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Lychee is an exotic tropical fruit with a distinct flavor. The genome of cultivar ‘Feizixiao’ was assembled into 15 pseudochromosomes, totaling ~470 Mb. High heterozygosity (2.27%) resulted in two complete haplotypic assemblies. A total of 13,517 allelic genes (42.4%) were differentially expressed in diverse tissues. Analyses of 72 resequenced lychee accessions revealed two independent domestication events. The extremely early maturing cultivars preferentially aligned to one haplotype were domesticated from a wild population in Yunnan, whereas the late-maturing cultivars that mapped mostly to the second haplotype were domesticated independently from a wild population in Hainan. Early maturing cultivars were probably developed in Guangdong via hybridization between extremely early maturing cultivar and late-maturing cultivar individuals. Variable deletions of a 3.7 kb region encompassed by a pair of CONSTANS -like genes probably regulate fruit maturation differences among lychee cultivars. These genomic resources provide insights into the natural history of lychee domestication and will accelerate the improvement of lychee and related crops. Two divergent haplotypes from a highly heterozygous lychee genome of the cultivar ‘Feizixiao’ and resequencing of 72 lychee accessions provide insights into the genome evolution and domestication history of lychee.

Grafting is a prevalent horticultural technique that enhances crop yields and stress resilience; nevertheless, compatibility issues frequently constrain its efficacy. This research examined the physiological, hormonal, and transcriptional factors regulating compatibility between the litchi (Litchi chinensis Sonn.) cultivars Feizixiao (FZX) and Ziniangxi (ZNX). The anatomical and growth investigations demonstrated significant disparities between compatible (FZX as scion and ZNX as rootstock) and incompatible (ZNX as scion and FZX as rootstock) grafts, with the latter showing reduced levels of indole acetic acid (IAA). Exogenous 1-naphthalene acetic acid (NAA) application markedly improved the graft survival, shoot development, and hormonal synergy, whereas the auxin inhibitor tri-iodobenzoic acid (TIBA) diminished these parameters. The incompatible grafts showed downregulation of auxin transporter genes, including ATP-binding cassette (ABC) transporter, AUXIN1/LIKE AUX1 (AUX/LAX), and PIN-FORMED (PIN) genes, suggesting impaired vascular tissue growth. Metabolomic profiling revealed dynamic interactions between auxin, salicylic acid, and jasmonic acid, with NAA-treated grafts exhibiting enhanced levels of stress-responsive metabolites. Transcriptome sequencing identified differentially expressed genes (DEGs) linked to auxin signaling (ARF, GH3), seven additional phytohormones, secondary metabolism (terpenoids, anthocyanins, and phenylpropanoids), and ABC transporters. Gene ontology and KEGG analyses highlighted the significance of hormone interactions and the biosynthesis of secondary metabolites in successful grafting. qRT-PCR validation substantiated the veracity of the transcriptome data, emphasizing the significance of auxin transport and signaling in effective graft development. This study provides an in-depth review of the molecular and physiological factors influencing litchi grafting. These findings provide critical insights for enhancing graft success rates in agricultural operations via targeted hormonal and genetic approaches.

Climate variability has increasingly disrupted the natural vegetative dormancy of litchi ( Litchi chinensis ), negatively impacting flowering, fruit set, and quality. This study evaluates the combined effect of paclobutrazol (PBZ) and micronutrients (Zinc Sulphate and Boric Acid) on the physical and biochemical quality of litchi fruits in a subtropical agro-climatic region. A factorial randomized block design was employed on 20-year-old litchi trees (cv. Dehradun) with 27 treatment combinations. Results revealed that PBZ @ 50 ppm followed by ZnSO 4 @ 1.0% significantly improved fruit length, weight, pulp percentage, and juice content. The same treatment also enhanced reducing sugars, total soluble solids (TSS), and ascorbic acid content, while optimizing the TSS: acid ratio. Zinc’s role as a cofactor in carbohydrate metabolism and antioxidant enzyme activity, along with PBZ’s vegetative growth suppression, synergistically improved nutrient allocation and fruit quality. Use of 50 ppm PBZ in month of October with 1% zinc sulphate at time of panicle emergence is an integrated approach for mitigating climate-related disruptions and improving litchi productivity and nutritional value.

Litchi is an important subtropical fruit, highly valued by consumers for its vibrant color and distinctive flavor. B-box (BBX) proteins, which are zinc finger transcription factors, play a crucial role in regulating plant growth, development, and stress responses. Nevertheless, the specific function of BBX genes in the development and coloration of litchi fruit remains inadequately understood. In this study, 21 LcBBX genes (designated as LcBBX1-LcBBX21) were identified within the litchi genome. These genes were categorized into five sub-families based on phylogenetic analysis and were found to be unevenly distributed across 12 chromosomes. Promoter analysis revealed a rich presence of light-responsive elements, such as the G-box, and abscisic acid (ABA) responsive elements, including ABRE, within the promoter regions of LcBBX genes. Protein–protein interaction predictions indicated that the majority of LcBBX genes have the potential to interact with the light-responsive factor HY5. Transcriptome analysis and qRT-PCR results demonstrated that LcBBX genes exhibit tissue-specific expression patterns. Notably, most LcBBX genes were highly expressed prior to fruit coloration, whereas LcBBX4 and LcBBX10 were upregulated during the fruit coloration phase. Furthermore, LcBBX1/4/6/7/15/19 were upregulated in response to light following the removal of shading. The findings suggest that LcBBX4 may directly regulate anthocyanin biosynthesis in litchi pericarp. This study provides critical insights into the molecular mechanisms underlying litchi fruit development and coloration.

Background Recent studies have demonstrated that cellular energy is a key factor switching on ripening and senescence of fruit. However, the factors that influence fruit energy status remain largely unknown. Results HPLC profiling showed that ATP abundance increased significantly in developing preharvest litchi fruit and was strongly correlated with fruit fresh weight. In contrast, ATP levels declined significantly during postharvest fruit senescence and were correlated with the decrease in the proportion of edible fruit. The five gene transcripts isolated from the litchi fruit pericarp were highly expressed in vegetative tissues and peaked at 70 days after flowering (DAF) consistent with fruit ADP concentrations, except for uncoupling mitochondrial protein 1 ( UCP1 ), which was predominantly expressed in the root, and ATP synthase beta subunit ( AtpB ), which was up-regulated significantly before harvest and peaked 2 days after storage. These results indicated that the color-breaker stage at 70 DAF and 2 days after storage may be key turning points in fruit energy metabolism. Transcript abundance of alternative oxidase 1 ( AOX1 ) increased after 2 days of storage to significantly higher levels than those of LcAtpB , and was down-regulated significantly by exogenous ATP. ATP supplementation had no significant effect on transcript abundance of ADP/ATP carrier 1 ( AAC1 ) and slowed the changes in sucrose non-fermenting-1-related kinase 2 ( SnRK2 ) expression, but maintained ATP and energy charge levels, which were correlated with delayed senescence. Conclusions Our results suggest that senescence of litchi fruit is closely related with energy. A surge of LcAtpB expression marked the beginning of fruit senescence. The findings may provide a new strategy to extend fruit shelf life by regulating its energy level.

As an important tropical and subtropical fruit, litchi’s inflorescence size and the number of florets per inflorescence are crucial factors affecting fruit set rate and yield. This study extensively collected a total of 219 litchi germplasm resources, including those from China and 11 other countries worldwide, systematically evaluating eight core phenotypic traits: inflorescence length (IL), inflorescence width (IW), number of secondary lateral inflorescences (NSLI), number of inflorescence internodes (NII), base to main axis length (BMAL), inverted 5th internode length (I5IL), number of female flowers per inflorescence (NFFI), and fertilization rate (FR). The research findings indicated significant correlations between these agronomic traits and fruit set rate, particularly with high fruit set rate litchi varieties showing notably lower trait expressions in IL, NSLI, NFFI, and NII compared to low fruit set rate varieties. Furthermore, through genome-wide association studies (GWAS), significant SNP loci were successfully identified for the two key traits, NSLI and NFFI, while other traits did not show significant associations. Transcriptome results revealed that differentially expressed genes between two typical inflorescence litchi varieties were mainly enriched in molecular function categories such as catalytic activity and transferase activity, affecting metabolic pathways and secondary metabolite synthesis. Joint analysis of GWAS and transcriptomics suggested that the NSLI-associated gene LITCHI016073 (UBP1-associated proteins) might regulate inflorescence development by influencing gibberellin signaling, while NFFI -associated genes LITCHI019855 (Solute carrier family), LITCHI011125 (SEC3A), LITCHI025977 (Acid phosphatase), and LITCHI023264 (Enolase) affected the development and number of female florets. The functions of these genes were further validated by transcriptome results. qRT-PCR analysis showed that in the Houxian variety (dense inflorescence), the expression levels of LITCHI016073, LITCHI011125, LITCHI025977, and LITCHI023264 during the three critical flowering stages were significantly higher than those in the Edanli variety, while the expression level of the LITCHI019855 gene was significantly lower, strongly demonstrating the important roles of these genes in inflorescence development and fruit set rate regulation. By employing large-scale sample analysis and multi-omics technologies, this study systematically unraveled the intrinsic relationships between litchi inflorescence traits and fruit set rate, providing a solid scientific basis and novel insights for litchi breeding practices.

Anthocyanin accumulation is crucial for the development of quality for most fruit. The mechanism underlying the regulation of anthocyanin biosynthesis by transcription factors in litchi fruit remains largely unknown. In this study, we isolated one NAC (NAM, ATAF1/2 and CUC2) TF gene, LcNAC13. Expression of LcNAC13 was upregulated as ripening proceeded, followed by the accumulation of anthocyanins. Electrophoretic mobility shift assay (EMSA) and transient expression assay showed that LcNAC13 could negatively regulate the expression of anthocyanin biosynthesis-related genes, including LcCHS1/2, LcCHI, LcF3H, LcF3’H, LcDFR, and LcMYB1. Furthermore, LcR1MYB1, as one R1-MYB type MYB, was identified to physically interact with LcNAC13 and reverse the effect of LcNAC13. Taken together, these results suggested that LcNAC13 and LcR1MYB1 may act together to antagonistically regulate anthocyanin biosynthesis during litchi fruit ripening, which helps to provide new insights into the regulatory networks of anthocyanin biosynthesis.

Litchi chinensis Sonn. is an important evergreen fruit crop cultivated in the tropical and subtropical regions. The edible portion of litchi fruit is the aril, which contains a high concentration of sucrose, glucose, and fructose. In this study, we review various aspects of sugar transport, metabolism, and signaling during fruit development in litchi. We begin by detailing the sugar transport and accumulation during aril development, and the biosynthesis of quebrachitol as a transportable photosynthate is discussed. We then document sugar metabolism in litchi fruit. We focus on the links between sugar signaling and seed development as well as fruit abscission. Finally, we outline future directions for research on sugar metabolism and signaling to improve fruit yield and quality.

Prolonged exposure to cold temperatures often results in a relatively low flowering rate in litchi (Litchi chinensis Sonn.) trees with younger leaves. This study aimed to verify the impact of stem girdling on litchi flowering by identifying and characterizing the induced metabolic changes. After a 60 day exposure to cold treatment at 15 °C/10 °C (12 h/12 h), the flowering rate of the girdled trees was 100%, while that of the non-girdled trees was 20%, indicating that girdling improved litchi flowering at its turning stage. The metabolic profiles of litchi leaves with and without stem girdling during floral induction were compared and 505 metabolites potentially associated with litchi flowering were detected. Most metabolites were involved in the metabolism of starch and sucrose, fatty acid, and phenylpyruvic acid. The metabolic pathways concerned with the biosynthesis of epinephrine, sucrose, and d-maltose were induced in leaves after girdling treatment. The level of galactitol, phenylpyruvic acid, acetyl-CoA, linoleic acid, alpha-linolenic acid, and 13-HPOT biosynthesis remained stable in the leaves from girdled trees but changed drastically in the leaves from non-girdled trees. In addition, 379 metabolites concerning flowering rate were characterized. Metabolism pathways of starch and sucrose, galactose, and linoleic acid are of great significance to the flowering of litchi. Linoleic acid exhibited the most significant variations between girdled trees and non-girdled trees with fold changes of up to 13.62. These results contribute to understanding the biological mechanism of litchi floral induction and the metabolic changes after stem girdling.

Background Lychee ( Litchi chinensis Sonn.), longan ( Dimocarpus longan Lour.), and rambutan ( Nephelium lappaceum L.) are popular tropical fruits in the family Sapindaceae, known for their succulent arils—specialized seed appendage with significant biological and commercial value. Despite their agricultural relevance, the molecular mechanisms underlying aril development in these species remain poorly understood. Results We conducted RNA-sequencing to profile transcriptomes during aril development, complemented by in-situ hybridization to validate the spatial expression of LcLBD1 . OrthoFinder identified species-specific and shared differentially expressed genes (DEGs), while functional enrichment analyses (GO, KEGG) and transcriptional network modeling elucidated regulatory pathways. After detailed analyses of transcriptomes, species-specific and shared DEGs were identified across lychee, longan, and rambutan using OrthoFinder. Members of the bHLH and MYB gene families were implicated in early aril development. Species-specific DEGs were primarily enriched in metabolic pathways. From shared DEGs, we identified ten transcription factors ( AGL8 , AP3 , SHP1 , WOX13 , LBD1 , LBD3, OBP1 , SPL2, SPL3, and SPL9 ) and three genes ( IAA8 , CSLD5 , and CYCD3;2 ) as key regulators. Interestingly, in-situ hybridization localized LcLBD1 expression to funicle and small aril cells, suggesting roles in cell differentiation and division. Conclusion We have identified ten transcription factors and three genes affecting aril development in lychee, longan, and rambutan, and validated the expression of LcLBD1 in funicle and aril cells. These results offer a new perspective on the molecular mechanism of aril development and lay the groundwork for future research into the functions and regulatory mechanisms of candidate genes.