比较转录组学揭示乙烯信号与表观遗传协同调控黄瓜性别决定

doi:10.13560/j.cnki.biotech.bull.1985.2025-0571

生物技术通报 ›› 2025, Vol. 41 ›› Issue (12): 139-155.doi: 10.13560/j.cnki.biotech.bull.1985.2025-0571

比较转录组学揭示乙烯信号与表观遗传协同调控黄瓜性别决定

杨宗辉¹(), 李利斌¹, 孟昭娟¹, 高天², 祝利霞³, 杜海梅⁴, 董伟伟⁵, 曹齐卫¹()

^1.山东省农业科学院蔬菜研究所农业农村部黄淮设施园艺工程重点实验室山东省大宗露地蔬菜育种重点实验室，济南 250100
^2.成都市农业技术推广总站，成都 610041
^3.济南大学生物科学与技术学院，济南 250022
^4.山东省泰安市宁阳县伏山镇农技站，泰安 271408
^5.山东省临沂市沂南县农业技术推广中心，临沂 276300

收稿日期:2025-06-03 出版日期:2025-12-26 发布日期:2026-01-06
通讯作者: 曹齐卫，男，硕士，研究员，研究方向：黄瓜遗传育种；E-mail: qiweicao1979@163.com
作者简介:杨宗辉，男，博士，助理研究员，研究方向：黄瓜分子育种；E-mail: ksprings@163.com
基金资助:
国家自然科学基金项目(32200506);国家自然科学基金项目(32402582);国家重点研发计划项目(2023YFD1201503);国家现代农业产业技术体系建设专项资金项目(CARS-23-G13);泰安市农业良种工程项目(2024NYLZ13);山东省科技型中小企业创新能力提升工程(2024TSGC0122);山东省农业科学院农业创新工程(CXGC2025B08);山东省农业科学院农业创新工程(CXGC2025C08)

Comparative Transcriptomics Reveals Synergistic Control of Cucumber Sex Determination by Ethylene Signaling and Epigenetic Regulation

YANG Zong-hui¹(), LI Li-bin¹, MENG Zhao-juan¹, GAO Tian², ZHU Li-xia³, DU Hai-mei⁴, DONG Wei-wei⁵, CAO Qi-wei¹()

^1.Shandong Key Laboratory of Bulk Open-field Vegetable Breeding, Ministry of Agriculture and Rural Affairs Key Laboratory of Huang Huai Protected Horticulture Engineering, Institute of Vegetables, Shandong Academy of Agricultural Sciences, Jinan 250100
^2.Chengdu Agricultural Technology Station, Chengdu 610041
^3.School of Biological Science and Technology, University of Jinan, Jinan 250022
^4.Agricultural Technology Station, Fushan Town, Ningyang County, Tai’an City, Shandong Province, Tai’an 271408
^5.Yinan County Agricultural Technology Center, Linyi City, Shandong Province, Linyi 276300

Received:2025-06-03 Published:2025-12-26 Online:2026-01-06

摘要/Abstract

摘要：

目的发掘调控黄瓜性别决定的关键基因及调控通路，为培育高产黄瓜品种提供理论依据，并为理解双子叶植物性别决定机制奠定基础。方法以黄瓜雌性系X8g（纯雌株）与普通系X8（雌雄株）近等基因系为材料，采用RNA-Seq技术对四叶一心期花芽分生组织进行转录组测序分析。通过差异表达分析、主成分分析和方差分解分析3种策略整合筛选关键基因。利用OrthoFinder鉴定黄瓜与拟南芥的直系同源基因，开展跨物种比较转录组分析，以探究调控网络的保守性与特异性。运用VIGS技术对核心候选基因CsACO2进行功能验证，采用qPCR检测基因沉默效率和特异性。使用DNA甲基化抑制剂5-氮杂胞苷处理雌性系植株验证表观遗传调控作用。结果在黄瓜雌性系与普通系之间共鉴定到197个差异表达基因，其中43个上调，154个下调，这些基因显著富集于花器官形态建成、α-亚麻酸（茉莉酸合成前体）代谢等通路。多维度分析共同确定了一些核心候选基因，包括已知的乙烯合成关键基因CsACO2和新发现的MADS-box家族转录因子AGL6、MADS4等。跨物种比较分析显示，黄瓜与拟南芥同源基因的表达模式总体相关性弱，但揭示了乙烯响应因子EIN3、NAC053转录因子靶基因集以及H3K27me3表观修饰在黄瓜性别调控中的潜在重要作用。功能验证实验证明，在雌性系中特异性沉默CsACO2能够诱导雄花和两性花的产生；而施用DNA甲基化抑制剂5-azacytidine同样能使雌性系植株开出雄花。结论系统揭示黄瓜性别决定是由乙烯信号通路主导，并可能由茉莉酸代谢、多类转录因子以及表观遗传协同作用的复杂分子网络。

关键词: 黄瓜, 性别决定, 比较转录组学, 乙烯信号通路, CsACO2, 表观修饰, 病毒诱导的基因沉默, 拟南芥

Abstract:

Objective To identify the key genes and regulatory pathways that control sex determination in cucumber (Cucumis sativus L.), with the aim of providing a theoretical basis for breeding high-yield cucumber varieties and laying a foundation for understanding the mechanisms of sex determination in dicotyledonous plants. Method Near-isogenic lines of cucumber, the gynoecious line X8g and the monoecious line X8, were used as materials. Transcriptome sequencing (RNA-Seq) analysis was conducted on the apical meristems of flower buds at the four-leaf-one-heart stage. An integrated strategy combining differential expression analysis, principal component analysis (PCA), and variance decomposition analysis was employed to screen for key genes. OrthoFinder was used to identify orthologous genes between cucumber and Arabidopsis thaliana to perform a cross-species comparative transcriptomic analysis, investigating the conservation and specificity of the regulatory networks. The function of the core candidate gene, CsACO2, was validated using Virus-Induced Gene Silencing (VIGS), and its silencing efficiency and specificity were assessed by qPCR. The role of epigenetic regulation was verified by treating the gynoecious line with the DNA methylation inhibitor 5-azacytidine. This study investigated key genes and pathways in cucumber sex determination using RNA-Seq analysis of gynoecious and monoecious lines. Result A total of 197 differentially expressed genes were identified between the gynoecious and monoecious lines, with 43 being upregulated and 154 downregulated. These genes were significantly enriched in pathways such as floral organ morphogenesis and α-linolenic acid (a precursor for jasmonic acid synthesis) metabolism. The multi-dimensional analysis identified a set of core candidate genes, including the known key ethylene synthesis gene CsACO2 and newly discovered MADS-box transcription factors like AGL6 and MADS4. The cross-species comparative analysis showed a weak overall correlation in expression patterns of orthologous genes but revealed the potential importance of target gene sets of the ethylene response factor EIN3, the NAC053 transcription factor, and H3K27me3 epigenetic modification in regulating cucumber sex. Functional validation experiments confirmed that the specific silencing of CsACO2 induced the formation of male and bisexual flowers in the gynoecious line. Similarly, treatment with 5-azacytidine also caused the gynoecious line to produce male flowers. Conclusion This study systematically reveals that cucumber sex determination is governed by a complex molecular network dominated by the ethylene signaling pathway, potentially involving jasmonic acid metabolism, various transcription factors, and epigenetic modifications.

Key words: Cucumis sativus L., sex determination, comparative transcriptomics, ethylene signaling pathway, CsACO2, epigenetic modification, virus-induced gene silencing (VIGS), Arabidopsis thaliana

杨宗辉, 李利斌, 孟昭娟, 高天, 祝利霞, 杜海梅, 董伟伟, 曹齐卫. 比较转录组学揭示乙烯信号与表观遗传协同调控黄瓜性别决定[J]. 生物技术通报, 2025, 41(12): 139-155.

YANG Zong-hui, LI Li-bin, MENG Zhao-juan, GAO Tian, ZHU Li-xia, DU Hai-mei, DONG Wei-wei, CAO Qi-wei. Comparative Transcriptomics Reveals Synergistic Control of Cucumber Sex Determination by Ethylene Signaling and Epigenetic Regulation[J]. Biotechnology Bulletin, 2025, 41(12): 139-155.

图/表 11

表1 测序数据的基本统计表

Table 1 Basic statistics of sequencing data

样本编号 Sample ID	清洁读数 Clean reads	清洁碱基数 Clean bases （bp）	GC 含量 GC content （%）	Q30 碱基比例 Q30 （%）
T01	25 139 532	7 511 087 362	44.41	93.75
T02	23 678 722	7 068 974 554	44.57	93.75
T03	29 026 750	8 662 561 328	44.31	94.09
T04	31 798 263	9 491 036 146	44.43	93.77
T05	26 566 141	7 941 970 238	44.24	93.74
T06	28 078 078	8 390 027 920	44.29	93.69

表2 比对结果统计表

Table 2 Statistics of mapping results

样本编号 Sample ID	总读数 Total reads	比对读数 Mapped reads	唯一比对读数 Uniquely mapped reads	多重比对读数 Multi-mapped reads	正链比对读数 Mapped reads on+strand	负链比对读数 Mapped reads on-strand
T01	50 279 064	48 741 549 （96.94%）	47 020 390 （93.52%）	1 721 159 （3.42%）	24 142 446	24 233 782
T02	47 357 444	45 842 026 （96.80%）	44 215 419 （93.37%）	1 626 607 （3.43%）	22 699 707	22 792 183
T03	58 053 500	56 296 505 （96.97%）	54 317 173 （93.56%）	1 979 332 （3.41%）	27 877 852	27 989 891
T04	63 596 526	61 603 424 （96.87%）	59 470 279 （93.51%）	2 133 145 （3.35%）	30 511 057	30 629 863
T05	53 132 282	51 558 779 （97.04%）	49 751 449 （93.64%）	1 807 330 （3.40%）	25 547 018	25 635 938
T06	56 156 156	54 471 955 （97.00%）	52 558 943 （93.59%）	1 913 012 （3.41%）	26 972 777	27 079 418

图1 黄瓜雌性系与普通系的转录组表达特征分析A：主成分分析（PCA）散点图展示样品间的整体表达差异；PC1和PC2分别解释38.4%和23.6%的表达变异；不同颜色表示不同基因型：雌性系（红色）和普通系（蓝色）；B：火山图展示差异表达基因的分布；红色和蓝色点分别表示显著上调（43个）和下调（154个）的基因（|log2FC|>=1，FDR<0.01）；突出显示了部分差异表达倍数超过3倍的基因；C：基因在PC1和PC2方向上的载荷值分布；点的颜色表示基因的差异表达状态；突出显示了部分具有高PC1载荷值的关键基因；D：基因表达方差分解分析；X轴表示基因型解释的方差占比，Y轴表示基因型方差与残差方差的对数比值；突出显示了部分基因型方差贡献率极高（图中示例为＞0.99）的基因，以直观展示其表达主要受基因型驱动；E：韦恩图展示3种基因筛选方法（差异表达分析、主成分分析和方差分解）结果的重叠情况；数字表示各区域基因数量及占比

Fig. 1 Transcriptome expression pattern analysis of gynoecious and monoecious cucumber linesA: Principal component analysis (PCA) plot showing overall expression differences among samples. PC1 and PC2 explain 38.4% and 23.6% of expression variation, respectively. Colors indicate different genotypes: gynoecious (red) and monoecious (blue). B: Volcano plot showing the distribution of differentially expressed genes. Red and blue dots represent significantly up-regulated (43) and down-regulated (154) genes (|log2FC|>=1, FDR<0.01). Highlighted are the genes with a fold change in expression exceeding 3 times. C: Distribution of gene loadings on PC1 and PC2. Dot colors indicate differential expression status. Key genes with high PC1 loadings are highlighted. D: Variance decomposition analysis of gene expression. The X-axis shows the distribution of genotype variance proportions, while the Y-axis displays the logarithmic ratio of genotype variance to residuals. Highlighted are the genes with a genotype variance proportion exceeding 0.99. E: Venn diagram showing the overlap among genes identified by three screening methods (differential expression analysis, principal component analysis, and variance decomposition). Numbers indicate gene counts and percentages in each region

表3 三种方法共同筛选的关键基因及其表达特征

Table 3 Key genes identified by three screening methods and their expression characteristics

基因编号 Gene ID	基因名称 Gene name	log₂倍数变化 log₂FC	表达调控 Regulation	PC1载荷值 PC1 loading	基因型方差占比 Fraction of variance across genotypes
CsaV3_2G032190	--	-1.23	下调	-0.020	0.927
CsaV3_3G040160	--	-1.74	下调	-0.020	0.931
CsaV3_4G028010	--	-2.43	下调	-0.032	0.998
CsaV3_4G037760	SPL14	1.26	上调	0.049	0.938
CsaV3_5G024890	--	-5.41	下调	-0.203	0.994
CsaV3_6G006010	AGL6	-1.98	下调	-0.028	0.999
CsaV3_6G008200	MADS4	-2.90	下调	-0.027	0.988
CsaV3_6G048630	CsACO2	-1.20	下调	-0.050	0.991
CsaV3_6G051850	--	2.81	上调	0.033	0.964

图2 功能富集分析揭示的关键代谢通路和生物学过程A：KEGG通路富集分析结果；气泡大小表示富集基因数目，颜色深浅表示校正后P值显著性水平；B：GO功能富集分析结果；气泡大小表示基因数目，颜色表示校正后P值；C：基于不同筛选策略的KEGG通路富集比较；热图中颜色表示富集得分（NES），黄色表示正向富集，蓝色表示负向富集；圆点大小表示显著性水平［-log10（P. adjust）］；D：不同筛选策略获得基因集的GO功能富集比较；热图中颜色表示富集得分（NES），黄色表示正向富集，蓝色表示负向富集。圆点大小表示显著性水平［-log10（P. adjust）］。FC：差异表达分析，PCA：主成分分析，VD：方差分解

Fig. 2 Functional enrichment analysis reveals key metabolic pathways and biological processesA: KEGG pathway enrichment analysis results. Bubble size indicates the number of enriched genes, and color intensity indicates the significance level (adjusted P-value). B: GO functional enrichment analysis results. Bubble size indicates gene count, and color indicates adjusted P-value. C: Comparison of KEGG pathway enrichment based on different screening strategies. Heatmap colors indicate enrichment scores (NES), with yellow indicating positive enrichment and blue indicating negative enrichment. The size of a dot indicates the significance level [-log10(P.adjust)]. D: Comparison of GO functional enrichment for gene sets obtained from different selection strategies. The colors in the heatmap indicate the enrichment score (NES), with yellow indicating positive enrichment and blue indicating negative enrichment. The size of a dot indicates the significance level [-log10(P.adjust)]. FC: Differential expression analysis; PCA: principal component analysis; VD: variance decomposition

图3 黄瓜与拟南芥同源基因表达模式比较分析A：黄瓜和拟南芥同源基因表达变化的散点图；横轴和纵轴分别表示黄瓜和拟南芥中基因的log2FC值；点的颜色表示不同的表达模式；重要基因用基因名标注；B：黄瓜特异差异表达基因的GO功能富集分析；气泡大小表示基因数量，颜色深浅表示校正后P值显著性水平（P. adjust）

Fig. 3 Comparative analysis of orthologus gene expression patterns between cucumber and ArabidopsisA: Scatter plot showing expression changes of orthologous genes between cucumber and Arabidopsis. X-axis and Y-axis indicate log2FC values in cucumber and Arabidopsis, respectively. Colors indicate different expression patterns. Key genes are labeled by gene names. B: GO functional enrichment analysis of cucumber-specific differentially expressed genes. Bubble size indicates gene count, and color intensity indicates significance level (adjusted P-value)

图4 黄瓜和拟南芥关键基因的表达热图分析热图展示了在黄瓜和拟南芥中差异表达并且有基因符号注释的101个基因表达模式；每1行代表1个基因，颜色表示基因表达水平的变化：黄色表示上调表达，蓝色表示下调表达；基因按照其表达模式聚类排列；右侧注释栏显示物种来源和基因型；每1行（即每个基因）的FPKM值进行Z-score标准化

Fig. 4 Expression heatmap analysis of key genes in cucumber and ArabidopsisThe heatmap displays the expression patterns of 101 differentially expressed genes with gene symbol annotations in cucumber and Arabidopsis. Each row indicates a gene, and the colors indicate changes in gene expression levels: yellow indicates upregulated expression, while blue indicates downregulated expression. The genes are clustered based on their expression patterns. The annotation bar on the right shows the species origin and genotype. The FPKM values of each row (i.e., each gene) are normalized to Z-score scale

图5 物种和基因型特异性基因的功能分析A：基因表达方差分布图；X轴表示物种间方差占比，Y轴表示基因型间方差占比；点的颜色表示不同类别：基因型方差占比高（红色）、物种方差占比高（绿色）和其他（灰色）；B：受基因型效应调控的基因KEGG通路富集分析结果；气泡大小表示基因数目，颜色深浅表示校正后P值，X轴表示富集倍数；C：受基因型效应调控的基因GO功能富集分析结果；气泡大小表示基因数目，颜色深浅表示校正后P值，X轴表示富集倍数；D：受基因型效应调控的基因GSEA富集分析结果；气泡大小表示基因数目，颜色表示校正后P值，X轴标准化富集分数（NES）

Fig. 5 Functional analysis of species- and genotype-specific genesA: Vriance distribution plot of gene expression. The X-axis indicates the fraction of variance across species, while the Y-axis indicates the fraction of variance across genotypes. The color of the points indicates different categories: high genotype variance proportion (red), high species variance proportion (green), and others (gray). B: KEGG pathway enrichment analysis results for genes regulated by genotype effects. The size of the bubbles indicates the number of genes, and the color intensity indicates the adjusted P-value. The X-axis indicates the enrichment fold change. C: GO functional enrichment analysis results for genes regulated by genotype effects. The size of the bubbles indicates the number of genes, and the color intensity indicates the adjusted P-value. The X-axis indicates the enrichment fold change. D: GSEA enrichment analysis results for genes regulated by genotype effects. The size of the bubbles indicates the number of genes set, the color indicates the adjusted P-value, and the X-axis indicates the normalized enrichment score (NES)

图6 PlantGSAD基因集富集分析A：受基因型效应调控的基因PlantGSAD基因集富集分析结果；棒棒糖图展示了显著富集的PlantGSAD基因集，气泡大小表示基因集大小，颜色深浅表示校正后P值，X轴表示标准化富集分数；B：EIN3靶基因集的富集分析结果；上方面板显示累积富集分数，下方面板展示基因在基因型方差占比排序中的分布；C：NAC053靶基因集的富集分析结果；同样展示了累积富集分数和基因分布图

Fig. 6 Gene set enrichment analysis of PlantGSADA: Enrichment analysis results for PlantGSAD gene sets regulated by genotype effects. The lollipop chart displays significantly enriched PlantGSAD gene sets, where the size of a bubble indicates the size of the gene sets, the color intensity indicates the adjusted P-value, and the X-axis indicates the normalized enrichment score. B: Enrichment analysis results for the EIN3 target gene set. The upper panel shows the running enrichment score, while the lower panel displays the distribution of genes in the ranking of genotype variance proportions. C: Enrichment analysis results for the NAC053 target gene set. It similarly displays the running enrichment score and the gene distribution plot

图7 黄瓜雌性系CsACO2基因的VIGS分析A：阴性对照（pTRSV2-空载体，CK），侵染后的雌性系黄瓜（X8g）只产生正常的雌花；B：阳性对照（pTRSV2-PDS），侵染后X8g植株的真叶出现明显的光漂白（白化）现象，证明VIGS系统有效；C：沉默CsACO2（pTRSV2-CsACO2， V1），侵染后的X8g植株上出现了雄花；D：沉默CsACO2（pTRSV2-CsACO2， V2），侵染后的X8g植株上出现了两性花；标尺=1 cm；E‒I：RT-qPCR检测结果显示CsACO2基因在沉默植株中表达显著下调，而其他ACO家族成员（CsACO1、CsACO3、CsACO4、CsACO5）表达无显著变化；CK：空载体对照；V1、V2：2个独立的CsACO2沉默植株；柱状图显示相对表达量（平均值±标准差），*** P<0.001

Fig. 7 VIGS analysis of the CsACO2 gene in gynoecious cucumberA: Negative control (pTRSV2-empty vector), in which the infected gynoecious cucumber (X8g) plant produces only normal female flowers. B: Positive control (pTRSV2-PDS), in which the leaves of the infected X8g plant show significant photobleaching, indicating the VIGS system is working. C: Silencing of CsACO2 (pTRSV2-CsACO2) induces the formation of male flowers on the infected X8g plant. D: Silencing of CsACO2 (pTRSV2-CsACO2) induces the formation of bisexual flowers on the infected X8g plant. Scale bar=1 cm. E‒I: RT-qPCR results showing significant downregulation of CsACO2 gene in silenced plants, while other ACO family members (CsACO1, CsACO3, CsACO4, CsACO5) showed no significant changes. CK: Empty vector control; V1, V2: two independent CsACO2-silenced plants. Bar charts show relative expression levels (mean±SD), ***P<0.001

图8 DNA甲基化抑制剂5-氮杂胞苷化学处理黄瓜雌性系展示了5-azacytidine处理组（5-az）与对照组（H2O）的表型差异。对照组的雌性系X8g植株正常生长并开出雌花，而经过5-az处理的植株产生了雄花。标尺=10 cm

Fig. 8 Chemical treatment of gynoecious cucumber with the DNA methylation inhibitor 5-azacytidinePhenotypic difference between the 5-azacytidine treatment group (5-az) and control group (H2O). The control gynoecious X8g plant grows normally and produces female flowers, whereas the 5-az-treated plant produces male flowers. Scale bar=10 cm

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比较转录组学揭示乙烯信号与表观遗传协同调控黄瓜性别决定

Comparative Transcriptomics Reveals Synergistic Control of Cucumber Sex Determination by Ethylene Signaling and Epigenetic Regulation

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