甘蓝叶酸合成代谢的转录组初步分析

doi:10.16420/j.issn.0513-353x.2025-0045

摘要/Abstract

摘要：

对127份甘蓝自交系材料的叶酸组分和含量进行了靶向代谢组分析，确定甘蓝中叶酸主要组分为5-甲基-四氢叶酸（占比60% ~ 80%）和5-甲酰-四氢叶酸（占比15% ~ 25%），筛选出早熟圆球型高叶酸自交系材料Q428和低叶酸自交系材料Q372。通过Q428和Q372比较转录组分析，鉴定出10 305个差异表达基因，在Q428中上调和下调表达的基因分别有5 178、5 127个。GO分析显示，差异表达基因与光合作用、光收集、蛋白质—发色团连接和叶绿素结合等相关；KEGG分析表明，差异表达基因主要集中于碳代谢、氨基酸生物合成及淀粉和蔗糖代谢等通路。通过与24个拟南芥叶酸合成代谢基因的共线性分析，在甘蓝中鉴定到叶酸合成代谢相关基因57个，其中12个关键基因在Q428和Q372中显著差异表达。与Q372相比，Q428中BoGCHI、GDC复合体相关编码基因（BoGCSH、BoGCSL、BoGCSP、BoGCST）、BoMTHFR和BoSHMT1a的表达量显著上调，而BoGGH在Q428中表达量显著下调。初步推测上述基因的差异表达是影响甘蓝叶酸含量的关键因素，可作为利用生物育种技术调控甘蓝叶酸含量的分子靶点。

关键词: 甘蓝, 叶酸, 转录组, 代谢组

Abstract:

A targeted metabolomic analysis was conducted on the folate composition and content of 127 cabbage inbred lines. The main folate components in cabbage were identified as 5-methyl- tetrahydrofolate（60%-80% of the total）and 5-formyl-tetrahydrofolate（15%-25% of the total）. Early-maturing，round-headed high-folate inbred line Q428 and low-folate inbred line Q372 were selected for further study. Comparative transcriptomic analysis of Q428 and Q372 identified 10 305 differentially expressed genes，with 5 178 genes upregulated and 5 127 genes downregulated in Q428. Gene Ontology analysis indicated that the differentially expressed genes were associated with processes such as photosynthesis，light harvesting，protein-chromophore interactions，and chlorophyll binding. KEGG pathway analysis revealed that these genes were primarily involved in carbon metabolism，amino acid biosynthesis，and starch and sucrose metabolism.Through a collinearity analysis with 24 Arabidopsis folate biosynthesis genes，a total of 57 folate-related genes were identified in cabbage，of which 12 key genes showed significant differential expression between Q428 and Q372. Compared to Q372，the expression levels of BoGCHI，genes associated with the GDC complex（BoGCSH，BoGCSL，BoGCSP，BoGCST），BoMTHFR，and BoSHMT1a were significantly upregulated in Q428，while the expression of BoGGH was significantly downregulated. The differential expression of these genes is preliminarily hypothesized to be a key factor affecting the folate content in cabbage，and these genes could serve as molecular targets for manipulating folate content in cabbage through biotechnological breeding techniques.

Key words: cabbage, folate, transcriptome, metabolome

张悦, 冯一了, 王蓓, 任文静, 姜春昱, 赵新宇, 王彩红, 杨丽梅, 庄木, 吕红豪, 王勇, 张扬勇, 季家磊. 甘蓝叶酸合成代谢的转录组初步分析[J]. 园艺学报, 2025, 52(5): 1301-1316.

ZHANG Yue, FENG Yiliao, WANG Bei, REN Wenjing, JIANG Chunyu, ZHAO Xinyu, WANG Caihong, YANG Limei, ZHUANG Mu, LÜ Honghao, WANG Yong, ZHANG Yangyong, JI Jialei. Preliminary Transcriptome Analysis of Folate Synthesis and Metabolism in Cabbage[J]. Acta Horticulturae Sinica, 2025, 52(5): 1301-1316.

图/表 13

图1 127份甘蓝自交系材料叶酸及其衍生物的含量

Fig. 1 The content of folate and derivatives in 127 cabbage inbred lines

表1 测序数据统计

Table 1 Sequencing data statistics

样品Sample	双端序列总数Paired-end reads counts	总碱基数Clean bases	GC含量/% GC Content	碱基质量值/% ≥ 30
Q372-1	20 186 702	6 043 240 774	46.57	94.02
Q372-2	21 382 384	6 402 029 466	46.70	94.50
Q372-3	19 720 185	5 902 457 860	46.32	94.24
Q428-1	21 147 787	6 332 933 914	47.79	93.93
Q428-2	23 999 831	7 185 985 424	47.75	94.32
Q428-3	19 953 645	5 975 348 582	47.70	94.16

图2 甘蓝自交系材料Q428（高叶酸）和Q372（低叶酸）FPKM的主成分分析

Fig. 2 PCA clustering of FPKM of cabbage inbred lines Q428（high folate）and Q372（low folate）

图3 甘蓝自交系材料Q428与Q372差异显著的前20个GO功能组

Fig. 3 The top 20 Gene Ontology terms exhibiting significant differential enrichment between cabbage inbred lines Q428 and Q372

图4 甘蓝自交系材料Q428和Q372差异表达基因的 KEGG 富集分析

Fig. 4 KEGG functional annotation of transcriptomic differences in cabbage inbred lines Q428 and Q372

表2 叶酸合成代谢相关基因

Table 2 Genes related to folate synthesis and metabolism

功能途径 Function pathway	基因 Gene	蛋白缩写 Protein abbreviation	拟南芥ID Arabidopsis thaliana ID	甘蓝ID Brassica oleracea ID	相似度/% Similarity	E值 E-value
pABA合成 pABA synthesis	ADCL	ADCL	AT1G50090.1	BolC02g022020.2J	80.548	0
				BolC03g082990.2J	85.955	0
				BolC06g004630.2J	89.045	0
	ADCS	ADCS	AT2G28880.1	BolC04g021330.2J	84.832	0
	ADCS	ADCS	AT2G28880.1	BolC04g055450.2J	81.031	0
喋啶合成 Pteridine synthesis	NUDT	DPP	AT1G68760.1	BolC02g025120.2J	82.270	9.78E-87
	DHNA	DHNA	AT3G11750.1	BolC01g050940.2J	87.500	3.6E-74
	GCHI	GCHI	AT3G07270.1	BolC05g058460.2J	82.303	0
	GCHI	GCHI	AT3G07270.1	BolC01g053860.2J	81.023	0
组装加尾 Assembly and taliling	DHTS/DHFR	DHFR	AT2G16370.1	BolC03g051860.2J	89.382	0
				BolC01g004210.2J	85.246	0
				BolC07g057740.2J	88.690	5.2E-103
	DHFS	DHFS	AT5G41480.1	BolC07g028910.2J	86.090	0
	HPPK/DHPS	HPPK/DHPS	AT4G30000.2	BolC01g009090.2J	85.257	0
分布转运 Distribution and transportation	FPGS	FPGS	AT3G10160.1	BolC01g052470.2J	82.083	0
分布转运 Distribution and transportation	GGH	GGH	AT1G78660.1	BolC02g034750.2J	85.893	0
降解回补Degradation and replenishment	PTAR	PTAR	AT1G10310.1	BolC08g021880.2J	92.181	5.2E-168
C1代谢 C1 metabolism	5FCL	5FCL	AT5G13050.1	BolC09g060020.2J	85.816	4.2E-165
	5FCL	5FCL	AT5G13050.1	BolC02g005400.2J	79.196	0
	5FCLL	5FCLL	AT1G76730.1	BolC06g030250.2J	86.517	0
	DHC	DHC	AT2G38660.1	BolC04g063230.2J	88.385	0
	FTHS	FTHS	AT1G31220.1	BolC05g029350.2J	83.390	1.4E-172
	GCSH	GCSH	AT1G32470.1	BolC08g011080.2J	94.012	3.1E-105
				BolC05g037930.2J	95.210	2.9E-107
				BolC05g030770.2J	93.413	6.4E-105
				BolC04g013540.2J	91.018	8E-101
	GCSL	GCSL	AT1G48030.1	BolC06g002320.2J	94.488	0
				BolC05g049030.2J	95.079	0
				BolC05g049060.2J	91.262	1.94E-57
	GCSP	GCSP	AT4G33010.1	BolC01g005590.2J	90.172	0
	GCST	GCST	AT1G11860.1	BolC08g055130.2J	97.066	0
	GCST	GCST	AT1G11860.1	BolC08g023150.2J	95.854	0
	MS	MS	AT5G17920.1	BolC03g009250.2J	97.781	0
				BolC09g055230.2J	97.520	0
				BolC02g008490.2J	97.258	0
				BolC03g036730.2J	95.953	0
				BolC05g061690.2J	95.181	0
				BolC03g011020.2J	91.054	0
				BolC02g025710.2J	95.200	8.66E-81
	MTHFR	MTHR	AT2G44160.1	BolC04g005400.2J	94.454	0
				BolC04g066800.2J	91.611	0
				BolC06g025320.2J	96.121	0
				BolC08g043230.2J	94.098	0
				BolC02g000140.2J	80.519	3.77E-35
	PURU	10-FDF	AT4G17360.1	BolC01g023770.2J	93.617	0
				BolC07g030320.2J	93.272	0
				BolC07g042860.2J	79.688	9.51E-27
				BolC07g030040.2J	82.759	9.29E-28
	SHMT1a	SHMTla	AT4G37930.1	BolC03g073550.2J	98.263	0
				BolC01g001230.2J	97.297	0
				BolC06g042720.2J	91.573	0
				BolC06g033950.2J	89.513	0
				BolC07g059720.2J	81.176	1.01E-35
	SHMT3	SHMT3	AT4G32520.1	BolC01g006620.2J	91.018	0
				BolC03g081120.2J	88.868	0
				BolC07g056500.2J	96.970	1.9E-14
				BolC07g056470.2J	96.970	1.9E-14

表2 叶酸合成代谢相关基因

Table 2 Genes related to folate synthesis and metabolism

功能途径 Function pathway	基因 Gene	蛋白缩写 Protein abbreviation	拟南芥ID Arabidopsis thaliana ID	甘蓝ID Brassica oleracea ID	相似度/% Similarity	E值 E-value
pABA合成 pABA synthesis	ADCL	ADCL	AT1G50090.1	BolC02g022020.2J	80.548	0
				BolC03g082990.2J	85.955	0
				BolC06g004630.2J	89.045	0
	ADCS	ADCS	AT2G28880.1	BolC04g021330.2J	84.832	0
	ADCS	ADCS	AT2G28880.1	BolC04g055450.2J	81.031	0
喋啶合成 Pteridine synthesis	NUDT	DPP	AT1G68760.1	BolC02g025120.2J	82.270	9.78E-87
	DHNA	DHNA	AT3G11750.1	BolC01g050940.2J	87.500	3.6E-74
	GCHI	GCHI	AT3G07270.1	BolC05g058460.2J	82.303	0
	GCHI	GCHI	AT3G07270.1	BolC01g053860.2J	81.023	0
组装加尾 Assembly and taliling	DHTS/DHFR	DHFR	AT2G16370.1	BolC03g051860.2J	89.382	0
				BolC01g004210.2J	85.246	0
				BolC07g057740.2J	88.690	5.2E-103
	DHFS	DHFS	AT5G41480.1	BolC07g028910.2J	86.090	0
	HPPK/DHPS	HPPK/DHPS	AT4G30000.2	BolC01g009090.2J	85.257	0
分布转运 Distribution and transportation	FPGS	FPGS	AT3G10160.1	BolC01g052470.2J	82.083	0
分布转运 Distribution and transportation	GGH	GGH	AT1G78660.1	BolC02g034750.2J	85.893	0
降解回补Degradation and replenishment	PTAR	PTAR	AT1G10310.1	BolC08g021880.2J	92.181	5.2E-168
C1代谢 C1 metabolism	5FCL	5FCL	AT5G13050.1	BolC09g060020.2J	85.816	4.2E-165
	5FCL	5FCL	AT5G13050.1	BolC02g005400.2J	79.196	0
	5FCLL	5FCLL	AT1G76730.1	BolC06g030250.2J	86.517	0
	DHC	DHC	AT2G38660.1	BolC04g063230.2J	88.385	0
	FTHS	FTHS	AT1G31220.1	BolC05g029350.2J	83.390	1.4E-172
	GCSH	GCSH	AT1G32470.1	BolC08g011080.2J	94.012	3.1E-105
				BolC05g037930.2J	95.210	2.9E-107
				BolC05g030770.2J	93.413	6.4E-105
				BolC04g013540.2J	91.018	8E-101
	GCSL	GCSL	AT1G48030.1	BolC06g002320.2J	94.488	0
				BolC05g049030.2J	95.079	0
				BolC05g049060.2J	91.262	1.94E-57
	GCSP	GCSP	AT4G33010.1	BolC01g005590.2J	90.172	0
	GCST	GCST	AT1G11860.1	BolC08g055130.2J	97.066	0
	GCST	GCST	AT1G11860.1	BolC08g023150.2J	95.854	0
	MS	MS	AT5G17920.1	BolC03g009250.2J	97.781	0
				BolC09g055230.2J	97.520	0
				BolC02g008490.2J	97.258	0
				BolC03g036730.2J	95.953	0
				BolC05g061690.2J	95.181	0
				BolC03g011020.2J	91.054	0
				BolC02g025710.2J	95.200	8.66E-81
	MTHFR	MTHR	AT2G44160.1	BolC04g005400.2J	94.454	0
				BolC04g066800.2J	91.611	0
				BolC06g025320.2J	96.121	0
				BolC08g043230.2J	94.098	0
				BolC02g000140.2J	80.519	3.77E-35
	PURU	10-FDF	AT4G17360.1	BolC01g023770.2J	93.617	0
				BolC07g030320.2J	93.272	0
				BolC07g042860.2J	79.688	9.51E-27
				BolC07g030040.2J	82.759	9.29E-28
	SHMT1a	SHMTla	AT4G37930.1	BolC03g073550.2J	98.263	0
				BolC01g001230.2J	97.297	0
				BolC06g042720.2J	91.573	0
				BolC06g033950.2J	89.513	0
				BolC07g059720.2J	81.176	1.01E-35
	SHMT3	SHMT3	AT4G32520.1	BolC01g006620.2J	91.018	0
				BolC03g081120.2J	88.868	0
				BolC07g056500.2J	96.970	1.9E-14
				BolC07g056470.2J	96.970	1.9E-14

图5 甘蓝叶酸相关基因染色体定位图

Fig. 5 Chromosome location map of folate-related genes in cabbage

图6 拟南芥与甘蓝自交系叶酸相关基因共线性图

Fig. 6 Collinearity mapping of folate biosynthesis genes in Arabidopsis thaliana and cabbage inbred lines

图7 甘蓝自交系叶酸合成代谢通路图参考De Lepeleire等（2018）和Lian等（2015）绘制参与叶酸合成代谢的酶。ADCS：氨基脱氧胆酸合成酶；ADCL：氨基脱氧胆酸裂解酶；FPGS：叶酰聚谷氨酸合成酶；PGH：pABA-谷氨酸水解酶；GGH：γ-谷酰基水解酶；GCHI：GTP 环化水解酶Ⅰ；HPPK/DHPS：二氢蝶呤焦磷酸激酶；DHFS：二氢叶酸合成酶；DHFR：二氢叶酸还原酶；GDC：甘氨酸脱羧酶；SHMT1a：丝氨酸羟甲基转移酶1a；MTHFR：亚甲基四氢叶酸还原酶；MS：蛋氨酸合成酶；FTHS：10-甲酰基四氢叶酸合成酶；DHC：5,10-亚甲基-四氢叶酸脱氢酶/5,10-亚甲基-四氢叶酸环水解酶

Fig. 7 Folate biosynthetic pathway in cabbage inbred lines Drawing based on De Lepeleire et al.，2018；Lian et al.，2015 Enzymes involved in folate synthesis. ADCS：Aminodeoxychorismate synthase；ADCL：Aminodeoxychorismate lyase；FPGS：Folylpolyglutamate synthetase；PGH：pABA-Glu hydrolase；GGH：γ-Glutamyl hydrolase；GCHI：GTP cyclohydrolaseⅠ；HPPK/DHPS：Dihydropterin pyrophosphokinase/dihydropteroate synthase；DHFS：Dihydrofolate synthetase；DHFR：Dihydrofolate reductase；GDC：Glycine decarboxylase；SHMT1a：Serine hydroxymethyl transferase 1a；MTHFR：Methylenetetrahydrofolate reductase；MS：Methionine synthase；FTHS：10-Formyltetrahydrofolate synthetase；DHC：5,10-Methylene-THF dehydrogenase/5,10-Methenyl-THF cyclohydrolase

图8 甘蓝自交系材料Q428和Q372差异表达基因RT-qPCR 验证柱上不同小写字母表示在0.05水平差异显著

Fig. 8 RT-qPCR validation of differentially expressed genes in cabbage inbred lines Q428 and Q372 Different lowercase letters above the bars mean significantly different at the 0.05 probability level

图9 甘蓝自交系材料Q428和Q372差异可变剪接事件 TTS：转录终止位点；TSS：转录起始位点

Fig. 9 Differential alternative splicing events between cabbage inbred lines Q428 and Q372 TTS：Transcription termination site；TSS：Transcription start site

图10 叶酸合成蛋白与一碳代谢关键蛋白网络分析模式图 ADCS：BolC04g021330.2J；ADCL：BolC02g022020.2J 蓝色线条：已知互作蛋白；绿色线条：基因邻域；浅绿线条：文本挖掘；黑色线条：基因共表达

Fig. 10 Network analysis model of folate biosynthesis proteins and one-carbon metabolism key proteins ADCS：BolC04g021330.2J；ADCL：BolC02g022020.2J. Blue Lines：known interactions；Green lines：gene neighborhood；Light green line：text mining；Black line：co-expression

图11 叶酸相关基因RT-qPCR验证

Fig. 11 RT-qPCR verification of folate-related genes BoGCH1：BolC05g058460.2J；BoPTAR：BolC08g021880.2J；Bo5FCL：BolC02g005400.2J；BoGCSH：BolC08g011080.2J；BoGCSL：BolC06g002320.2J；BoGCSP：BolC01g005590.2J；BoGCST：BolC08g055130.2J；BoMTHFR：BolC04g005400.2J；BoSHMT1a：BolC03g073550.2J；BoGGH：BolC02g034750.2J t-test. **：α = 0.01；***：α = 0.001

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