Fruit acidity, a key quality trait, is primarily determined by malic acid in many fruit crops. However, the molecular machinery governing its accumulation, particularly in response to hormonal cues like auxin, remains a "black box." Here, we systematically deconstruct the regulatory pathway controlling malic acid in litchi (Litchi chinensis). We first identify the tonoplast-localized transporter LcALMT1 as the principal channel for malate sequestration into the vacuole. We then uncover its upstream regulatory module, revealing that the R2R3-MYB transcription factor LcMYB70 directly binds the LcALMT1 promoter but lacks intrinsic transcriptional activity. Instead, LcMYB70 functions as a molecular scaffold to recruit the Auxin Response Factor LcARF10, which confers transcriptional repression upon the complex. This LcMYB70-LcARF10 repressor module is negatively regulated by auxin signaling, providing a direct molecular link between the decline in endogenous auxin during fruit maturation and the attenuation of malate accumulation. Critically, we identified a single-nucleotide polymorphism in the LcARF10 gene that governs the divergence between high- and low-acid cultivars. The functional C allele in low-acid cultivars enables the formation of the repressor complex. In contrast, the T allele in high-acid cultivars contains a premature stop codon that results in a non-functional, truncated protein, preventing complex assembly and causing the high-acid phenotype. Our study defines a complete pathway from hormone to trait and its genetic basis, revealing a novel MYB-ARF scaffold module; a definitive molecular link between auxin withdrawal and metabolic reprogramming; and the functional integrity of a corepressor as a new paradigm for trait diversification.

Low-temperature stress (LTS) inhibits the growth and yield of pitaya. HuBBX1, a cold-tolerance transcription factor, was identified based on the physiological and transcriptomic analyses between two pitaya cultivars. HuBBX1 enhances plant cold tolerance via the activation of cold-regulated (COR) genes. Low-temperature stress (LTS) affects fruit quality and yields. Pitaya plants are sensitive to LTS; however, the molecular mechanisms underlying LTS in pitaya remain poorly understood. In this study, the chlorophyll fluorescence, photosynthetic system, cold tolerance-associated physiological indexes, and differentially expressed genes (DEGs) were compared using two pitaya cultivars, i.e., ‘SCAU-NH’ (resistant to low temperature) and ‘SCAU-KX’ (sensitive to low temperature) at the LTS. Six candidate transcription factors (TFs) related to LTS were identified according to their expression profiles. Yeast growth assay and GUS activity analysis showed that HubZIP6, HuOFP12, HuBBX1, HuHY5, HuBOA1, and HuERF39 could enhance cold resistance. Among them, HuBBX1 is a nuclear protein with transcriptional activation capability. Overexpression of HuBBX1 enhanced cold tolerance in Arabidopsis thaliana and tomato. Dual-luciferase reporter assays (DLR), yeast one hybrid (Y1H), and EMSA showed that HuBBX1 promotes the expression of cold-regulated (COR) genes (HuCOR15A and HuRD29A) by directly bounding to the G-box in their promoters to increase plant cold tolerance. The present work provides a foundation for further study of the molecular mechanisms of pitaya’s response to LTS.

Organ abscission is a core developmental process that allows plants to optimize resource allocation, maximize reproductive fitness, and respond to environmental cues. In agricultural systems, however, premature fruit abscission can severely reduce yield. Here, we investigate premature fruit drop in litchi and identify the hexokinase homolog LcHXK1 as a nonglycolytic hexose sensor that suppresses abscission by activating a pedicel lignification program. LcHXK1 physically associates with and phosphorylates the WRKY transcription factor LcWRKY42, a modification that enhances its stability and transcriptional activity in inducing laccase and peroxidase genes required for lignin polymerization, promoting lignin deposition and reinforcing the pedicel to prevent organ detachment. Over expression of LcHXK1 or LcWRKY42 in litchi callus and in Arabidopsis elevates lignin content, increases laccase and peroxidase activities, and delays organ abscission, revealing a conserved sugar-responsive pathway. LcWRKY42 also upregulates LcHXK1, forming a positive feedback loop that amplifies hexose signaling. Together, these findings define a sugar-sensing regulatory module that couples carbon status to pedicel lignification, providing a mechanistic framework for improving fruit retention in crops.

Wampee (Clausena lansium) is a tropical and southern subtropical fruit tree whose productivity is limited by low-temperature stress (LTS). This study investigated the physiochemical and ‌molecular mechanisms by which melatonin (MLT) enhances chilling tolerance in wampee. MLT treatment improved membrane stability and reduced oxidative damage by enhancing antioxidant capacity and osmotic adjustment. Metabolomic and transcriptomic analyses revealed that differentially expressed genes and metabolites were primarily associated with flavonoid biosynthesis and starch and sucrose metabolism pathways. Eleven key candidate genes were identified, including sucrose synthase, granule-bound starch synthase, trehalose-6-phosphate synthase, chalcone-flavonone isomerase, flavonoid 3',5'-hydroxylase, and UDP-glycosyltransferase. MLT treatment also increased soluble carbohydrate levels, such as sucrose and fructose, and enhanced sucrose phosphate synthase activity. Transcription factors ClbHLH2 and ClNAC1 enhanced wampee's cold tolerance by activating the sucrose-biosynthetic genes ClSUS2 and ClSPS1, respectively. These findings provide insights into the molecular and physiological mechanisms underlying wampee adaptation to LTS and highlight MLT as a potential tool to improve wampee's cold tolerance.

Longan (Dimocarpus longan Lour.) is highly sensitive to low temperature, which severely restricts its cultivation and industrial development. MYB transcription factors serve as key regulators in plant responses to cold stress. In this study, an R2R3-MYB gene DlMYB108 was cloned from ‘Shixia’ longan. Sequence analysis showed that DlMYB108 contains two typical MYB repeats and shares high homology with cold-responsive MYB108 proteins from other plants. Expression pattern analysis revealed that DlMYB108 is highly expressed in young leaves, which are more sensitive to cold stress, and is significantly induced by low-temperature treatment. Subcellular localization and transcriptional activation assays confirmed that DlMYB108 is a nuclear-localized transcriptional activator. Yeast one-hybrid and dual-luciferase assays demonstrated that DlMYB108 specifically binds to the promoters of DlCBF2 and DlCBF3 and activates their transcription. Heterologous expression of DlMYB108 in Arabidopsis significantly enhanced cold tolerance, accompanied by reduced ion leakage, malondialdehyde (MDA) content and reactive oxygen species (ROS) accumulation, as well as upregulated expression of CBF and cold-responsive genes. Collectively, DlMYB108 positively regulates longan cold tolerance through activating DlCBF2 and DlCBF3 expression, providing a valuable candidate gene for cold-tolerant longan breeding.

Cold stress severely limits the yield and quality of fruit crops, yet its regulatory mechanisms in pitaya remain poorly understood. Here, we identified a cold-inducible bZIP transcription factor, HubZIP6, that plays a central role in enhancing cold tolerance in pitaya. HubZIP6 is a nuclear-localized protein with transcriptional activation activity, and its overexpression in Arabidopsis and tomato significantly improved cold tolerance, as reflected by higher survival rates, reduced ion leakage, and lower reactive oxygen species accumulation. Mechanistically, HubZIP6 directly binds to ACGT motifs in the promoters of HuCBF1 and HuCBF3, thereby activating their expression under cold stress. In addition, HubZIP6 physically interacts with the salicylic acid-binding protein HuSABP2, which synergistically enhances the transcriptional activation of HuCBF genes. Notably, HubZIP6 also directly activates HuSABP2, forming a regulatory loop that connects CBF transcriptional control with salicylic acid signaling. Consistently, overexpression of HuSABP2 further enhances cold tolerance in transgenic plants. Collectively, these findings demonstrate that cold tolerance is enhanced through HubZIP6-mediated integration of CBF activation and salicylic acid signaling, providing a promising genetic target for improving stress resilience in fruit crops.

Seed abortion is a critical agronomic trait affecting both fruit quality and yield. Cell wall invertase (CWIN) hydrolyzes sucrose into glucose and fructose, which serve as both nutrients and signaling molecules to regulate seed development, with its activity suppressed by invertase inhibitor (INH). However, the transcriptional regulators controlling INH expression remain unknown. Here, we identify the MADS-box transcription factor LcMADS28 as a direct activator of LcINH1. LcMADS28 is highly expressed in the funicle and embryo of the abortive-seeded cultivar 'Nuomici' at 15 days after anthesis, whereas its expression is much lower in the big-seeded cultivar 'Heiye'. Further analysis reveals that LcMADS28 interacts with LcMADS27 to form a heterodimer that directly binds to the LcINH1 promoter and activates its transcription. Silencing LcMADS28 in 'Nuomici' reduces LcINH1 expression, which increases CWIN activity, promotes embryo and seed development, and lowers fruit abscission. RNA-seq analysis indicates that genes associated with auxin and sucrose metabolism are activated after LcMADS28 silencing. In addition, heterologous overexpression of LcMADS28 in tomato and Arabidopsis increases seed abortion. Together, our results indicate that LcMADS28 and LcMADS27 coordinately activate LcINH1 to regulate early seed development in lychee and provide a mechanistic framework linking MADS-box transcription factors with the invertase/INH module.

Fruit quality in wampee is strongly influenced by the accumulation of key metabolites, including anthocyanins, sugars, and organic acids, yet their metabolic dynamics during fruit development remain poorly understood. In this study, we analyzed metabolite profiles and the expression of metabolism-related genes in the pulps of two wampee cultivars, “Jixin” (JX) and “Zirou” (ZR), across multiple fruit developmental stages. Two anthocyanins, 17 sugars, and 32 organic acids were identified. Total phenolics, flavonoids, starch, and soluble sugars accumulated mainly during early fruit development. “JX” wampee exhibited higher ascorbic acid levels than “ZR” wampee. Sucrose and citric acid were the predominant sugars and organic acids in both cultivars. Transcriptomic analysis revealed 37 anthocyanin-related, 29 sugar-related, and 18 organic acid-related genes. Strong correlations between candidate gene expression and metabolite levels suggest that these genes play key roles in regulating the biosynthesis and accumulation of anthocyanins, sugars, and organic acids in wampee.

Wampee (Clausena lansium), a tropical evergreen fruit from the Rutaceae family renowned for its rich nutrient profile and bioactive compounds, presents a fascinating case study in fruit coloration. However, changes in anthocyanins, and expressions of metabolism-associated genes during fruit maturation of red-pericarp wampee ('ZR') are not documented. In this study, metabolic and gene expression profiles of anthocyanin across different fruit developmental stages of red and yellow-pericarp wampees were analyzed. A total of 38 distinct anthocyanins were identified from the comparison of 'ZR3' and 'JX3' wampees and categorized into 17 differential anthocyanin metabolites (DAMs). Among these DAMs, fifteen were up-regulated in 'ZR3', while two were down-regulated compared with 'JX3'. The delphinidin 3-[6-(4-(caffeoylrhamnosyl)glucoside)] was the predominant anthocyanins in 'ZR' wampee. A total of 1135 metabolics mainly including amino acid metabolites and flavonoids were detected in the 'ZR' and 'JX' wampees. Significant differences were mainly concentrated in the biosynthesis of secondary metabolites in terms of flavonoid biosynthesis, ABC transporters, and anthocyanin biosynthesis. According to the combined analyses of qRT-PCR and transcriptome, the transcript levels of PAL1, PAL2, CHS1 and UFGT1 in 'ZR' wampee were two to eight-fold higher than those in 'JX' wampee during fruit pigmentation. Our study offers valuable insights into the mechanisms of anthocyanin accumulation in the red pericarp of wampee which is helpful to regulate fruit coloration of wampee.

Litchi chinensis Sonn. is an important economic fruit tree in tropical and subtropical regions. Regrettably, the efficiency of plant regeneration via somatic embryogenesis in litchi is typically low due to the poor conversion of embryos to plants. The purpose of this study was to establish a regeneration system via somatic embryogenesis from immature embryos explants in 'Heiye' cultivar of litchi. Our results demonstrated that MS medium supplemented with 2.0 mg L-1 2,4-D was optimal for callus induction. For somatic embryo (SE) induction, MS medium containing 0.5 g L-1 activated charcoal (AC) was the most effective, while the use of zeatin (ZT) and thidiazuron (TDZ) resulted in abnormal somatic embryos. The rooting and regeneration rate of 2.15% and 17.5%, respectively, were achieved using MS medium supplemented with 0.5 g L-1 AC. Furthermore, transcriptome analysis was performed on embryogenic callus (EC), globular embryo (GE), and heart embryo (HE) to explore the molecular mechanisms of early somatic embryogenesis. 2,587 common differentially expressed genes (DEGs) between EC_vs_GE and EC_vs_HE were identified, and the expression patterns of these common DEGs were separated into twelve major clusters. GO annotation and KEGG pathway analysis revealed that these common DEGs were implicated in plant hormone signal transduction, auxin-activated signaling pathway, and other biological processes. Additionally, differentially expressed transcription factors were identified, and the function of LcBBM2 which is specifically highly expressed during early somatic embryogenesis was verified. Overexpression of LcBBM2 in tomato promotes callus and shoot formation. Therefore, this study can provide a theoretical basis and technical support for genetic breeding improvement of litchi.

Basic helix-loop-helix (bHLH) proteins have been recognized as activators of anthocyanin in many plant species, but their role as inhibitors of anthocyanin is seldom reported. In this study, LcbHLH107 was identified as a transcription repressor regulating anthocyanin biosynthesis in litchi. LcbHLH107 was up-regulated in the red hairy roots overexpressing LcMYB1, which was the key transcription activator in litchi anthocyanin biosynthesis. Dual luciferase assay and yeast one-hybrid assay confirmed that LcbHLH107 was regulated by LcMYB1. LcbHLH107 could suppresses anthocyanin accumulation through transient transformation in petunia leaves and overexpression in litchi callus. Moreover, LcbHLH107 directly bound to the promoter of LcDFR, and inhibited its expression. Furthermore, protein sequence mutation and functional verification revealed that the EAR motif was essential for the inhibitory function of LcbHLH107. In summary, LcbHLH107 is a repressor that inhibits anthocyanin biosynthesis in litchi, providing a negative feedback mechanism to regulate anthocyanin accumulation at transcriptional level.

Pitaya is an important perennial herbaceous fruit tree. The color of fruit determines pitaya nutritive (and attractive) value, which is considered as an important objective in breeding improvement. In this study, we reported the first telomere-to-telomere (T2T) gap-free genome of "Shuangse No. 1" pitaya (Hylocereus polyrhizus; red peel). Two high-quality genomes for "Dahong" (H. polyrhizus; red peel) and "Honghuaqinglong" (H. stenopterus; stay-green) were further assembled, aiming to explore the genetic diversity of pitaya genomes. In further analysis, we noticed a high proportion of viral contamination in pitaya tissues, which hindered the efficient utilization of transcriptomic data. To address this issue, we analyzed 111 pitaya transcriptome data from different geographic regions to characterize and separate viral components. Then we developed an efficient, novel, and universal transcript purification system for pitaya transcriptomes by applying it to 27 samples from different tissues and species, thereby enhancing the utility for transcriptomic and broader biological research. Combining the purified transcriptomic data with comparative genomic analyses, we identified HuERF72, a transcription factor (TF) that potentially regulates chlorophyll degradation in pitaya. Interaction assays and plant transformation elucidated that HuERF72 acts as a repressive TF by directly binding to the promoter of HuSGR1, a key structural gene in the chlorophyll degradation pathway. This study provides high-quality genomic resources and novel methodologies for molecular investigations in pitaya. Additionally, the proposed regulatory network advances our understanding of the transcriptional regulatory mechanisms underlying chlorophyll degradation, offering valuable insights into the genetic improvement of pitaya.

Pitaya canker disease, caused by Neoscytalidium dimidiatum, is the primary threat to pitaya cultivation, significantly compromising fruit quality and reducing yield. WRKY transcription factors are essential regulators in plant pathogen recognition and defense mechanisms, yet their specific roles in the development of pitaya canker disease remain largely unexplored. In this study, five genes (HmeWRKY33, HmeWRKY51, HmePR1, HmeHsp70, and HmeSERK) associated with pitaya canker disease were identified through RNA-Seq analysis. The expression levels of HmeWRKY33 and HmeWRKY51 were upregulated following N. dimidiatum infection. Transient transformation revealed that these five genes negatively influenced the resistance of Nicotiana benthamiana leaves to canker disease while promoting the accumulation of reactive oxygen species and inducing cell death. Yeast one-hybrid and dual luciferase reporter assays revealed that HmeWRKY33 directly activated the expression of HmeSERK, while HmeWRKY51 directly inhibited the expression of HmePR1 and HmeHsp70, coparticipating in regulating the susceptibility of 'Youcihuanglong' pitaya to canker. These findings provide a theoretical basis for breeding new canker-resistant pitaya varieties through genetic transformation.

Glycosylation of anthocyanin plays an important role in increasing its stability and diversity in plants. Here, we identified a glucosyltransferase gene responsible for the anthocyanin components in Litchi chinensis Sonn. Cyanidin-3-rutinoside is the main anthocyanins of pericarps and red hairy roots overexpressing MYB transcription factor LcMYB1 in the late maturing cultivars. However, in the early maturing cultivars, the anthocyanins in the pericarps is dominated by cyanidin-3-glucoside, and the anthocyanins in the red hairy roots overexpressing LcMYB1 is dominated by cyanidin-3-rutinoside. Enzyme assays highlighted notable differences in flavonoid 3-O-rhamnosyltransferase (F3RT) activity between the pericarps and red hairy roots overexpressing LcMYB1 in the early maturing cultivars. Two differentially expressed genes (DEGs), LcF3RT1 and LcF3RT2, were significantly up-regulated in the red hairy roots overexpressing LcMYB1. Yeast one-hybrid and dual luciferase reporter assays revealed that LcMYB1 could bind to the promoter of LcF3RT2 and significantly activate its expression. Functional validation showed that LcF3RT2 could catalyze the conversion of cyanidin-3-glucoside into cyanidin-3-rutinoside, leading to the differences on anthocyanin components in pericarps and red hairy roots of early maturing litchi cultivars. Our results will provide insights into the regulation and glycosylation modification of anthocyanins in litchi as well as in other plants.

Polyploidy in plants can enhance stress resistance and secondary metabolite production, offering potential benefits for Clausena lansium (L.) Skeel, a medicinally valuable species. However, systematic studies of polyploidy-induced morphological, anatomical, and metabolic changes in this species are lacking. This study aimed to induce and characterize polyploid C. lansium lines, assess ploidy-dependent variations, and evaluate their impact on bioactive metabolite accumulation. Three cultivars were hybridized, treated with colchicine, and bred, yielding 13 stable polyploid lines confirmed by flow cytometry and chromosome counting. The polyploids exhibited distinct traits, including larger pollen grains, altered leaf margins, increased leaflet numbers, enlarged guard cells with reduced stomatal density, and thicker leaf tissues. Metabolomic analysis revealed that tetraploids accumulated significantly higher levels of flavonoids, alkaloids, and phenolic acids compared to diploids, while triploids showed moderate increases. These findings demonstrate that polyploidization, particularly tetraploidy, enhances C. lansium’s medicinal potential by boosting pharmacologically active compounds. The study expands germplasm resources and supports the development of high-quality cultivars for pharmaceutical applications.

Fruit size is an important quantitative trait that directly affects yield and quality. However, fruits are generally small in the current main litchi cultivars, which seriously influence yield. In this study, we characterized the fruit phenotype and histology of large-fruited cultivars 'Ziniangxi' (ZNX) and 'Hehuadahongli' (HHDHL) and smallfruited cultivars 'Chenzi' (CZ) and 'Guiwei' (GW) at different developmental stages. Large-fruited cultivars (ZNX and HHDHL) had greater pericarp weight and thickness, aril weight, aril cell size, seed weight, and seed cell size compared to small-fruited cultivars (CZ and GW). ZNX had the largest single fruit weight at maturity, while CZ had the smallest fruit size. Then, the pericarps, arils, seeds, and the early developing fruits of CZ and ZNX at different developmental stages were used for transcriptome sequencing to unravel the mechanism underlying fruit size in litchi. A total of 21,672 DEGs were identified by pairwise comparisons of young fruits, pericarp, aril, and seeds at each developmental stage between CZ and ZNX cultivars. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis revealed that numerous genes associated with cytokinin, auxin, gibberellin and brassinosteroid exhibited differential expression between large- and smallfruited litchi cultivars, such as LcBEH2, LcIPT, LcGH3.1, LcCYP72A219. These results provide a theoretical basis for the regulation of fruit size in litchi breeding.

Soluble sugar is an important factor in determining fruit quality and flavor. In this study, the sugar accumulation mechanisms in wampee (Clausena lansium) fruits were investigated by using two cultivars-'Huami' (sweet) and 'Jinjixin' (sweet and sour)-at five developmental stages. Transcriptome analysis revealed a strong correlation between ClSWEET3a expression and total soluble sugar/sucrose content. Functional characterization demonstrated that ClSWEET3a, a plasma membrane-localized transporter, facilitates glucose and sucrose uptake in yeast. Silencing of ClSWEET3a in 'Jinjixin' fruits significantly decreased both sucrose and hexose levels, confirming its role in sugar accumulation. Furthermore, we identified two transcription factors (ClbZIP3 and ClERF062) that activate the ClSWEET3a promoter, with ClbZIP3 exhibiting stronger regulatory effects. Yeast one-hybrid assays confirmed their direct binding to the ClSWEET3a promoter. Our findings elucidate a molecular framework for sugar accumulation in wampee and provide insights for targeted breeding strategies to improve fruit quality.

It is essential to introduce new cultivars to diversify the pomelo industry in China. This paper compared the agronomic and environmental performances of new Tabtim Siam (TS) and Xishi (XS) pomelos with the local cultivars (Red-fleshed Sweet (RS) and Shatian (ST)) in Dabu County. We have generally evaluated the phenological, physiological, fruit quality, stress resistance, and storage characteristics. Findings indicated that TS and XS grew up well, and the phenological stages were adjusted to the local conditions. They had a high pollen viability and equivalent photosynthetic capacity. XS and TS had the highest yield and good fruit quality in terms of higher edible rates, more juice rate, and balanced sugar–acid content. Both the introduced cultivars had greater cold resistance compared with the control with lower semi-lethal temperatures. Polyethylene film at low temperatures to preserve the quality of storage was effective. Compared with RS and ST, TS and XS had a higher price in the market economically. The use of molecular markers (SCoT and SRAP) was able to discriminate all cultivars, which proved genetic uniqueness. In summary, TS and XS have potential to be grown in the Meizhou area and provide high quality, good adaptability, and greater market potential.

Flowering time and subsequent fruiting significantly influence the economic value of fruit trees. However, the regulatory mechanisms underlying the vegetative-to-reproductive transition remain understudied, particularly at single-cell and spatial levels. Here, we present a single-nucleus (snRNA-seq) and spatial transcriptomic (stRNA-seq) atlas of shoot apices in loquat (Eriobotrya japonica), a perennial fruit crop with both nutritional and medicinal importance. From the snRNA-seq dataset, 42,546 nuclei were profiled and resolved into 22 clusters corresponding to seven major cell types. Pseudotime analysis reconstructed developmental trajectories, revealing bifurcated lineages toward external and internal tissues, and identified genes dynamically associated with cell differentiation. Comparative analysis between the pre-initiation and onset stages of floral bud initiation uncovered 3,329 differentially expressed genes, including 67 homologs of Arabidopsis flowering-related genes, with the most pronounced transcriptional changes observed in epidermal and shoot meristematic cells, underscoring their central roles in floral initiation. Moreover, 43 key candidate genes, such as EjCRY2 and EjAGL79, associated with pseudotime branch points critical for cell fate decisions were predicted to act within a regulatory network dominated by photoperiod- and circadian rhythm-related pathways. Finally, integration with stRNA-seq demonstrated well concordance with snRNA-seq results and supported cell-type annotations particularly for epidermal and shoot meristematic cells. Collectively, the marker genes and associated datasets generated here provide a valuable resource for advancing single-cell and spatial transcriptomic research in loquat and potentially other fruit tree species. In addition, the identified candidate genes represent promising targets for in-depth functional studies and for breeding strategies aimed at manipulating flowering and fruiting time in loquat.

Litchi has great economic significance as a global fruit crop. However, the advancement of litchi functional genomics has encountered substantial obstacles due to its recalcitrance to stable transformation. Here, we present an efficacious Agrobacterium tumefaciens-mediated transformation system in somatic embryos of ‘Heiye’ litchi. This system was developed through the optimization of key variables encompassing explant selection, A. tumefaciens strain delineation, bacterium concentration, infection duration, and infection methodology. The subsequent validation of the transformation technique in litchi was realized through the ectopic expression of LcMYB1, resulting in the generation of transgenic calli. However, the differentiation of transgenic calli into somatic embryos encountered substantial challenges. To delineate the intricate molecular underpinnings of LcMYB1’s inhibitory role in somatic embryo induction, a comprehensive transcriptome analysis was conducted that encompassed embryogenic calli (C), globular embryos (G), and transgenic calli (TC). A total of 1,166 common differentially expressed genes (DEGs) were identified between C-vs.-G and C-vs.-TC. Gene Ontology (GO) annotation and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis revealed that these common DEGs were mostly related to plant hormone signal transduction pathways. Furthermore, RT-qPCR corroborated the pronounced down-regulation of numerous genes that are associated with somatic embryo induction within the transgenic calli. The development of this transformation system provides valuable support for functional genomics research in litchi.