Regulation Mechanism of Plant Hormones Related to Onion Bulb Enlargement and Development Based on Transcriptome Analysis

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

Abstract

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

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.

Figures/Tables 10

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

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

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

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

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

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

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

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

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

Fig. 8 RT-qPCR verification of DEGs

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