基于转录组与代谢组解析红肉葡萄及其自交后代果肉类黄酮积累特征

doi:10.3864/j.issn.0578-1752.2026.16.013

中国农业科学 ›› 2026, Vol. 59 ›› Issue (16): 3655-3672.doi: 10.3864/j.issn.0578-1752.2026.16.013

基于转录组与代谢组解析红肉葡萄及其自交后代果肉类黄酮积累特征

吴培景²(), 苏玲¹(), 陈迎春¹, 孟冬², 杨清², 张曼², 周小苗², 陶建敏³, 郑焕³, 李勃¹, 宫磊¹^,³()

¹ 山东省葡萄研究院/济南市果品品质调控与精深加工重点实验室，济南 250100
² 北京林业大学林学院，北京 100083
³ 南京农业大学园艺学院，南京 210095

收稿日期:2026-04-25 接受日期:2026-06-26 出版日期:2026-08-16 发布日期:2026-08-17
通信作者:
宫磊，E-mail：glflysky@163.com。
联系方式: 吴培景，E-mail：wu15318838869@163.com。苏玲，E-mail：susulingzi@126.com。吴培景和苏玲为同等贡献作者。
基金资助:
山东省农业科学院农业科技创新工程(CXGC2026A08); 国家葡萄产业技术体系(CARS-29)

Integrative Transcriptomic and Metabolomic Analyses Reveal Flavonoid Accumulation Characteristics in the Flesh of Red-Fleshed Grape and Self-Pollinated Progenies

WU PeiJing²(), SU Ling¹(), CHEN YingChun¹, MENG Dong², YANG Qing², ZHANG Man², ZHOU XiaoMiao², TAO JianMin³, ZHENG Huan³, LI Bo¹, GONG Lei¹^,³()

¹ Shandong Academy of Grape, Jinan Key Laboratory of Fruit Quality Control and Deep Processing, Jinan 250100
² College of Forestry, Beijing Forestry University, Beijing 100083
³ College of Horticulture, Nanjing Agricultural University, Nanjing 210095

Received:2026-04-25 Accepted:2026-06-26 Published:2026-08-16 Online:2026-08-17

摘要/Abstract

摘要：

【目的】研究红肉葡萄及其自交后代果肉类黄酮的基因表达及代谢组分差异，解析类黄酮生物合成的代谢积累特征并提供转录调控线索，为提高葡萄果实类黄酮含量及培育葡萄新品种提供理论基础。【方法】以红肉葡萄新种质‘钟山红玉’（ZSHY）和自交后代‘南19’（N19）、‘南30’（N30），以及‘玫瑰香’（MGX）为试验材料，设置ZSHY_vs_MGX、N30_vs_ZSHY、N19_vs_MGX和N30_vs_N19四个组别，进行果肉类黄酮靶向代谢组学和转录组学（RNA-seq）检测，通过富集分析鉴定类黄酮代谢物积累、合成关键基因以及转录调控的网络。【结果】基于类黄酮靶向代谢组学技术，检测出104种表达差异的类黄酮代谢物，并鉴定出62种显著差异的核心类黄酮代谢物，其中‘ZSHY’和‘N19’中黄酮醇、黄烷醇等多数代谢物积累量显著高于‘N30’和‘MGX’。KEGG通路富集分析显示差异代谢物显著富集于类黄酮生物合成相关通路，特别是花青素苷、黄酮与黄酮醇生物合成途径。转录组学分析共筛选到758个差异表达基因（DEGs），显著富集于类黄酮、苯丙烷类生物合成等通路。进一步鉴定出30个核心差异表达的类黄酮合成关键结构基因，其表达模式与类黄酮代谢物积累趋势基本一致，即在‘ZSHY’和‘N19’中表达量高，在‘N30’和‘MGX’中表达量低。此外，筛选出22个与类黄酮合成结构基因显著相关的转录因子，主要包括WRKY、MYB、ERF等家族。【结论】红肉葡萄与其自交后代间存在显著的类黄酮代谢差异，‘ZSHY’和‘N19’果肉中类黄酮的较高积累与其合成通路关键结构基因的高表达密切相关，且转录因子可能对类黄酮合成基因具有调控作用。

关键词: 红肉葡萄, 果肉, 自交后代, 类黄酮, 转录组, 代谢组

Abstract:

【Objective】 This study investigated differences in flavonoid-related gene expression and metabolite profiles in the flesh of red-fleshed grape berries and their self-pollinated progenies, aiming to elucidate the metabolic accumulation characteristics of flavonoid biosynthesis, and provide insights into transcriptional regulation, so as to lay a theoretical foundation for improving flavonoid contents in grape berries and breeding new grape varieties. 【Method】 The red-fleshed grape germplasm Zhongshanhongyu (ZSHY), its self-pollinated progenies Nan 19 (N19) and Nan 30 (N30), and Muscat (MGX) were used as materials. Four pairwise comparison groups (ZSHY_vs_MGX, N30_vs_ZSHY, N19_vs_MGX, and N30_vs_N19) were established for targeting flavonoid metabolomics alongside transcriptome sequencing (RNA-seq) of berry flesh. Enrichment analyses were subsequently conducted to characterize flavonoid metabolites accumulation, identify key structural genes, and dissect the transcriptional regulatory networks involved in flavonoid biosynthetic pathway. 【Result】 Based on targeted flavonoid metabolomics technology, a total of 104 differentially accumulated flavonoid metabolites were detected, and 62 core metabolites exhibiting significant differences were further identified. Notably, most flavonols and flavanols accumulated to substantially higher levels in ZSHY and N19 than in N30 and MGX. KEGG enrichment analysis revealed that these differential metabolites were predominantly enriched in flavonoid biosynthesis pathways, particularly responsible for anthocyanin, flavone, and flavonol biosynthesis. Transcriptome profiling identified 758 differentially expressed genes (DEGs), which were significantly overrepresented in flavonoid and phenylpropanoid biosynthesis pathways. Furthermore, 30 core DEGs directly involved in flavonoid biosynthesis were screened, whose expression patterns were broadly consistent with the metabolite accumulation profiles, showing high transcript abundance in ZSHY and N19, but low expression in N30 and MGX. In addition, 22 transcription factors (TFs) significantly correlated with flavonoid structural genes were identified, mainly belonging to the WRKY, MYB, and ERF families. 【Conclusion】 Significant differences existed in flavonoid metabolism between the red-fleshed grape and its self-pollinated progenies. The elevated flavonoid accumulation in the flesh of ZSHY and N19 was closely associated with the upregulation of the key structural genes in the flavonoid pathway, and the identified TFs might play important regulatory roles in this process.

Key words: red-fleshed grape, fruit flesh, self-progeny, flavonoids, transcriptome, metabolomics

吴培景, 苏玲, 陈迎春, 孟冬, 杨清, 张曼, 周小苗, 陶建敏, 郑焕, 李勃, 宫磊. 基于转录组与代谢组解析红肉葡萄及其自交后代果肉类黄酮积累特征[J]. 中国农业科学, 2026, 59(16): 3655-3672.

WU PeiJing, SU Ling, CHEN YingChun, MENG Dong, YANG Qing, ZHANG Man, ZHOU XiaoMiao, TAO JianMin, ZHENG Huan, LI Bo, GONG Lei. Integrative Transcriptomic and Metabolomic Analyses Reveal Flavonoid Accumulation Characteristics in the Flesh of Red-Fleshed Grape and Self-Pollinated Progenies[J]. Scientia Agricultura Sinica, 2026, 59(16): 3655-3672.

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基因Gene	基因ID Gene ID	引物序列Primers sequence (5′-3′)
Actin	—	F: CTTGGCTGATAGGCTGGCGAAG R: TCCACATCTGCTCAAAGGTGCTTAG
PAL	VIT_13s0019g04460	F: ATGAGGTGAAGCGGATGGTG R: GCCTTTACTCCCTCTCTCGC
CYP73A4	VIT_06s0004g08150	F: AATCCTGGTGAACGCATGGT R: TTGGCCTCAACCTTGGACTC
4CL2	VIT_11s0052g01090	F: CCAGATCATCTTCCGCTGCA R: GCCTTGCTTGATCCCCATCT
CHS	VIT_14s0068g00920	F: CCAAAATCGAACGCCCACTC R: TGGAAATCAACCCTGGGACG
CHIL2	VIT_13s0067g02870	F: CAAGGGTTCACAGTACGGGG R: TCCAAAGCTTCCTCCTCCTCT
CHI	VIT_13s0067g03820	F: TGGAGTCCATCATCGGCAAG R: TTCTCATCCCCAGCCTCCTT
HCT	VIT_11s0037g00440	F: GCCTCTCCCATGATCAACCC R: GCGTTGCGAATCCTCTGAAC
CYP75B2	VIT_17s0000g07210	F: CCTCTACCACTTCCTCACGC R: GCCCATACGGAGATGCATGA
CYP75A1	VIT_06s0009g02970	F: TTATGGGGCAAGGTGGAAGC R: TTAACATCTCCGGCACCACC
DFR	VIT_18s0001g12800	F: AATGAAATCGTGTGCTGCCG R: ACTCCAGCAGCTTTCATCGT
LDOX	VIT_02s0025g04720	F: ATGGTGACTTCAGTGGCTCC R: GAACCTGAGGCCCTTCATCC
UFGT	VIT_16s0039g02230	F: AATGGGAGGATGGTGGAGGA R: TAGGACCAACTGCCCTGTCT

样品 Sample	原始数据 Raw reads (M)	过滤后数据 Clean reads (M)	过滤后碱基总数 Clean bases (G)	有效碱基百分比 Valid bases (%)	碱基质量值 Q30 (%)	GC含量 GC content (%)	特异比对率 Unique map (%)
MGX-1	44.82	44.71	6.70	99.77	97.94	46.24	86.00
MGX-2	46.83	46.74	7.00	99.80	97.89	45.98	88.42
MGX-3	45.39	45.27	6.78	99.73	97.95	46.56	86.93
N30-1	46.26	46.12	6.90	99.71	97.99	46.26	86.66
N30-2	46.78	46.68	6.99	99.79	97.86	46.32	85.48
N30-3	46.69	46.56	6.97	99.72	97.96	46.35	86.81
ZSHY-1	46.35	46.22	6.92	99.72	98.00	47.08	83.65
ZSHY-2	46.29	46.14	6.91	99.68	98.02	46.56	86.76
ZSHY-3	46.15	46.05	6.90	99.77	98.01	46.80	86.10
N19-1	46.91	46.67	6.97	99.47	97.94	46.17	85.52
N19-2	46.70	46.50	6.95	99.55	97.92	46.33	85.43
N19-3	47.25	47.11	7.05	99.70	97.89	46.30	85.44

基因名称 Gene name	基因 Gene	基因ID Gene ID	数量 Count	编号 KO ID
苯丙氨酸解氨酶 Phenylalanine ammonia-lyase	PAL	VIT_13s0019g04460	1	K10775
肉桂酸-4-羟化酶 Cinnamate-4-hydroxylase	CYP73A	VIT_06s0004g08150	1	K00487
4-香豆酸辅酶A连接酶 4-coumarate coenzyme A ligase	4CL2	VIT_11s0052g01090; VIT_16s0039g02040	2	K01904
查尔酮合成酶 Chalcone synthase	CHS	VIT_16s0022g01020; VIT_05s0136g00260; VIT_14s0068g00920; VIT_16s0022g01140; VIT_16s0022g01190; VIT_00s1492g00010; VIT_16s0022g01000	7	K00660
查尔酮异构酶样蛋白 Chalcone-flavanone isomerase-related	CHIL2	VIT_13s0067g02870	1	K01859
查尔酮异构酶Chalcone isomerase	CHI	VIT_13s0067g03820	1	K01859
莽草酸O-羟基肉桂酰转移酶 Shikimate O-hydroxycinnamoyltransferase	HCT	VIT_11s0037g00440	1	K13065
黄烷酮3'羟化酶Flavonoid 3'- hydroxylase	CYP75B2	VIT_17s0000g07200; VIT_17s0000g07210	2	K05280
类黄酮3', 5'羟基化酶 Flavonoid 3', 5'-hydroxylase	CYP75A1	VIT_06s0009g02970; VIT_06s0009g02840; VIT_06s0009g02860	3	K13083
	CYP75A2	VIT_06s0009g02830	1	K13083
	CYP75A3	VIT_06s0009g02920; VIT_06s0009g02880; VIT_06s0009g02810	3	K13083
类黄酮 O-甲基转移酶 Flavonoid O-methyltransferase	FAOMT	VIT_01s0010g03510; VIT_01s0010g03470; IT_01s0010g03490; VIT_01s0010g03460	4	K13272
二氢黄酮醇-4-还原酶 Dihydroflavonol 4-reductase	DFR	VIT_18s0001g12800	1	K13802
无色花青素双加氧酶 Leucoanthocyanin dioxygenase	LDOX	VIT_02s0025g04720	1	K05277
UDP类黄酮-3-O-葡萄糖基转移酶 UDP flavonoid-3-O-glucosyltransferase	UFGT	VIT_16s0039g02230	1	K12930

基于转录组与代谢组解析红肉葡萄及其自交后代果肉类黄酮积累特征

Integrative Transcriptomic and Metabolomic Analyses Reveal Flavonoid Accumulation Characteristics in the Flesh of Red-Fleshed Grape and Self-Pollinated Progenies

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