Integrated Transcriptomic and Metabolomic Analysis of OsMRS2-6 in Rice Growth and Chloroplast Traits

Background/Objectives: OsMRS2-6 is a member of the MRS2/MGT family, but its relationship with chloroplast status and growth and development in rice remains incompletely understood. Methods: In this study, we generated OsMRS2-6 knockout and overexpression lines and combined transient subcellular localization, chloroplast ultrastructural analysis, plastid gene-expression profiling, transcriptomics and metabolomics to investigate the biological functions of OsMRS2-6. Results: OsMRS2-6 was localized to chloroplasts and was preferentially expressed in mature flag leaves. Loss of OsMRS2-6 was associated with reduced seedling growth, plant dwarfing, disorganized thylakoid structures and increased plastoglobule abundance. In addition, OsMRS2-6 knockout altered the editing efficiency of eight chloroplast RNA-editing sites and disrupted the expression of genes associated with NADH dehydrogenase-like complexes, photosystems and chloroplast ribosomes. By contrast, OsMRS2-6 overexpression was associated with earlier heading and increased bleaching of panicle tissues. Transcriptomic and metabolomic analyses identified 691 shared differentially expressed genes and 270 shared differential metabolites in the knockout-versus-wild-type and overexpression-versus-wild-type comparisons, respectively. Integrated analysis further identified 11 pathways jointly involving genes and metabolites, mainly related to sugar metabolism, energy production, amino-acid turnover, antioxidant metabolism and secondary metabolism. Conclusions: Together, these findings extend previous knowledge of OsMRS2-6/OsMGT3 beyond its reported roles in chloroplast Mg²⁺ uptake and photosynthetic regulation by associating altered OsMRS2-6 expression with chloroplast ultrastructure, plastid RNA editing, reproductive-stage phenotypes and coordinated transcriptomic and metabolomic responses in rice.