Sunburn is a major abiotic stress in fruit crops, leading to significant economic losses due to reduced fruit quality and marketability. Wampee (Clausena lansium), a tropical specialty fruit with growing industrial interest, is particularly vulnerable to sunburn-induced peel browning during ripening. To elucidate the underlying mechanisms, we conducted comprehensive field surveys and integrated physiological, biochemical, metabolomic, and transcriptomic analyses. Our integrated analyses suggest that strong light exposure is a key environmental trigger for sunburn, while shading treatments effectively mitigated damage despite elevated bag temperatures. Physiological assessments revealed that sunburn progression involved reactive oxygen species (ROS) accumulation, membrane lipid peroxidation, and dynamic changes in antioxidant enzymes (SOD, CAT, APX) and osmotic regulators. Metabolomic analysis identified 277 differentially accumulated metabolites, with significant enrichment of phenylpropanoid and flavonoid compounds such as coniferol, dihydrokaempferol, and naringenin—under severe stress. Transcriptomic data further highlighted coordinated upregulation of phenylpropanoid biosynthesis, flavonoid biosynthesis, and heat stress response pathways. We identified 28 structural genes and 56 transcription factors (including WRKY28, bHLH30, and HSFC1) as central regulators. Integrative analysis suggested that WRKY and bHLH transcription factors are associated with the upregulation of key genes (e.g., PAL and 4CL) and the accumulation of antioxidant metabolites, implying a potential role in improving photo-thermal tolerance. This study provides valuable physiological and molecular insights into sunburn response in wampee fruit and offers potential strategies for breeding resistant varieties and developing postharvest management practices to enhance fruit quality in industrial cultivation.

Intestinal health is critical for efficient swine production, yet effective intervention strategies remain limited. This study evaluated the impacts of dietary Brevibacillus laterosporus BL1 (live or heat-killed form) on finishing pigs, focusing on serum parameters, antioxidant capacity, intestinal barrier, cecal microbiota, and microbial metabolic profiles. Results demonstrated that relative to the control group (CON), B. laterosporus BL1 (both live and heat-killed forms) decreased serum pro-inflammatory cytokines, ameliorated serum lipids, and enhanced systemic antioxidant capacity. Moreover, the heat-killed form was comparable to the live bacteria in strengthening the intestinal barrier, as evidenced by improved intestinal morphology, upregulated barrier-related proteins (ZO-1, Muc-1, and Muc-2), decreased serum lipopolysaccharide levels, and raised intestinal anti-inflammatory cytokines (IL-10 and IL-22) and immunoglobulins (IgG and IgM). Further, metagenomic analysis of cecal digesta demonstrated that heat-killed B. laterosporus BL1 elevated the proportions of potentially beneficial genera Limosilactobacillus and Lactobacillus, while suppressed potential pathogens Clostridium and Terrisporobacter. Consistently, heat-killed B. laterosporus BL1 increased cecal levels of lactate, total short-chain fatty acids (SCFAs), acetic acid, and butyric acid, while decreasing the concentration of phenol, indole, skatole, and biogenic amines (total amines, methylamine, cadaverine, and putrescine). Thus, heat-killed B. laterosporus BL1 emerges as a promising agent for promoting overall physiological status and intestinal health in finishing pigs.

[Objective]To elucidate the microbiological mechanisms through which long-term straw return influences the severity of bacterial diseases in paddy fields,thereby providing a theoretical basis for precise disease prevention and control.[Method]Based on a long-term field location experiment in Huizhou,Guangdong Province,this study implemented three treatments:1.3 times the amount of full straw returned(S30,with a seasonal application rate of 8 425 kg·hm-2),full straw returned(CKS,with a seasonal application rate of 6 400 kg·hm-2),and no straw returned(CK).Using metagenomic sequencing,we systematically compared the dynamics of soil bacterial community structure and the relative abundance of key pathogenic species(including Burkholderia glumae,Xanthomonas oryzae,and Dickeya oryzae)under different straw management practices,and examined their relationships with environmental factors through correlation analysis.[Result]Straw returning significantly enhanced the species richness of soil bacterial communities(P<0.05)and altered their structural composition.Among the detected phyla,Proteobacteria,Chloroflexi and Acidobacteria were identified as the dominant taxa,and their relative abundances were significantly influenced by both the amount of returned straw and the growth stages of rice.Redundancy analysis confirmed that soil pH served as a key environmental factor driving shifts in community structure(P=0.024).Straw returning generally reduced the abundance of three pathogenic bacteria during the tillering stage.It also lowered the disease severity indices for bacterial leaf blight,leaf streak,and panicle blight of rice,though not significantly,and even carried a potential risk of increasing foot rot incidence.At the maturity stage,S30 significantly increased the abundance of B.glumae and X.oryzae,while the relative abundance of D.oryzae was markedly reduced.Additionally,S30 significantly promoted the aggravation of bacterial leaf blight and raised the incidence of leaf streak and foot rot.In contrast,CKS showed no significant negative impact on the occurrence of most bacterial diseases.Its disease incidence was only slightly higher than that of CK,and the disease index performance remained relatively moderate.Correlation analysis revealed that at maturity,the abundances of Burkholderia and Xanthomonas were significantly positively correlated with soil pH,while at the tillering stage,Dickeya abundance showed a strong association with soil available phosphorus content.[Conclusion]Long-term straw returning is altering the soil microenvironment,resulting in dual specificity on the type and growth stage of bacterial diseases in rice.At the tillering stage,it reduced the disease indices of bacterial leaf blight,leaf streak,and panicle blight,though not significantly,while even increasing the risk of bacterial foot rot.At maturity,however,straw returning promoted different bacterial diseases depending on the amount applied.Among the treatments,S30 showed the most pronounced effects,providing a scientific basis for ecologically sustainable management of bacterial diseases in rice.

Background Beneficial plant-associated microorganisms are key drivers of sustainable agriculture. However, their discovery and practical application remain insufficiently explored. Here, we present the first comprehensive comparative genomic analysis of a newly identified Sinomonas strain together with all publicly available genomes to assess its agronomic potential Results Our results demonstrate that Sinomonas has an open pangenome and harbors multiple pathways for IAA biosynthesis, including a rare pathway found in only a limited number of bacterial taxa. The genus also contains genes involved in the synthesis of cytokinin analogues. In addition, genomic annotation identified ten genes putatively associated with phosphorus solubilization. A total of sixteen distinct biosynthetic gene clusters were identified, covering pathways for the biosynthesis of stenothricin, dactylocycline, aborycin, reveromycin, michiganin A, ikarugamycin, and peucechelin, all of which are compounds with reported antibacterial activity. In addition, Sinomonas carries multiple genes potentially involved in improving plant stress tolerance, including genes related to the biosynthesis of spermidine, 2,3-butanediol, acetoin, betaine, proline, and trehalose. Conclusion Overall, these findings highlight the functional diversity of the Sinomonas genome and provide preliminary insights into its potential agricultural applications.

Hydrothermal carbonization (HTC) offers a sustainable pathway to convert agricultural wastes into multifunctional hydrochars, yet the stability of hydrochars and the biotoxicity of hydrocharderived dissolved organic matter (DOM) as amendments for contaminated farmland soils remained understudied. Herein, this study investigates feedstock-dependent (straw: HS, swine manure: HSM, and cattle manure: HCM) and time-resolved variations in hydrochar and the derived DOM characteristics for farmland remediation potentials. Feedstock type dominated hydrochars and DOM functionality that manure-based hydrochars exhibited superior metal adsorption capacity (100 % Pb removal by HSM and 51.7-76.2 % by HCM), more biologically suitable C/N ratios (HSM: 15.0-16.5, HCM: 21.4-23.5), and germination index (HSM: 51.1-76.7 %, HCM: 56.2-82.2 %), correlating with the reduced phytotoxicity. The DOM derived from manure-based hydrochar contained more macromolecular fluorescent humus contents and various organic functional groups, while HS released more phytotoxic DOM with 44.3-68.3 % germination inhibition. DOM removal enhanced Pb adsorption capacities by 56.1-97.3 % for lignocellulose-rich HS. With elemental analysis and 2D-FTIR-COS analysis, the prolonged hydrothermal duration enhanced structural stability, reducing DOM release by 19.6-40.5 % through dehydration and decarboxylation. In addition, the stability of hydrochar, alongside the N content and the degree of dehydration and decarboxylation, significantly affected their toxicity to seed germination. In conclusion, the type of feedstock has the most substantial impact on hydrochars and DOM properties that HCM emerged as the most viable candidate due to synergistic benefits, while optimizing hydrothermal time improved performance agricultural remediation.

A novel strain of the genus Sinomonas, designated G460-2 T, was isolated from rice paddy soil. The cells of strain G460-2 T were Gram-positive, aerobic, and non-motile rods. The optimal growth conditions for this strain were observed at 30 °C and a pH of 7.0. Phylogenetic analysis based on 16S rRNA gene sequencing revealed that strain G460-2 T shared the highest sequence similarity (98.41

The prevalence of antibiotic resistance genes (ARGs) in agricultural soils has garnered significant attention. However, the long-term impacts of various nitroge (N)-substitution fertilization regimes on the distribution of soil ARGs and their dominant drivers in a subtropical triple-cropping system remain largely unexplored. This study employed a metagenomic approach to analyze soil ARGs, microbial communities, mobile genetic elements (MGEs), and viruses from a maize-maize-cabbage rotation field experiment with five different fertilization regimes. Soil samples were collected in 2012 and 2021. A total of 615 unique ARG subtypes were identified, with multidrug, bacitracin, and rifamycin resistance genes being the most abundant. Notably, ARG types. the continuous application of fresh chicken manure (CM) over 10 years significantly increased both the count of unique ARG subtypes and the total ARG abundance compared to other fertilization regimes, such as inorganic fertilizer and composted chicken manure. Specifically, the abundance of genes associated with antibiotic target replacement (e.g., sul1 and sul2) in the CM-treated soil rose by 8.83-fold from 2021 to 2012. Our random forest analysis revealed that the abundance of three MGEs (QacEdelta, plasmids, and IstB), two viral families (Myoviridae and Podoviridae), two bacterial phyla (Chloroflexi and Planctomycetes), and two environmental factors (pH and soil organic matter (SOM)) significantly influenced the distribution of ARGs. Furthermore, variance decomposition analysis underscored the critical roles of the three MGEs and the two viral families in the dissemination of ARGs, suggesting that horizontal gene transfer (HGT) may play a key role in ARG spread. These findings enhance our understanding of how different fertilization practices influence ARG dissemination in subtropical triple-cropping agroecosystems over the long term and provide valuable insights for optimizing fertilization management strategies.

An adaptable, low-cost, and easy-to-operate biological treatment system for pollutant abatement in aquaculture water at the field pond scale needs to be developed. In this study, the pollutant removal capacity of a stable bioreactor for aquaculture wastewater was assessed, and the related mechanism was elucidated via an analysis of the microbial community’s characteristics and functions. The average removal efficiencies of chemical oxygen demand, suspended solids, total nitrogen, and total phosphorus were 40%, 86.22%, 38.62%, and 53.74%, respectively. The effluent quality meets the Requirement for Water Discharge from Freshwater Aquaculture Pond, SC/T9101-2007. The results indicate that the fillers under anaerobic conditions could attract Denitratisoma and unclassified_Rhodocyclaceae, promoting the denitrification reaction. This aligns with the characteristic that total nitrogen in aquaculture sewage mainly exists in the form of nitrate nitrogen. An anaerobic atmosphere helps degrade organic contaminants at liquid interfaces and remove nitrogen in the solid phase. The fillers under anaerobic conditions could attract Bacteroidota and promote the production of polysaccharides to form biofilms, which may be associated with phosphorus removal. The results indicate that the anaerobic stage can promote the formation of biofilm on the fillers to remove pollutants, thus achieving higher aquaculture sewage treatment efficiency.

Interplanting crops is the best method to grow crops synergistically for better utilization of land and agro-resources. Grape (Vitis vinifera) and potato (Solanum tuberosum L.) have highly efficient agricultural planting systems in China, however, how soil physicochemical properties and soil microbial communities and metabolites affect the output of grape-potato interplanting remained unknown. In this study, we employed three planting patterns (CK: grape monocropping; YY: grape interplanted with potato (variety ‘Favorita’); LS: grape interplanted with potato (variety ‘Longshu7’)) at two experimental sites i.e., the Huizhou (2022) site and the Qingyuan site (2023). The grape variety for all planting patterns was ‘Sunshine Rose’. Soil samples (top 0-20 cm) at both sites were collected to observe the diversity of bacterial communities and soil metabolites. Our findings revealed that, compared with monocropping, the interplanted systems resulted in higher concentrations of total nitrogen, available phosphorus, and available potassium and enhanced the activities of acid phosphatase, urease, and protease. The potato root exudates also altered the relative abundance of Bacillus, Kaistobacter, and Streptomyces in the rhizosphere. Among the soil metabolites, lipids and organic acids showed the most significant changes. Notably, 13-L-hydroperoxylinoleic acid is the key differentially abundant metabolite involved in the regulation of linoleic acid metabolism pathways. The association analyses of the metabolome, microbiome, and soil physicochemical properties revealed that the interactions of microbes and metabolites resulted in differences in the soil nutrient content, whereas the interactions of 13-L-hydroperoxylinoleic acid and Firmicutes improved the soil nutrient levels and bacterial composition in the interplanting systems. In summary, our findings demonstrated that intercropping grapes with potato ‘Favorita’ was better with respect to improving soil nutrients, soil enzyme activity, the diversity of soil bacteria, and soil metabolites without causing adverse impacts on grape yield. Overall, this study explained the physiological mechanisms by which soil microorganisms and metabolites promote potato growth in grape interplanting and provided new perspectives for the utilization of soil resources in vineyards.

The preharvest internal browning of Nane plum fruit, with no visible effects on the appearance of the fruit, has become a serious problem in recent years in its production area in Guangdong Province, China. This study investigated the effects of environmental factors, including temperature, on Nane plum internal browning. Plum orchards at different elevations with different incidences of internal browning were selected. Using fruits with different internal browning incidence levels, the internal browning mechanism was analyzed with transcriptome and metabolome analyses. The results revealed decreased internal browning at high altitudes. Shading treatment significantly reduced internal browning, whereas bagging and insect-proof net-covering treatments significantly increased internal browning. Because bagging and net coverings increase the local ambient temperature, the findings suggest that high temperature is an important factor influencing the internal browning of Nane plum. The metabolome experiments showed that with increased internal browning, the levels of phenolic hydroxyls such as catechol increased, with simultaneous increases in hydrogen peroxide content and oxidase activity. It can be speculated that the oxidation of phenolic hydroxyl substances is the main cause of the preharvest browning of Nane plum. Transcriptome analysis revealed the increased expression of calcium signaling-related and downstream effector genes and indicated an important role of calcium in internal browning, possibly due to its increased content in the fruit. Further, with increasingly serious internal browning, genes related to photosynthesis were down-regulated, while genes related to senescence were up-regulated, thus suggesting the up-regulation of the process of cell senescence during internal browning. In conclusion, heat stress should be eliminated to reduce preharvest internal browning in Nane plum.

Phage therapy has the potential to alleviate plant bacterial wilt. However, the knowledge gap concerning the phage-agrochemical interaction impedes the broader application of phages in agriculture. This study characterized a phage isolate and investigated its interactions with agrochemicals. A novel species within the Ampunavirus genus was proposed, serving phage LPRS20 as a type phage with a broad lytic range and significant antibacterial activity against Ralstonia solanacearum strains infecting tobacco, chili, or tomato. Sensory evaluation of the morphology of tobacco leaves suggested that phage application resulted in negligible harm to plants. Investigations into phage-agrochemical interactions revealed synergisms when LPRS20 was delivered 4 h before thiodiazole-copper as well as LPRS20 in combination with low-concentration berberine. Overall, our findings reveal that phage LPRS20 represents a novel, effective, and eco-friendly biocontrol agent against tobacco bacterial wilt in vivo and in vitro and contributes to the potential integration of phages and agrochemicals for controlling soil-borne pathogens.

Bacillus velezensis is well known as a plant growth-promoting rhizobacteria (PGPR) and biocontrol agent. Nevertheless, there are very few reports on the study of B. velezensis on tomato early blight, especially the biocontrol effects among different inoculation concentrations. In this study, an IAA-producing strain, Bacillus velezensis YXDHD1-7 was isolated from the tomato rhizosphere soil, which had the strongest inhibitory effect against Alternaria solani. Inoculation with bacterial suspensions of this strain promoted the growth of tomato seedlings effectively. Furthermore, inoculations at 106, 107, and 108 cfu/mL resulted in control efficacies of 100%, 83.15%, and 69.90%, respectively. Genome sequencing showed that it possesses 22 gene clusters associated with the synthesis of antimicrobial metabolites and genes that are involved in the production of IAA. Furthermore, it may be able to produce spermidine and volatile compounds that also enhance plant growth and defense responses. Our results suggest that strain YXDHD1-7 prevents early blight disease by promoting growth and enhancing the defense enzyme activities in tomato plants. This strain is a promising candidate for an excellent microbial inoculant that can be used to enhance tomato production.

Mulberry leaves are rich in nutrients but contain anti-nutrient factors that hinder their digestion and absorption. Feeding animals with mulberry leaves directly could harm their health. The microbial fermentation of mulberry leaves could reduce their anti-nutritional factors’ content and improve their nutritional value. Sequencing and analyzing mulberry leaves before and after fermentation showed that fermentation increased the relative abundance of Pediococcus, Bradyrhizobium, Hydrotalea, and Rhodanobacteria, and decreased that of Enterobacter. Fermentation improved the quality of mulberry leaves by rebuilding the bacterial community. Finishing pigs were raised on fermented mulberry leaves (FML), and their carcass performance, meat quality, economic benefits, and gut microbiome were evaluated. FML had no negative impact on pig carcass performance, meat quality, and antioxidant capacity, and could somewhat improve the economic benefits. FML decreased the relative abundance of Proteobacteria in the colon and Streptococcus in the feces, and increased that of Actinobacteria (cecum, colon, feces) and Prevotella (colon). The gut core microorganisms in the FML group were mainly enriched with Actinobacteria, Bifidobacterium, Bifidobacteriaceae, Bifidobacteriales, and other beneficial microorganisms. Dietary FML reduced ammonia, indole, and skatole contents in the feces. In conclusion, FML reshaped the gut microbiota without negatively affecting pig product performance, produced cleaner waste, and improved environmental protection and sustainability, making it an attractive prospective feed for pigs.

Paddy fields are the main agricultural source of greenhouse gas methane (CH4) emissions. To enhance rice yield, various fertilization practices have been employed in rice paddies. However, the key microbial and abiotic factors driving CH4 emissions under different fertilization practices in paddy fields remain largely uncharted. This study conducted field experiments in a traditional double-cropping rice area in South China, utilizing five different fertilization practices to investigate the key factors influencing CH4 emissions. High-throughput sequencing and PICRUSt2 functional prediction were employed to investigate the contributions of soil physicochemical properties, CH4-metabolizing microorganisms (methanogens and methanotrophs), and key genes (mcrA and pmoA) on CH4 emissions. The results showed that CH4 emission fluxes exhibited seasonal variations, with consistent patterns of change observed across all treatments for both early- and late-season rice. Compared to the no-fertilization (NF) treatment, cumulative CH4 emissions were lower in early-season rice with green manure (GM) and straw returning (SR) treatments, as well as in late-season rice with GM treatment, while rice yields were maintained at higher levels. High-throughput sequencing analysis revealed that potential methanogens were primarily distributed among four orders: Methanobacteriales, Methanocellales, Methanomicrobiales, and Methanosarcinales. Furthermore, there was a significant positive correlation between the relative abundance of the CH4-related key gene mcrA and these microorganisms. Functional analysis indicated that these potential methanogens primarily produce methane through the acetoclastic and hydrogenotrophic pathways. Aerobic CH4-oxidizing bacteria, predominantly from the genus Methylocystis, were detected in all the treatments, while the CH4 anaerobic-oxidizing archaea ANME-1b was only detected in chemical fertilization (CF) and cow manure (CM) treatments. Our random forest analysis revealed that the relative abundance of two methanogens (Methanocellales and Methanosarcinales) and two environmental factors (pH and DOC) had significant impacts on the cumulative CH4 emissions. The variance decomposition analysis highlighted the CH4-metabolizing microorganisms explained 50% of the variance in the cumulative CH4 emissions, suggesting that they are the key microbial factors driving CH4 emissions. These findings provide guidance for the development of rational measures to reduce CH4 emissions in paddy fields.

Wampee ( Clausena lansium ) is an economically significant subtropical fruit tree widely cultivated in Southern China. High-quality genomic resources are unavailable, but they are essential for functional genomics and germplasm enhancement of wampee. Here, we provide a chromosome-level genome sequence for the wampee cultivar JinFeng and a population genomic analysis of 266 accessions. The 297.1 Mb wampee genome, containing nine chromosomes with a scaffold N50 of 29.2 Mb and encoding 23,468 protein-coding genes, showed a significant improvement over the previous version. We dissected the wampee population structure and genetic differentiation in China using population genomic analysis, which detected 110 and 671 genes under a selective sweep associated with sour and sweet wampee evolution in domesticated clones, respectively. Homozygous non-synonymous single nucleotide polymorphisms are likely associated with fruit flavor differentiation. A genome-wide association study identified 220 remarkable marker-trait associations for total acid content, harboring 289 genes encoding transcription factors, transporters, and enzymes involved in sugar and acid metabolism, which are potentially useful for sour and sweet taste development in wampee fruit. Furthermore, the ethylene response factor family gene ClERF061 and the SWEET family gene ClSWEET7 were identified. Linkage assessment between the relative expression levels of ClERF061 or ClSWEET7 and the total acid/total sugar contents implied their potential involvement in sugar-acid metabolism in wampee fruits. High-quality genome resources are valuable for expediting wampee research and genome-assisted breeding. ### Competing Interest Statement The authors have declared no competing interest.

Inadequately managed solid organic waste generation poses a threat to the environment and human health globally. Biotransformation with the black soldier fly larvae (BSFL) is emerging as talent technology for solid waste management. However, there is a lack of understanding of whether BSFL can effectively suppress potential pathogenic microorganisms during management and the underlying mechanisms. In this study, we investigated the temporal variations of microorganisms in two common types of solid waste, i.e., kitchen waste (KW) and pig manure (PM). Natural composting and composting with BSFL under three different pH levels (pH 5, 7, and 9) were established to explore their impact on microbial communities in compost and the gut of BSFL. The results showed that the compost of kitchen waste and pig manure led to an increase in relative abundance of various potentially pathogenic bacteria. Temporal gradient analyses revealed that the most substantial reduction in the relative abundance and diversity of potentially pathogenic microorganisms occurred when the initial pH of both two wastes were adjusted to 7 upon the introduction of BSFL. Through network and pls-pm analysis, it was discovered that the gut microbiota of BSFL occupied an ecological niche in the compost, inhibiting the proliferation of potentially pathogenic microorganisms. This study has revealed the potential of BSFL in reducing public health risks during the solid waste management process, providing robust support for sustainable waste management.

Biochar was popularly used for reducing greenhouse gas (GHG) emissions in vegetable production, but using biochar does not necessarily guarantee a reduction in GHG emissions. Herein, it's meaningful to elucidate the intricate interplay among biochar properties, soil characteristics, and GHG emissions in vegetable production to provide valuable insights for informed and effective mitigation strategies. Therefore, in current research, a meta-analysis of 43 publications was employed to address these issues. The boost-regression analysis results indicated that the performance of biochar in inhibiting N2O emissions was most affected by the N application rate both in high and low N application conditions. Besides, biochar had dual roles and showed well performance in reducing GHG emissions under low N input (≤300 kg N ha-1), while having the opposite effect during high N input (>300 kg N ha-1). Specifically, applying biochar under low N fertilization input could obviously reduce soil N2O emissions, CO2 emissions, and CH4 emissions by 18.7 %, 17.9 %, and 16.9 %, respectively. However, the biochar application under high N fertilization input significantly (P < 0.05) increased soil N2O emissions, CO2 emissions, and CH4 emissions by 39.7 %, 43.0 %, and 27.7 %, respectively. Except for the N application rate, the soil pH, SOC, biochar C/N ratio, biochar pH, and biochar pyrolysis temperature are also the key factors affecting the control of GHG emissions in biochar-amended soils. The findings of this study will contribute to deeper insights into the potential application of biochar in regulating GHG under consideration of N input, offering scientific evidence and guidance for sustainable agriculture management.

Wampee (Clausena lansium) is an economically significant subtropical fruit tree widely cultivated in Southern China. To provide high-quality genomic resources for C. lansium, we report a chromosome-level genome sequence for the "JinFeng" cultivar. The 297.1 Mb C. lansium genome contained nine chromosomes with a scaffold N50 of 29.2 Mb and encoded 23,468 protein-coding genes. Selective sweep analysis between sweet and sour C. lansium varieties and genome-wide association analysis identified 14 candidate genes putatively involved in sugar and acid accumulation. ClERF061, encoding an ethylene response factor, and ClSWEET7, encoding a Sugars Will Eventually be Exported Transporters (SWEET) family protein, were proposed as key regulators of the sweet and sour tastes of the wampee fruit. ClERF061 and ClSWEET7 overexpression in tomatoes increased the total sugar and acid content in fruits. ClSWEET7 promoter activation by ClERF061 was confirmed via Nicotiana benthamiana transient expression. Our study provides valuable genomic resources for C. lansium genetics and breeding.