葡萄TPS基因家族全基因组鉴定及VvTPS4在单萜形成中的功能验证

doi:10.3864/j.issn.0578-1752.2025.07.012

Abstract

Abstract:

【Objective】Based on grape genome information, this study identifies and analyzes the terpene synthase (TPS) gene family expression in grapes using bioinformatics methods. This research lays an important foundation for subsequent studies on the biological functions of VvTPSs and grape breeding. 【Method】The VvTPS gene family was identified using the protein sequences of Arabidopsis AtTPS gene family members and the reported Hidden Markov model (HMM) files PF01397 and PF03936. Various bioinformatics tools, including Expasy, Tbtools, MEME, MEGA, MCScanX, SPOMA, WoLF PSORT, and PlantCARE were used to analyze the physicochemical characteristics, phylogenetic tree, chromosomal distributions, gene structure, subcellular localization, secondary structure of protein, and cis-acting elements in the promoters of gape TPS family genes. Additionally, the expression profiles of TPS genes in two aromatic grape varieties Red Globe (neutral) and Muscat Hamburg (muscat) were analyzed using qPCR. The transgenic tomato overexpressed VvTPS4 was used to study its function in influencing the muscat aroma by metabolomics. 【Result】A total of 65 VvTPS gene family members were identified, encoding proteins ranging from 339 to 840 amino acids, with an average molecular mass of 64.13 kDa and theoretical isoelectric points of 4.93 to 7.65. Most members have 7 exon structures. Phylogenetic analysis classified the grape TPS genes into five subfamilies: TPS-a, TPS-b, TPS-c, TPS-e/f, and TPS-g. Subcellular localization analysis indicated that most VvTPS proteins are localized in chloroplasts and cytoplasm, with 10 members from the TPS-g subfamily found in plastids. Promoter analysis revealed numerous cis-acting elements associated with responses to light, temperature, drought, hormones, and defense mechanisms. Of the 29 VvTPS genes cloned, most showed higher expression levels in the muscat-flavored grape variety compared to the non-aromatic variety. In transgenic tomatoes overexpressing VvTPS4, volatile monoterpenoids were significantly accumulated, with linalool levels increasing 20.73-fold and L-α-terpineol levels rising 14.55-fold compared to the wild type. Flavor characteristics analysis demonstrated these two compounds have floral aroma and are the main characteristic substances affecting the aroma of muscat fragrance.【Conclusion】Sixty-five VvTPS genes were identified in grapes, showing high conservation with some variations. Several TPS genes showed significantly expressed in muscat-flavored grape varieties. Overexpression of VvTPS4 led to a significant increase the accumulation of volatile monoterpenoids, which may play an essential role in developing the muscat aroma in grapes.

Key words: grape, TPS gene family, expression analysis, aroma, metabolomics

YANG CaiLi, LI YongZhou, HE LiangLiang, SONG YinHua, ZHANG Peng, LIU ZhaoXian, LI PengHui, LIU SanJun. Genome-Wide Identification and Analysis of TPS Gene Family and Functional Verification of VvTPS4 in the Formation of Monoterpenes in Grape[J].Scientia Agricultura Sinica, 2025, 58(7): 1397-1417.

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URL: https://www.chinaagrisci.com/EN/10.3864/j.issn.0578-1752.2025.07.012

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Figures/Tables 11

Table 1

Information about TPS gene family members of grape"

蛋白质 Protein	基因ID Gene ID	长度 Length (aa)	分子量 MW (kDa)	等电点 pI	酸性氨基酸比例 Asp+Glu (%)	碱性氨基酸比例 Arg+Lys (%)	不稳定指数 Instability index		总平均亲水性 GRAVY
VvTPS1	VIT_00s0266g00010.t01	507	58.11	5.51	14.20	10.26	38.89	稳定Stable	-0.274
VvTPS2	VIT_00s0266g00020.t01	487	55.90	5.87	13.55	10.88	40.98	不稳定Unstable	-0.309
VvTPS3	VIT_00s0266g00070.t01	517	59.72	5.74	14.12	11.41	39.52	稳定Stable	-0.341
VvTPS4	VIT_00s0271g00010.t01	492	56.48	5.53	14.43	10.77	40.33	不稳定Unstable	-0.323
VvTPS5	VIT_00s0271g00030.t01	482	55.27	5.5	13.90	9.34	39.76	稳定Stable	-0.3
VvTPS6	VIT_00s0271g00060.t01	577	66.27	5.77	13.34	9.71	43.3	不稳定Unstable	-0.348
VvTPS7	VIT_00s0361g00060.t01	566	64.82	5.21	13.07	9.72	44.22	不稳定Unstable	-0.196
VvTPS8	VIT_00s0372g00020.t01	406	46.55	5.65	13.30	9.85	36.91	稳定Stable	-0.254
VvTPS9	VIT_00s0372g00040.t01	507	58.01	5.51	14.20	10.26	37.89	稳定Stable	-0.274
VvTPS10	VIT_00s0372g00070.t01	645	74.07	5.83	12.25	9.46	40.03	不稳定Unstable	-0.144
VvTPS11	VIT_00s0385g00010.t01	490	56.17	5.91	13.67	10.82	34.9	稳定Stable	-0.284
VvTPS12	VIT_00s0385g00020.t01	508	58.19	5.65	14.76	11.02	35.13	稳定Stable	-0.365
VvTPS13	VIT_00s0392g00060.t01	419	47.52	5.41	12.89	9.79	46.18	不稳定Unstable	-0.158
VvTPS14	VIT_00s0450g00010.t01	840	96.05	5.83	12.74	10.48	50.92	不稳定Unstable	-0.214
VvTPS15	VIT_00s0572g00010.t01	450	51.49	5.59	13.56	10.22	42.28	不稳定Unstable	-0.288
VvTPS16	VIT_00s0572g00020.t01	507	58.06	5.56	14.00	10.26	38.38	稳定Stable	-0.284
VvTPS17	VIT_00s0692g00020.t01	555	64.36	5.94	13.15	10.63	39.16	稳定Stable	-0.346
VvTPS18	VIT_00s0724g00010.t01	517	61.02	5.89	14.31	12.38	48.11	不稳定Unstable	-0.371
VvTPS19	VIT_00s0847g00020.t01	545	62.43	5.45	14.13	9.91	40.48	不稳定Unstable	-0.316
VvTPS20	VIT_00s1319g00010.t01	832	95.67	5.75	12.86	9.86	41.75	不稳定Unstable	-0.286
VvTPS21	VIT_00s2271g00010.t01	495	58.39	5.23	15.76	11.52	50.48	不稳定Unstable	-0.427
VvTPS22	VIT_07s0151g01040.t01	828	94.39	6.21	12.44	11.35	45.81	不稳定Unstable	-0.291
VvTPS23	VIT_07s0151g01070.t01	790	90.39	5.36	13.92	10.51	43.28	不稳定Unstable	-0.308
VvTPS24	VIT_10s0116g00750.t01	817	94.37	5.84	13.10	10.53	43.66	不稳定Unstable	-0.266
VvTPS25	VIT_12s0059g02710.t01	519	59.74	5.45	15.22	12.91	47.03	不稳定Unstable	-0.446
VvTPS26	VIT_12s0059g02720.t01	388	44.99	5.36	15.21	12.37	42.38	不稳定Unstable	-0.324
VvTPS27	VIT_12s0134g00020.t01	601	69.76	5.81	15.31	12.65	51.07	不稳定Unstable	-0.397
VvTPS28	VIT_12s0134g00030.t01	579	67.09	6.04	15.20	13.47	47.6	不稳定Unstable	-0.395
VvTPS29	VIT_13s0019g00060.t01	594	69.40	5.28	13.47	10.10	42.16	不稳定Unstable	-0.307
VvTPS30	VIT_13s0067g00050.t01	585	68.49	5.86	14.36	12.14	46.96	不稳定Unstable	-0.393
VvTPS31	VIT_13s0067g00130.t01	521	60.98	7.22	12.67	12.67	43.01	不稳定Unstable	-0.343
VvTPS32	VIT_13s0067g00370.t01	590	68.87	5.62	14.07	11.19	44.69	不稳定Unstable	-0.373
VvTPS33	VIT_13s0067g00380.t01	339	39.94	7.65	13.57	13.86	46.95	不稳定Unstable	-0.476
VvTPS34	VIT_13s0067g03700.t01	566	66.05	5.23	15.02	11.48	48.26	不稳定Unstable	-0.322
VvTPS35	VIT_13s0067g03740.t01	422	49.57	4.93	14.69	10.19	45.77	不稳定Unstable	-0.263
VvTPS36	VIT_13s0067g03790.t01	593	69.40	5.44	13.49	10.62	41.55	不稳定Unstable	-0.326
VvTPS37	VIT_13s0067g03830.t01	440	51.56	5.98	12.27	10.45	39.53	稳定Stable	-0.322
VvTPS38	VIT_13s0084g00010.t01	551	64.65	5.29	15.61	11.43	44.85	不稳定Unstable	-0.413
VvTPS39	VIT_18s0001g04050.t01	535	62.00	5.11	15.89	10.84	44.71	不稳定Unstable	-0.278
VvTPS40	VIT_18s0001g04080.t01	627	72.75	5.16	16.27	11.16	47.2	不稳定Unstable	-0.31
VvTPS41	VIT_18s0001g04120.t01	561	64.68	5.34	15.15	11.05	52.65	不稳定Unstable	-0.354
VvTPS42	VIT_18s0001g04170.t01	515	59.92	5.33	15.34	11.46	46.65	不稳定Unstable	-0.312
VvTPS43	VIT_18s0001g04220.t01	505	58.38	5.3	14.85	11.68	51.24	不稳定Unstable	-0.416
VvTPS44	VIT_18s0001g04280.t01	555	64.37	5.46	15.14	11.71	49.39	不稳定Unstable	-0.308
VvTPS45	VIT_18s0001g04780.t01	561	65.10	5.34	15.15	11.05	52.99	不稳定Unstable	-0.37
VvTPS46	VIT_18s0001g04870.t01	555	64.53	5.6	14.95	11.89	50.54	不稳定Unstable	-0.353
VvTPS47	VIT_18s0001g05230.t01	555	64.43	5.65	14.77	11.89	46.44	不稳定Unstable	-0.349
VvTPS48	VIT_18s0001g05240.t01	561	65.13	5.52	14.62	11.23	55.08	不稳定Unstable	-0.351
VvTPS49	VIT_18s0001g05290.t01	616	71.11	5.91	13.47	11.36	49.31	不稳定Unstable	-0.254
VvTPS50	VIT_18s0001g05360.t01	368	42.57	6.37	12.77	11.68	40.84	不稳定Unstable	-0.113
VvTPS51	VIT_18s0001g05430.t01	482	55.67	5.42	14.94	11.20	50.14	不稳定Unstable	-0.382
VvTPS52	VIT_18s0001g05460.t01	586	67.92	5.68	14.16	11.26	48.87	不稳定Unstable	-0.245
VvTPS53	VIT_18s0001g05470.t01	527	61.61	5.38	15.56	11.57	51.96	不稳定Unstable	-0.326
VvTPS54	VIT_19s0014g01060.t01	559	64.02	5.51	14.13	11.27	47.23	不稳定Unstable	-0.25
VvTPS55	VIT_19s0014g01070.t01	560	65.09	5.19	15.54	11.43	52.7	不稳定Unstable	-0.343
VvTPS56	VIT_19s0014g02550.t01	595	69.06	5.32	15.13	11.60	43.87	不稳定Unstable	-0.282
VvTPS57	VIT_19s0014g02580.t01	517	60.54	5.33	15.67	12.57	43.1	不稳定Unstable	-0.3
VvTPS58	VIT_19s0014g02590.t01	561	64.99	5.07	15.86	11.05	44.53	不稳定Unstable	-0.297
VvTPS59	VIT_19s0014g04800.t01	593	68.81	5.64	14.50	12.14	44.49	不稳定Unstable	-0.37
VvTPS60	VIT_19s0014g04810.t01	559	64.70	5.33	15.03	11.99	46.25	不稳定Unstable	-0.367
VvTPS61	VIT_19s0014g04900.t01	557	64.36	5.48	14.90	11.13	47.66	不稳定Unstable	-0.295
VvTPS62	VIT_19s0014g04930.t01	557	64.32	5.52	14.54	10.77	46.28	不稳定Unstable	-0.252
VvTPS63	VIT_19s0015g02070.t01	562	65.38	5.61	14.59	10.68	52.08	不稳定Unstable	-0.327
VvTPS64	VIT_19s0085g00830.t01	826	93.75	5.91	12.71	10.90	47.51	不稳定Unstable	-0.186
VvTPS65	VitviT2T_020264	422	48.89	5.31	14.93	10.66	49.07	不稳定Unstable	-0.272

Table 1

Table 2

Secondary structure and subcellular localization of grape TPS proteins"

蛋白质 Protein	α-螺旋 α-helix (%)	延伸链 Extended strand (%)	β-转角 β-turn (%)	无规则卷曲 Random coil (%)	亚细胞定位 Subcellular location
VvTPS1	72.58	3.35	3.35	20.71	叶绿体Chloroplast
VvTPS2	72.48	2.87	4.31	20.33	细胞核Nucleus
VvTPS3	70.60	4.45	4.26	20.70	细胞核Nucleus
VvTPS4	71.54	2.85	4.27	21.34	叶绿体Chloroplast
VvTPS5	73.03	3.94	4.77	18.26	叶绿体Chloroplast
VvTPS6	68.80	2.77	3.47	24.96	叶绿体Chloroplast
VvTPS7	69.43	3.36	3.18	24.03	细胞质Cytoplasm
VvTPS8	71.18	4.19	2.22	22.41	叶绿体Chloroplast
VvTPS9	74.56	2.76	3.55	19.13	叶绿体Chloroplast
VvTPS10	61.40	8.53	4.34	25.74	叶绿体Chloroplast
VvTPS11	64.29	5.10	3.47	27.14	叶绿体Chloroplast
VvTPS12	64.17	3.54	3.54	28.74	细胞质Cytoplasm
VvTPS13	74.94	0.48	3.10	21.48	细胞质Cytoplasm
VvTPS14	63.93	3.10	2.74	30.24	质膜Plasmalemma
VvTPS15	71.78	3.56	4.44	20.22	叶绿体Chloroplast
VvTPS16	73.96	3.16	3.75	19.13	叶绿体Chloroplast
VvTPS17	65.41	3.24	2.70	28.65	细胞核Nucleus
VvTPS18	69.44	2.71	2.51	25.34	叶绿体Chloroplast
VvTPS19	71.38	2.20	3.12	23.30	细胞质Cytoplasm
VvTPS20	58.17	5.53	3.37	32.93	细胞质Cytoplasm
VvTPS21	71.52	2.63	3.84	22.02	细胞质Cytoplasm
VvTPS22	57.49	5.43	4.23	32.85	细胞质Cytoplasm
VvTPS23	57.22	5.32	3.67	33.80	叶绿体Chloroplast
VvTPS24	56.18	6.24	3.55	34.03	细胞质Cytoplasm
VvTPS25	68.02	3.85	3.28	24.86	叶绿体Chloroplast
VvTPS26	63.66	4.12	2.32	29.90	叶绿体Chloroplast
VvTPS27	67.22	3.33	3.00	26.46	叶绿体Chloroplast
VvTPS28	68.05	2.76	3.63	25.56	线粒体Mitochondrion
VvTPS29	65.15	3.54	4.04	27.27	叶绿体Chloroplast
VvTPS30	66.67	4.62	3.59	25.13	线粒体Mitochondrion
VvTPS31	67.37	4.41	3.45	24.76	细胞质Cytoplasm
VvTPS32	66.95	2.88	3.56	26.61	叶绿体Chloroplast
VvTPS33	65.49	5.01	2.65	26.84	叶绿体Chloroplast
VvTPS34	67.67	3.18	3.89	25.27	叶绿体Chloroplast
VvTPS35	72.27	3.79	3.79	20.14	细胞质Cytoplasm
VvTPS36	65.60	3.88	3.20	27.32	叶绿体Chloroplast
VvTPS37	68.64	1.82	2.27	27.27	叶绿体Chloroplast
VvTPS38	70.42	3.45	3.45	22.69	细胞质Cytoplasm
VvTPS39	70.47	5.05	4.11	20.37	细胞质Cytoplasm
VvTPS40	68.90	4.78	2.55	23.76	内质网Endoplasmicreticulum
VvTPS41	67.91	5.35	3.57	23.17	内质网Endoplasmicreticulum
VvTPS42	67.77	5.05	3.69	23.50	细胞质Cytoplasm
VvTPS43	67.33	5.15	3.17	24.36	细胞核Nucleus
VvTPS44	69.19	4.14	3.96	22.70	细胞质Cytoplasm
VvTPS45	67.02	4.99	3.39	24.60	细胞核Nucleus
VvTPS46	68.83	4.32	3.24	23.60	细胞质Cytoplasm
VvTPS47	68.65	4.6	3.78	22.88	细胞质Cytoplasm
VvTPS48	67.74	4.63	3.21	24.42	细胞核Nucleus
VvTPS49	61.36	7.47	3.57	27.60	叶绿体Chloroplast
VvTPS50	73.10	2.99	2.45	21.47	质膜Plasmalemma
VvTPS51	69.71	3.94	4.15	22.20	线粒体Mitochondrion
VvTPS52	65.53	6.14	3.41	24.91	叶绿体Chloroplast
VvTPS53	73.62	4.17	3.23	18.98	叶绿体Chloroplast
VvTPS54	67.26	4.47	3.22	25.04	叶绿体Chloroplast
VvTPS55	67.68	4.82	3.21	24.29	细胞质Cytoplasm
VvTPS56	65.38	4.37	3.03	27.23	线粒体Mitochondrion
VvTPS57	66.92	4.45	3.09	25.53	细胞质Cytoplasm
VvTPS58	68.81	5.17	3.39	22.64	叶绿体Chloroplast
VvTPS59	66.95	5.90	3.04	24.11	细胞质Cytoplasm
VvTPS60	68.69	5.01	3.40	22.90	细胞质Cytoplasm
VvTPS61	70.38	4.85	3.41	21.36	叶绿体Chloroplast
VvTPS62	68.22	6.46	4.13	21.18	叶绿体Chloroplast
VvTPS63	68.51	5.16	3.02	23.31	细胞质Cytoplasm
VvTPS64	62.59	5.57	4.24	27.60	细胞核Nucleus
VvTPS65	72.99	3.55	3.32	20.14	细胞质Cytoplasm

Table 2

Fig. 1

Fig. 2

Fig. 3

Table 3

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Fig. 7

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基因对Gene pairs	Ka	Ks	Ka/Ks
VvTPS25/MD17G0079700	0.423	1.805	0.235
VvTPS64/MD10G0181600	0.237	0.949	0.250
VvTPS61/MD11G0189300	0.277	1.412	0.196
VvTPS61/MD17G0079700	0.542	2.558	0.212
VvTPS59/MD03G0176900	0.297	1.161	0.255
VvTPS22/MD11G0231900	0.248	1.559	0.159
VvTPS22/MD03G0216300	0.271	2.019	0.134
VvTPS7/MD17G0078700	0.432	2.276	0.190
VvTPS9/MD05G0280700	0.271	1.216	0.223
VvTPS8/MD05G0280900	0.512	1.508	0.340
VvTPS27/ONI13020	0.592	1.868	0.317
VvTPS59/ONI13020	0.303	1.162	0.261
VvTPS59/ONI12956	0.319	1.025	0.311
VvTPS64/ONI11835	0.209	0.904	0.231
VvTPS59/ONI12905	0.324	1.696	0.191
VvTPS22/ONH93575	0.211	1.631	0.129
VvTPS7/ONI10138	0.312	1.133	0.275
VvTPS7/ONI13020	0.602	2.450	0.246
VvTPS8/ONI12958	0.664	1.766	0.376
VvTPS9/ONI12959	0.655	2.753	0.238
VvTPS12/ONI12902	0.595	2.069	0.287
VvTPS11/ONI12905	0.621	2.249	0.276
VvTPS9/ONI13050	0.657	2.950	0.223

Genome-Wide Identification and Analysis of TPS Gene Family and Functional Verification of VvTPS4 in the Formation of Monoterpenes in Grape

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