[1] Zhang X, Wu Y, Li Z, Song C, Wang X. 2021. Advancements in plant regeneration and genetic transformation of grapevine (Vitis spp.). Journal of Integrative Agriculture 20:1407−34 doi: 10.1016/S2095-3119(20)63586-9
[2] Jang M, Cai L, Udeani GO, Slowing KV, Thomas CF, et al. 1997. Cancer chemopreventive activity of resveratrol, a natural product derived from grapes. Science 275:218−20 doi: 10.1126/science.275.5297.218
[3] Fiod Riccio BV, Fonseca-Santos B, Colerato Ferrari P, Chorilli M. 2020. Characteristics, biological properties and analytical methods of t rans-resveratrol: a review. Critical Reviews in Analytical Chemistry 50:339−58 doi: 10.1080/10408347.2019.1637242
[4] Vannozzi A, Dry IB, Fasoli M, Zenoni S, Lucchin M. 2012. Genome-wide analysis of the grapevine stilbene synthase multigenic family: genomic organization and expression profiles upon biotic and abiotic stresses. BMC Plant Biology 12:130 doi: 10.1186/1471-2229-12-130
[5] Halls C, Yu O. 2008. Potential for metabolic engineering of resveratrol biosynthesis. Trends in Biotechnology 26:77−81 doi: 10.1016/j.tibtech.2007.11.002
[6] Dubrovina AS, Kiselev KV. 2017. Regulation of stilbene biosynthesis in plants. Planta 246:597−623 doi: 10.1007/s00425-017-2730-8
[7] Zhou Y, Massonnet M, Sanjak JS, Cantu D, Gaut BS. 2017. Evolutionary genomics of grape (Vitis vinifera ssp. vinifera) domestication. PNAS 114:11715−20 doi: 10.1073/pnas.1709257114
[8] Yin X, Singer SD, Qiao H, Liu Y, Jiao C, et al. 2016. Insights into the mechanisms underlying ultraviolet-c induced resveratrol metabolism in grapevine (V. amurensis Rupr.) cv. "Tonghua-3". Frontiers in Plant Science 7:503 doi: 10.3389/fpls.2016.00503
[9] Wang J, Ma L, Xi H, Wang L, Li S. 2015. Resveratrol synthesis under natural conditions and after UV-C irradiation in berry skin is associated with berry development stages in 'Beihong' (V. vinifera × V. amurensis). Food Chemistry 168:430−38 doi: 10.1016/j.foodchem.2014.07.025
[10] Crupi P, Pichierri A, Basile T, Antonacci D. 2013. Postharvest stilbenes and flavonoids enrichment of table grape cv Redglobe (Vitis vinifera L.) as affected by interactive UV-C exposure and storage conditions. Food Chemistry 141:802−8 doi: 10.1016/j.foodchem.2013.03.055
[11] Hasan M, Bae H. 2017. An overview of stress-induced resveratrol synthesis in grapes: perspectives for resveratrol-enriched grape products. Molecules 22:294 doi: 10.3390/molecules22020294
[12] Leng F, Cao J, Ge Z, Wang Y, Zhao C, et al. 2020. Transcriptomic analysis of root restriction effects on phenolic metabolites during grape berry development and ripening. Journal of Agricultural and Food Chemistry 68:9090−99 doi: 10.1021/acs.jafc.0c02488
[13] Höll J, Vannozzi A, Czemmel S, D'Onofrio C, Walker AR, et al. 2013. The R2R3-MYB transcription factors MYB14 and MYB15 regulate stilbene biosynthesis in Vitis vinifera. The Plant Cell 25:4135−49 doi: 10.1105/tpc.113.117127
[14] Fang L, Hou Y, Wang L, Xin H, Wang N, et al. 2014. Myb14, a direct activator of STS, is associated with resveratrol content variation in berry skin in two grape cultivars. Plant Cell Reports 33:1629−40 doi: 10.1007/s00299-014-1642-3
[15] Vannozzi A, Wong DCJ, Höll J, Hmmam I, Matus JT, et al. 2018. Combinatorial regulation of stilbene synthase genes by WRKY and MYB transcription factors in grapevine (Vitis vinifera L.). Plant and Cell Physiology 59:1043−59 doi: 10.1093/pcp/pcy045
[16] Jiang J, Xi H, Dai Z, Lecourieux F, Yuan L, et al. 2019. VvWRKY8 represses stilbene synthase genes through direct interaction with VvMYB14 to control resveratrol biosynthesis in grapevine. Journal of Experimental Botany 70:715−29 doi: 10.1093/jxb/ery401
[17] Wang L, Wang Y. 2019. Transcription factor VqERF114 regulates stilbene synthesis in Chinese wild Vitis quinquangularis by interacting with VqMYB35. Plant Cell Reports 38:1347−60 doi: 10.1007/s00299-019-02456-4
[18] Jaillon O, Aury JM, Noel B, Policriti A, Clepet C, et al. 2007. The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla. Nature 449:463−7 doi: 10.1038/nature06148
[19] Sweetman C, Wong DCJ, Ford CM, Drew DP. 2012. Transcriptome analysis at four developmental stages of grape berry (Vitis vinifera cv. Shiraz) provides insights into regulated and coordinated gene expression. BMC Genomics 13:691 doi: 10.1186/1471-2164-13-691
[20] Balic I, Vizoso P, Nilo-Poyanco R, Sanhueza D, Olmedo P, et al. 2018. Transcriptome analysis during ripening of table grape berry cv. Thompson Seedless. PLoS One 13:e0190087 doi: 10.1371/journal.pone.0190087
[21] Zhong H, Zhang F, Pan M, Wu X, Zhang W, et al. 2020. Comparative phenotypic and transcriptomic analysis of Victoria and flame seedless grape cultivars during berry ripening. FEBS Open Bio 10:2616−30 doi: 10.1002/2211-5463.12996
[22] Gambino G, Boccacci P, Pagliarani C, Perrone I, Cuozzo D, et al. 2021. Secondary metabolism and defense responses are differently regulated in two grapevine cultivars during ripening. International Journal of Molecular Sciences 22:3045 doi: 10.3390/ijms22063045
[23] He L, Meng N, Castellarin SD, Wang Y, Sun Q, et al. 2021. Combined metabolite and transcriptome profiling reveals the norisoprenoid responses in grape berries to abscisic acid and synthetic auxin. International Journal of Molecular Sciences 22:1420 doi: 10.3390/ijms22031420
[24] Wang ZG, Guo LL, Ji XR, Yu YH, Zhang GH, Guo DL. 2019. Transcriptional analysis of the early ripening of 'Kyoho' grape in response to the treatment of riboflavin. Genes 10:514 doi: 10.3390/genes10070514
[25] Kong Q, Deng R, Li X, Zeng Q, Zhang X, et al. 2020. Based on RNA-Seq analysis identification and expression analysis of Trans-scripusinA synthesize-related genes of UV-treatment in postharvest grape fruit. Archives of Biochemistry and Biophysics 690:108471 doi: 10.1016/j.abb.2020.108471
[26] Zhang X, Zhang L, Ji M, Wu Y, Zhang S, et al. 2021. Genome-wide identification and expression analysis of the B-box transcription factor gene family in grapevine (Vitis vinifera L.). BMC Genomics 22:221 doi: 10.1186/s12864-021-07479-4
[27] Valletta A, Iozia LM, Leonelli F. 2021. Impact of environmental factors on stilbene biosynthesis. Plants 10:90 doi: 10.3390/plants10010090
[28] Li X, Wu B, Wang L, Li S. 2006. Extractable amounts of trans-resveratrol in seed and berry skin in Vitis evaluated at the germplasm level. Journal of Agricultural and Food Chemistry 54:8804−11 doi: 10.1021/jf061722y
[29] Leng F, Ye Y, Zhou J, Jia H, Zhu X, et al. 2021. Transcriptomic and weighted gene co-expression correlation network analysis reveal resveratrol biosynthesis mechanisms caused by bud sport in grape berry. Frontiers in Plant Science 12:690095 doi: 10.3389/fpls.2021.690095
[30] Zheng X, Shi J, Yu Y, Shen Y, Tan B, et al. 2017. Exploration of elite stilbene synthase alleles for resveratrol concentration in wild Chinese Vitis spp. and Vitis cultivars. Frontiers in Plant Science 8:487 doi: 10.3389/fpls.2017.00487
[31] Kersey PJ, Allen JE, Armean I, Boddu S, Bolt BJ, et al. 2016. Ensembl Genomes 2016: more genomes, more complexity. Nucleic Acids Research 44:D574−D580 doi: 10.1093/nar/gkv1209
[32] Gu B, Zhang B, Ding L, Li P, Shen L, Zhang J. 2020. Physiological change and transcriptome analysis of Chinese wild Vitis amurensis and Vitis viniferain response to cold stress. Plant Molecular Biology Reporter 38:478−90 doi: 10.1007/s11105-020-01210-5
[33] Li R, Xie X, Ma F, Wang D, Wang L, et al. 2017. Resveratrol accumulation and its involvement in stilbene synthetic pathway of Chinese wild grapes during berry development using quantitative proteome analysis. Scientific Reports 7:9295 doi: 10.1038/s41598-017-10171-x
[34] Park SC, Pyun JW, Jeong YJ, Park SH, Kim S, et al. 2021. Overexpression of VlPRX21 and VlPRX35 genes in Arabidopsis plants leads to bioconversion of trans-resveratrol to δ-viniferin. Plant Physiology and Biochemistry 162:556−63 doi: 10.1016/j.plaphy.2021.03.015
[35] Yan C, Yang N, Wang X, Wang Y. 2021. VqBGH40a isolated from Chinese wild Vitis quinquangularis degrades trans-piceid and enhances trans-resveratrol. Plant Science 310:110989 doi: 10.1016/j.plantsci.2021.110989
[36] Wang K, Li C, Lei C, Zou Y, Li Y, et al. 2021. Dual function of VvWRKY18 transcription factor in the β-aminobutyric acid-activated priming defense in grapes. Physiologia Plantarum 172:1477−92 doi: 10.1111/ppl.13341
[37] Wang D, Jiang C, Liu W, Wang Y. 2020. The WRKY53 transcription factor enhances stilbene synthesis and disease resistance by interacting with MYB14 and MYB15 in Chinese wild grape. Journal of Experimental Botany 71:3211−26 doi: 10.1093/jxb/eraa097
[38] Jiang C, Wang D, Zhang J, Xu Y, Zhang C, et al. 2021. VqMYB154 promotes polygene expression and enhances resistance to pathogens in Chinese wild grapevine. Horticulture Research 8:151 doi: 10.1038/s41438-021-00585-0
[39] Orduña L, Li M, Navarro-Payá D, Zhang C, Santiago A, et al. 2022. Direct regulation of shikimate, early phenylpropanoid and stilbenoid pathways by Subgroup 2 R2R3-MYBs in grapevine. The Plant Journal 110:529−47 doi: 10.1111/tpj.15686
[40] Wang D, Jiang C, Li R, Wang Y. 2019. VqbZIP1 isolated from Chinese wild Vitis quinquangularis is involved in the ABA signaling pathway and regulates stilbene synthesis. Plant Science 287:110202 doi: 10.1016/j.plantsci.2019.110202
[41] Trapnell C, Pachter L, Salzberg SL. 2009. TopHat: discovering splice junctions with RNA-Seq. Bioinformatics 25:1105−11 doi: 10.1093/bioinformatics/btp120
[42] Pertea M, Pertea GM, Antonescu CM, Chang TC, Mendell JT, et al. 2015. StringTie enables improved reconstruction of a transcriptome from RNA-seq reads. Nature Biotechnology 33:290−95 doi: 10.1038/nbt.3122
[43] Trapnell C, Williams BA, Pertea G, Mortazavi A, Kwan G, et al. 2010. Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nature Biotechnology 28:511−15 doi: 10.1038/nbt.1621
[44] Schulze SK, Kanwar R, Gölzenleuchter M, Therneau TM, Beutler AS. 2012. SERE: single-parameter quality control and sample comparison for RNA-Seq. BMC Genomics 13:524 doi: 10.1186/1471-2164-13-524
[45] Wang L, Feng Z, Wang X, Wang X, Zhang X. 2010. DEGseq: an R package for identifying differentially expressed genes from RNA-seq data. Bioinformatics 26:136−38 doi: 10.1093/bioinformatics/btp612
[46] Benjamini Y, Hochberg Y. 1995. Controlling the false discovery rate: a practical and powerful approach to multiple testing. Journal of the Royal Statistical Society: Series B (Methodological) 57:289−300 doi: 10.1111/j.2517-6161.1995.tb02031.x
[47] Young MD, Wakefield MJ, Smyth GK, Oshlack A. 2010. Gene ontology analysis for RNA-seq: accounting for selection bias. Genome Biology 11:R14 doi: 10.1186/gb-2010-11-2-r14
[48] Ai C, Kong L. 2018. CGPS: A machine learning-based approach integrating multiple gene set analysis tools for better prioritization of biologically relevant pathways. Journal of Genetics and Genomics 45:489−504 doi: 10.1016/j.jgg.2018.08.002
[49] Langfelder P, Horvath S. 2008. WGCNA: an R package for weighted correlation network analysis. BMC Bioinformatics 9:559 doi: 10.1186/1471-2105-9-559
[50] Langfelder P, Zhang B, Horvath S. 2008. Defining clusters from a hierarchical cluster tree: the Dynamic Tree Cut package for R. Bioinformatics 24:719−20 doi: 10.1093/bioinformatics/btm563
[51] Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, et al. 2003. Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Research 13:2498−504 doi: 10.1101/gr.1239303
[52] Livak KJ, Schmittgen TD. 2001. Analysis of relative gene expression data using real-time quantitative PCR and the 2ΔΔCᴛ method. Methods 25:402−8 doi: 10.1006/meth.2001.1262