Graft incompatibility remains a significant challenge to the sustainable development of the longan (Dimocarpus longan Lour.) industry, yet the physiological mechanisms associated with scion genotype divergence are not fully understood. This study examined the effects of scion genotype on rootstock–scion interactions using the main cultivar ‘Shixia’ as rootstock. Two scion genotypes from an F1 population of ‘Dawuyuan’ × ‘Shuguan’ were selected: one compatible (DS237) and one incompatible (DS297). Leaf anatomy, photosynthetic physiology, and mineral element composition were analyzed to assess differences in leaf functionality between these two genotypes. The incompatible scion genotype (DS297) showed a trend toward lower potassium and higher magnesium concentrations; however, individual ion comparisons did not remain significant after FDR correction, whereas the K/Mg ratio was significantly altered in both scion and rootstock, being lower in the incompatible scion but higher in the incompatible rootstock. Anatomical analysis revealed reductions in cambium thickness, phloem thickness, vessel diameter, and vessel density in incompatible grafts, as well as thinner upper epidermis and palisade tissue. These structural differences may be associated with altered bidirectional transport. The observed changes may contribute to decreased photoassimilate export and qualitatively assessed starch accumulation in mesophyll cells, and may further contribute to the decline in leaf photosynthetic performance. These findings raise the possibility that mineral-associated developmental defects may be associated with scion genetic composition in this specific longan scion–rootstock combination. However, these findings are based on one compatible and one incompatible genotype on a single rootstock without self-grafted controls or histological evidence from the graft union itself, and should therefore be considered preliminary pending confirmation in additional genotype pairs and direct functional measurements.

The rapid accumulation of genome-scale data has transformed plant biology from descriptive genetics to predictive and increasingly mechanistic genomics. Longan (Dimocarpus longan Lour.) is an economically important subtropical fruit tree in China and Southeast Asia, but compared with model plants and major temperate fruit crops, its genomic resources and functional studies have developed relatively late. Here, we review recent progress in longan genomics with emphasis on three interrelated areas: genome assembly and annotation, transcriptomic resources, and representative gene family studies associated with flowering, somatic embryogenesis, and transporter-mediated stress tolerance. The progression from the first draft genome of ‘Honghezi’ to the chromosome-scale assemblies of ‘Jidanben’ and ‘Shixia’ has substantially improved contiguity and gene annotation, thereby enabling population-genomic analysis, genome-wide gene family identification, and candidate-gene discovery. Available transcriptomic datasets further support studies of reproductive development, stress responses, and embryogenic competence, although cross-study integration remains limited. We also summarize how gene family analyses have advanced the current understanding of floral induction, continuous flowering, somatic embryogenesis, mineral transport, and sugar transport in longan. Importantly, the field is still dominated by cataloguing and expression-based inference, whereas causal validation, pan-genomic analysis, and multi-omics integration remain insufficient. We therefore argue that future progress in longan molecular breeding will depend on integrating high-quality genomic resources with functional validation, standardized comparative annotation, and improved transformation or regeneration systems.