Fruit acidity determines the organoleptic quality and nutritive value of most fruits. In litchi, although the organic acid composition of pulps is known, the molecular mechanisms and genes underlying variation in fruit acidity remain elusive. Herein, developing pulps of two contrasting litchi varieties, Huaizhi (HZ, low-acidity) and Boye_No.8 (B8, high-acidity), were subjected to metabolomics and transcriptomics, and the dynamic metabolome and transcriptional changes were determined. Measurements revealed that the dominant acidity-related organic acid in litchi pulps is malate, followed in low levels by citrate and tartrate. Variation in litchi pulps’ acidity is mainly associated with significant differences in malate and citrate metabolisms during fruit development. Malic acid content decreased by 91.43% and 72.28% during fruit ripening in HZ and B8, respectively. The content of citric acid increased significantly in B8, while in HZ it was reduced considerably. Differentially accumulated metabolites and differentially expressed genes analyses unveiled fumarate, succinate, 2-oxoglutarate, GABA (γ-aminobutyric acid), phosphoenolpyruvate, and citrate metabolisms as the key driving pathways of litchi fruits’ acidity variation. The drastic malate and citrate degradation in HZ was linked to higher induction of fumarate and GABA biosynthesis, respectively. Thirty candidate genes, including three key genes (LITCHI026501.m2, fumarase; LITCHI020148.m5, glutamate decarboxylase; and LITCHI003343.m3, glutamate dehydrogenase), were identified for functional studies toward genetic modulation of litchi fruit acidity. Our findings provide insights into the molecular basis of acidity variation in litchi and provide valuable resources for fruit quality improvement.

Litchi chinensis Sonn. is an economically and culturally significant fruit crop in China, valued for its distinctive flavor, which arises from the combined contributions of taste and aroma metabolites. While the accumulation of sugars, organic acids, and volatile terpenes in litchi has been extensively studied, the role of nitrogenous flavor compounds, particularly free amino acids (FAAs), remains poorly characterized across diverse germplasm. To address this gap, high-performance liquid chromatography (HPLC) was employed to quantify 20 free amino acids in the pulp of 148 distinct litchi germplasm accessions. Comprehensive statistical analyses, including non-parametric tests, correlation analysis, and hierarchical clustering, were performed to elucidate compositional variations. Alanine (Ala), glutamate (Glu), and γ-aminobutyric acid (GABA) were the most abundant FAAs, contributing strongly to sweetness and umami. FAA profiles differed significantly among genomic groups, and clustering analysis identified three major chemotypes: Glu-accumulating, GABA-accumulating, and Ala-accumulating types. This study provides the first large-scale survey of FAA diversity in litchi germplasm and establishes a foundation for selecting cultivars with desirable flavor attributes and for future genomic dissection of amino acid metabolism.

The late spring cold spell severely affects the growth of litchi flower buds. Melatonin, as a signaling molecule, can enhance the plant’s ability to resist abiotic stress by regulating multiple physiological processes. However, there are few studies on the function of melatonin in litchi under cold stress. In the present study, 100 μM of melatonin was selected based on the ABA content in litchi seedlings. To identify genes potentially involved in melatonin and cold stress conditions in litchi, four RNA-seq libraries of litchi leaves under melatonin and cold conditions were constructed. In total, 6.4–8.5 Gb of trimmed bases were generated in each library. Thirty-five genes were randomly selected for qRT-PCR analysis. The results showed a strong positive correlation between the data from qRT-PCR and RNA-seq. A total of 4590 differentially expressed genes (DEGs) were identified in the treatment of melatonin (1845) and melatonin in cold condition (2745). The expression of several genes belonging to starch and sucrose metabolism, plant hormones (auxin, ABA), MAPK, and alpha-linolenic acid metabolism pathways were differentially expressed. The enhanced carbohydrate metabolism might lead to litchi seedlings treated with melatonin to produce more metabolic energy. Abscisic acid can improve cold tolerance. Collectively, our results reveal that pretreatment with melatonin (100 μM) protects litchi seedlings from cold stress through plant hormones and carbohydrate metabolism and provides potential genes for future research.

Sugars function as essential signaling molecules and metabolic substrates in plant growth, development, yield formation, and fruit quality. The aril of litchi (Litchi chinensis Sonn.) accumulates high levels of hexoses, primarily glucose and fructose; however, the molecular mechanisms underlying this process remain poorly characterized. This study aimed to systematically identify the monosaccharide transporter (MST) gene family in litchi and elucidate its role in aril sugar accumulation. Through a comprehensive analysis of the litchi genome, we identified a total of 45 LcMST genes, which were classified into seven distinct subfamilies: STP, ERD6L, PLT, INT, pGlcT, TMT, and VGT. Analysis of gene structure and conserved motifs revealed notable conservation among members within the same subfamily. Collinearity and gene duplication analyses suggested that the LcMST family expanded through both tandem and whole-genome duplication events, a process primarily governed by purifying selection. Expression profiling across diverse tissues demonstrated that LcMST genes exhibit distinct tissue-specific expression patterns. During fruit development in the hexose-dominant cultivar ‘Tianshuili’, the expression of the tonoplast monosaccharide transporter gene LcTMT1 exhibited a significant positive correlation with the accumulation of fructose, glucose, and total sugars. Heterologous functional complementation assays in yeast confirmed the ability of LcTMT1 to transport both glucose and fructose. In conclusion, this study presents the first genome-wide identification and characterization of the MST gene family in litchi, and identifies LcTMT1 as a key contributor of hexose accumulation in the aril. These findings establish a foundation for elucidating the molecular mechanisms of sugar accumulation in litchi fruit and for guiding future genetic improvement of fruit quality.

Lychee (Litchi chinensis Sonn.) is a major subtropical fruit crop, yet the regulatory hierarchy underlying edible ratio (flesh weight/whole fruit weight, %) and juice yield (juice weight/whole fruit weight, %), the core processing-quality traits, remains unresolved. We phenotyped 301 accessions from ten origins under uniform conditions and used hierarchical regression to predict and evaluate edible ratio and juice yield based on structural and physiological fruit traits, thereby separating the contributions of structural constraints and physiological modulation. Both traits exhibited broad population variation and were significantly modulated by maturity stage, with late-maturing accessions outperforming early types. A strong positive correlation (r = 0.679, p < 0.001) supported the identification of “double-high” germplasm combining superior edible ratio and juice yield. Kernel ratio emerged as the dominant structural constraint on edible ratio (R² = 0.6699, p < 0.001), while the combined inedible fraction served as the basal limiting factor for juice yield (R² = 0.4262, p < 0.001). Critically, after controlling for structural variation, physiological traits contributed an independent 9.2% of explained variance (ΔR² = 0.092, p < 0.001). pH was identified as the primary positive physiological predictor (β = 0.322, p < 0.001), whereas soluble solids content (SSC) exhibited a weak negative effect (β = −0.064, p = 0.008), indicating that high sugar content is not a priority target for processing-oriented breeding. An Integrated Ideotype Score (IIS) was constructed to objectively rank germplasm; elite accessions including ‘10_269’, ‘Yujinqiu’ and ‘Nuomici’ combined edible ratio > 75% with juice yield > 40%. These findings establish a “structural constraint-physiological modulation” two-tier regulatory hierarchy for lychee processing quality and provide a multivariate framework for germplasm evaluation and breeding selection.