Litchi is one of the ancient fruits that originated in China, renowned for its high nutrition and rich flavor, and Xianjinfeng (XJF) stands as one of the most notable varieties in terms of its flavor. Investigating the metabolic changes in taste compounds during fruit development offers deeper insights into the formation patterns of fruit quality. In this study, we conducted extensive metabonomic research on the accumulation patterns of taste compounds (carbohydrates, organic acids, and amino acids) across three developmental stages of XJF litchi. A total of 238 taste metabolites were detected. Cluster analysis and PCA revealed significant changes in metabolite composition and content across different stages, closely correlating with the developmental phase. The abundance of total taste metabolites in stage S1 was notably lower than stages S2 and S3. The total abundance of sugar continued to rise, yet monosaccharides and disaccharides exhibited distinct behaviors, highlighting the characteristic accumulation of reducing sugars. Most organic acids demonstrated a notable downward trend, whereas the abundance of most essential and flavor-contributing amino acids showed an upward trend. The number of DAMs across the three stages followed the trend of S1 vs. S3 > S1 vs. S2 > S2 vs. S3. KEGG functional annotation and enrichment revealed that amino acid biosynthesis, D-amino acid metabolism, 2-oxocarboxylic acid metabolism, glyoxylate and dicarboxylate metabolism, the pentose phosphate pathway, the tricarboxylic acid cycle, and carbon metabolism were the most significantly enriched primary metabolic pathways. More differential metabolites and metabolic pathways indicated that the critical stage from the green fruit stage to the color transition stage laid a solid foundation for litchi flavor. This experiment will offer valuable references for cultivation, breeding, processing, and consumption.

Litchi (Litchi chinensis Sonn.) is a highly valuable fruit crop that is widely grown in tropical and subtropical areas of the world. Studying its genetic diversity and population structure is critical for effective conservation and breeding programs. In this study, we developed 150 single-nucleotide polymorphism (SNP) markers that were evenly spaced across litchi genome and applied them to the evaluation of the genetic diversity of 84 litchi accessions, including old cultivars, modern cultivars, hybrids from known parents and wild accessions. Ninety-one SNP markers, showing high levels of polymorphism and high genotyping success rates, were used for further analysis. The newly developed SNP markers captured a relatively higher level of genetic diversity (He = 0.364) in litchi cultivars and could be successfully applied for the identification of synonymous cultivars and hybrids with close genetic backgrounds. Cluster analysis grouped all genotypes into three clusters that showed perfect association with their fruit maturation period, among which wild accessions clustered with their corresponding domesticated cultivars, and hybrids from different parent combinations showed different inheritance tendencies. Our study not only provided a set of efficient SNP markers for future genetic research, but also laid an important foundation for the conservation and genetic breeding of litchi.

Flower color variations have increasingly been recognized as playing an important role in the adaptation to UV-B radiation; however, the underlying mechanism is poorly understood in perennial fruit trees. Litchi is an important fruit tree, and extremely early maturing (EEM) and middle-to-late-maturing (MLM) cultivars that originated from regions with high and low UV-B radiation have dark brown and light yellow flower buds, respectively, while their hybrid early-maturing (EM) cultivars have an intermediate brown flower bud. This study comprehensively analyzed the metabolome and transcriptome of flower buds of litchi EEM, EM and MLM cultivars to explore the mechanism underlying flower color variation during the adaptation to UV-B radiation for the first time. Metabolomic analysis identified 72 flavonoids in litchi flower buds, among which a higher accumulation of flavonol glycosides was responsible for darker flower buds of EEM cultivars. And transcriptome analysis revealed key structural genes, including LcCHI, LcFLS and seven UGTs, together with two transcription factors (LcMYB12 and LcMYB111), which could be directly up-regulated by UV-B radiation, playing critical roles in regulating the differential accumulation of flavonol glycosides. These results provide new insights into the molecular mechanism underlying adaptation to UV-B radiation and provide a genetic basis for future breeding of stress-tolerant cultivars of litchi.

Flavonol synthase (FLS) is the crucial enzyme of the flavonol biosynthetic pathways, and its expression is tightly regulated in plants. In our previous study, two alleles of LcFLS, LcFLS-A and LcFLS-B, have been identified in litchi, with extremely early-maturing (EEM) cultivars only harboring LcFLS-A, while middle-to-late-maturing (MLM) cultivars only harbor LcFLS-B. Here, we overexpressed both LcFLS alleles in tobacco, and transgenic tobacco produced lighter-pink flowers and showed increased flavonol levels while it decreased anthocyanin levels compared to WT. Two allelic promoters of LcFLS were identified, with EEM cultivars only harboring proLcFLS-A, while MLM cultivars only harbor proLcFLS-B. One positive and three negative R2R3-MYB transcription regulators of LcFLS expression were identified, among which only positive regulator LcMYB111 showed a consistent expression pattern with LcFLS, which both have higher expression in EEM than that of MLM cultivars. LcMYB111 were further confirmed to specifically activate proLcFLS-A with MYB-binding element (MBE) while being unable to activate proLcFLS-B with mutated MBE (MBEm). LcHY5 were also identified and can interact with LcMYB111 to promote LcFLS expression. Our study elucidates the function of LcFLS and its differential regulation in different litchi cultivars for the first time.