{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,8]],"date-time":"2026-10-08T22:26:59Z","timestamp":1791498419783,"version":"4.3.4"},"reference-count":50,"publisher":"MDPI AG","issue":"5","license":[{"start":{"date-parts":[[2026,3,1]],"date-time":"2026-03-01T00:00:00Z","timestamp":1772323200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Innovation Guidance and Technology-based Enterprise Incubation Program","award":["202304BT090020"],"award-info":[{"award-number":["202304BT090020"]}]},{"name":"Innovation Guidance and Technology-based Enterprise Incubation Program","award":["202204BI090016"],"award-info":[{"award-number":["202204BI090016"]}]},{"name":"Academician Expert Workstation in Yunnan Province","award":["202405AF140080"],"award-info":[{"award-number":["202405AF140080"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Foods"],"abstract":"<jats:p>Table grapes are widely consumed fruits, and their quality is largely determined by aroma, texture, and the accumulation of health-promoting compounds such as flavonoids. In this study, we systematically compared the edible quality and molecular basis of flavonoid biosynthesis among three major table grape cultivars: Crimson Seedless (CRS), Red Globe (RG), and Shine Muscat (SM). An integrated approach combining physicochemical assays, Gas chromatography\u2013ion mobility spectrometry (GC-IMS)-based volatile profiling, and transcriptome sequencing (RNA-seq) was employed. Among the three cultivars, SM exhibited superior fruit quality, characterized by the highest firmness, total soluble solids, ascorbic acid, total phenolic content, and flavonoid content, whereas CRS showed the highest titratable acidity. Volatile compound analysis revealed distinct aroma profiles among the cultivars. SM was enriched in ethanol and 2-methylbutanal, contributing sweet and fruity notes, while CRS contained higher levels of C6 aldehydes, such as hexanal and (E)-2-hexenal, which are associated with green and leafy aromas. RG exhibited a relatively simpler volatile profile with lower overall abundance. Transcriptome analysis identified 20 differentially expressed genes involved in the flavonoid biosynthetic pathway, including PAL, C4H, 4CL, CHI, F3H, F3\u2032H, and DFR, of which ten were significantly upregulated in SM. Eight of these genes showed strong positive correlations (r &gt; 0.8) with flavonoid content. These results provide a comprehensive understanding of the metabolic and genetic mechanisms underlying cultivar-specific quality traits and identify promising candidate genes for breeding table grapes with enhanced flavor and health-promoting properties.<\/jats:p>","DOI":"10.3390\/foods15050823","type":"journal-article","created":{"date-parts":[[2026,3,4]],"date-time":"2026-03-04T08:51:33Z","timestamp":1772614293000},"page":"823","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":1,"title":["Comparative Profiling of Aroma Volatiles and Flavonoid Biosynthesis in Crimson Seedless, Red Globe, and Shine Muscat Table Grapes Using GC-IMS and RNA-Seq"],"prefix":"10.3390","volume":"15","author":[{"given":"Xiaoxue","family":"Kong","sequence":"first","affiliation":[{"name":"Agro-Products Processing Research Institute, Yunnan Academy of Agricultural Sciences, Kunming 650221, China"},{"name":"School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing 210023, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Fang","family":"Yang","sequence":"additional","affiliation":[{"name":"Agro-Products Processing Research Institute, Yunnan Academy of Agricultural Sciences, Kunming 650221, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Qiuqiu","family":"Huang","sequence":"additional","affiliation":[{"name":"Agro-Products Processing Research Institute, Yunnan Academy of Agricultural Sciences, Kunming 650221, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Fang","family":"Fang","sequence":"additional","affiliation":[{"name":"Agro-Products Processing Research Institute, Yunnan Academy of Agricultural Sciences, Kunming 650221, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yuxing","family":"Guo","sequence":"additional","affiliation":[{"name":"School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing 210023, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Qin","family":"Zou","sequence":"additional","affiliation":[{"name":"Agro-Products Processing Research Institute, Yunnan Academy of Agricultural Sciences, Kunming 650221, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5978-707X","authenticated-orcid":false,"given":"Haibo","family":"Luo","sequence":"additional","affiliation":[{"name":"School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing 210023, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2989-3442","authenticated-orcid":false,"given":"Lijuan","family":"Yu","sequence":"additional","affiliation":[{"name":"Agro-Products Processing Research Institute, Yunnan Academy of Agricultural Sciences, Kunming 650221, China"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2026,3,1]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"131","DOI":"10.1016\/j.scienta.2018.10.018","article-title":"Estimates of repeatability for selection of genotypes of seedless table grapes for Brazilian semiarid regions","volume":"245","author":"Sales","year":"2019","journal-title":"Sci. Hortic."},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"116823","DOI":"10.1016\/j.foodres.2025.116823","article-title":"Effects of elevated temperature and shaded UV-B radiation exclusion on berry biochemical composition in four grape (Vitis vinifera L.) cultivars with distinct anthocyanin profiles","volume":"218","author":"Wang","year":"2025","journal-title":"Food Res. Int."},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"1582620","DOI":"10.1155\/ijfo\/1582620","article-title":"Analysis of the nutritional content, phytochemicals, and antioxidant properties of the unexploited wild grape variety Ampelocissus indica (L.) Planch in Comparison to Vitis vinifera L","volume":"2025","author":"Nandasiri","year":"2025","journal-title":"Int. J. Food Sci."},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"142678","DOI":"10.1016\/j.foodchem.2024.142678","article-title":"Post-harvest quality preservation of red globe grapes using grape juice-based edible coatings combined with UVC treatment","volume":"470","author":"Palou","year":"2025","journal-title":"Food Chem."},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"112778","DOI":"10.1016\/j.postharvbio.2024.112778","article-title":"Process parameters optimization for red globe grapes to enhance shelf-life using non-equilibrium cold plasma jet","volume":"210","author":"Mishra","year":"2024","journal-title":"Postharvest Biol. Technol."},{"key":"ref_6","doi-asserted-by":"crossref","unstructured":"Abou, E.M.K., ElHennawy, H.M., Samaan, M.S.F., Salaheldin, T.A., Ahmed, A.E., and ElKereamy, A. (2021). Using zinc oxide nanoparticles to improve the color and berry quality of table grapes Cv. crimson seedless. Plants, 10.","DOI":"10.3390\/plants10071285"},{"key":"ref_7","doi-asserted-by":"crossref","unstructured":"Petoumenou, D.G., and Patris, V. (2021). Effects of several preharvest canopy applications on yield and quality of table grapes (Vitis vinifera L.) Cv. crimson seedless. Plants, 10.","DOI":"10.3390\/plants10050906"},{"key":"ref_8","doi-asserted-by":"crossref","unstructured":"Sayed, M.E.A., Hammam, A.A., Fayed, A.S.K., Rebou, N.Y.H., and Eldin, R.M.B. (2024). Improving water use efficiency, yield, and fruit quality of crimson seedless grapevines under drought stress. Horticulturae, 10.","DOI":"10.3390\/horticulturae10060576"},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"142546","DOI":"10.1016\/j.foodchem.2024.142546","article-title":"Effects of temperature on the physicochemical properties and volatile profiles of \u2018Shine Muscat\u2019 grape during postharvest storage","volume":"469","author":"Jiang","year":"2024","journal-title":"Food Chem."},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"143255","DOI":"10.1016\/j.foodchem.2025.143255","article-title":"Supplementary light with different wavelengths improved the monoterpenes aroma and quality traits of \u2018Shine Muscat\u2019 grape berries under facility cultivation","volume":"474","author":"Li","year":"2025","journal-title":"Food Chem."},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"3016","DOI":"10.1093\/jxb\/eraf082","article-title":"Grape volatile organic compounds (VOCs)-analysis, biosynthesis and profiling","volume":"76","author":"Tomaz","year":"2025","journal-title":"J. Exp. Bot."},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"116568","DOI":"10.1016\/j.foodres.2025.116568","article-title":"Characterize and explore the dynamic changes in the volatility profiles of sauce-flavor baijiu during different rounds by GC-IMS, GC\u2013MS and GC\u00d7GC\u2013MS combined with machine learning","volume":"213","author":"Niu","year":"2025","journal-title":"Food Res. Int."},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"116404","DOI":"10.1016\/j.foodres.2025.116404","article-title":"Formation of volatile compounds in mutton during air fryer roasted mutton by means of GC-MS and GC-IMS","volume":"211","author":"Hua","year":"2025","journal-title":"Food Res. Int."},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"102853","DOI":"10.1016\/j.fochx.2025.102853","article-title":"Pre-harvest Chitooligosaccharide application enhances phenolic composition, antioxidant capacity, and sensory quality of cabernet Gernischt grapes (Vitis vinifera L.) and wine","volume":"29","author":"Zhao","year":"2025","journal-title":"Food Chem. X"},{"key":"ref_15","doi-asserted-by":"crossref","unstructured":"Salama, A.M., Abdelsalam, M.A., Rehan, M., Elansary, M., and Shereif, A.E. (2023). Anthocyanin accumulation and its corresponding gene expression, total phenol, antioxidant capacity, and fruit quality of \u2018Crimson seedless\u2019 grapevine (Vitis vinifera L.) in response to grafting and pre-harvest applications. Horticulturae, 9.","DOI":"10.3390\/horticulturae9091001"},{"key":"ref_16","doi-asserted-by":"crossref","unstructured":"Wu, J., Wang, P., Xie, R., Nie, H., Wu, X., Ma, Y., Lu, C., Yang, E., Li, N., and Ma, Y. (2025). StMYB308L and its regulatory role in flavonoid biosynthesis pathways in potato. BMC Plant Biol., 25.","DOI":"10.1186\/s12870-025-06897-w"},{"key":"ref_17","doi-asserted-by":"crossref","unstructured":"Liu, G., Gao, H., Song, Y., Wang, H., Zhang, D., Wang, Y., Liu, S., Li, Z., Liu, C., and Sun, Y. (2025). Multiomic analysis reveals that the flavonoid biosynthesis pathway is associated with cold tolerance in Heracleum moellendorffii Hance. Front. Plant Sci., 16.","DOI":"10.3389\/fpls.2025.1544898"},{"key":"ref_18","doi-asserted-by":"crossref","unstructured":"Zhang, B., Lam, T.K.Y., Chen, L., Zhang, C., Zhu, L., Zhang, H., Wang, P., Wang, J., Cai, Z., and Xia, Y. (2025). Single-cell transcriptomics and time-series metabolite profiling reveal the spatiotemporal regulation of flavonoid biosynthesis genes and phytohormone homeostasis by PAP1 in Arabidopsis. BMC Biol., 23.","DOI":"10.1186\/s12915-025-02297-6"},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"133052","DOI":"10.1016\/j.foodchem.2022.133052","article-title":"Metabolomic and biochemical analysis of mesocarp tissues from table grape berries with contrasting firmness reveals cell wall modifications associated to harvest and cold storage","volume":"389","author":"Patricio","year":"2022","journal-title":"Food Chem."},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"117958","DOI":"10.1016\/j.lwt.2025.117958","article-title":"The combined use of 1-MCP and laser microporous film packaging maintains the quality of Shine Muscat grapes by inhibiting oxidative stress and cell wall catabolism","volume":"225","author":"Kong","year":"2025","journal-title":"LWT-Food Sci. Technol."},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"165","DOI":"10.1006\/abio.1995.1127","article-title":"Extraction and determination of ascorbate and dehydroascorbate from plant tissue","volume":"225","author":"Kampfenkel","year":"1995","journal-title":"Anal. Biochem."},{"key":"ref_22","doi-asserted-by":"crossref","unstructured":"He, Y., Cao, X., Pan, K., Shi, W., and Ying, Y. (2024). Integrated transcriptome and metabolome analyses provided insight into the variation in quality of green bamboo (Bambusa oldhamii) shoots at different growth stages. Forests, 15.","DOI":"10.3390\/f15091582"},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"100254","DOI":"10.1016\/j.fochx.2022.100254","article-title":"Impact of melatonin application on lignification in water bamboo shoot during storage","volume":"13","author":"Yang","year":"2022","journal-title":"Food Chem. X"},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"i884","DOI":"10.1093\/bioinformatics\/bty560","article-title":"fastp: An ultra-fast all-in-one FASTQ preprocessor","volume":"34","author":"Chen","year":"2018","journal-title":"Bioinformatics"},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"644","DOI":"10.1038\/nbt.1883","article-title":"Full-length transcriptome assembly from RNA-Seq data without a reference genome","volume":"29","author":"Grabherr","year":"2011","journal-title":"Nat. Biotechnol."},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"59","DOI":"10.1038\/nmeth.3176","article-title":"Fast and sensitive protein alignment using DIAMOND","volume":"12","author":"Buchfink","year":"2015","journal-title":"Nat. Methods"},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"357","DOI":"10.1038\/nmeth.1923","article-title":"Fast gapped-read alignment with Bowtie 2","volume":"9","author":"Langmead","year":"2012","journal-title":"Nat. Methods"},{"key":"ref_28","doi-asserted-by":"crossref","unstructured":"Li, B., and Dewey, C.N. (2011). RSEM: Accurate transcript quantification from RNA-Seq data with or without a reference genome. BMC Bioinform., 12.","DOI":"10.1186\/1471-2105-12-323"},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"550","DOI":"10.1186\/s13059-014-0550-8","article-title":"Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2","volume":"15","author":"Love","year":"2014","journal-title":"Genome Biol."},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"fyaf026","DOI":"10.1093\/fqsafe\/fyaf026","article-title":"Integrative transcriptomics and metabolomics reveal the possible lignification mechanism of Lei bamboo shoots during ambient temperature storage","volume":"9","author":"Chen","year":"2025","journal-title":"Food Qual. Saf."},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"113117","DOI":"10.1016\/j.scienta.2024.113117","article-title":"The effect of pre-harvest and post-harvest aloe vera gel treatments on fruit quality and storage performance of table grapes","volume":"331","author":"Donat","year":"2024","journal-title":"Sci. Hortic."},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"113192","DOI":"10.1016\/j.postharvbio.2024.113192","article-title":"Cell wall and reactive oxygen metabolism responses of stored Shine Muscat grapes to combined melatonin and 24-epibrassinolide treatment","volume":"219","author":"Zeng","year":"2025","journal-title":"Postharvest Biol. Tecnol."},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"100457","DOI":"10.1016\/j.atech.2024.100457","article-title":"SSC and pH prediction and maturity classification of grapes based on hyperspectral imaging","volume":"8","author":"Gao","year":"2024","journal-title":"Smart Agric. Technol."},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"115810","DOI":"10.1016\/j.lwt.2024.115810","article-title":"Sensory characteristics of \u201cShine Muscat\u201d grapes based on consumer reviews and human and intelligent sensory evaluation","volume":"195","author":"Qi","year":"2024","journal-title":"LWT-Food Sci. Technol."},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"117314","DOI":"10.1016\/j.lwt.2024.117314","article-title":"The potential of enzymatic hydrolysis with HS-SPME-GC\u00d7GC-ToFMS for the study of volatile signature of grapes","volume":"215","author":"Fonseca","year":"2025","journal-title":"LWT-Food Sci. Technol."},{"key":"ref_36","doi-asserted-by":"crossref","unstructured":"Liu, Y., Cao, W., Zhang, B., Qin, H., Wang, Y., Yang, Y., Xu, P., Wang, Y., Fan, S., and Li, C. (2025). Effects of different shaping methods and loading on fruit quality and volatile compounds in \u2018Beibinghong\u2019 grapes. Foods, 14.","DOI":"10.3390\/foods14050772"},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"141958","DOI":"10.1016\/j.foodchem.2024.141958","article-title":"Postharvest changes in the phenolic and free volatile compound contents in Shine Muscat grapes at room temperature","volume":"465","author":"Wang","year":"2025","journal-title":"Food Chem."},{"key":"ref_38","doi-asserted-by":"crossref","first-page":"111018","DOI":"10.1016\/j.postharvbio.2019.111018","article-title":"Enhancement of table grape flavor by postharvest application of monoterpenes in modified atmosphere","volume":"159","author":"Tyagi","year":"2020","journal-title":"Postharvest Biol. Tecnol."},{"key":"ref_39","doi-asserted-by":"crossref","first-page":"346","DOI":"10.1016\/j.foodchem.2015.01.018","article-title":"Study of free and glycosidically bound volatile compounds in air-dried raisins from three seedless grape varieties using HS\u2013SPME with GC\u2013MS","volume":"177","author":"Wang","year":"2015","journal-title":"Food Chem."},{"key":"ref_40","doi-asserted-by":"crossref","first-page":"571","DOI":"10.1002\/pts.2903","article-title":"Grape by-products for smart packaging films: Antioxidant, pH-sensitive, uv-blocking and antimicrobial properties for food preservation","volume":"38","author":"Schmitz","year":"2025","journal-title":"Packaging Technol. Sci."},{"key":"ref_41","doi-asserted-by":"crossref","first-page":"142058","DOI":"10.1016\/j.foodchem.2024.142058","article-title":"Cold liquid stabulation: Impact on the phenolic, antioxidant, and aroma characteristics of wines from aroma-neutral white grape varieties","volume":"465","author":"Paolis","year":"2024","journal-title":"Food Chem."},{"key":"ref_42","doi-asserted-by":"crossref","first-page":"112178","DOI":"10.1016\/j.postharvbio.2022.112178","article-title":"Genome-wide identification of the CsPAL gene family and functional analysis for strengthening green mold resistance in citrus fruit","volume":"196","author":"Wei","year":"2023","journal-title":"Postharvest Biol. Tecnol."},{"key":"ref_43","doi-asserted-by":"crossref","unstructured":"Soostani, S.B., Ranjbar, M., Memarian, A., Mohammadi, M., and Yaghini, Z. (2025). Regulation of APX, SOD, and PAL genes by chitosan under salt stress in rapeseed (Brassica napus L.). BMC Plant Biol., 25.","DOI":"10.1186\/s12870-025-06815-0"},{"key":"ref_44","doi-asserted-by":"crossref","unstructured":"Qin, W., Deng, J., Guo, J., Yang, W., and Liu, J. (2025). Metabolic reallocation in soybeans under shade stress alters phenylpropanoid profiles with implications for stress adaptation and seed composition. BMC Plant Biol., 25.","DOI":"10.1186\/s12870-025-06893-0"},{"key":"ref_45","doi-asserted-by":"crossref","unstructured":"Keykha Akhar, F., Bagheri, A., Moshtaghi, N., and Zarei, A. (2025). Downregulation of chalcone isomerase in petunia hybrida: Profound effects on floral morphology and transcriptional remodeling of the flavonoid biosynthetic pathway. BMC Plant Biol., 25.","DOI":"10.1186\/s12870-025-07607-2"},{"key":"ref_46","doi-asserted-by":"crossref","first-page":"229","DOI":"10.1016\/j.fbp.2024.09.016","article-title":"CcCHIL, a type IV chalcone isomerase that can improve (2S)-naringenin production in Saccharomyces cerevisiae","volume":"148","author":"Zhang","year":"2024","journal-title":"Food Bioprod. Process"},{"key":"ref_47","doi-asserted-by":"crossref","first-page":"806","DOI":"10.1104\/pp.109.152801","article-title":"Ectopic expression of apple F3\u2019H genes contributes to anthocyanin accumulation in the Arabidopsis tt7 mutant grown under nitrogen stress","volume":"153","author":"Han","year":"2010","journal-title":"Plant Physiol."},{"key":"ref_48","doi-asserted-by":"crossref","first-page":"42","DOI":"10.1007\/s00425-022-03952-w","article-title":"PHR1 positively regulates phosphate starvation-induced anthocyanin accumulation through direct upregulation of genes F3\u2019H and LDOX in Arabidopsis","volume":"256","author":"Liu","year":"2022","journal-title":"Planta"},{"key":"ref_49","doi-asserted-by":"crossref","first-page":"333","DOI":"10.1007\/s13258-015-0373-3","article-title":"Overexpressing the wheat dihydroflavonol 4-reductase gene TaDFR increases anthocyanin accumulation in an Arabidopsis dfr mutant","volume":"38","author":"Shin","year":"2016","journal-title":"Genes Genom."},{"key":"ref_50","doi-asserted-by":"crossref","unstructured":"An, Y., Li, N., Zhang, R., Wang, S., and Wang, J. (2025). Identification and characterization of DFR gene family and cloning of candidate genes for anthocyanin biosynthesis in pepper (Capsicum annuum L.). BMC Plant Biol., 25.","DOI":"10.1186\/s12870-025-06743-z"}],"container-title":["Foods"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/2304-8158\/15\/5\/823\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,3,4]],"date-time":"2026-03-04T09:35:10Z","timestamp":1772616910000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/2304-8158\/15\/5\/823"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,3,1]]},"references-count":50,"journal-issue":{"issue":"5","published-online":{"date-parts":[[2026,3]]}},"alternative-id":["foods15050823"],"URL":"https:\/\/doi.org\/10.3390\/foods15050823","relation":{},"ISSN":["2304-8158"],"issn-type":[{"value":"2304-8158","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,3,1]]}}}