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Issues Mol. Biol.","CIMB"],"abstract":"<jats:p>Leaf-color mutants are crucial for elucidating chlorophyll metabolism mechanisms. Here, we identified yel, a stably inherited rice mutant with a dwarf and yellow-green leaf phenotype controlled by a single recessive nuclear gene. Using BSA-seq, we mapped the candidate causal gene to OsMPEC, encoding a magnesium protoporphyrin IX monomethyl ester cyclase with a G\u2192T substitution. Multi-omics analysis revealed that the functional deficiency of OsMPEC protein\u2014despite unchanged transcript levels\u2014triggers global transcriptional repression of the chlorophyll metabolic network. This defect caused distinct metabolic consequences: impaired synthesis at the early stage (yel1) and toxic metabolite accumulation at the later stage (yel2). Furthermore, metabolic collapse induced systemic reprogramming of hormone signaling, shifting from pro-growth to stress and senescence modes. We propose that the yel phenotype is associated with a self-reinforcing inhibitory loop of \u201cpassive synthesis inhibition\u201d and \u201cactive degradation acceleration.\u201d This study clarifies OsMPEC\u2019s role in chlorophyll homeostasis and demonstrates how a single genetic defect drives phenotype- through to network-level cascading effects.<\/jats:p>","DOI":"10.3390\/cimb48080848","type":"journal-article","created":{"date-parts":[[2026,8,20]],"date-time":"2026-08-20T16:05:19Z","timestamp":1787241919000},"page":"848","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Integrative Multi-Omics Analysis Reveals Systemic Transcriptional and Hormonal Reprogramming Associated with a Rice Yellow-Green Leaf Mutant"],"prefix":"10.3390","volume":"48","author":[{"given":"Guang","family":"Li","sequence":"first","affiliation":[{"name":"College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang 524088, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jiawei","family":"Liu","sequence":"additional","affiliation":[{"name":"College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang 524088, China"},{"name":"College of Agriculture, South China Agricultural University, Guangzhou 510642, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xiao","family":"Yang","sequence":"additional","affiliation":[{"name":"College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang 524088, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mangu","family":"Hu","sequence":"additional","affiliation":[{"name":"College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang 524088, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yongxiang","family":"Huang","sequence":"additional","affiliation":[{"name":"College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang 524088, China"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2026,8,20]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"363","DOI":"10.1016\/j.tplants.2011.03.004","article-title":"Agricultural biotechnology for crop improvement in a variable climate: Hope or hype?","volume":"16","author":"Varshney","year":"2011","journal-title":"Trends Plant Sci."},{"key":"ref_2","doi-asserted-by":"crossref","unstructured":"Yu, K., Wang, J., Sun, C., Liu, X., Xu, H., Yang, Y., Dong, L., and Zhang, D. 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