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However, the molecular mechanism and signaling pathways underlying this disorder remain largely unexplored. In this study, we identified a unique hybrid from a cross between Kiyomi (Citrus unshiu Marc \u00d7 Citrus sinensis Osbeck) and Egan No. 1 tangerine (Citrus reticulata Blanc.) that exhibits the juice sac granulation from the onset of fruit development. Compared to normal fruits, \u201cKS\u201d fruit exhibited significantly elevated levels of lignin and brassinolide (BR). Through resequencing and transcriptome analyses, we identified 4-Coumarate CoA ligase 1-like\u03b1 (Ci4CL1-like\u03b1) as a key gene involved in lignin biosynthesis. Notably, a single nucleotide polymorphism (SNP, A\/T) in the promoter region of Ci4CL1-like\u03b1 between KS (carrying T) and normal (carrying A) allowed the former to be successfully targeted and positively regulated by CiMYB306. In addition, both CiMYB306 and Ci4CL1-like\u03b1 were positively regulated by CiNAC9 through interacting with the NARC motifs in a BR-inducible way. Genetic evidences confirmed that CiMYB306 and CiNAC9 regulated lignin biosynthesis in a Ci4CL1-like\u03b1-dependent manner. Taken together, our findings reveal that the mutation of A into T in the promoter of Ci4CL1-like\u03b1 creates a binding site recognized and positively activated by CiMYB306, which acts in synergy with CiNAC9 in a BR-responsive way, leading to enhanced lignin synthesis and fruit granulation. These findings gain valuable insight into the BR-mediated transcriptional regulatory module involved in fruit granulation and unravel potential targets for mitigating this disorder.<\/jats:p>","DOI":"10.1093\/plcell\/koag276","type":"journal-article","created":{"date-parts":[[2026,9,11]],"date-time":"2026-09-11T11:47:48Z","timestamp":1789127268000},"source":"Crossref","is-referenced-by-count":0,"title":["A single nucleotide polymorphism in the\n                    <i>4-Coumarate CoA ligase 1-like\u03b1<\/i>\n                    promoter induces juice sac granulation by promoting brassinolide-mediated lignin synthesis in citrus"],"prefix":"10.1093","volume":"38","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-4158-6015","authenticated-orcid":false,"given":"Lele","family":"Chu","sequence":"first","affiliation":[{"name":"National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, College of Horticulture and Forestry Science, Huazhong Agricultural University , 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Huazhong Agricultural University , No. 1 Shizishan Street, Wuhan, Hubei 430070 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0000-3302-9262","authenticated-orcid":false,"given":"Wenqiang","family":"Hu","sequence":"additional","affiliation":[{"name":"National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, College of Horticulture and Forestry Science, Huazhong Agricultural University , No. 1 Shizishan Street, Wuhan, Hubei 430070 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0006-1925-7158","authenticated-orcid":false,"given":"Ligang","family":"He","sequence":"additional","affiliation":[{"name":"Hubei Key Laboratory of Germplasm Innovation and Utilization of Fruit Trees, Research of Institute of Fruit and Tea, Hubei Academy of Agricultural Sciences , No. 10 Nanhu Avenue, Wuhan, Hubei 430064 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