article-title":"The amylose content in rice endosperm is related to the post-transcriptional regulation of the waxy gene","volume":"7","author":"Wang","year":"1995","journal-title":"Plant J."},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"131","DOI":"10.1270\/jsbbs.52.131","article-title":"Molecular characterization of Wx-mq, a novel mutant gene for low-amylose content in endosperm of rice (Oryza sativa L.)","volume":"52","author":"Satoh","year":"2002","journal-title":"Breed. Sci."},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"595","DOI":"10.1111\/pbr.12088","article-title":"Development of AS-PCR marker based on a key mutation confirmed by resequencing of Wx-mp in Milky Princess and its application in japonica soft rice (Oryza sativa L.) breeding","volume":"132","author":"Yang","year":"2013","journal-title":"Plant Breed."},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"609","DOI":"10.1007\/s11103-009-9544-4","article-title":"Identification and characterization of a novel Waxy allele from a Yunnan rice landrace","volume":"71","author":"Liu","year":"2009","journal-title":"Plant Mol. Biol."},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"979","DOI":"10.1007\/s00122-008-0729-z","article-title":"Allelic diversification at the Wx locus in landraces of Asian rice","volume":"116","author":"Mikami","year":"2008","journal-title":"Theor. Appl. Genet."},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"1157","DOI":"10.1016\/j.molp.2019.05.011","article-title":"Wxlv, the ancestral allele of rice waxy gene","volume":"12","author":"Zhang","year":"2019","journal-title":"Mol. Plant."},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"2164","DOI":"10.1111\/pbi.13391","article-title":"Creating novel Wx alleles with fine-tuned amylose levels and improved grain quality in rice by promoter editing using CRISPR\/Cas9 system","volume":"18","author":"Huang","year":"2020","journal-title":"Plant Biotechnol. J."},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"6219","DOI":"10.1093\/nar\/gkm685","article-title":"Differentiation of core promoter architecture between plants and mammals revealed by LDSS analysis","volume":"35","author":"Yamamoto","year":"2007","journal-title":"Nucleic Acids Res."},{"key":"ref_20","doi-asserted-by":"crossref","unstructured":"Yamamoto, Y.Y., Ichida, H., Matsui, M., Obokata, J., Sakurai, T., Satou, M., Seki, M., Shinozaki, K., and Abe, T. (2007). Identification of plant promoter constituents by analysis of local distribution of short sequences. BMC Genom., 8.","DOI":"10.1186\/1471-2164-8-67"},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"7040","DOI":"10.1038\/s41467-025-62087-0","article-title":"A transcription factor ensemble orchestrates bundle sheath expression in rice","volume":"16","author":"Hua","year":"2025","journal-title":"Nat. Commun."},{"key":"ref_22","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","year":"2021","journal-title":"Nat. Plants"},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"32","DOI":"10.4038\/tar.v29i1.8295","article-title":"In silico promoter analysis reveals rice Wx promoter could be a TATA-less promoter with a putative pyrimidine rich region","volume":"29","author":"Hemage","year":"2017","journal-title":"Trop. Agric. Res."},{"key":"ref_24","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":"Lemmon","year":"2017","journal-title":"Cell"},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"4349","DOI":"10.1093\/jxb\/erad175","article-title":"Promoter editing for the genetic improvement of crops","volume":"74","author":"Shi","year":"2023","journal-title":"J. Exp. Bot."},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"149","DOI":"10.1038\/s41586-019-1711-4","article-title":"Search-and-replace genome editing without double-strand breaks or donor DNA","volume":"576","author":"Anzalone","year":"2019","journal-title":"Nature"},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"3544","DOI":"10.1093\/jxb\/erad112","article-title":"Fine mapping of the grain chalkiness quantitative trait locus qCGP6 reveals the involvement of Wx in grain chalkiness formation","volume":"74","author":"Li","year":"2023","journal-title":"J. Exp. Bot."},{"key":"ref_28","doi-asserted-by":"crossref","unstructured":"Tang, W., Chen, H., Zhang, S., Tang, J., Lin, J., Fang, X., Chen, G., and Zhang, Y. (2024). A novel allele in the promoter of Wx decreases gene expression and confers lower apparent amylose contents in japonica rice (Oryza sativa L.). Plants, 13.","DOI":"10.3390\/plants13050745"},{"key":"ref_29","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","year":"2020","journal-title":"Nat. Biotechnol."},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"1278","DOI":"10.1111\/pce.14378","article-title":"Genetic architecture of seed glycerolipids in Asian cultivated rice","volume":"46","author":"Hong","year":"2022","journal-title":"Plant Cell Environ."},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"1046","DOI":"10.1016\/j.scib.2024.11.040","article-title":"Two major rice loci determine rice-staple food populations differences in vitamin B1 deficiency levels","volume":"70","author":"Li","year":"2025","journal-title":"Sci. Bull."},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"350","DOI":"10.1111\/j.1365-313X.2009.03958.x","article-title":"Heterogeneity of Arabidopsis core promoters revealed by high-density TSS analysis","volume":"60","author":"Yamamoto","year":"2009","journal-title":"Plant J."},{"key":"ref_33","first-page":"334","article-title":"A simplified assay for milled-rice amylose","volume":"16","author":"Juliano","year":"1971","journal-title":"Cereal Sci. Today"},{"key":"ref_34","doi-asserted-by":"crossref","unstructured":"Zhou, L., Cheung, M.Y., Li, M.W., Fu, Y., Sun, Z., Sun, S.M., and Lam, H.M. (2010). Rice hypersensitive induced reaction protein 1 (OsHIR1) associates with plasma membrane and triggers hypersensitive cell death. BMC Plant Biol., 10.","DOI":"10.1186\/1471-2229-10-290"}],"container-title":["International Journal of Molecular Sciences"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/1422-0067\/27\/18\/8386\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,9,22]],"date-time":"2026-09-22T16:34:15Z","timestamp":1790094855000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/1422-0067\/27\/18\/8386"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,9,20]]},"references-count":34,"journal-issue":{"issue":"18","published-online":{"date-parts":[[2026,9]]}},"alternative-id":["ijms27188386"],"URL":"https:\/\/doi.org\/10.3390\/ijms27188386","relation":{},"ISSN":["1422-0067"],"issn-type":[{"value":"1422-0067","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,9,20]]}}}