Integrated metabolomics and transcriptomics reveal the tissue-specific distribution patterns and potential molecular mechanisms in flavonoids between Citrus reticulata ‘Shiyue Ju’ and its mutant C. reticulata ‘Denglong Ju’

Citrus reticulata ‘Shiyue Ju’ (STJ) and its mutant C. reticulata ‘Denglong Ju’ (DLJ) are characterized by distinct phenotypes and varying levels of nutritional components. Flavonoids, known for their significant bioactive properties in citrus, have not been systematically elucidated between these two cultivars. The present study employs comparative metabolomics to comprehensively analyze flavonoid profiles across STJ and DLJ tissues, revealing the identification of 129 flavonoid compounds predominantly represented by flavones, flavanones, and flavonols. 34 flavonoids were significantly accumulated in the peel of STJ, while another 39 flavonoids were notably enriched in the peel of DLJ. Our findings demonstrate that the distinct tissue-specific flavonoid profiles likely underpin the significant separation observed between STJ and DLJ. Transcriptomic analysis identified critical genes associated with flavonoid biosynthesis pathways: OMTs and UGTs. Notably, the intense pigmentation observed in the peel of DLJ appears to be linked to the pronounced upregulation of PAL and ANR genes. Additionally, the integration of transcriptomic and metabolomic datasets using weighted gene co-expression network analysis (WGCNA) revealed that two genes (LOC18034981 and LOC18037750) might play vital roles in the differential flavonoid production observed between STJ and DLJ. This study establishes a molecular foundation for elucidating the biosynthesis of flavonoids in these two citrus species while offering novel insights into enhancing citrus fruit quality as functional food resources.