基于转录组分析植物激素对洋葱鳞茎膨大发育的调控机制

doi:10.13560/j.cnki.biotech.bull.1985.2024-0671

摘要/Abstract

摘要：

目的通过对洋葱发育不同阶段的鳞茎组织进行转录组比较分析，为研究植物激素在洋葱鳞茎形成过程中的分子调控机制提供依据。方法分别取洋葱出苗后33、47、61和75 d的鳞茎部位为试验材料，通过酶联免疫吸附法和气相色谱法检测，了解生长素、细胞分裂素、赤霉素3、脱落酸以及乙烯（前体ACC）含量在鳞茎膨大过程中的变化趋势；利用高通量测序技术进行转录组测序分析，从分子水平阐述植物激素对鳞茎发育的影响。结果从4个发育阶段的鳞茎中共检测到11 814个差异表达基因（DEGs），其中共同DEGs有3 311个；KEGG富集分析显示，不同发育阶段比较组DEGs均显著富集到“植物激素信号转导”通路，并对该通路上筛选到的36个主要DEGs进行表征；结合WGCNA分析每个模块与性状的r和P值，筛选到2个关键模块，通过转录因子预测，挖掘到3 028个转录因子unigenes与13个植物激素信号结构基因unigenes共表达，转录因子unigenes功能注释来自46个基因家族，最多的为锌指蛋白（C₂C₂、C₃H），其次为bHLH、NAC、ERF基因家族。结论通过转录组分析揭示了植物激素信号转导途径参与洋葱鳞茎膨大发育的相关基因。

关键词: 洋葱, 鳞茎膨大, 转录组分析, 植物激素, 转录因子

Abstract:

Objective The comparative transcriptome of bulb tissues at different stages of onion development was analyzed to provide a basis for studying the molecular mechanism of plant hormones in onion (Allium cepa L.) bulb formation. Method Onion bulbs at 33, 47, 61 and 75 d after seedling emergence were collected as experimental materials. ELISA and gas chromatography were used to quantify the contents of auxin, cytokinin, gibberellin3, abscisic acid and ethylene (precursor ACC) during the bulb enlargement and development. Transcriptome sequencing was performed using high-throughput sequencing technology to elucidate the effects of plant hormones on bulb development at molecular level. Result A total of 11 814 differentially expressed genes (DEGs) were detected from bulbs tissue at four developmental stages, of which 3 311 were shared DEGs. KEGG enrichment analysis revealed that DEGs were significantly enriched into "plant hormone signal transduction" pathway in different comparison groups, and 36 major DEGs were screened and characterized in this pathway. Combining the r and P values of each module and trait in WGCNA (weighted gene co-expression network analysis) analysis, two key modules were screened out. Through transcription factor prediction, 3 028 transcription factor unigenes were found to be co-expressed with 13 plant hormone signaling genes. The functional annotation of transcription factor unigenes were derived from 46 gene families, the most important of which were zinc finger protein (C₂C₂, C₃H), followed by bHLH, NAC and ERF gene families. Conclusion The genes related to plant hormone signal transduction pathway involved in onion bulb development is preliminarily revealed by transcriptome analysis.

Key words: onion, bulb enlargement, transcriptome analysis, plant hormone, transcription factor

李艳伟, 杨妍妍, 孙亚玲, 霍雨猛, 王振宝, 刘冰江. 基于转录组分析植物激素对洋葱鳞茎膨大发育的调控机制[J]. 生物技术通报, 2025, 41(2): 187-201.

LI Yan-wei, YANG Yan-yan, SUN Ya-ling, HUO Yu-meng, WANG Zhen-bao, LIU Bing-jiang. Regulation Mechanism of Plant Hormones Related to Onion Bulb Enlargement and Development Based on Transcriptome Analysis[J]. Biotechnology Bulletin, 2025, 41(2): 187-201.

图/表 10

表1 RT-qPCR引物序列信息

Table 1 Information of RT-qPCR primer sequences

基因名称Gene name	上游引物Forward primer （5′-3′）	下游引物Reverse primer （5′-3′）
SAUR40	F： AGGAGAAGAGATGAAGAGGT	R： TTACAAAAAGAAAAGGAGGA
SAUR50	F： GCAATGAAGTAAGTGAAAGG	R： GGAAAATAGTAAAGAGGTGT
SAUR32	F： TTCAGCCAGACCTAAGAGCG	R： CATAGCAACCACAGAACCCA
SCL32	F： AGAGGATAGAGAGGTCGGA	R： ATAGGCATTTTCTTTGGTT
XTH22	F： ATACAAGAACTTCAAGGCAG	R： ATTTTACAATAAGCACACCA
SUS	F： AATGCTTCACTTCCCCGCC	R： TCGCCCCAACCCTTCTCTA
GLU2	F： GGTGGGATGGGAAACATAGGA	R： AAAGGAGGGTGGAAGTGGAGA
PGIP2	F： CCCTTCTTTTCTCGCTAACCT	R： ATACCCCATTGTGGCACTCCT
LSH4A	F： TTGACCAGTTTGGAAAGACC	R： GCAGTAGCAGTAACAGGAGC
LSH4B	F： GCAGCGGGAGAGGGTAAGG	R： AAAAAGGCGGAAGGAAAAA
Actin	F： ACACGGCCTGGATAGCAACAT	R： AGAGCAGTATTCCCAAGCATT

图1 不同发育阶段洋葱鳞茎形态变化A：不同发育阶段洋葱鳞茎形态，P1：四叶期，P2：膨大初期，P3：膨大中期，P4：膨大后期，比例尺为5 mm；B：不同发育阶段时间点的鳞茎直径统计，*表示0.05水平差异显著。下同

Fig. 1 Morphological changes of onion bulb at different developmental stagesA: Morphology of onion bulb at different developmental stages; P1: four-leaf stage; P2: early formation stage; P3: middle formation stage; P4: later formation stage. Scale=5 mm. B: The length of bulb diameter at different developmental stage points, * indicates significant difference at 0.05 level. The same below

图2 不同发育阶段鳞茎中各类激素含量分析**表示0.01水平差异显著，***表示0.001水平差异显著；下同

Fig. 2 Analysis of various hormone contents in bulb at different developmental stages** indicates significant difference at 0.01 level， and *** indicates significant difference at 0.001 level. The same below

表2 转录组测序数据统计与质量评估

Table 2 Statistics and quality assessment of transcriptome sequencing data assembly

样品 Sample	原始数据 Raw data/Gb	干净数据 Clean data/Gb	Q20/%	Q30/%	GC含量 GC Content/%	外显子 Exon/%	内含子 Intron/%	基因间区 Intergenic/%
P1-1	5.39	4.98	98.72	94.77	43	86.68	2.92	10.40
P1-2	5.6	5.05	98.81	95.25	43	87.15	2.69	10.16
P1-3	5.54	5.07	98.86	95.44	43	87.22	2.86	9.92
P2-1	6.16	5.79	98.79	95.04	42	85.83	2.95	11.23
P2-2	6.27	5.89	98.71	93.70	42	86.29	2.92	10.79
P2-3	6.53	6.1	98.81	94.27	42	85.88	2.93	11.19
P3-1	6.26	5.88	98.82	95.23	42	84.54	3.44	12.02
P3-2	6.24	5.89	98.74	94.94	42	83.91	3.72	12.37
P3-3	5.41	4.94	98.68	94.81	42	84.10	3.40	12.51
P4-1	6.42	5.86	98.85	95.40	42	84.44	3.47	12.08
P4-2	5.99	5.47	98.76	95.19	42	84.55	3.62	11.83
P4-3	6.28	5.79	98.78	95.08	42	85.08	3.29	11.62

图3 鳞茎不同发育阶段差异表达基因分析A：差异表达基因数量；B：差异表达基因的韦恩图；C：3个比较组间共有差异基因的趋势分析

Fig. 3 DEGs analysis in different developmental stages of bulbA: Numbers of DEGs. B: Venn diagram of DEGs. C: STEM analysis of shared DEGs among the three comparison groups

图4 不同比较组差异表达基因的KEGG富集通路

Fig. 4 KEGG enrichment pathway of DEGs in different comparison groups

图5 生长素、细胞分裂素、赤霉素、脱落酸以及乙烯信号转导途径差异表达基因分析A：生长素、细胞分类素、赤霉素、脱落酸、乙烯信号转导途径；B：植物激素信号转导相关基因热图。热图表示不同处理间差异基因的FPKM值，颜色越红，数值越高；从左到右样本依次为P1、P2、P3和P4

Fig. 5 Analysis of DEGs in IAA, CTK, GA, ABA, and ETH signal transduction pathwaysA: IAA, CTK, GA, ABA, and ETH signal transduction pathway. B: Heat map of plant hormone signal transduction metabolism-related genes. The heat map showed the FPKM value of different genes at different stages and the higher the value, the redder the color. From left to right, the samples are P1, P2, P3 and P4

图6 基因共表达网络的可视化A：最佳软阈值的选择；B：差异表达基因的系统聚类树和基因模块，不同颜色代表不同的模块；C：各模块中的基因数量

Fig. 6 Visualization of gene co-expression networksA: Selection of optimal soft threshold. B: Cluster dendrogram and gene modules of DEGs. Different colors indicate different modules. C: Gene number of each module

图7 模块与表型的相关性分析及核心基因共表达网络可视化A：植物激素信号转导模块相关基因的共表达网络可视化；转录因子用三角形表示，结构基因用红色圆形表示，图形越大表明基因连通度越高；B：模块与鳞茎直径相关性热图，每个格子的值分别表示相关系数R2 和P值，红色表示正相关，蓝色表示负相关

Fig. 7 Correlation analysis between modules and phenotypes and co-expression networks visualization of core genesA: Co-expression network visualization of plant hormone signal transduction modules. Transcription factors are represented by triangles, while structural genes are represented by red circles. The larger the graph, the higher the connectivity of genes. B: Correlation heat map between module and trait. The values of each lattice indicate the correlation coefficients R2 and P, respectively. Red indicates positive correlation, and blue indicates negative correlation

图8 差异表达基因RT-qPCR验证

Fig. 8 RT-qPCR verification of DEGs

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