Linking genetic and chemical diversity in mandarin germplasm: Implications for taxonomy and Huanglongbing resistance breeding

Huanglongbing (HLB) is a devastating disease threating global citrus production, yet the role of intraspecific metabolic and genetic diversity in host resistance breeding remains largely unexplored. This study conducted a breeding-oriented evaluation of 216 mandarin ( Citrus reticulata ) accessions by integrating leaf volatile profiling and start codon targeted (SCoT) polymorphism genotyping. Leaf volatile profiling identified 121 metabolites, predominantly monoterpenes (14.9–94.9%) and sesquiterpenes (0.5–75.8%). Total volatile content varied up to 12.5-fold among cultivars, with the hybrid Calamondin exhibiting a distinctive sesquiterpene-rich chemotype dominated by germacrene D (75.8%). Multivariate analyses distinguished mandarin groups and highlighted thymol methyl ether (4.8–9.5%) as a potential antimicrobial biomarker associated with HLB tolerance. SCoT markers revealed high genetic diversity (82.1% polymorphism), and a significant correlation between genotype and metabolite profiles was observed (Mantel test: R = 0.314, P < 0.0001). Multiple regression identified specific SCoT loci (e.g., Sp14–1) significantly associated with key volatiles, providing potential targets for marker-assisted selection. Our work establishes a transferable dual-omics framework that not only advances understanding of mandarin biodiversity but also provides a directly applicable strategy for accelerating the development of HLB-resistant cultivars, with significant implications for sustainable citrus production worldwide.